Paul Bodelier

Dr. Paul Bodelier

Senior Researcher
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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands



I am a microbial ecologist with a strong interest in biogeochemistry with a focus on the functional ecology of the microbes involved. My special attention goes to microbes involved in the production and degradation of greenhouse gases.


Paul Bodelier has been a senior scientist at the Netherlands Institute of Ecology in Wageningen, the Netherlands since 2008. He obtained his PhD at the University of Nijmegen in 1997 focusing on nitrogen cycling in the rhizosphere of wetland plants. From 1997-1999 the scope of his work was expanded to methane cycling in rice paddies during a post-doc stay at the Max-Planck Institute for terrestrial Microbiology in Marburg, Germany, working together with the inspiring mentor Prof. Peter Frenzel. The MPI period was followed by a post-doc position at the Centre for Limnology of the Netherlands Institute of Ecology in Nieuwersluis, the Netherlands which was continued in 2008 by a tenured position at the same Institute.

The research in that period as well as the current research topics are reflected in his broad interest and perspective on ecology and interactions between microbes and their biotic and abiotic environment. His work has always spanned multiple levels of biological organization. The central topic of his current research line is the biogeochemical cycling of carbon and nutrients in wetlands and soils, mainly related to methane production and consumption. This area of research has proven particularly well-suited to link even combined multi-level effects to global element cycles, as the factors ultimately controlling atmospheric methane emissions include both physical (e.g. flooding, fertilizer use, temperature) and biotic factors (community composition, protozoa, macrofauna, plants, animals). For these studies, he used microbiological, biogeochemical, molecular biological, analytical chemical as well as isotopic approaches spanning the organization levels from genes to ecosystems. In addition, he actively seeks cooperation with researchers to make use of the current rapid development of new techniques to unravel the ecology of microbes in natural systems (e.g. massive parallel sequencing and protein stable isotope labeling).

Besides following his personal research interests he serves the scientific community by editorial activities (specialty chief editor at Frontiers in Terrestrial Microbiology (2010-2022); Section editor at Plant and Soil, editorial board member at ISME Journal (2012-2021) and Applied and Environmental Microbiology; ad hoc reviewer for more than 30 journals; grant reviewing activities NSF, NERC, NWO, ERC, Czech science foundation, Danish research Council Finnish Academy, etc.).

Next to these activities he also has a strong interest in the well-being of his colleagues, whose interest he represents by being the chairman of the personnel representative committee of the Netherlands Institute of Ecology and member of the employee council of the Royal Netherlands Academy of Arts and Sciences.

Research groups

Research Expertise

Microbial ecology



  • 2008–Present
    Senior Scientist Microbial Ecology (NIOO-KNAW)
  • 1999–2008
    Post-doc at Centre for Limnology (NIOO-KNAW), Nieuwersluis, the Netherlands.
  • 1997–1999
    Post-doc at Max Planck Institute for terrestrial Microbiology, Marburg, Germany.


  • 1992–1997
    PhD student, Centre for terrestrial Ecology (NIOO-KNAW), Heteren, the Netherlands.
  • 1985–1991
    Msc Biology at Radboud University Nijmegen, the Netherlands.


  • 2022
    NWO-NWA Climate Smart Soils.
    Budget: €1,376,812
    Utrecht University, Aeres University of Applied Sciences, Louis Bolk Institute, VA, BVOR, DSV, Joordens Seeds, Eurofins, Melioraad, DAW, ILVO
  • 2022
    NWO-TTW perspectief. Soil Pros. Soil biodiversity analysis for sustainable production systems.
    Budget: €3,969,062
    Hogere Agrarische School, Universiteit van Amsterdam, Utrecht Universiteit, Universiteit Twente, Wageningen University and Research
  • 2019
    EU-EFRO province of Gelderland. Fiber2Fiber.
    Budget: €1,500,000
    Natural Soil improvement, Kennis centrum papier en karton, SGI Compliance, Waterschap Drentse Overijselse Delta, Grondslag, CSE, Westerdijk Fungal Biodiversity Institute.
  • 2018
    NWO-TTW. Open Technology programme. SmartResidue. Evaluating Compost and bio-based residues as methane mitigation strategy creating climate smart agricultural soils. “Putting microbes to work”.
    Budget: €663,000
    Wageningen University, BioClear Earth, Natural Soil Improvement, Vereniging van afval bedrijven
  • 2016
    NIOO Strategic funds
    Budget: €132,000
    NIOO departments of Microbial Ecology and Aquatic Ecology,
  • 2015
    NWO thematic call "Green". Clever Cover Cropping.
    Budget: €890,000
    Wageningen University, Agrifirm, Joordens zaden, P.H. Petersen Saatzucht GMBH, VanDijke Semo seeds and services,
  • 2013
    NWO open science programme. LifeMOB. Unravelling life strategies of methane-oxidizing bacteria using a proteomic approach.
    Budget: €249,000
    UFZ Leipzig
  • 2012
    BE-Basic. SURESUPPORT. Towards a quick decision SUPPORT tool for SUstainable use of harvest RESidues (SURE/SUPPORT)
    Budget: €459,396
    BLGG Research B.V. Bioclear B.V., BioDetection Systems B.V., ClearDetections B.V., Wageningen University - Nematology, VU University Amsterdam
  • 2011
    BE-Basic. Assessing impacts of land-use for bio-based economy on soil and sediment biodiversity, ecosystem processes and services
    Budget: €1,100,000
    BioClear, BLGG, Deltares
  • 2010
    ESF-EuroEEFG. MECOMECON. Methanotrophic Diversity and Gene Expression as a Controlling Factor of Global Methane Consumption
    Budget: €240,000
    Max-Planck Institute for terrestrial Microbiology, Marburg; ETH Zurich; University of Tromso; University of East Anglia, Norwich; University of Zurich; Helmholtz center, Leipzig; VU Amsterdam.
  • 2006
    ESF-Eurodiversity. METHECO. The role of microbial diversity in the dynamics and stability of global methane consumption: microbial methane oxidation as a model-system for microbial ecology
    Budget: €202,214
    Max-Planck Institute for terrestrial Microbiology, Marburg; University of East Anglia, Norwich; Agricultural University Uppsala; University of Tromso; Austrian Institute of Technology, Seibersdorf.

Editorial board memberships

  • 2000–Present
    Applied and Environmental Microbiology
  • 2012–2021
    ISME Journal
  • 2010–2022
    Frontiers in Microbiology
  • 2012–Present
    Plant and Soil

PhD students

  • 2018–Present
    German Perez
    Netherlands Institute of Ecology, Wageningen University, ANII Uruguay
    Promotors and Copromotors: Prof. Wietse de Boer, dr Paul L.E. Bodelier
  • 2019–2023
    Vania Scarlet Chavez-Rico
    Wetsus, Wageningen University
    Promotors and Copromotors: Prof. dr. Cees Buisman, dr. Miriam van Eekert, dr. Paul L.E. Bodelier
  • 2019–Present
    Stijn van den Bergh
    Netherlands Institute of Ecology, Wageningen University
    Promotors and Copromotors: Prof. Wietse de Boer, dr. Paul L.E. Bodelier
  • 2015–2022
    Sytske M. Drost
    Netherlands Institute of Ecology, Wageningen University
    Promotors and Copromotors: Prof. Wietse de Boer, dr. Paul L.E. Bodelier
  • 2014–2018
    Amber Heijboer
    Netherlands Institute of Ecology, Wageningen University, Utrecht University
    Promotors and Copromotors: Prof. George Kowalchuk, prof Peter de Ruiter, dr. Paul L.E. Bodelier
  • 2014–2017
    Elvyra Schnyder
    University of Zurich
    Promotors and Copromotors: Prof. Bernard Schmidt, dr. Pascal Niklaus, dr. Paul L.E. Bodelier
  • 2010–2014
    Anne Daebeler
    Netherlands Institute of Ecology, Utrecht University
    Promotors and Copromotors: Prof. Riks Laanbroek, dr. Mariet Hefting, dr Paul L.E. Bodelier
  • 2008–2012
    Anne Steenbergh
    Netherlands Institute of Ecology, Utrecht University
    Promotors and Copromotors: Prof. Riks Laanbroek, dr Paul L.E. Bodelier
  • 2008–2012
    Liesbeth Vissers
    Netherlands Institute of Ecology, Utrecht University
    Promotors and Copromotors: Prof. Riks Laanbroek, prof. Gerard Muyzer, dr Paul L.E. Bodelier
  • 2007–2011
    Juanjuan Wang
    Netherlands Institute of Ecology, Utrecht University
    Promotors and Copromotors: Prof. Riks Laanbroek, prof. Gerard Muyzer, dr Paul L.E. Bodelier
  • 2003–2007
    Marzia Miletto
    Netherlands Institute of Ecology, Utrecht University
    Promotors and Copromotors: Prof. Riks Laanbroek, prof. Gerard Muyzer, dr Paul L.E. Bodelier
  • 2003–2007
    Manuela Coci
    Netherlands Institute of Ecology, Utrecht University
    Promotors and Copromotors: Prof. Riks Laanbroek, dr Paul L.E. Bodelier
  • 2023–Present
    Ruchen Tian
    Netherlands Institute of Ecology, Wageningen University
    Promotors and Copromotors: Wim van der Putten, Paul Bodelier, Kyle Mason-Jones
  • 2022–Present
    Lourens van Langeveld
    Wetsus, Wageningen University
    Promotors and Copromotors: Cees Buisman, Miriam van Eekert, Paul Bodelier

Ancillary activities


Peer-reviewed publications

  • Soil Biology and Biochemistry

    Soil aggregate stability governs field greenhouse gas fluxes in agricultural soils

    Stijn van den Bergh, Iris Chardon, Marcio Fernandes Alves Leite, Gerard Korthals, Jochen Mayer, Mathias Cougnon, Dirk Reheul, Wietse de Boer, Paul Bodelier
    Agriculture is responsible for 30–50% of the yearly CO2, CH4, and N2O emissions. Soils have an important role in the production and consumption of these greenhouse gases (GHGs), with soil aggregates and the inhabiting microbes proposed to function as biogeochemical reactors, processing these gases. Here we studied, for the first time, the relationship between GHG fluxes and aggregate stability as determined via laser diffraction analysis (LDA) of agricultural soils, as well as the effect of sustainable agricultural management strategies thereon. Using the static chamber method, all soils were found to be sinks for CH4 and sources for CO2 and N2O. The application of organic amendments did not have a conclusive effect on soil GHG fluxes, but tilled soils emitted more CO2. LDA was a useful and improved method for assessing soil aggregate stability, as it allows for the determination of multiple classes of aggregates and their structural composition, thereby overcoming limitations of traditional wet sieving. Organic matter content was the main steering factor of aggregate stability. The presence of persistent stable aggregates and the disintegration coefficient of stable aggregates were improved in organic-amended and no-tilled soils. Predictive modelling showed that, especially in these soils, aggregate stability was a governing factor of GHG fluxes. Higher soil CH4 uptake rates were associated with higher aggregate stability, while CO2 and N2O emissions increased with higher aggregate stability. Altogether, it was shown that sustainable agricultural management strategies can be used to steer the soil's aggregate stability and, both consequently and outright, the soil GHG fluxes, thereby creating a potential to contribute to the mitigation of agricultural GHG emissions.
  • Microorganisms

    Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils

    German Perez, Sascha Krause, Paul Bodelier, Marion Meima-Franke, Leonardo Pitombo, Pilar Irisarri
    Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria–methanotrophs and their respective traits.
  • Ecology

    Experimental erosion of microbial diversity decreases soil CH4 consumption rates

    Elvira Schnyder, Paul Bodelier, Martin Hartmann, Ruth Henneberger, Pascal A. Niklaus

    Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 101–107-fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.
  • Waste Management

    The intrinsic methane mitigation potential and associated microbes add product value to compost

    Stijn van den Bergh, Iris Chardon, Marion Meima-Franke, Ohana Costa, Gerard Korthals, Wietse de Boer, Paul Bodelier
    Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h−1 g dw compost−1 and 25.19 ± 6.75 pmol h−1 g dw compost−1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.
  • Soil Biology and Biochemistry

    Do temporal and spatial heterogeneity modulate biodiversity–functioning relationships in com-munities of methanotrophic bacteria?

    Elvira Schnyder, Paul Bodelier, Martin Hartmann, Ruth Henneberger, Pascal A. Niklaus

    Positive relationships between biodiversity functioning have been found in communities of plants but also of soil microbes. The beneficial effects of diversity are thought to be driven by niche partitioning among community members, which leads to more complete or more efficient community-level resource use through various mechanisms. An intriguing related question is whether environmentally more heterogeneous habitats provide a larger total niche space and support stronger diversity—functioning relationships because they harbor more species or allow species to partition the available niche space more efficiently. Here, we tested this hypothesis by assembling communities of 1, 2 or 4 methanotrophic isolates and exposing them to temporally (constant or diurnal temperature cycling) and structurally (one or two aggregate size classes) more heterogeneous conditions. In total, we incubated 396 microcosms for 41 days and found that more biodiverse communities consumed more methane (CH4) and tended to have a larger community size (higher pmoA copy numbers). Diurnal temperature cycling strongly reduced CH4 oxidation and growth, whereas soil aggregate composition and diversity had no detectable effect. Biodiversity effects varied greatly with the identity of the community members that were combined. With respect to community level CH4 consumption, strain interactions were positive or neutral but never negative, and could neither be explained by 14 structural and function traits we collected or by the observed competitive hierarchy among the strains. Overall, our results indicate that methanotrophic diversity promotes methanotrophic community functioning. The strains that performed best varied with environmental conditions, suggesting that a high biodiversity is important for maintaining methanotrophic functioning as environmental conditions fluctuate over time.
  • Science of the Total Environment

    Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave

    Xiaoyu Cheng, Zhilin Zeng, Xiaoyan Liu, Lu Li, Hongmei Wang, Rui Zhao, Paul Bodelier, Weiqi Wang, Yiheng Wang, Olli H. Tuovinen
    Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogenic community composition and their interaction with MOBs in the Heshang Cave to comprehensively understand methane cycling in subsurface biosphere. MOBs in karst cave were dominated by high-affinity MOB, upland soil cluster (USC), with USCγ pmoA gene abundance within the range of 1.34 × 104 to 1.8 × 107 copies·g−1 DW. In contrast, methanogens were dominated by Methanoregula and cluster ZC-I. The mcrA numbers were 7.21 × 103 to 8.31 × 104 copies·g−1 DW, 1–3 orders of magnitude lower than those of MOB. The inter-domain network analysis indicated that MOBs and methanogens cooperated more in the interior of the cave. Despite of the higher number of methanogenic nodes in the network, MOB dominated the keystone taxa, suggesting a leading functional role of MOB. MOB in caves showed a comparable with or higher potential methane oxidizing rate (PMOR, 0.63 ng CH4·g−1 DW·h−1 in sediment versus 11.02 ng CH4·g−1 DW·h−1 in weathered rock) than those in soils, whereas methane produced by methanogens was undetected. Collectively, high absolute abundances of MOB, high PMORs, the dominance of methanotrophic keystone taxa in the inter-domain network confirmed the superiority of MOBs over methanogens in the oligotrophic karst cave, mounting new evidence on caves as an important methane sink in terms of the interaction between methanogens and MOBs.
  • Environmental Technology & Innovation

    Effect of pre-treatment processes of organic residues on soil aggregates

    Vania Scarlet Chavez-Rico, Stijn van den Bergh, Paul Bodelier, Miriam van Eekert, Yujia Luo, Klaas G.J. Nierop, Valentina Sechi, Adrie Veeken, Cees N.J. Buisman
    Process technologies, such as composting, anaerobic digestion, or lactic acid fermentation, greatly influence the resulting organic amendments (OAs) characteristics even when the same raw material is used. However, it is still unclear how these process technologies indirectly modify the effect of OAs on soil microbial activity and soil aggregation. To determine the effect of OA produced using pre-treatment technologies on the soil microbial activity and soil aggregation, we ran a soil column experiment in which we applied compost, digestate and lactic acid fermentation product made of the same model bio-waste. The results indicated that OAs produced under anaerobic conditions (fermented product and digestate) increased microbial activity, biomass, and soil micro- and macro-aggregation compared to compost and control treatments. Soil microbial activity strongly correlated to C, Ca, Mg, extracellular polymeric substances (EPS), fungal biomass, and macroaggregate formation (, ). Simultaneously, soil macroaggregate formation strongly correlated to water-extractable C, EPS, cation exchange capacity, K, Mg, Na, and bacterial biomass (, ). This study demonstrated that the effect of an organic substrate on soil properties can be modified towards desired effects using different pre-treatment technologies, suggesting the possibility of “engineer” OAs.
  • Frontiers in Microbiology

    Archaea and their interactions with bacteria in a karst ecosystem

    Xiaoyu Cheng, Xing Xiang, Yuan Yun, Weiqi Wang, Hongmei Wang, Paul Bodelier
    Karst ecosystems are widely distributed around the world, accounting for 15–20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4+ availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2−. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.
  • Frontiers in Environmental Science

    Relief of phosphate limitation stimulates methane oxidation

    Thomas P. A. Nijman, André M. Amado, Paul Bodelier, Annelies Veraart
    Aquatic ecosystems such as shallow lakes and wetlands are important emitters of the greenhouse gas methane (CH4). Increased phosphorus (P) loading is expected to increase CH4 production in these ecosystems. This increased CH4 production can potentially be mitigated by increased CH4 oxidation, but how P availability affects methane-oxidizing bacterial (MOB) community composition and potential CH4 oxidation remains to be tested. Here, we incubated MOB from sediments of four subtropical lakes of different trophic states for 7 days at different phosphate (PO43-) concentrations to determine the effects of P on MOB community composition and potential CH4 oxidation. We measured CH4 consumption daily and compared CH4 oxidation during the exponential growth phase. Furthermore, we determined MOB community composition at the end of the incubations using qPCR of the pmoA gene. To test for differences in N and P uptake, we determined bacterial biomass N and P content. We found that increases in PO43- concentrations until 10 µM significantly increased CH4 oxidation. PO43- also increased bacterial biomass P content, while N content was not affected. MOB community composition was not affected by PO43- but more strongly correlated to lake of origin, likely due to the short duration of the incubations. Our results show that PO43- can not only stimulate CH4 oxidation indirectly through increased CH4 production, but also directly by increasing MOB growth. Importantly, these effects only occur at low PO43- concentrations, indicating that at high nutrient loads the increased CH4 oxidation will likely not mitigate the increased CH4 production.
  • International Journal of Systematic and Evolutionary Microbiology

    Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster

    Martin W. Hahn, Alexandra Pitt, Johanna Schmidt, Ulrike Koll, Jacqueline Wolf, William B. Whitman, Paul Bodelier, Meina Neumann-Schaal

    We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65T (=CCUG 56422T=DSM 107630T) and MWH-P2sevCIIIbT (=CCUG 56420T=DSM 107629T), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family Alcaligenaceae and revealed Orrella amnicola and Orrella marina (= Algicoccus marinus) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus Orrella represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65T and the new genus Jezberella gen. nov. and the new species J. montanila-cus sp. nov. to harbour strain MWH-P2sevCIIIbT. Furthermore, we propose the reclassification of the species Orrella amnicola in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.
  • 2022

    Microbial trait-based approaches for agroecosystems

    Sascha Krause, S.A. Bertilsson, Hans-Peter Grossart, Paul Bodelier, Peter M. van Bodegom, J.T. Lennon, Laurent Philippot, X. Le Roux
    Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning toward more sustainable practices. In particular, innovation and developments targeting the aboveground and belowground components of agroecosystems should be informed by frameworks and approaches that harness the—in particular functional—diversity of complex microbial communities. Here, we review and discuss microbial trait-based approaches that will help us understand and steer agroecosystem functioning in the face of global change. We highlight how trait-based approaches can improve agricultural practices related to soil functioning (e.g., soil fertility and aggregation); climate regulation (e.g., carbon storage and greenhouse gas emissions) and adaptation to climate change; plant health; and reduction of contaminant-related hazards for human health. We also consider how microbial trait-based approaches can be used as a tool to improve cultivated plant performance through artificial selection and microbiome engineering. Last, we discuss the inherent obstacles associated with the development and implementation of trait-based approaches owing to strong interactions within microbial communities and linkages between plants and the soil environment. Despite these obstacles, microbial trait-based approaches hold promise for the sustainable management of agricultural ecosystems needed to feed and nourish a rapidly growing human population.
  • Frontiers in Microbiology

    Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities

    Gabriel G.T.N. Monteiro, Dayane J. Barros, Gabriele V.M. Gabriel, Andressa M. Venturini, Tomás G.R. Veloso, Gisele Herbst Vazquez, Luciana C. Oliveira, Vania Neu, Paul Bodelier, Cleber Fernando M. Mansano, Siu Mui Tsai, Acácio A. Navarrete

    Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2), which can be further oxidized to nitrate (NO3). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 and NO3, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4+) and NO3—and NO2—dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.
  • Hydrobiologia

    A combination of host ecology and habitat but not evolutionary history explains differences in the microbiomes associated with rotifers

    Ester M. Eckert, Tommaso Cancellario, Paul Bodelier, Steven A.J. Declerck, Liang Diwen, Sainur Samad, Monika Winder, Libin Zhou, Diego Fontaneto
    The holobiont concept places emphasis on the strict relationship between a host and its associated microbiome, with several studies supporting a strong effect of the quality of the microbiome on the host fitness. The generalities of the holobiont have been questioned for several invertebrates, including zooplankton. Here we assess the role of host ecology, habitat, and evolutionary history to explain the differences in the microbiomes associated with rotifers, across a broad taxonomic spectrum and from different habitats. The analyses of 93 rotifer-associated microbiomes from 23 rotifer host species revealed that a combination of effects from the host ecology and its habitat seem to be stronger than host phylogenetic distances in explaining differences in microbial composition of the microbiomes. This pattern is in line with the idea of habitat filtering being a stronger explanation than co-evolution in shaping the relationship between a microbiome and its rotifer host.
  • Frontiers in Microbiology

    Methane-Derived Carbon As A Driver For Cyanobacterial Growth

    Slawek Cerbin, German Perez, Michal Rybak, Łukasz Wejnerowski, Adam Konowalczyk, Nico Helmsing, Suzanne M.H. Naus-Wiezer, Marion Meima-Franke, Łukasz Pytlak, Ciska Raaijmakers, Witold Nowak, Paul Bodelier
    Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ13C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, 13C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.
  • Microorganisms

    Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments

    Júlia B. Gontijo, Fabiana S. Paula, Andressa M. Venturini, Jéssica A. Mandro, Paul Bodelier, Siu Mui Tsai

    Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains.
  • Microorganisms


    Ohana Costa, Mattias De Hollander, Eiko Kuramae, Paul Bodelier

    The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.
  • Nature Microbiology

    Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem

    R. Van Spanning, Q. Guan, Chrats Melkonian, James Gallant, Lubos Polerecky, Jean-François Flot, Bernd W Brandt, M. Braster, Paul Iturbe-Espinoza, Joost Aerts, Marion Meima-Franke, S. Piersma, Catalin M. Bunduc, Roy Ummels, Arnab Pain, Emily J. Fleming, Nicole van der Wel, Vasile D. Gherman, Serban M. Sarbu, Paul Bodelier, W. Bitter
    So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth’s atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using 13C-labelled methane confirmed that Candidatus M. methanotrophicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.
  • Waste Management

    Producing organic amendments: physicochemical changes in biowaste used in anaerobic digestion, composting, and fermentation

    Vania Chavez, Paul Bodelier, M.H.A. van Eekert, Valentina Sechi, Annegreet Veeken, Cees N.J. Buisman
    Organic amendments (OAs) produced via composting, anaerobic digestion, or lactic acid fermentation, can be used to replenish soil carbon. Not all OAs production technologies preserve C and nutrients in the same way. In this study, we compared the influence of these technologies (i.e., treatments) on C and nutrient preservation and OAs chemical composition after production. We produced compost, digestate, and lactic-acid fermentation product using the same biowaste-resembling model substrate using three reactors under laboratory conditions. We compared the chemical conversions and end-products using mass balances over C, N, and P. Overall results show that losses are minimal under reducing production conditions. Fermentation and digestion conserved 99% and 64% of C; and 93% and 100% of N, respectively. While compost conservation of nutrients was limited to 25% of C and 38% of N. Digestate had the highest concentrations of C, N, and P in the water-soluble phase, enabling their accessibility for soil microbes. Concentrations in the fermentation product were one order of magnitude lower but still higher than in compost. The treatments also influence the final availability of C, N, and P, which could potentially improve the fertilising and soil-improving properties of produced OAs. Our results show that under reducing conditions, losses of C, N, and P can be decreased while increasing OAs applications in terms of sources for soil-microbial development.
  • Biology and Fertility of Soils

    Greenhouse gas (CO2, CH4, and N2O) emissions after abandonment of agriculture, and insights on the response of the (de)nitrifier

    Alaa H.M. El-Hawwary, Kristof Brenzinger, Hyo Jung Lee, Annelies Veraart, Elly Morrien, Michael Schloter, Wim H. van der Putten, Paul Bodelier, Adrian Ho
    The GHG (CO2, CH4, N2O) emission potential along a chronosequence of former agricultural soils abandoned for 9 to 32 years were compared to an actively managed (on-going) agricultural soil (reference). The soils were incubated in mesocosms with and without manure amendment, and microbial functional groups involved in nitrous oxide emission were quantitatively assessed. Carbon dioxide emission significantly increased after agriculture abandonment (< 24 years) consistent with higher decomposition rate, but total emission decreased in the long term (> 29 years). With the cessation of agriculture, the abandoned sites generally became a net methane sink. Notably, total nitrous oxide emission showed a significant monotonic decrease over years of abandonment in response to manure amendment, possibly reflecting an altered capacity for (de)nitrification as indicated in the response of the (de)nitrifier abundance. Overall, our findings suggest that the GHG legacy of agriculture diminishes over time (> 29 years), with lowered GHG emissions and global warming potential (GWP) after abandonment of agriculture.
  • Environmental Microbiology Reports

    Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves

    Xiaoyu Cheng, Hongmei Wang, Zhilin Zeng, Lu Li, Rui Zhao, Paul Bodelier, Yiheng Wang, Xiaoyan Liu, Chuntian Su, Shuangjiang Liu

    Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g−1 DW h−1, which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.
  • Freshwater Biology

    Trophic and non-trophic effects of fish and macroinvertebrates on carbon emissions

    Maite Colina, M. Meerhoff, German Perez, Annelies Veraart, Paul Bodelier, Antoon van der Horst, Sarian Kosten
    Shallow aquatic systems exchange large amounts of carbon dioxide (CO2) and methane (CH4) with the atmosphere. The production and consumption of both gases is determined by the interplay between abiotic (such as oxygen availability) and biotic (such as community structure and trophic interactions) factors.
    Fish communities play a key role in driving carbon fluxes in benthic and pelagic habitats. Previous studies indicate that trophic interactions in the water column, as well as in the benthic zone can strongly affect aquatic CO2 and CH4 net emissions. However, the overall effect of fish on both pelagic and benthic processes remains largely unresolved, representing the main focus of our experimental study.
    We evaluated the effects of benthic and pelagic fish on zooplankton and macroinvertebrates; on CO2 and CH4 diffusion and ebullition, as well as on CH4 production and oxidation, using a full-factorial aquarium experiment. We compared five treatments: absence of fish (control); permanent presence of benthivorous fish (common carps, benthic) or zooplanktivorous fish (sticklebacks, pelagic); and intermittent presence of carps or sticklebacks.
    We found trophic and non-trophic effects of fish on CO2 and CH4 emissions. Intermittent presence of benthivorous fish promoted a short-term increase in CH4 ebullition, probably due to the physical disturbance of the sediment. As CH4 ebullition was the major contributor to the total greenhouse gas (GHG) emissions, incidental bioturbation by benthivorous fish was a key factor triggering total carbon emissions from our aquariums.
    Trophic effects impacted GHG dynamics in different ways in the water column and the sediment. Fish predation on zooplankton led to a top-down trophic cascade effect on methane-oxidising bacteria. This effect was, however, not strong enough as to substantially alter CH4 diffusion rates. Top-down trophic effects of zooplanktivorous and benthivorous fish on benthic macroinvertebrates, however, were more pronounced. Continuous fish predation reduced benthic macroinvertebrates biomass decreasing the oxygen penetration depth, which in turn strongly reduced water–atmosphere CO2 fluxes while it increased CH4 emission.
    Our work shows that fish can strongly impact GHG production and consumption processes as well as emission pathways, through trophic and non-trophic effects. Furthermore, our findings suggest their impact on benthic organisms is an important factor regulating carbon (CO2 and CH4) emissions.
  • Microbiology spectrum

    USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves

    Xiaoyu Cheng, Xiaoyan Liu, Hongmei Wang, Chuntian Su, Rui Zhao, Paul Bodelier, Weiqi Wang, Liyuan Ma, Xiaolu Lu
    Karst caves have recently been demonstrated to act as a sink for atmospheric methane, due in part to consumption by microbes residing in caves that can oxidize methane at atmospheric levels. However, our knowledge about the responsible atmospheric methane-oxidizing bacteria (atmMOB) in this vast habitat remains limited to date. To address this issue, weathered rock samples from three karst caves were collected in Guilin City and subjected to high-throughput sequencing of pmoA and 16S rRNA genes. The results showed that members of the high-affinity upland soil cluster (USC), especially upland soil cluster gamma (USCγ), with absolute abundances of 104 to 109 copies · g−1 dry sample, dominated the atmMOB communities, while Proteobacteria and Actinobacteria dominated the overall bacterial communities. Moreover, USCγ was a keystone taxon in cooccurrence networks of both the atmMOB and the total bacterial community, whereas keystone taxa in the bacterial network also included Gaiella and Aciditerrimonas. Positive links overwhelmingly dominated the cooccurrence networks of both atmMOB and the total bacterial community, indicating a consistent response to environmental disturbances. Our study shed new insights on the diversity and abundances underlining atmMOB and total bacterial communities and on microbial interactions in subterranean karst caves, which increased our understanding about USC and supported karst caves as a methane sink.
    IMPORTANCE Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidation in these ecosystems. Our pmoA high-throughput results from weathered rock samples from three karst caves in Guilin City confirm the wide occurrence of atmospheric methane-oxidizing bacteria in this habitat, especially those affiliated with the upland soil cluster, with a gene copy number of 104 to 109 copies per gram dry sample. Methanotrophs and the total bacterial communities had more positive than negative interactions with each other as indicated by the cooccurrence network, suggesting their consistent response to environmental disturbance. Our results solidly support caves as an atmospheric methane sink, and they contribute to a comprehensive understanding of the diversity, distribution, and interactions of microbial communities in subsurface karst caves.
  • Biology and Fertility of Soils

    Steering microbiomes by organic amendments towards climate-smart agricultural soils

    Kristof Brenzinger, Ohana Costa, Adrian Ho, Guusje Koorneef, Bjorn J.M. Robroek, Douwe Molenaar, Gerard Korthals, Paul Bodelier
    We steered the soil microbiome via applications of organic residues (mix of cover crop residues, sewage sludge + compost, and digestate + compost) to enhance multiple ecosystem services in line with climate-smart agriculture. Our result highlights the potential to reduce greenhouse gases (GHG) emissions from agricultural soils by the application of specific organic amendments (especially digestate + compost). Unexpectedly, also the addition of mineral fertilizer in our mesocosms led to similar combined GHG emissions than one of the specific organic amendments. However, the application of organic amendments has the potential to increase soil C, which is not the case when using mineral fertilizer. While GHG emissions from cover crop residues were significantly higher compared to mineral fertilizer and the other organic amendments, crop growth was promoted. Furthermore, all organic amendments induced a shift in the diversity and abundances of key microbial groups. We show that organic amendments have the potential to not only lower GHG emissions by modifying the microbial community abundance and composition, but also favour crop growth-promoting microorganisms. This modulation of the microbial community by organic amendments bears the potential to turn soils into more climate-smart soils in comparison to the more conventional use of mineral fertilizers.
  • Microbiology Resource Announcements

    Complete and Draft Genome Sequences of Aerobic Methanotrophs Isolated from a Riparian Wetland

    Ohana Costa, Marion Meima-Franke, Paul Bodelier
    Wetlands are important sources of methane emissions, and the impacts of these emissions can be mitigated by methanotrophic bacteria. The genomes of methanotrophs Methylomonas sp. strain LL1 and Methylosinus sp. strain H3A, as well as Methylocystis sp. strains H4A, H15, H62, and L43, were sequenced and are reported here.
  • Biology and Fertility of Soils

    Discrepancy in exchangeable and soluble ammonium-induced effects on aerobic methane oxidation

    Hester van Dijk, Thomas Kaupper, Clemens Bothe, Hyo Jung Lee, Paul Bodelier, Marcus A. Horn, Adrian Ho
    Ammonium-induced stimulatory, inhibitory, and/or neutral effects on soil methane oxidation have been attributable to the ammonium concentration and mineral forms, confounded by other edaphic properties (e.g., pH, salinity), as well as the site-specific composition of the methanotrophic community. We hypothesize that this inconsistency may stem from the discrepancy in the cation adsorption capacity of the soil. We postulate that the effects of ammonium on the methanotrophic activity in soil are more accurately portrayed by relating methane uptake rates to the soluble ammonium (bioavailable), rather than the exchangeable (total) ammonium. To reduce adsorption (exchangeable) sites for ammonium in a paddy soil, two successive pre-incubation steps were introduced resulting in a 1000-fold soil dilution (soil enrichment), to be compared to a soil slurry (tenfold dilution) incubation. Ammonium was supplemented as NH4Cl at 0.5–4.75gL−1 after pre-incubation. While NH4Cl significantly stimulated the methanotrophic activity at all concentrations in the soil slurry incubation, methane uptake showed a dose-dependent effect in the soil enrichment. The trend in methane uptake could be explained by the soluble ammonium concentration, which was proportionate to the supplemented ammonium in the soil enrichment. In the soil slurry incubation, a fraction (36–63%) of the supplemented ammonium was determined to be adsorbed to the soil. Accordingly, Methylosarcina was found to predominate the methanotrophic community after the incubation, suggesting the relevance of this methanotroph at elevated ammonium levels (< 3.25gL−1 NH4Cl). Collectively, our results showed that the soluble, rather than the exchangeable ammonium concentration, is relevant when determining the effects of ammonium on methane oxidation, but this does not exclude other (a)biotic factors concurrently influencing methanotrophic activity.
  • Biogeochemistry

    Active methane processing microbes and the disproportionate role of NC10 phylum in methane mitigation in Amazonian floodplains

    Marília de S. Bento, Dayane J. Barros, Maria Gabriella S. Araújo, Rafael Da Róz, Glauber Altrão Carvalho, Janaina Braga do Carmo, Rogério H. Toppa, Vania Neu, Bruce R. Forsberg, Paul Bodelier, Siu Mui Tsai, Acácio A. Navarrete
    Here we use a top-down and bottom-up approach in landscape ecology to analyze the active microbes processing methane fluxes (FCH4) in seasonally flooded-forest (FOR) and -traditional farming systems (TFS) in Amazonian floodplains flooded with black, white, and clear water. Our results revealed higher CH4 emissions from water-atmosphere interface in clear water floodplain, followed by black and white water floodplain, respectively. Active methanogenic and methanotrophic taxa were ubiquitous at 0–15 and 15–30 cm soil layer in FOR and TFS, with differences among the water types with respect to the richness, evenness and diversity of the methanogenic communities. These ecological results were not generalizable regarding to FOR and TFS sites, soil layers, and non-flooded and flooded periods. Despite the predominant oxidation of CH4 in the non-flooded period, higher richness and diversity of methanotrophs were revealed for FOR and TFS in the flooded period. In turn, the structure of the methanogenic and methanotrophic communities and their variation were influenced mainly by soil physicochemical factors, water type, soil depth and the presence of nitrifiers, as Nitrososphaera and Nitrospira. Our study reveals a signature across methanotrophic communities in soils from Amazon floodplain with different water types, with a putative disproportionate role of NC10 phylum in CH4 mitigation in natural and agricultural Amazonian floodplains. These findings open the possibilities to explore the role of NC10 phylum in the carbon cycling in Amazon.
  • Canadian Journal of Microbiology

    Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor

    Yan Zheng, Xiaolong Hu, Zhongjun Jia, Paul Bodelier, Zhiying Guo, Yong Zhang, Fangli Li, Xuesli Li, Peixin He
    It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4+, available P, available K, and Ca2+) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.
  • Journal of Applied Ecology

    Plant community flood resilience in intensively managed grasslands and the role of the plant economic spectrum

    Natalie Oram, Gerlinde De Deyn, Paul Bodelier, J.H.C. Cornelissen, J.W. van Groeningen, Diego Abalos
    The increasing frequency of extreme weather events, such as floods, requires management strategies that promote resilience of grassland productivity. Mixtures of plant species may better resist and recover from flooding than monocultures, as they could combine species with stress‐coping and resource acquisition traits. This has not yet been tested in intensively managed grasslands despite its relevance for enhancing agroecosystem resilience.
    Using intact soil cores from an 18‐month‐old field experiment, we tested how 11 plant communities (Festuca arundinacea, Lolium perenne, Poa trivialis and Trifolium repens in monoculture, two‐ and four‐species mixtures) resist and recover from repeated flooding in a 4‐month greenhouse experiment.
    We found that plant community composition, not whether the community was a mixture or monoculture, influenced the community's resistance to flooding, although most communities were able to resist and recover from both floods.
    The plant community's position on the leaf economic spectrum in flooded conditions was related to its resistance to and recovery from flooding. Resistance to and recovery from a severe flood were related to flood‐induced intraspecific trait variation, causing a shift in the community's position on the leaf resource economic spectrum. In flooded conditions, resource‐conservative communities (characterized by low specific leaf area, low leaf nitrogen content and high leaf dry matter content) better resisted and recovered from flooding. The community's position on the root resource economic spectrum was less connected to the community's resistance and recovery.
    Synthesis and applications. Our study shows that in flooded conditions, resource‐conservative plant communities are more resilient to flooding than resource‐acquisitive communities in an intensively managed grassland. This suggests that plant community position on the leaf economic spectrum, as well as species’ flood‐induced intraspecific variation, should be considered when designing grasslands to withstand increasing flood frequency and severity.
  • Frontiers in Microbiology

    Grand challenges in Terrestrial Microbiology: moving on from a decade of progress in microbial biogeochemistry

    Paul Bodelier, Sara Hallin
    Grand Challenges in Terrestrial Microbiology: Moving on From a Decade of Progress in Microbial Biogeochemistry
  • Frontiers in Microbiology

    Niche Differentiation of Host-associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes

    Sainur Samad, Hyo Jung Lee, Slawek Cerbin, Marion Meima-Franke, Paul Bodelier
    It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their “host”. However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and phytoplankton-&-particle-associated (PPA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PPA and zooplankton associated microbes; and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PPA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analysed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PPA. Indicator species analysis showed that 9 %, 8 % 12 % and 21% unique OTUs were significantly associated with copepods, cladocerans, bacterioplankton, and PPA, respectively. Surprisingly, genera of methane oxidizing bacteria (MOB), methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PPA. Our study clearly demonstrates niche differentiation of pelagic microbes which is affected by warming with possible impact on biogeochemical cycling in freshwater systems.
  • Soil Biology & Biochemistry

    DNA stable-isotope probing highlights the effects of temperature on functionally active methanotrophs in natural wetlands

    Liyan Zhang, Marc G. Dumont, Paul Bodelier, Jonathan M. Adams, Dan He, Haiyan Chu
    Microbial methane (CH4) oxidation is a major global sink of CH4. Aerobic CH4-oxidizing bacteria (methanotrophs) represent a biological model system for CH4 consumption and is very sensitive to climate warming, but still poorly understood. Here we used DNA stable-isotope probing (SIP) coupled with high-throughput sequencing of 13C-DNA to compare active methanotrophs incubated at 10, 15, 20, and 25 °C in 13CH4-fed microcosms from two geographically distinct natural wetlands: Sanjiang Plain wetland in northeast China and Haibei wetland in Tibet Plateau. In both wetlands, CH4 oxidation potential was enhanced with increasing temperature. Community profiling revealed that type I methanotrophs dominated CH4 oxidation, although a small portion (2.76%–17.14%) of type II methanotrophs (Methylocystis, Methylosinus/Methylocystis) were significantly stimulated at 20 °C and 25 °C. 13C-labeled indicator species included Methylobacter, Methylocystis, and Methylosarcina species in Sanjiang Plain, and Methylobacter and Methylosarcina species in Haibei. Network analysis demonstrated positive co-occurrence of species between genera of Methylobacter, Methylosarcina, and Methylocystis with shifts in temperature, while interspecies interactions between Methylobacter and Methylomonas correlated negatively, and Methylobacter and Methylosinus/Methylocystis positively. Partial least squares path modeling illustrated that the direct effects of temperature on CH4 oxidation were stronger in northeast China than Tibet Plateau, and temperature could also indirectly influence CH4 oxidation via shifts in the methanotroph communities. Collectively, these results provide insights into how temperature could influence methanotrophy in natural wetlands under future climate scenarios.
  • Science of the Total Environment

    Can flooding-induced greenhouse gas emissions be mitigated by trait-based plant species choice?

    Natalie J. Orama, J.W. van Groeningen, Paul Bodelier, Kristof Brenzinger, Johannes H. C. Cornelissen, Gerlinde De Deyn, Diego Abalos
  • FEMS Microbiology Ecology

    Response of a methane-driven interaction network to stressor intensification

    Adrian Ho, L.W. Mendes, Hyo Jung Lee, Thomas Kaupper, Yongliang Mo , Anja Poehlein, Paul Bodelier, Zhongjun Jia, Marcus A. Horn
    Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5–4.75 g L−1, in 0.25–0.5 g L−1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.
  • mSphere

    Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments

    Mohammad Ghashghavi, Svetlana Belova, Paul Bodelier, Svetlana Dedysh, Martine A.R. Kox, Daan Speth, P. Frenzel, Mike S.M. Jetten, Sebastian Lücker, Claudia Lüke
  • Soil Biology & Biochemistry

    Rice straw serves as additional carbon source for rhizosphere microorganisms and reduces root exudate consumption

    Sarah A. Maarastawi, Katharina Frindte, Paul Bodelier, C. Knief
    Straw application is a common agricultural fertilisation practice, providing an additional carbon and nutrient source for soil microorganisms. We investigated the influence of rice straw application on root exudate consuming microorganisms in the rhizosphere of Zea mays based on 13CO2 pulse labelling and phospholipid fatty acid stable isotope probing (PLFA-SIP) in a paddy soil under rice-maize crop rotation. The application of straw decreased the labelling of microbial PLFAs in the rhizosphere of 30 and 40 day old maize plants by 70% compared to treatments without straw. This decrease could partially be explained by a lower rate of CO2 assimilation of the plant in the presence of rice straw. In addition, the uptake of root exudates by rhizosphere organisms was decreased due to the presence of the rice straw, which serves as an additional carbon source for these microorganisms.
  • Water Research

    Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater

    Marcelle van der Waals, Caroline M. Plugge, Marion Meima-Franke, Pieter de Waard, Paul Bodelier, Hauke Smidt, Jan Gerritse
    EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater was used to (i) assess the potential for EtBE degradation, (ii) resolve the EtBE degradation pathway and (iii) characterize the phylogenetic composition of the bacterial community involved in EtBE degradation in contaminated groundwater. In an unamended microcosm, algal growth was observed after eight weeks when exposed to a day-night light cycle. In the fed-batch reactor, oxygen produced by the algae Scenedesmus and Chlorella was used by bacteria to degrade 50 μM EtBE replenishments with a cumulative total of 1250 μM in a day/night cycle (650 lux), over a period of 913 days. The microbial community in the fed-batch reactor degraded EtBE, using a P450 monooxygenase and 2-hydroxyisobutyryl-CoA mutase, to tert-butyl alcohol (TBA), ethanol and CO2 as determined using 13C nuclear magnetic resonance spectroscopy (NMR) and gas chromatography. Stable isotope probing (SIP) with 13C6 labeled EtBE in a fed-batch vessel showed no significant difference in community profiles of the 13C and 12C enriched DNA fractions, with representatives of the families Halomonadaceae, Shewanellaceae, Rhodocyclaceae, Oxalobacteraceae, Comamonadaceae, Sphingomonadaceae, Hyphomicrobiaceae, Candidatus Moranbacteria, Omnitrophica, Anaerolineaceae, Nocardiaceae, and Blastocatellaceae. This is the first study describing micro-oxic degradation of EtBE by an algal-bacterial culture. This algal-bacterial culture has advantages compared with conventional aerobic treatments: (i) a lower risk of EtBE evaporation and (ii) no need for external oxygen supply in the presence of light. This study provides novel leads towards future possibilities to implement algal-bacterial consortia in field-scale groundwater or wastewater treatment.
  • Soil Biology & Biochemistry

    Unexpected role of canonical aerobic methanotrophs in upland agricultural soils.

    Adrian Ho, Hyo Jung Lee, Max Reumer, Marion Meima-Franke, Ciska Raaijmakers, Hans Zweers, Wietse de Boer, Wim H. van der Putten, Paul Bodelier
    Aerobic oxidation of methane at (circum-)atmospheric concentrations (<40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have been detected along with the high-affinity ones, their role as a methane sink in upland soils remains enigmatic. Here, we show that canonical methanotrophs can contribute to (circum-)atmospheric methane uptake in agricultural soils. We performed a stable-isotope 13CCH4 labelling incubation in the presence and absence of bio-based residues that were added to the soil to track the flow of methane. Residue amendment transiently stimulated methane uptake rate (<50 days). Soil methane uptake was sustained throughout the incubation (130 days), concomitant to the enrichment of 13CCO2. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs with cultured representatives. 16S rRNA and pmoA gene sequence analyses revealed that the as-yet-uncultured high-affinity methanotrophs were virtually absent in these soils. The stable-isotope labelling approach allowed to attribute soil methane uptake to canonical methanotrophs, whereas these were not expected to consume (circum-)atmospheric methane. Our findings thus revealed an overlooked reservoir of high-affinity methane-oxidizers represented by the canonical methanotrophs in agriculture-impacted upland soils. Given that upland agricultural soils have been thought to marginally or do not contribute to atmospheric methane consumption due to the vulnerability of the high-affinity methanotrophs, our findings suggest a thorough revisiting of the contribution of agricultural soils, and the role of agricultural management to mitigation of climate change.
  • 2019

    Methanotroph Ecology, Environmental distribution and functioning.

    Paul Bodelier, German Perez, Annelies Veraart, Sascha Krause
    The dynamics of methane concentrations in the atmosphere in recent decades has demonstrated many anomalies which are poorly understood. The only biological way of degrading this potent greenhouse gas is by microbial oxidation. Aerobic methanotrophic bacteriaAerobic methanotrophic bacteria(MB) play an important role in many ecosystems worldwide degrading methane before it can escape to the atmosphere. This group of bacteria has intensively been studied as a model microbial functional guild because there is a strong link between the consumption of methane and the composition of MB communities, facilitating the study of microbial ``behavior'' in the environment. These studies have revealed a strong biogeographyBiogeographyof MB which is displayed in their phylogenyPhylogenynot only on the basis of single functional marker genes but also on genomeGenomesequence basis. Novel environmental controlling factors have been revealed (e.g. rare earth metals) as well as novel organisms with as yet unknown traits for MB. The resistance and resilience of methane consumption and methane consuming communities have been shown to depend on specific community members. The current knowledge on environmental distribution and of MB has led to propose a life-history scheme, classifying MB communities on their collective traits rather than singly on their capacity the oxidise methane alone.
  • Applied and Environmental Microbiology

    Impact of peat mining, and restoration on methane turnover potentials and methane-cycling microorganisms in a northern bog

    Max Reumer, M. Harnisz, Hyo Jung Lee, Andreas Reim, O. Grunert, A. Putkinen, Hannu Fritze, Paul Bodelier, Adrian Ho
    Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing its carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the peat physico-chemical properties, and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum post-harvest, methane turnover potentials and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in a natural (as a reference), actively mined, abandoned, and restored peatland over two consecutive years. In all sites, the methanogenic and methanotrophic population size were enumerated using qPCR assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition was determined using Illumina MiSeq sequencing of the mcrA gene, and a pmoA-based t-RFLP analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potentials, but rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.
  • Scientific Reports

    Environmental legacy contributes to the resilience of methane consumption in a laboratory microcosm system

    Sascha Krause, Marion Meima-Franke, Annelies Veraart, G. Ren, Adrian Ho, Paul Bodelier
    The increase of extreme drought and precipitation events due to climate change will alter microbial processes. Perturbation experiments demonstrated that microbes are sensitive to environmental alterations. However, only little is known on the legacy effects in microbial systems. Here, we designed a laboratory microcosm experiment using aerobic methane-consuming communities as a model system to test basic principles of microbial resilience and the role of changes in biomass and the presence of non-methanotrophic microbes in this process. We focused on enrichments from soil, sediment, and water reflecting communities with different legacy with respect to exposure to drought. Recovery rates, a recently proposed early warning indicator of a critical transition, were utilized as a measure to detect resilience loss of methane consumption during a series of dry/wet cycle perturbations. We observed a slowed recovery of enrichments originating from water samples, which suggests that the community’s legacy with a perturbation is a contributing factor for the resilience of microbial functioning.
  • Frontiers in Microbiology

    Resistance and Recovery of Methane Oxidizing Communities depends on Stress Regime and History

    Henri van Kruistum, Paul Bodelier, Adrian Ho, Marion Meima-Franke, Annelies Veraart
    Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors.
  • ISME Journal

    Living apart together – Bacterial volatiles influence methanotrophic growth and activity.

    Annelies Veraart, Paolina Garbeva, Femke van Beersum, Adrian Ho, Cees Hordijk, Marion Meima-Franke, Hans Zweers, Paul Bodelier
    Volatile organic compounds play an important role in microbial interactions. However, little is known about how volatile-mediated interactions modulate biogeochemical processes. In this study, we show the effect of volatile-mediated interaction on growth and functioning of aerobic methane-oxidizing bacteria, grown in co-culture with five different heterotrophs. Both growth and methane oxidation of Methylobacter luteus were stimulated by interaction with specific heterotrophs. In Methylocystis parvus, we observed significant growth promotion, while methane oxidation was inhibited. Volatolomics of the interaction of each of the methanotrophs with Pseudomonas mandelii, revealed presence of a complex blend of volatiles, including dimethylsulfide, dimethyldisulfide, and bicyclic sesquiterpenes. Although the ecological role of the detected compounds remains to be elucidated, our results provide unprecedented insights into interspecific relations and associated volatiles for stimulating methanotroph functioning, which is of substantial environmental and biotechnological significance.
  • Quaternary Science Reviews

    Abundance and δ13C values of fatty acids in lacustrine surface sediments: Relationships with in-lake methane concentrations

    Tabea Stötter, David Bastviken, Paul Bodelier, Maarten van Hardenbroek, Päivi Rinta, Jos Schilder, Carsten J. Schubert, Oliver Heiri
    Proxy-indicators in lake sediments provide the only approach by which the dynamics of in-lake methane cycling can be examined on multi-decadal to centennial time scales. This information is necessary to constrain how lacustrine methane production, oxidation and emissions are expected to respond to global change drivers. Several of the available proxies for reconstructing methane cycle changes of lakes rely on interpreting past changes in the abundance or relevance of methane oxidizing bacteria (MOB), either directly (e.g. via analysis of bacterial lipids) or indirectly (e.g. via reconstructions of the past relevance of MOB in invertebrate diet). However, only limited information is available about the extent to which, at the ecosystem scale, variations in abundance and availability of MOB reflect past changes in in-lake methane concentrations. We present a study examining the abundances of fatty acids (FAs), particularly of 13C-depleted FAs known to be produced by MOB, relative to methane concentrations in 29 small European lakes. 39 surface sediment samples were obtained from these lakes and FA abundances were compared with methane concentrations measured at the lake surface, 10 cm above the sediments and 10 cm within the sediments. Three of the FAs in the surface sediment samples, C16:1ω7c, C16:1ω5c/t, and C18:1ω7c were characterized by lower δ13C values than the remaining FAs. We show that abundances of these FAs, relative to other short-chain FAs produced in lake ecosystems, are related with sedimentary MOB concentrations assessed by quantitative polymerase chain reaction (qPCR). We observed positive relationships between methane concentrations and relative abundances of C16:1ω7c, C16:1ω5c/t, and C18:1ω7c and the sum of these FAs. For the full dataset these relationships were relatively weak (Spearman's rank correlation (rs) of 0.34–0.43) and not significant if corrected for multiple testing. However, noticeably stronger and statistically significant relationships were observed when sediments from near-shore and deep-water oxic environments (rs = 0.57 to 0.62) and those from anoxic deep-water environment (rs = 0.55 to 0.65) were examined separately. Our results confirm that robust relationships exist between in-lake CH4 concentrations and 13C-depleted groups of FAs in the examined sediments, agreeing with earlier suggestions that the availability of MOB-derived, 13C-depleted organic matter for aquatic invertebrates increases with increasing methane concentrations. However, we also show that these relationships are complex, with different relationships observed for oxic and anoxic sediments and highest values measured in sediments deposited in oxic environments overlain with relatively methane-rich water. Furthermore, although all three 13C-depleted FA groups identified in our survey are known to be produced by MOB, they also receive contributions by other organism groups, and this will have influenced their distribution in our dataset.
  • Frontiers in Microbiology

    Organic residue amendments to modulate greenhouse gas emissions from agricultural soils

    Kristof Brenzinger, Sytske Drost, Gerard Korthals, Paul Bodelier
    Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH4 oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO2 and N2O differed considerably between the treatments, CH4 fluxes remained stable. In contrast, in vitro CH4 oxidation showed a clear increase for all amendments over time. CO2 fluxes were mostly dependent on the amount of organic residue that was used, while N2O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO2, CH4, and/or N2O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.
  • Ecology

    Positive diversity-functioning relationships in model communities of methanotrophic bacteria

    Elvyra Schnyder, Paul Bodelier, Martin Hartmann, Ruth Henneberger, Pascal A. Niklaus
    Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding-effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH4 at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH4 consumption and community size was positively correlated. The temporal CH4 consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity–ecosystem function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.
  • Frontiers in Microbiology

    Modulation of litter decomposition by the soil microbial food web under influence of land use change

    Amber Heijboer, P.C. de Ruiter, Paul Bodelier, George Kowalchuk
    Soil microbial communities modulate soil organic matter (SOM) dynamics by catalyzing litter decomposition. However, our understanding of how litter-derived carbon (C) flows through the microbial portion of the soil food web is far from comprehensive. This information is necessary to facilitate reliable predictions of soil C cycling and sequestration in response to a changing environment such as land use change in the form of agricultural abandonment. To examine the flow of litter-derived C through the soil microbial food web and it’s response to land use change, we carried out an incubation experiment with soils from six fields; three recently abandoned and three long term abandoned fields. In these soils, the fate of 13C-labeled plant litter was followed by analyzing phospholipid fatty acids (PLFA) over a period of 56 days. The litter-amended soils were sampled over time to measure 13CO2 and mineral N dynamics. Microbial 13C-incorporation patterns revealed a clear succession of microbial groups during litter decomposition. Fungi were first to incorporate 13C-label, followed by G- bacteria, G+ bacteria, actinomycetes and micro-fauna. The order in which various microbial groups responded to litter decomposition was similar across all the fields examined, with no clear distinction between recent and long-term abandoned soils. Although the microbial biomass was initially higher in long-term abandoned soils, the net amount of 13C-labeled litter that was incorporated by the soil microbial community was ultimately comparable between recent and long-term abandoned fields. In relative terms, this means there was a higher efficiency of litter-derived 13C-incorporation in recent abandoned soil microbial communities compared to long-term abandoned soils, most likely due to a net shift from SOM-derived C towards root-derived C input in the soil microbial food web following land-abandonment.
  • Biogeosciences

    Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions

    Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, M.E. Bottcher, Matthias Winkel, Paul Bodelier, Susanne Liebner
    The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5mS cm−1, respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re)establishment of methanogens and slow (re)establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting.
  • Soil Biology & Biochemistry

    Soil warming and fertilization altered rates of nitrogen transformation processes and selected for adapted ammonia-oxidizing archaea in sub-arctic grassland soil

    Anne Daebeler, Paul Bodelier, Mariet M. Hefting, Tobias Rütting, (Riks) H.J. Laanbroek
    Abstract The balance of microbial nitrogen (N) transformation processes in sub-arctic terrestrial ecosystems is most likely affected by global change, with potential feedbacks to greenhouse gas emissions and eutrophication. Soil temperature and N availability – their global increases being two of the most pressing global change features - will be prime drivers of N dynamics and microbial community structure, but little is known about their interactive effects in these ecosystems. We utilized geothermally warmed soils from Iceland as a natural experiment for assessing fertilization and warming effects on gross soil N transformation processes. Experimental incubations of these soils at different temperatures coupled with a dual 15N-labelling/-tracing approach and pyrotag transcript-sequencing allowed for the analysis of independent and combined impacts of N fertilization and temperature shifts on gross N mineralisation, nitrification, and ammonium and nitrate immobilisation rates and archaeal ammonia-oxidizing (AOA) communities, being the key ammonia oxidizers in this soil. Gross nitrification in warmed soil was increased in relation to ambient temperature soil and exhibited a higher temperature optimum. Concomitantly, our results revealed a selection of AOA populations adapted to in situ soil temperatures. Phylogenetically distinct populations of actively ammonia-oxidizing archaea exhibited conserved temperature optima. N mineralization and nitrification showed higher sensitivities in response to short-term temperature changes if the soils had been warmed. In part, the influence of short-term temperature changes could however be neutralized by the effects of N fertilization. Long-term N fertilization alone affected only gross N mineralization. However, all gross N transformation rates were significantly altered by the interactive effects of N fertilization and soil warming. We conclude that in order to reliably predict effects of global change on sub-arctic soil N transformation processes we need to consider multiple interactions among global change factors and to take into account the capacity of soil microbial populations to adapt to global change conditions.
  • FEMS Microbiology Ecology

    Revisiting life strategy concepts in environmental microbial ecology

    Adrian Ho, Paolo Di Lonardo, Paul Bodelier
    Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies and determine at least to some extent their prevalence and distribution in the environment. Unlike animals and plants, there is an unprecedented diversity and intractable metabolic versatility among bacteria, making classification or grouping these microorganisms based on their functional traits as has been done in animal and plant ecology challenging. Nevertheless, based on representative pure cultures, microbial traits distinguishing different life strategies had been proposed, and had been the focus of previous reviews. In the environment, however, the vast majority of naturally-occurring microorganisms have yet to be isolated, restricting the association of life strategies to broad phylogenetic groups and/or physiological characteristics. Here, we reviewed the literature to determine how microbial life strategy concepts (i.e. copio- and oligo-trophic strategist, and Competitor-Stress tolerator-Ruderals, CSR framework) are applied in complex microbial communities. Because of the scarcity of direct empirical evidence elucidating the associated life strategies in complex communities, we rely heavily on observational studies determining the response of microorganisms to (a)biotic cues (e.g. resource availability) to infer microbial life strategies. Although our focus is on the life strategies of bacteria, parallels were drawn from the fungal community. Our literature search showed inconsistency in the community response of proposed copiotrophic- and oligotrophic-associated microorganisms (phyla level) to changing environmental conditions. This suggests that tracking microorganisms at finer phylogenetic and taxonomic resolution (e.g. family level or lower) may be more effective to capture changes in community response and/or that edaphic factors exert a stronger effect in community response. We discuss the limitations, and provide recommendations for future research applying microbial life strategies in environmental studies.
  • Global Change Biology Bioenergy

    Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition.

    Adrian Ho, Umer Zeeshan Ijaz, Thierry K.S. Janssens, Rienke Ruijs, Sang Yoon Kim, Wietse de Boer, Aad J Termorshuizen, Wim H. van der Putten, Paul Bodelier
    With the projected rise in the global human population, agriculture intensification and land-use conversion to arable fields is anticipated to meet the food and bio-energy demand to sustain a growing population. Moving towards a circular economy, agricultural intensification results in the increased re-investment of bio-based residues in agricultural soils, with consequences for microbially-mediated greenhouse gas (GHG) emission, as well as other aspects of soil functioning. To date, systematic studies to address the impact of bio-based residue amendment on the GHG balance, including the soil microorganisms, and nutrient transformation in agricultural soils are scarce. Here, we assess the Global Warming Potential (GWP) of in-situ GHG (i.e. CO2, CH4, and N2O) fluxes after application of six bio-based residues with broad C:N ratios (5-521) in two agricultural soils (sandy loam and clay; representative of vast production areas in north-western Europe). We relate the GHG emission to the decomposability of the residues in a litter bag assay, and determined the effects of residue input on crop (common wheat) growth after incubation. The shift in the bacterial community composition and abundance was monitored using IonTorrentTM sequencing and qPCR, respectively by targeting the 16S rRNA gene. The decomposability of the residues, independent of C:N ratio, was proportional to the GWP derived from the GHG emitted. The soils harbored distinct bacterial communities, but responded similarly to the residue amendments, because both soils exhibited the highest mean GWP after addition of the same residues (sewage sludge, aquatic plant material, and compressed beet leaves). Our results question the extent of using the C:N ratio alone to predict residue-induced response in GHG emission. Taken together, we show that although soil properties strongly affect the bacterial community composition, microbially-mediated GHG emission is residue-dependent.
  • 2017

    Microbial Ecosystem Functions in Wetlands Under Disturbance

    Anne Steenbergh, Annelies Veraart, Adrian Ho, Paul Bodelier
  • Proceedings of the Royal Society B-Biological Sciences

    Trophic state changes can affect the importance of methane-derived carbon in aquatic food webs

    Jos Schilder, M. Van Hardenbroek, Paul Bodelier, Emiliya P. Kirilova, Markus Leuenberger, A.F. Lotter, O. Heiri
    Methane-derived carbon, incorporated by methane-oxidizing bacteria, has been identified as a significant source of carbon in food webs of many lakes. By measuring the stable carbon isotopic composition (δ13C values) of particulate organic matter, Chironomidae and Daphnia spp. and their resting eggs (ephippia), we show that methane-derived carbon presently plays a relevant role in the food web of hypertrophic Lake De Waay, The Netherlands. Sediment geochemistry, diatom analyses and δ13C measurements of chironomid and Daphnia remains in the lake sediments indicate that oligotrophication and re-eutrophication of the lake during the twentieth century had a strong impact on in-lake oxygen availability. This, in turn, influenced the relevance of methane-derived carbon in the diet of aquatic invertebrates. Our results show that, contrary to expectations, methane-derived relative to photosynthetically produced organic carbon became more relevant for at least some invertebrates during periods with higher nutrient availability for algal growth, indicating a proportionally higher use of methane-derived carbon in the lake's food web during peak eutrophication phases. Contributions of methane-derived carbon to the diet of the investigated invertebrates are estimated to have ranged from 0–11% during the phase with the lowest nutrient availability to 13–20% during the peak eutrophication phase.
  • Nature Communications

    Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils

    Yuanfeng Cai, Yan Zheng, Paul Bodelier, R. Conrad, Zhongjun Jia
    Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ~1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this ‘high-affinity’ methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane.
  • Frontiers in Microbiology

    Recurrence and frequency of disturbance have cumulative effect on methanotrophic activity, abundance, and community structure.

    Adrian Ho, E. van den Brink, Andreas Reim, Sascha Krause, Paul Bodelier
    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency.
  • Frontiers in Microbiology

    Biotic interactions in microbial communities as modulators of biogeochemical processes: Methanotrophy as a model system.

    Adrian Ho, R. Angel, Annelies Veraart, Anne Daebeler, Z. Jia, Sang Yun Kim, F.M. Kerckhof, N. Boon, Paul Bodelier
    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.
  • Nature

    Sustainability: Bypassing the methane cycle

    A genetically modified rice with more starch in its grains also provides fewer nutrients for methane-producing soil microbes. This dual benefit might help to meet the urgent need for globally sustainable food production.
  • Plant and Soil

    Diazotrophic methanotrophs in peatlands: the missing link?

    Adrian Ho, Paul Bodelier

    A recent publication in Plant and Soil (Leppänen et al. 2015) reports on the effect of peat moss species and water table on the N2 fixation rate in boreal peatlands and forests. The lack of CH4-stimulated N2 fixation led the authors to conclude that methanotrophs do not contribute significantly to the N-supply of the mosses. This is in contrast to other studies in peatlands which suggest that methanotrophs may be responsible for the “unaccounted” N-input. The importance of peatlands in the global carbon cycle, combined with the crucial role of N not only in ombotrophic peatlands but also in thawing permafrost warrants a synthesis of these controversies.

    Evidence for and against diazotrophic N-provision by aerobic methanotrophs in peatlands

    Ombrotrophic peatlands are nitrogen poor environments, relying solely on atmospheric N deposition. Yet, there is an imbalance in atmospheric N deposition and N accumulation in Sphagnum mosses, with N accumulation by far exceeding N-deposition
  • Microbes and Environments

    Phylogenetic characterization of phosphatase-expressing bacterial communities in Baltic Sea sediments

    Anne Steenbergh, Paul Bodelier, H.L. Hoogveld, C.P Slomp, (Riks) H.J. Laanbroek
    Phosphate release from sediments hampers the remediation of aquatic systems from a eutrophic state. Microbial phosphatases in sediments release phosphorus during organic matter degradation. Despite the important role of phosphatase-expressing bacteria, the identity of these bacteria in sediments is largely unknown. We herein presented a culture-independent method to phylogenetically characterize phosphatase-expressing bacteria in sediments. We labeled whole-cell extracts of Baltic Sea sediments with an artificial phosphatase substrate and sorted phosphatase-expressing cells with a flow cytometer. Their phylogenetic affiliation was determined by Denaturing Gradient Gel Electrophoresis. The phosphatase-expressing bacterial community coarsely reflected the whole-cell bacterial community, with a similar dominance of Alphaproteobacteria.
  • Geoderma

    Beyond nitrogen: the importance of phosphorus for CH4 oxidation in soils and sediments

    Annelies Veraart, Anne Steenbergh, Adrian Ho, Sang Yun Kim, Paul Bodelier
    Wetlands, lakes and agricultural soils are important sources and sinks of the greenhouse gas methane. The only known methane sink of biological nature is the oxidation by methanotrophic microorganisms, these organisms therefore provide an important ecosystem service. To protect this ecosystem service, it is important to maintain methanotrophic microorganism diversity, especially under increased anthropogenically-induced environmental pressures, such as imbalanced input of nutrients to ecosystems. There is therefore an urgent need to understand how N and P affect the structure and activity of methane oxidizing communities. Numerous research studies have already shown variable effects of N-addition on methane oxidation: small additions tend to stimulate methane oxidation, whereas large additions are inhibitory. There is however still a large knowledge gap concerning effects of P on methane oxidation. Here, we present data on the relation between methane oxidation and various measures of P in 50 drainage ditches, and summarize literature reporting relations between P and methane oxidation in wetlands and soils. Additionally, we review experiments on effects of P, N and N + P addition on both low affinity and high affinity methane oxidation. In our set of drainage ditches, as well as studies on wetland and permafrost soils, P content is positively correlated to methane oxidation, though it also co-correlates with many other variables. However, results from P-additions in rice paddies, agricultural soils, landfills, peat bogs, permafrost soils and forests were more variable: sometimes inhibiting (2 studies), other times stimulating methane oxidation (4 studies), and sometimes showing no effect (5 studies). Two studies report increased methanotroph (pmoA) abundance following P-fertilization, but little is known about effects of P on methanotroph community structure and its consequences for methane consumption. By mining methanotrophic genomes for genes involved in N and P-related processes, we demonstrate that variability in N/P related traits (influencing acquisition, uptake and metabolism) does not reflect DNA-based phylogeny. This review points to a need for better mechanistic understanding of the effects of P on methane oxidation, and the role of traits of methanotrophic community members in regulating this process
  • Geoderma

    Combined effects of carbon, nitrogen and phosphorus on CH4 production and denitrification in wetland sediments

    Sang Yun Kim, Annelies Veraart, Marion Meima-Franke, Paul Bodelier
    Anthropogenic impacts and associated climate change are anticipated to change nutrient availability in wetlands. Changes in nutrient availability can affect major biogeochemical reactions (i.e., methanogenesis, denitrification) which impact greenhouse gas emissions and trophic status of ecosystems. However, the modulating role of nutrients in C and N cycles, and their resulting effects on interactions between methanogenesis and denitrification are poorly understood. Here, anaerobic slurry incubations were carried out to test the sole and combined effects of C, N and P on methanogenesis and denitrification in wetland sediments. Three levels of N (as KNO3) were added, and three levels of P (as KH2PO4), either with or without C (as CH3COOH) additions during laboratory slurry incubations. We investigated potential CH4 production, denitrification, physico-chemical properties of sediment and pore water and abundances of methanogens and denitrifiers by using functional genes (mcrA and nirS). N addition significantly inhibited CH4 production (Mean 8.6 ± 10.8 μmol g− 1 d.w) compared to the treatment without N addition (Mean 28.2 ± 18.1 μmol g− 1 d.w) during incubation, irrespective of C addition. P addition did not directly influence methanogenesis. However, combined N and P addition decreased CH4 production (Mean 7.2 ± 10.2 μmol g− 1 d.w) to a larger extent than sole N addition (Mean 11.3 ± 11.9 μmol g− 1 d.w) due to increased substrate competition with denitrifiers. Interestingly, N and P addition in combination with C addition led to inhibition of CH4 production as well as denitrification. Combined with increasing ammonium and accumulating nitrite (NO2−), the observed inhibition suggests that a change of electron flow towards dissimilatory nitrate reduction to ammonium (DNRA) consumed more electron donors (i.e., acetate) in the process, reducing methanogenesis and denitrification. Our result suggests that P, especially in combination with other substrates, should be considered as an important modulating factor in greenhouse gas emissions (in particular CH4 and N2O) from wetlands.
  • Global Change Biology

    Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application

    Adrian Ho, Andreas Reim, Sang Yun Kim, Marion Meima-Franke, Aad J Termorshuizen, Wietse de Boer, Wim H. van der Putten, Paul Bodelier
    Intensification of agriculture to meet the global food, feed, and bioenergy demand entail increasing re-investment of carbon compounds (residues) into agro-systems to prevent decline of soil quality and fertility. However, agricultural intensification decreases soil methane uptake, reducing and even causing the loss of the methane sink function. In contrast to wetland agricultural soils (rice paddies), the methanotrophic potential in well-aerated agricultural soils have received little attention, presumably due to the anticipated low or negligible methane uptake capacity in these soils. Consequently, a detailed study verifying or refuting this assumption is still lacking. Exemplifying a typical agricultural practice, we determined the impact of bio-based residue application on soil methane flux, and determined the methanotrophic potential, including a qualitative (diagnostic microarray) and quantitative (group-specific qPCR assays) analysis of the methanotrophic community after residue amendments over two months. Unexpectedly, after amendments with specific residues we detected a significant transient stimulation of methane uptake confirmed by both the methane flux measurements and methane oxidation assay. This stimulation was apparently a result of induced cell-specific activity, rather than growth of the methanotroph population. Although transient, the heightened methane uptake offsets up to 16% of total gaseous CO2 emitted during the incubation. The methanotrophic community, predominantly comprised of Methylosinus may facilitate methane oxidation in the agricultural soils. While agricultural soils are generally regarded as a net methane source or a relatively weak methane sink, our results show that methane oxidation rate can be stimulated, leading to higher soil methane uptake. Hence, even if agriculture exerts an adverse impact on soil methane uptake, implementing carefully designed management strategies (e.g. repeated application of specific residues) may compensate for the loss of the methane sink function following land-use change.
  • Geoderma

    Mechanisms controlling greenhouse gas emissions from soils

    P.J. Kim, Paul Bodelier, Y. Lu
    The following set of papers presents a special section of the outputs from 20th World Congress of Soil Science, the international conference of the International Union of Soil Sciences (IUSS). The conference was held in the International Convention Center (ICC) Jeju, Republic of Korea, from June 8 to 13, 2014. It was organized by the Korean Society of Soil Science and Fertilizer as the local organizer under the auspices of the IUSS. More than 2500 participants from 87 countries from around the world attended the congress.
  • Environmental Microbiology

    Field-scale tracking of active methane-oxidizing communities in a landfill-cover soil reveals spatial and seasonal variability

    R. Henneberger, E. Chiri, Paul Bodelier, P. Frenzel, C. Luke, M.H. Schroth
    Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4. Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.
  • FEMS Microbiology Ecology

    Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows

    Sascha Krause, Pascal A. Niklaus, Sara Badwan Morcillo, Marion Meima-Franke, Claudia Lüke, Andreas Reim, Paul Bodelier
    The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity, and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but neither to major changes in abundances of MOB nor in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabelling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.
  • Journal of Ecology

    Peatland vascular plant functional types affect methane dynamics by altering microbial community structure

    B.J.M. Robroek, Vincent E.J. Jassey, Martine A.R. Kox, Roeland L. Berendsen, Robert T.E. Mills, Lauric Cécillon, Jérémy Puissant, Marion Meima-Franke, Peter A.H.M. Bakker, Paul Bodelier
    Peatlands are natural sources of atmospheric methane (CH4), an important greenhouse gas. It is established that peatland methane dynamics are controlled by both biotic and abiotic conditions, yet the interactive effect of these drivers is less studied, and consequently poorly understood. Climate change affects the distribution of vascular plant functional types (PFTs) in peatlands. By removing specific PFTs, we assessed their effects on peat organic matter chemistry, microbial community composition and on potential methane production (PMP) and oxidation (PMO) in two microhabitats (lawns and hummocks). Whilst PFT removal only marginally altered the peat organic matter chemistry, we observed considerable changes in microbial community structure. This resulted in altered PMP and PMO. PMP was slightly lower when graminoids were removed, whilst PMO was highest in the absence of both vascular PFTs (graminoids and ericoids), but only in the hummocks. Path analyses demonstrate that different plant–soil interactions drive PMP and PMO in peatlands, and that changes in biotic and abiotic factors can have auto-amplifying effects on current CH4 dynamics. Synthesis. Changing environmental conditions will, both directly and indirectly, affect peatland processes, causing unforeseen changes in CH4 dynamics. The resilience of peatland CH4 dynamics to environmental change therefore, depends on the interaction between plant community composition and microbial communities.
  • FEMS Microbiology Ecology

    Ammonia-limited conditions cause of Thaumarchaeal dominance in volcanic grassland soil

    Anne Daebeler, Paul Bodelier, Mariet M. Hefting, (Riks) H.J. Laanbroek
    The first step of nitrification is carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA). It is largely unknown, by which mechanisms these microbes are capable of coexistence and how their respective contribution to ammonia oxidation may differ with varying soil characteristics. To determine how different levels of ammonium availability influence the extent of archaeal and bacterial contributions to ammonia oxidation, microcosm incubations with controlled ammonium levels were conducted. Net nitrification was monitored and ammonia oxidizer communities were quantified. Additionally, the nitrification inhibitor allylthiourea (ATU) was applied to discriminate between archaeal and bacterial contributions to soil ammonia oxidation. Thaumarchaeota, which were the only ammonia oxidizers detectable at the start of the incubation, grew in all microcosms, but AOB later became detectable and grew as well. Low and high additions of ammonium increasingly stimulated AOB growth, while AOA were only stimulated by the low addition. Treatment with ATU had no effect on net nitrification and sizes of ammonia-oxidizing communities suggesting that the effective concentration of ATU to discriminate between archaeal and bacterial ammonia oxidation is not the same in different soils. Our results support the niche differentiating potential of ammonium concentration for AOA and AOB and we conclude that ammonium limitation can be a major reason for absence of detectable AOB in soil.Keywordsammonia-oxidizing archaeaammonia-oxidizing bacterianitrificationallylthioureaammonium© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions{at}
  • Biology and Fertility of Soils

    Manure-associated stimulation of soil-borne methanogenic activity in agricultural soils

    Adrian Ho, Alaa H.M. El-Hawwary, Sang Yun Kim, Marion Meima-Franke, Paul Bodelier
    The growing human population and scarcity of arable land necessitate agriculture intensification to meet the global food demand. Intensification of agricultural land entails manure input into agrosystems which have been associated to increased methane emission. We investigated the immediate short-term response of methane production and the methanogens after manure amendments in agricultural soils and determined the relevance of the manure-derived methanogenic population in its contribution to soil methane production. We followed methane production in a series of unamended and manure-amended batch incubations: (i) manure and soil, (ii) sterilized manure and soil, and (iii) manure and sterilized soil. Moreover, we determined the methanogenic abundance using a quantitative PCR targeting the mcrA gene. Results show that the soil-borne methanogenic community was significantly stimulated by manure amendment, resulting in increased methane production and mcrA gene abundance; manure-derived methanogenic activity contributed only marginally to overall methane production. Accordingly, our results highlighted the importance of the resident methanogenic community and physiochemical properties of a residue when considering methane mitigation strategies in agricultural soils.
  • PLoS One

    Effect of redox conditions on bacterial community structure in Baltic Sea sediments with contrasting redox conditions

    Anne Steenbergh, Paul Bodelier, C.P Slomp, (Riks) H.J. Laanbroek
    Phosphorus release from sediments can exacerbate the effect of eutrophication in coastal marine ecosystems. The flux of phosphorus from marine sediments to the overlying water is highly dependent on the redox conditions at the sediment-water interface. Bacteria are key players in the biological processes that release or retain phosphorus in marine sediments. To gain more insight in the role of bacteria in phosphorus release from sediments, we assessed the effect of redox conditions on the structure of bacterial communities. To do so, we incubated surface sediments from four sampling sites in the Baltic Sea under oxic and anoxic conditions and analyzed the fingerprints of the bacterial community structures in these incubations and the original sediments. This paper describes the effects of redox conditions, sampling station, and sample type (DNA, RNA, or whole-cell sample) on bacterial community structure in sediments. Redox conditions explained only 5% of the variance in community structure, and bacterial communities from contrasting redox conditions showed considerable overlap. We conclude that benthic bacterial communities cannot be classified as being typical for oxic or anoxic conditions based on community structure fingerprints. Our results suggest that the overall structure of the benthic bacterial community has only a limited impact on benthic phosphate fluxes in the Baltic Sea.
  • Frontiers in Microbiology

    Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

    Sascha Krause, X. Le Roux, P.A. Niklaus, P.M. Van Bodegom, J.T. Lennon, S.A. Bertilsson, Hans-Peter Grossart, L. Philippot, Paul Bodelier
    In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.
  • ISME Journal

    Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil

    Anne Daebeler, Paul Bodelier, Yan Zheng, M.M. Hefting, Z. Jia, (Riks) H.J. Laanbroek
    Ammonium/ammonia is the sole energy substrate of ammonia oxidizers, and is also an essential nitrogen source for other microorganisms. Ammonia oxidizers therefore must compete with other soil microorganisms such as methane-oxidizing bacteria (MOB) in terrestrial ecosystems when ammonium concentrations are limiting. Here we report on the interactions between nitrifying communities dominated by ammonia-oxidizing archaea (AOA) and Nitrospira-like nitrite-oxidizing bacteria (NOB), and communities of MOB in controlled microcosm experiments with two levels of ammonium and methane availability. We observed strong stimulatory effects of elevated ammonium concentration on the processes of nitrification and methane oxidation as well as on the abundances of autotrophically growing nitrifiers. However, the key players in nitrification and methane oxidation, identified by stable-isotope labeling using 13CO2 and 13CH4, were the same under both ammonium levels, namely type 1.1a AOA, sublineage I and II Nitrospira-like NOB and Methylomicrobium-/Methylosarcina-like MOB, respectively. Ammonia-oxidizing bacteria were nearly absent, and ammonia oxidation could almost exclusively be attributed to AOA. Interestingly, although AOA functional gene abundance increased 10-fold during incubation, there was very limited evidence of autotrophic growth, suggesting a partly mixotrophic lifestyle. Furthermore, autotrophic growth of AOA and NOB was inhibited by active MOB at both ammonium levels. Our results suggest the existence of a previously overlooked competition for nitrogen between nitrifiers and methane oxidizers in soil, thus linking two of the most important biogeochemical cycles in nature.
  • Journal of Evolutionary Biology

    Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria.

    Sascha Krause, P.M. Van Bodegom, W.K. Cornwell, Paul Bodelier
    The presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between relatedness and physiological traits exists for aerobic methane-oxidizing bacteria (MOB). We generated a comprehensive data set that included 30 MOB strains with quantitative physiological trait information. Phylogenetic trees were built from the 16S rRNA gene, a common phylogenetic marker, and the pmoA gene which encodes a subunit of the key enzyme involved in the first step of methane oxidation. We used a Blomberg's K from comparative biology to quantify the strength of phylogenetic signal of physiological traits. Phylogenetic signal was strongest for physiological traits associated with optimal growth pH and temperature indicating that adaptations to habitat are very strongly conserved in MOB. However, those physiological traits that are associated with kinetics of methane oxidation had only weak phylogenetic signals and were more pronounced with the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results give evidence that approaches based solely on taxonomical information will not yield further advancement on microbial eco-evolutionary interactions with its environment. This is a novel insight on the connection between function and phylogeny within microbes and adds new understanding on the evolution of physiological traits across microbes, plants and animals.
  • 2014

    Microbial Ecosystems, Protection of

    Synonyms Conservation of microbial diversity and ecosystem functions provided by microbes; Preservation of microbial diversity and ecosystem functions provided by microbes Definition The use, management, and conservation of ecosystems in order to preserve microbial diversity and functioning. Introduction Ecosystems collectively determine biogeochemical processes that regulate the Earth system. Loss of biodiversity is generally regarded as detrimental to ecosystems and ecosystem functioning and therefore has been a central issue for environmental scientists during the last decades (Hooper et al. 2012). Microorganisms (i.e., bacteria, archaea, protozoa, and fungi) comprise a major part of the total biomass of organisms inhabiting on Earth and represent the largest source of biodiversity. They play critical roles in biogeochemical processes and ecosystem functioning and are fundamental to many ecosystem services (e.g., soil health, wastewater treatment, nutrient recycling, human health, carbon
  • Microbial Ecology

    Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only

    Yao Pan, G.C.J. Abell, Paul Bodelier, Marion Meima-Franke, A. Sessitsch, L. Bodrossy
    Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities (i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community
  • 2014

    Extraction Methods, Variability Encountered in

    Synonyms Bias in DNA extractions methods; Variation in DNA extraction methods Definition The variability in extraction methods is defined as differences in quality and quantity of DNA observed using various extraction protocols, leading to differences in outcome of microbial community composition assessments using genomic approaches. Introduction Microbial communities are at the very basis of life on Earth, catalyzing biogeochemical reactions and driving global nutrient cycles (Falkowski et al. 2008). As yet, they are not on the global biodiversity conservation agenda, implying that microbial diversity is not under any threat by anthropogenic disturbance or climate change. However, this maybe a misconception caused by the rudimentary knowledge we have concerning microbial communities in their natural habitats as compared to the knowledge we have on plants and animals. The inability to culture the vast majority of microbes present in ecosystems prevents the detailed study of their ecology an
  • 2014

    Interactions between methane and nitrogen cycling; current metagenomics studies and future trends

    Paul Bodelier, Anne Steenbergh
    Wetlands, lakes, soils and sediments are the most important biological sources as well sinks of the greenhouse gas methane. However, the dynamics, variability and uncertainty in methane emission models from these systems is high necessitating better knowledge of the underlying microbial processes. The impact of nitrogenous fertilizers and atmospheric nitrogen deposition on methane production and consumption in freshwater ecosystems (wetlands, lakes, rice paddies) as well as in upland soils has been the subject of intense research the past decades. However, our mechanistic understanding of the observed effects on methane and nitrogen cycling interactions in these ecosystems is poor which is even more so considering the novel microbial groups and pathways discovered. This chapter gives an overview of the main ways the nitrogen cycle interacts with the microbial methane cycling in freshwater wetlands, soils and sediments and summarizes the main current metagenomic studies that carried out on microbial groups involved. It can be concluded that metagenomic techniques developed and applied have the potential to obtain an integrative view of microbial communities and interactions and bear the potential to discover new pathways and organisms. The way forward is to apply these techniques in replicated, manipulative experimental set ups to obtain mechanistic understanding of methane-nitrogen cycle interactions.
  • Biogeosciences

    Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    Yan Zheng, Rong Huang, B. Wang, Paul Bodelier, Z. Jia
    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and pmoA genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity by 6-fold during a 19 day incubation period, while ammonia oxidation activity was significantly inhibited in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like type Ia MOB, and nitrifying communities appeared to be suppressed by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to equal increase in Methylosarcina and Methylobacter-related MOB, indicating the differential growth requirements of representatives of these genera. Strikingly, type Ib MOB did not respond to methane nor to urea. Increase in 13C-assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, in addition of nitrite-oxidizing bacteria. These results provide comprehensive insights in the interactions between actively growing methanotrophs and ammonia oxidizers in a complex soil ecosystem.
  • Current Opinion in Environmental Sustainability

    Interactions between methane and the nitrogen cycle in light of climate change

    Paul Bodelier, Anne Steenbergh
    Next to carbon dioxide, methane is the most important greenhouse gas which predominantly is released from natural wetlands and rice paddies. Climate change predictions indicate enhanced methane emission from global ecosystems under elevated CO2 and temperature. However, the extent of this positive feedback is far from clear and depends on factors modulating microbial responses of microbes involved in methane cycling in various ecosystems. Nitrogen input by atmospheric deposition or fertilizer additions, is such a factor with a range of possible effects on microbial methane production and consumption. In this paper we discuss the crucial lacks in knowledge preventing a better understanding and predictions of climate change effects on global methane emissions.
  • PLoS One

    Cattle Manure Enhances Methanogens Diversity and Methane Emissions Compared to Swine Manure under Rice Paddy

    Sang Yun Kim, Prabhat Pramanik, Paul Bodelier, Pil Joo Kim

    Livestock manures are broadly used in agriculture to improve soil quality. However, manure application can increase the availability of organic carbon, thereby facilitating methane (CH4) production. Cattle and swine manures are expected to have different CH4 emission characteristics in rice paddy soil due to the inherent differences in composition as a result of contrasting diets and digestive physiology between the two livestock types. To compare the effect of ruminant and non-ruminant animal manure applications on CH4 emissions and methanogenic archaeal diversity during rice cultivation (June to September, 2009), fresh cattle and swine manures were applied into experimental pots at 0, 20 and 40 Mg fresh weight (FW) ha−1 in a greenhouse. Applications of manures significantly enhanced total CH4 emissions as compared to chemical fertilization, with cattle manure leading to higher emissions than swine manure. Total organic C contents in cattle (466 g kg−1) and swine (460 g kg−1) manures were of comparable results. Soil organic C (SOC) contents were also similar between the two manure treatments, but dissolved organic C (DOC) was significantly higher in cattle than swine manure. The mcrA gene copy numbers were significantly higher in cattle than swine manure. Diverse groups of methanogens which belong to Methanomicrobiaceae were detected only in cattle-manured but not in swine-manured soil. Methanogens were transferred from cattle manure to rice paddy soils through fresh excrement. In conclusion, cattle manure application can significantly increase CH4 emissions in rice paddy soil during cultivation, and its pretreatment to suppress methanogenic activity without decreasing rice productivity should be considered.
  • Archaea

    Temporal and spatial coexistence of archaeal and bacterial amoA genes and gene transcripts in Lake Lucerne

    E.W. Vissers, F.S. Anselmetti, Paul Bodelier, G. Muyzer, C. Schleper, M. Tourna, (Riks) H.J. Laanbroek
    Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO). This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA) and bacteria (AOB) over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42 m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton.
  • International Journal of Systematic and Evolutionary Microbiology

    Methylomonas paludis sp. nov., the first acid-tolerant member of the genus Methylomoas, from an acidic wetland

    O.V. Danilova, I.S. Kulichevskaya, O.N. Rozova, E.N. Detkova, Paul Bodelier, Y.A. Trotsenko, S.N. Dedysh
    An aerobic methanotrophic bacterium was isolated from an acidic (pH 3.9) Sphagnum peat bog in north-eastern Russia and designated strain MG30T. Cells of this strain are Gram-negative, pale-pink-pigmented, non-motile, thick rods that are covered by large polysaccharide capsules and contain an intracytoplasmic membrane system typical of type I methanotrophs. They possess a particulate methane monooxygenase enzyme (pMMO) and utilize only methane and methanol. Carbon is assimilated via the ribulose-monophosphate pathway; nitrogen is fixed via an oxygen-sensitive nitrogenase. Strain MG30T grows in a pH range of 3.8-7.3 (optimum pH 5.8-6.4) and at temperatures between 8 and 30°C (optimum 20-25°C). The major cellular fatty acids are C16:1ω5t, C16:1ω8c, C16:1ω7c, and C14:0; the DNA G+C content is 48.5 mol%. The isolate belongs to the family Methylococcaceae of the class Gammaproteobacteria and displays 94.7-96.9% 16S rRNA gene sequence similarity to members of the genus Methylomonas. However, strain MG30T differs from all taxonomically characterized members of this genus by the absence of motility, the ability to grow in acidic conditions, and low DNA G+C content. Therefore, we propose to classify this strain as a novel, acid-tolerant species of the genus Methylomonas, Methylomonas paludis sp. nov. Strain MG30T (=DSM 24973T = VKM B-2745T) is the type strain.
  • 2013

    Microbiology of wetlands

    Paul Bodelier, S.N. Dedysh
    Watersaturated soil and sediment ecosystems (i.e. wetlands) are ecologically as well as economically important systems due to their high productivity, their nutrient (re)cycling capacities and their prominent contribution to global greenhouse gas emissions. Being on the transition between terrestrial and – aquatic ecosystems, wetlands are buffers for terrestrial run off thereby preventing eutrophication of inland as well as coastal waters. The close proximity of oxic-anoxic conditions, often created by wetland plant roots, facilitates the simultaneous activity of aerobic as well as anaerobic microbial communities. Input of nutrients and fast recycling due to active aerobes and anaerobes makes these systems highly productive and therefore attractive for humans as well as many other organisms. Wetlands globally are under high pressure due to anthropogenic activities as well as climate change. Changes of land-use as well as altered hydrology due to climate change will lead to disturbance and loss of these habitats. However, the diversity and functioning of microbial communities in wetlands systems in highly underexplored in comparison to soils and aquatic ecosystems. Given the importance of wetlands and their immediate threats combined with the lack of knowledge on the microbiology of these systems is the basis for this special issue, focusing on the current microbiological knowledge and gaps therein to be assessed in future wetland research. Papers (research papers, reviews, perspectives, opinion papers) are welcomed that focus on all aspects that regulate the functioning and community composition of microbes (i.e. bacteria, archaea, protozoa, fungi) in wetland ecosystems (peat, coastal as well as freshwater marshes, flood plains, rice paddies, littoral zones of lakes etc) from all geographic regions. Welcomed topics are physiology, ecology, functioning, biodiversity, biogeography of microbes involved in nutrient cycling (C, N, P, Fe, Mn), green house gas emissions as well as plant-microbe interactions. These studies can be multidisciplinary and cover topics from the molecular to the community level.
  • ISME Journal

    Microbial minorities modulate methane consumption through niche partitioning

    Paul Bodelier, Marion Meima-Franke, Cees Hordijk, Anne Steenbergh, M.M. Hefting, L. Bodrossy, M. von Bergen, J. Seifert
    Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity–ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy. Keywords: biodiversity–ecosystem functioning; methane oxidation; stable isotope labeling; proteomics; wetlands
  • FEMS Microbiology Ecology

    Spatial patterns of methanotrophic communities along a hydrological gradient in a riparian wetland

    Sascha Krause, Marion Meima-Franke, M.M. Hefting, Paul Bodelier
    Microbial communities display a variety of biogeographical patterns mainly driven by large-scale environmental gradients. Here, we analysed the spatial distribution of methane-oxidizing bacteria (MOB) and methane oxidation in a strongly fluctuating environment. We investigated whether the spatial variability of the MOB community can be explained by an environmental gradient and whether this changes with different plot sizes. We applied a pmoA-specific microarray to detect MOB, measured methane oxidation, methane emissions and soil properties. All variables were measured in a 10 × 10 m, 1 × 1 m and 20 × 20 cm plot and interpreted using a geostatistical approach. Methane oxidation as well as MOB displayed spatial patterns reflected in the underlying flooding gradient. Overlapping and contrasting spatial patterns for type I and type II MOB suggested different ecological life strategies. With smaller plot size, the environmental gradient could not explain the variability in the data and local factors became more important. In conclusion, environmental gradients can generally explain variability in microbial spatial patterns; however, we think that this does not contribute to a mechanistic explanation for microbial diversity because the relevant scales for microorganisms are much smaller than those normally measured.
  • Environmental Microbiology

    Does microbial stoichiometry modulate eutrophication of aquatic ecosystems?

    Anne Steenbergh, Paul Bodelier, M. Heldal, C.P Slomp, (Riks) H.J. Laanbroek
    The stoichiometry of prokaryotes (Bacteria and Archaea) can control benthic phosphorus (P) fluxes relative to carbon (C) and nitrogen (N) during organic matter remineralization. This paper presents the first experimental data on benthic microbial stoichiometry. We used X-ray microanalysis to determine C:N:P ratios of individual prokaryotes from C-limited Baltic Sea sediments incubated under oxic or anoxic conditions. At approximately 400:1, C:P ratios of prokaryotes from both oxic and anoxic incubations were higher than the Redfield ratio for marine organic matter (106:1), whereas prokaryotic C:N ratios (6.4:1) were close to the Redfield ratio. We conclude that high microbial C:P ratios contribute to the enhanced remineralization of P from organic matter relative to C and N observed in many low oxygen marine settings.
  • International Journal of Systematic and Evolutionary Microbiology

    Methylocystis bryophila sp. nov., a Novel Facultatively Methanotrophic Bacterium from Acidic Sphagnum Peat, and Emended Description of the Genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993

    S.E. Belova, I.S. Kulichevskaya, Paul Bodelier, S.N. Dedysh
    A new species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2sT and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2sT and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aero-tolerant nitrogenase. Strains H2sT and S284 develop between pH 4.2 and 7.6 (optimum pH 6.0-6.5), and at temperatures between 8 and 37°C (optimum 25-30°C). The major fatty acids are C18:1w8c, C18:1w7c, and C16:1w7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2sT and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3% similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2sT and S284 are classified as a novel species, for which the name Methylocystis bryophila sp. nov. is proposed. Strain H2sT (=DSM 21852T = VKM B-2545T) is the type strain of Methylocystis bryophila.
  • Frontiers in Microbiology

    Microbiology of wetlands

    Paul Bodelier, S.N. Dedysh
    Wetlands are ecologically as well as economically important systems due to their high productivity, their nutrient (re)cycling capacities, and their prominent contribution to global greenhouse gas emissions. Being on the transition between terrestrial and—aquatic ecosystems, wetlands are buffers for terrestrial run off thereby preventing eutrophication of inland as well as coastal waters. The close proximity of oxic–anoxic conditions, often created by wetland plant roots, facilitates the simultaneous activity of aerobic as well as anaerobic microbial communities. Input of nutrients and fast recycling due to active aerobes and anaerobes makes these systems highly productive and therefore attractive for humans as well as many other organisms. Wetlands globally are under high pressure due to anthropogenic activities as well as climate change. Changes of land-use as well as altered hydrology due to climate change will lead to disturbance and loss of these habitats. However, the diversity and functioning of microbial communities in wetland systems is highly underexplored in comparison to soils and aquatic ecosystems.
  • Environmental Microbiology Reports

    Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies

    Adrian Ho, F.M. Kerckhof, C. Luke, Andreas Reim, Sascha Krause, N. Boon, Paul Bodelier
    Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids, and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal (C-S-R) functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal (C-R) while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.
  • FEMS Microbiology Ecology

    Seasonal and vertical distribution of putative ammonia-oxidizing thaumarchaeotal communities in an oligotrophic lake

    E.W. Vissers, C.I. Blaga, Paul Bodelier, G. Muyzer, C. Schleper, J.S. Sinninghe Damsté, M. Tourna, (Riks) H.J. Laanbroek
    The discovery of Archaea carrying an amoA gene coding for the A-subunit of ammonia monooxygenase gave a boost to studies aimed at detecting this gene under diverse conditions. Despite numerous studies describing the archaeal amoA gene abundance and richness in different habitats, the understanding of the freshwater ecology of potentially archaeal ammonia oxidizers, recently positioned in the phylum Thaumarchaeota, is still lacking. In a seasonal and vertical study of deep oligotrophic Lake Lucerne, Switzerland, with high Thaumarchaeota-specific crenarchaeol concentrations, we showed that all archaeal 16S rRNA genes found belong to the thaumarchaeotal phylum. The abundances of archaeal 16S rRNA and amoA genes remained in the same order of magnitude (average 6 × mL−1) and displayed matching seasonal dynamics within 16 monthly collected samples at three different water depths (r2 = 0.80, slope of 1.06). The Thaumarchaeota in this lake form a distinct cluster in both the 16S rRNA and amoA gene phylogenies, are affiliated to other thaumarchaeotal freshwater sequences within group 1.1a Archaea, and fall in the low saline cluster of the amoA phylogeny. In accordance with temperature and conductivity, the Thaumarchaeota in the surface water showed a significantly different seasonality and lower abundance than their counterparts in the deeper waters. This study indicates that the ecology of Thaumarchaeota, with their potential in nitrogen cycling, may differ per water depth in deep freshwater ecosystems.
  • Plant and Soil

    Effect of the aerenchymatous helophyte Glyceria maxima on the sulfate-reducing communities in two contrasting riparian grassland soils

    M. Miletto, Paul Bodelier, F.G. Ferdelman, B.B. Jørgensen, (Riks) H.J. Laanbroek
    Aims The research aimed at studying the effect of flooding with sulfate-rich water on the activity, abundance and diversity of sulfate-reducing micro-organisms present in the root zone of an oxygen-releasing plant growing on two riparian grassland soils with contrasting amounts of iron. Methods A series of microcosms was used to investigate the effects. Plants were grown under controlled conditions in microcosms containing a rhizosphere and bulk soil compartment for a period of 12 weeks in the presence of sulfate-rich flood water. Molybdate-treated systems served as non-sulfate-reducing controls. Results At harvest, activity and numbers of sulfate-reducing micro-organisms were higher in the absence of molybdate, but a rhizosphere effect and an impact of the presence of high levels of iron were not observed on activity and numbers. Both soils had in common a diverse community of sulfate-reducing micro-organisms covering all major cultured bacterial taxa. The appearance of members of the Desulfovibrionaceae exclusively in the rhizosphere of G. maxima was the only unambiguous indication of a plant effect. Conclusion The presence of sulfate-rich flood water stimulated the activity and growth of a part of the sulfate-reducing community leading to a change in community composition. The proximity of aerenchymatous plant roots and the abundance of iron in the soil had a negligible effect on the sulfate-reducing community.
  • Freshwater Science

    Methane as a carbon source for the food web in raised bog pools

    G.A. Van Duinen, K. Vermonden, Paul Bodelier, A.J. Hendriks, R.S.E.W. Leuven, J.J. Middelburg, G. Van der Velde, W.C.E.P. Verberk
    Raised bog pools are extremely nutrient poor and rich in humic substances, and these features limit primary production. To assess the base of the invertebrate food web in bog pools we measured the stable-isotopic signatures of primary producers, dead organic matter, and invertebrates, and the composition and stable-C-isotope ratio of their phospholipid-derived fatty acids (PLFAs). The stableisotopic signatures showed the presence of multiple trophic levels and differential use of basal food sources by the invertebrates among and within species, individuals, and size classes. Carnivorous and omnivorous invertebrates assimilated polyunsaturated fatty acids (PUFAs) derived from algae, and possibly macrophytes, and fatty acids that are specific for methane-oxidizing bacteria (MOB). Part of the bacterial biomass conveyed to higher trophic levels in the bog pools originated from MOB. Pelagic zooplankton appeared to rely more on bacteria, whereas insects relied more on algae. Periphyton, a primary algal food source, was the basal food source most depleted in 13C and was inferred to sustain §½ the invertebrate food web. The relatively depleted d13C values of PUFAs in invertebrates suggest a role for methane-derived C. We argue that the CO2 assimilated by the algae could be derived from MOB. Therefore, depleted d13C values of invertebrates do not necessarily indicate a direct pathway between MOB and these invertebrates because algae may form an intermediate level.
  • Geomicrobiology Journal

    Bacterial diversity and geochemical profiles in sediments from eutrophic Azorean lakes

    G. da Costa Martins, I. Henriques, D.C Ribeiro, A. Correia, Paul Bodelier, J.V. Cruz, A.G. Brito, R. Nogueira
    In the Azores, the advanced trophic state of the lakes requires a fast intervention to achieve the good ecological status prescribed by the Water Framework Directive. Despite the considerable effort made to describe the phytoplankton growing on the water column, the lack of information regarding the microbial processes in sediments is still high. Thus, for the successful implementation of internal management actions, the present work explored the relationships between geochemical profiles and dominant members of the bacterial community in sediments from eutrophic Azorean lakes. Lake Azul geochemical profiles were quite homogeneous for all parameters, while in lake Furnas the total iron profile presented a peak below the aerobic layer. For lake Verde, the concentrations of all studied parameters (20 ± 2% loss-on-ignition; 2.10 ± 0.08 mg g−1 total phosphorus; 1.31 ± 0.50 mg g−1 total nitrogen; 8.06 ± 0.13 mg g−1 total iron) in the uppermost sediment layer were approximately two times higher than the ones in sediments from other lakes, decreasing with sediment depth. The higher amounts of phosphorus and organic matter in lake Verde suggested a higher internal contribution of phosphorus to eutrophication. The dominant members of the sediment bacterial community, investigated by denaturing gradient gel electrophoresis, were mostly affiliated to Proteobacteria phylum (Alpha-, Delta-, and Gamma-subclasses), group Bacteroidetes/Chlorobi and phylum Chloroflexi. The Cyanobacteria phylum was solely detected in sediments from lake Verde and lake Furnas that presented the highest amounts of nitrogen and phosphorus both in the water column and sediments, while the other phyla were detected in sediments from the three studied lakes. In conclusion, management measurers to achieve the good ecological status until 2015 should be distinct for the different lakes taking into account the relative magnitude of the nutrient sources and the bacterial diversity in sediments.
  • Frontiers in Microbiology

    Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

    Anne Daebeler, G.C.J. Abell, Paul Bodelier, L. Bodrossy, D.M. Frampton, M.M. Hefting, (Riks) H.J. Laanbroek
    The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.
  • Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology

    Characterization of Methylobacterium strains isolated from the phyllosphere and description of Methylobacterium longum sp nov

    C. Knief, V. Dengler, Paul Bodelier, J.A. Vorholt
    Methylobacterium strains are abundantly found in the phyllosphere of plants. Morphological, physiological and chemotaxonomical properties of 12 previously isolated strains were analyzed in order to obtain a more detailed overview of the characteristics of phyllosphere colonizing Methylobacterium strains. All strains showed the typical properties of the genus Methylobacterium, including pink pigmentation, facultative methylotrophy, a fatty acid profile dominated by C18:1 ω7c, and a high G+C content of 65 mol % or more. However, some strains showed only weak growth on methanol and pigmentation varied from pale pink to red. Strains grew best under mesophilic, neutrophilic conditions and low salt (≤1%) concentrations, but variation was seen with respect to the temperature and pH range under which growth occurred. Likewise, differences were seen with respect to carbon source utilization. Some strains were versatile and utilized diverse organic acids, amino acids and sugars, while others could only metabolize a restricted number of organic acids. The strains that were most distinct from existing type strains based on 16S rRNA gene sequence analysis were selected for DNA–DNA hybridization experiments to analyze whether they are sufficiently different at the genomic level from existing type strains to justify their classification as new species. This resulted in the delineation of strain 440 and its description as Methylobacterium longum sp. nov. strain 440 (=DSM 23933T = CECT 7806T). A main characteristic of this species is the formation of relatively long rods compared to other Methylobacterium species.
  • Ecology and Evolution

    Structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils

    Paul Bodelier, Marie-Jose Bär-Gilissen, Marion Meima-Franke, Cees Hordijk
    Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils. This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.
  • International Journal of Systematic and Evolutionary Microbiology

    Singulisphaera rosea sp. nov., a planctomycete from acidic Sphagnum peat, and emended description of the genus Singulisphaera

    I.S. Kulichevskaya, E.N. Detkova, Paul Bodelier, W.I.C. Rijpstra, J.S. Sinninghe Damsté, S.N. Dedysh
    A novel species, Singulisphaera rosea sp. nov., is proposed for aerobic, pink-pigmented, budding bacterium isolated from an acidic Sphagnum peat bog of northwestern Russia. This bacterium, designated strain S26T, has non-motile, spherical cells that occur singly, in pairs or in short chains and attach to surfaces by means of a holdfast material. Novel isolate is moderately acidophilic, mesophilic organism capable of growth at pH values between 3.2 and 7.1 (with an optimum at pH 4.8-5.0) and at temperatures between 4 and 33°C (with an optimum at 20-26°C). Most sugars, several organic acids and polyalcohols are the preferred growth substrates. The major fatty acids are C16:0, C18:1ω9c and C18:2ω6c,12c. The major neutral lipids are n-C31:9 hydrocarbon and squalene; the polar lipids are phosphatidylglycerol, phosphatidylcholine, and an unknown group of intact polar lipids. The G+C content of the DNA is 62.2 mol%. 16S rRNA gene sequence analysis showed that strain S26T is a member of the order Planctomycetales. Among taxonomically characterized representatives of this order, the highest sequence similarity (95.1-95.2%) was observed with non-filamentous, peat-inhabiting planctomycete Singulisphaera acidiphila. However, compared with S. acidiphila, the novel isolate is pigmented, displays significant differences in substrate utilization pattern, has greater tolerance of acidic conditions and contains the C16:1ω9c fatty acid. These differences indicate that strain S26T (=DSM 23044T = VKM B-2599T) represents a novel species of the genus Singulisphaera, Singulisphaera rosea sp. nov.
  • Frontiers in Microbiology

    Spatial patterns of iron- and methane-oxidizing bacterial communities in an irregularly flooded, riparian wetland

    JuanJuan Wang, Sascha Krause, Gerard Muyzer, Marion Meima-Franke, (Riks) H.J. Laanbroek, Paul Bodelier
    Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circum-neutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR-DGGE and QPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidisers (FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Gallionella-related FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of FeOB was assessed using PCR-DGGE and the abundance of both FeOB and MOB by QPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Gallionella-related numbers of FeOB outnumbered the MOB subgroups indicating their competitiveness or the prevalence of Fe2+ over CH4 oxidation in this floodplain.
  • Current Opinion in Environmental Sustainability

    Interactions between nitrogenous fertilizers and methane cycling in wetland and upland soils

    Recent dynamics and uncertainties in global methane budgets necessitate research of controls of sources and sinks of atmospheric methane. Production of methane by methanogenic archaea in wetlands is a major source while consumption by methane oxidizing bacteria in upland soils is a major sink. Methane formation as well as consumption is affected by nitrogenous fertilizers as has been studied intensively. This review synthesizes the results of these studies which are contradictory and await mechanistic explanations. These can be found in the community composition and the traits of the microbes involved in methane cycling. Molecular microbial investigations, use of stable isotope labeling techniques, discoveries and isolation of new species and pathways offer new insight into interactions between nitrogen and methane cycling.
  • Environmental Microbiology Reports

    Acetate utilization as a survival strategy of peat-inhabiting Methylocystis spp

    S.E. Belova, M. Baani, N.E. Suzina, Paul Bodelier, W. Liesack, S.N. Dedysh
    Representatives of the genus Methylocystis are traditionally considered to be obligately methanotrophic bacteria, which are incapable of growth on multicarbon substrates. Here, we describe a novel member of this genus, strain H2s, which represents a numerically abundant and ecologically important methanotroph population in northern Sphagnum-dominated wetlands. This isolate demonstrates a clear preference for growth on methane but is able to grow slowly on acetate in the absence of methane. Strain H2s possesses both forms of methane monooxygenase (particulate and soluble MMO) and a well-developed system of intracytoplasmic membranes (ICM). In cells grown for several transfers on acetate, these ICM are maintained, although in a reduced form, and mRNA transcripts of particulate MMO are detectable. These cells resume their growth on methane faster than those kept for the same period of time without any substrate. Growth on acetate leads to a major shift in the phospholipid fatty acid composition. The re-examination of all type strains of the validly described Methylocystis species showed that Methylocystis heyeri H2T and Methylocystis echinoides IMET10491T are also capable of slow growth on acetate. This capability might represent an important part of the survival strategy of Methylocystis spp. in environments where methane availability is variable or limited.
  • FEMS Microbiology Ecology

    Strain-specific incorporation of methanotrophic biomass into eukaryotic grazers in a rice field soil revealed by SIP-PLFA

    J. Murase, Cees Hordijk, I. Tayasu, Paul Bodelier
    In wetland ecosystems, methane is actively utilized by methanotrophs. The immobilized methane carbon is then passed on to other organisms such as grazers. Here, we traced the incorporation of methanotrophic biomass into eukaryotes in a rice field soil using phospholipid fatty acid stable-isotope probing (PLFA-SIP). Addition of 13C-labeled cells of five methanotrophs to soil (5 × 107 cells g−1 soil) did not affect the CO2 release rate, but significantly increased the carbon isotopic ratio within 24 h. In 48 h, 2–7% of the added bacterial biomass carbon was detected as 13CO2. The soil with Methylobacter luteus released the highest amount of 13CO2, comparable to that with Escherichia coli. The amount of polyunsaturated PLFAs (C18:3ω6c and C20:4ω6c) was not affected by the addition of bacterial cells to soil, but their carbon isotopic ratio increased significantly within 24–48 h. The extent of 13C-enrichment in PLFAs differed between the added methanotrophs, with the highest labeling upon addition of M. luteus. The relative abundance of 13C-labeled C18:3ω6c to C20:4ω6C also differed between the strains. The results indicated that the eukaryotes in soil, probably protozoa, preferentially graze on specific methanotrophs and immediately incorporate their biomass.
  • FEMS Microbiology Ecology

    Hydrology is reflected in the functioning and community composition of methanotrophs in the littoral wetland of a boreal lake

    H.M.P. Siljanen, A. Saari, Sascha Krause, A. Lensu, G.C.J. Abell, L. Bodrossy, Paul Bodelier, P.J. Martikainen
    In lake ecosystems a major proportion of methane emissions originate from the littoral zone which can have a great spatial variability in hydrology, soil quality and vegetation. Hitherto, spatial heterogeneity and the effects it has on functioning and diversity of methanotrophs in littoral wetlands is poorly understood. A diagnostic microarray based on the particulate methane monooxygenase gene coupled with geostatistics was used to analyze spatial patterns of methanotrophs in the littoral wetland of a eutrophic boreal lake (Lake Kevätön, Eastern Finland). The wetland had a hydrology gradient with mean water table varying from −8 cm to −25 cm. The wettest area comprising the highest methane oxidation, had the highest abundance and species richness of methanotrophs. High water table favoured the occurrence of type Ib methanotrophs whereas type Ia and type II were found under all moisture conditions. Thus the spatial heterogeneity in functioning and diversity of methanotrophs in littoral wetlands is highly dependent on water table which in turn varies spatially in relation to the geomorphology of the wetland. We suggest that changes in water levels resulting from regulation of lakes and/or global change will affect the abundance, activity, diversity of methanotrophs and consequently methane emissions from such systems.
  • Applied and Environmental Microbiology

    Distribution and diversity of gallionella-like neutrophilic iron oxidizers in a tidal freshwater marsh

    JuanJuan Wang, S. Vollrath, T. Behrends, Paul Bodelier, G. Muyzer, F. Den Oudsten, Marion Meima-Franke, P. Cappellen, (Riks) H.J. Laanbroek
    Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
  • Frontiers in Microbiology

    Toward understanding, managing, and protecting microbial ecosystems

    Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.
  • Ecology

    Aquatic herbivores facilitate the emission of methane from wetlands

    Wetlands are significant sources of atmospheric methane. Methane produced by microbes enters roots and escapes to the atmosphere through the shoots of emergent wetland plants. Herbivorous birds graze on helophytes, but their effect on methane emission remains unknown. We hypothesized that grazing on shoots of wetland plants can modulate methane emission from wetlands. Diffusive methane emission was monitored inside and outside bird exclosures, using static flux chambers placed over whole vegetation and over single shoots. Both methods showed significantly higher methane release from grazed vegetation. Surface-based diffusive methane emission from grazed plots was up to five times higher compared to exclosures. The absence of an effect on methane-cycling microbial processes indicated that this modulating effect acts on the gas transport by the plants. Modulation of methane emission by animal–plant–microbe interactions deserves further attention considering the increasing bird populations and changes in wetland vegetation as a consequence of changing land use and climate change.
  • Limnology and Oceanography

    Phosphatases relieve carbon limitation of microbial activity in Baltic Sea sediments along a redox-gradient

    Anne Steenbergh, Paul Bodelier, H.L. Hoogveld, C.P Slomp, (Riks) H.J. Laanbroek
    The relationship between phosphatase activity and the element limiting microbial activity (carbon [C], nitrogen [N], or phosphorus [P]) was studied experimentally in sediment from four stations in the Baltic Sea located along a depth transect from oxic to anoxic bottom waters. The role of extracellular phosphatases was assessed by determining the percentages of intact cells that could be labeled with an artificial substrate for phosphatases (i.e., enzyme-labeled fluorescence 97 phosphatase substrate [ELF]) using a flow cytometer. Phosphatase activity was detected in sediment slurries from all sites either with or without prior incubation under oxic or anoxic conditions. In addition, ELF-labeled cells were detected in all incubated sediments, indicating that intact cells bearing phosphatases contribute to the phosphatase activity. Phosphatase activities and percentages of ELF-labeled cells were lower for the anoxic than for the oxic slurry incubations. Phosphatases are likely used to relieve the limitation of microbial activity by utilizable C in these recently deposited, organic C–rich sediments in the Baltic Sea. In marine sediments overlain by anoxic bottom waters, the biological and chemical mechanisms of P retention are often less efficient than in oxic settings and the P released to relieve C limitation escapes to the overlying water. This explains the ongoing higher P fluxes from sediments overlain by anoxic bottom waters.
  • Journal of Paleolimnology

    Fossil chironomid δ13C as a proxy for past methanogenic contribution to benthic food webs in lakes?

    M. Van Hardenbroek, O. Heiri, J. Grey, Paul Bodelier, F. Verbruggen, A.F. Lotter
    We used a series of experiments to determine whether stable carbon isotope analysis of modern and fossil larval head capsules of chironomids allowed identification of their dietary carbon source. Our main focus was to assess whether carbon from naturally 13C-depleted methane-oxidizing bacteria (MOB) can be traced in chironomid cuticles using stable carbon isotope analysis. We first showed that a minimum sample weight of ~20 μg was required for our equipment to determine head capsule δ13C with a standard deviation of 0.5‰. Such a small minimum sample weight allows taxon-specific δ13C analyses at a precision sufficient to differentiate whether head capsules consist mainly of carbon derived from MOB or from other food sources commonly encountered in lake ecosystems. We then tested the effect of different chemical pre-treatments that are commonly used for sediment processing on δ13C measurements on head capsules. Processing with 10% KOH (2 h), 10% HCl (2 h), or 40% HF (18 h) showed no detectable effect on δ13C, whereas a combination of boiling, accelerated solvent extraction and heavy chemical oxidation resulted in a small (0.2‰) but statistically significant decrease in δ13C values. Using culturing experiments with MOB grown on 13C-labelled methane, we demonstrated that methanogenic carbon is transferred not only into the larval tissue, but also into chironomid head capsules. Taxon-specific δ13C of fossil chironomid head capsules from different lake sediments was analyzed. δ13C of head capsules generally ranged from −28 to −25.8‰, but in some instances we observed δ13C values as low as −36.9 to −31.5‰, suggesting that carbon from MOB is traceable in fossil and subfossil chironomid remains. We demonstrate that stable carbon isotope analyses of fossil chironomid head capsules can give insights into dietary links and carbon cycling in benthic food webs in the past and that the method has the potential to reconstruct the importance of MOB in the palaeo-diet of chironomid larvae and, indirectly, to infer past changes in methane flux at the sediment water interface in lakes.
  • FEMS Microbiology Ecology

    Biphasic kinetics of a methanotrophic community is a combination of growth and increased activity per cell

    Anne Steenbergh, M. Meima, M.P. Kamst-van Agterveld, Paul Bodelier
    Since methane-oxidizing bacteria (MOB) are the only biological sink for the greenhouse gas methane, knowledge about the functioning of these bacteria in various ecosystems is needed to understand the dynamics observed in global methane emission. The activity of MOB is commonly assessed by methane oxidation assays. The resulting methane depletion curves often follow a biphasic pattern of initial and induced methane oxidation activity, often interpreted as representing the in situ active and total MOB community, respectively. The application of QPCR on soil incubations, that were stopped before, at, and after the transition point in the methane-depletion curve demonstrated that both pmoA-mRNA was produced as well as substantial cell growth took place already in the initial phase. In addition, type Ia and II MOB displayed markedly different behaviour which can be interpreted as ecologically different strategies. For the correct interpretation of methane oxidation assays, it is recommend using small time windows to calculate methane oxidation activities as to avoid substantial cell growth.
  • Microbial Ecology

    Response of the sulfate-reducing community to the re-establishment of estuarine conditions in two contrasting soils: a mesocosm approach

    M. Miletto, R. Loeb, A.M. Antheunisse, Paul Bodelier, (Riks) H.J. Laanbroek
    We studied the response of the sulfate-reducing prokaryote (SRP) communities to the experimental variation of salinity and tide in an outdoor mesocosm setup. Intact soil monoliths were collected at two areas of the Haringvliet lagoon (The Netherlands): one sampling location consisted of agricultural grassland, drained and fertilized for at least the last century; the other of a freshwater marshland with more recent sea influence. Two factors, i.e., “salinity” (freshwater/oligohaline) and “tide” (nontidal/tidal), were tested in a full-factorial design. Soil samples were collected after 5 months (June–October). Dissimilatory (bi)sulfite reductase β subunit-based denaturing gradient gel electrophoresis (dsrB-DGGE) analysis revealed that the SRP community composition in the agricultural grassland and in the freshwater marshland was represented mainly by microorganisms related to the Desulfobulbaceae and the Desulfobacteraceae, respectively. Desulfovibrio-related dsrB were detected only in the tidal treatments; Desulfomonile-related dsrB occurrence was related to the presence of oligohaline conditions. Treatments did have an effect on the overall SRP community composition of both soils, but not on the sulfate depletion rates in sulfate-amended anoxic slurry incubations. However, initiation of sulfate reduction upon sulfate addition was clearly different between the two soils.
  • Applied and Environmental Microbiology

    Quantitative assessment of ammonia-oxidizing bacterial communities in the epiphyton of submerged macrophytes in shallow lakes

    Manuela Coci, G.W. Nicol, G.N. Pilloni, M. Schmid, M.P. Kamst-van Agterveld, Paul Bodelier, (Riks) H.J. Laanbroek
    In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However, the diversity, numbers, and activity of epiphytic ammonia-oxidizing bacteria have long been overlooked. In the present study, we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On the basis of the m2 of the lake surface, the gene copy numbers of epiphytic ammonia oxidizers were not significantly different from those in the benthic and pelagic compartments. The potential ammonia-oxidizing activities measured in the epiphytic compartment were also not significantly different from the activities determined in the benthic compartment. No potential ammonia-oxidizing activities were observed in the pelagic compartment. No activity was detected in the epiphyton of Chara aspera, the dominant submerged macrophyte in Lake Nuldernauw in The Netherlands. The presence of ammonia-oxidizing bacterial cells in the epiphyton of Potamogeton pectinatus was also demonstrated by fluorescent in situ hybridization microscopy images. By comparing the community composition as assessed by the 16S rRNA gene PCR-denaturing gradient gel electrophoresis approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Of the environmental parameters examined, only the water retention time, the Kjeldahl nitrogen content, and the total phosphorus content correlated with potential ammonia-oxidizing activities. None of these parameters correlated with the numbers of gene copies related to ammonia-oxidizing betaproteobacteria
  • Applied and Environmental Microbiology

    Impacts of Inter- and Intralaboratory Variations on the Reproducibility of Microbial Community Analyses

    Yao Pan, L. Bodrossy, P. Frenzel, A.-G. Hestnes, Sascha Krause, C. Lüke, M. Franke, H. Siljanen, M.M. Svenning, Paul Bodelier
    With the advent of molecular biological techniques, especially next-generation sequencing and metagenomics, the number of microbial biogeography studies is rapidly increasing. However, these studies involve the synthesis of data generated by different laboratories using different protocols, chemicals, etc., all with inherent biases. The aim of this study was to assess inter- as well as intralaboratory variations in microbial community composition when standardized protocols are applied to a single soil sample. Aliquots from a homogenized soil sample from a rice field in Italy were sent to five participating laboratories. DNA was extracted by two investigators per laboratory using an identical protocol. All DNA samples were sent to one laboratory to perform DNA quantification, quantitative PCR (QPCR), and microarray and denaturing gradient gel electrophoresis (DGGE) analyses of methanotrophic communities. Yields, as well as purity of DNA, were significantly different between laboratories but in some cases also between investigators within the same laboratory. The differences in yield and quality of the extracted DNA were reflected in QPCR, microarray, and DGGE analysis results. Diversity indices (Shannon-Wiener, evenness, and richness) differed significantly between laboratories. The observed differences have implications for every project in which microbial communities are compared in different habitats, even if assessed within the same laboratory. To be able to make sensible comparisons leading to valid conclusions, intralaboratory variation should be assessed. Standardization of DNA extraction protocols and possible use of internal standards in interlaboratory comparisons may help in rendering a "quantifiable" bias.
  • Proceedings of the National Academy of Sciences of the United States of America

    Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2

    Barbara Drigo, Agata Pijl, Henk Duyts, Anna Kielak, H.A. Gamper, M.J. Houtekamer, H.T.S. Boschker, Paul Bodelier, A.S. Whiteley, Hans van Veen, George Kowalchuk
    Rising atmospheric CO2 levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics; however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO2 modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO2 conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric CO2 clearly evokes the emergence of distinct opportunistic plant-associated microbial communities. Analyses involving RNA-based stable isotope probing, neutral/phosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric CO2 concentrations and terrestrial ecosystems.
  • International Journal of Systematic and Evolutionary Microbiology

    Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog

    I.S. Kulichevskaya, O.I. Baulina, Paul Bodelier, W.I.C. Rijpstra, J.S. Sinninghe Damsté, S.N. Dedysh
    An aerobic, pink-pigmented, budding and rosette-forming bacterium was isolated from an acidic Sphagnum peat bog and designated strain A10T. The 16S rRNA gene sequence analysis showed that strain A10T was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Gemmata, with 90 % sequence similarity to that of Gemmata obscuriglobus, the only taxonomically described organism of this group. Ellipsoid-shaped cells of strain A10T were uniformly covered with crateriform pits and possessed long (up to 10–15 µm) and unusually thick (0.5–0.7 µm) stalks of a unique ultrastructure. Thin sections revealed a complex intracellular membrane system compartmentalizing the cells. Strain A10T was a moderately acidophilic, mesophilic organism capable of growth at pH values between 3.8 and 7.2 (with an optimum at pH 5.5–6.0) and at temperatures between 10 and 30 °C (with an optimum at 20–25 °C). The major fatty acids were C18 : 0, C18 : 15c and C16 : 15c and the major quinone was MK-6. Cells of strain A10T contained high amounts of bound saturated and monounsaturated C26–C32 (-1) hydroxy fatty acids. The G+C content of the DNA was 62.5 mol%. The unique cell morphology, the capability of growth in acidic conditions and a number of chemotaxonomic and genotypic characteristics served to differentiate strain A10T from G. obscuriglobus. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Zavarzinella formosa gen. nov., sp. nov. is proposed The type strain is A10T (=DSM 19928T=VKM B-2478T).
  • International Journal of Systematic and Evolutionary Microbiology

    Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene

    A.V. Vorob'ev, Wietse de Boer, L.B. Folman, Paul Bodelier, N.V. Doronina, N.E. Suzina, Y.A. Trotsenko, S.N. Dedysh
    Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beech wood blocks during decay by the white-rot fungus Hypholoma fasciculare (Folman et al., 2008) and were designated strains BW863T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH values between 3.1 and 6.5 (with an optimum at pH 4.5-5.0) and at temperatures between 4 and 30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually high amounts (about 90%) of 18:17c fatty acid, thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of novel isolates is 61.8-62.8 mol %. On the basis of 16S rRNA gene sequence identity, strains BW863T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2 (96.5-97 %). Comparative sequence analysis of mxaF, the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity values between the MxaF sequences of the acidophilic isolates and the MxaF sequences from known alpha-, beta- and gammaproteobacterial methylotrophs comprised 69-75%, 61-63% and 64-67%, respectively. The data therefore suggest that strains BW863T and BW872 represent a novel genus and species of methylotrophic bacteria; the name Methylovirgula ligni gen. nov., sp. nov. is proposed, with strain BW863T (=DSM 19998T = NCIMB 14408T) as the type strain.
  • ISME Journal

    A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria

    Paul Bodelier, Marie-Jose Bär-Gilissen, Cees Hordijk, J.S. Sinninghe Damsté, W.I.C. Rijpstra, J.A.J. Geenevasen, P.F. Dunfield
    Aerobic methane-oxidizing bacteria (MB) are the primary terrestrial sinks for the greenhouse gas methane. A distinct characteristic of MB is the presence of specific phospholipid ester-linked fatty acids (PLFA) in their membranes that differentiate them from each other and also from all other organisms. These distinct PLFA patterns facilitate microbial ecology studies. For example, the assimilation of C from methane into PLFA can be traced in environmental samples using stable isotope (13C) probing (SIP), which links the activity of MB to their community composition in situ. However, the phylogenetic resolution of this method is low because of a lack of PLFA profiles from cultured MB species. In this study, PLFA profiles of 22 alphaproteobacterial (type II) MB were analysed after growth on methane, methanol or both substrates together. Growth on different substrates did not affect the PLFA profiles of the investigated strains. A number of Methylocystis strains contained novel C18:2 fatty acids (7c,12c and 6c,12c) that can be used as diagnostic biomarkers. The detection of these novel PLFA, combined with the analyses of multiple type II strains, increased the phylogenetic resolution of PLFA analysis substantially. Multivariate analysis of the expanded MB PLFA database identified species groups that closely reflected phylogenies based on 16S rRNA and pmoA gene sequences. The PLFA database therefore provides a robust framework for linking identity to activity in MB communities with a higher resolution than was previously possible.
  • Environmental Microbiology

    Whole community genome amplification (WCGA) leads to compositional bias in methane oxidizing communities as assessed by pmoA based microarray analyses and QPCR

    Paul Bodelier, M.P. Kamst-van Agterveld, Marion Meima-Franke, N. Stralis-Pavese, L. Bodrossy
    Whole-genome amplification (WGA) using multiple displacement amplification (MDA) has recently been introduced to the field of environmental microbiology. The amplification of single-cell genomes or whole-community metagenomes decreases the minimum amount of DNA needed for subsequent molecular community analyses. The resolution of profiling methods of environmental microbial communities will increase substantially by the use of the whole-community genome amplification (WCGA) procedure, assuming that the original community composition is not affected qualitatively as well as quantitatively. The present study aims to test if WCGA introduces a bias when applied to aerobic proteobacterial methanotrophic communities. For this, first, we subjected samples from freshwater lake sediment to WCGA, and amplified using primers targeting the pmoA gene coding for the α-subunit of the methane monooxygenase enzyme. Second, we analysed community composition using a diagnostic microarray and quantitative PCR (QPCR) assays. These methods clearly demonstrated that the WCGA amplification introduced a bias. Thus, numbers of γ-proteobacterial methanotrophs ('type Ia') increased significantly while the α-proteobacterial methanotrophs ('type II') were not amplified by the WCGA procedure. It is hypothesized that this bias is caused by the differences in GC content, which may compromise the efficiency of the MDA reaction.
  • FEMS Microbiology Letters

    A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples

    E.W. Vissers, Paul Bodelier, G. Muyzer, (Riks) H.J. Laanbroek
    In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for denaturing gradient gel electrophoresis (DGGE) with primer sets 21F–958R and Parch519f–Arch915r, respectively. After sequencing of the DGGE bands obtained by this nested method, 93% of the sequences were of archaeal origin. More diverse archaeal DGGE patterns were found as compared with other PCR methods. The nested PCR-DGGE method presented here is therefore a reliable tool to analyze the archaeal diversity in freshwater habitats, revealing even more widespread diversity of the archaea.
  • ISME Journal

    Diversity of iron oxidizers in wetland soils revealed by novel 16S rRNA primers targeting Gallionella-related bacteria

    JuanJuan Wang, G. Muyzer, Paul Bodelier, (Riks) H.J. Laanbroek
    Neutrophilic iron-oxidizing bacteria (FeOB) are important catalysts of iron cycling in wetland environments. However, little is known about their diversity and distribution in various environments. The aim of this study was to develop a PCR-DGGE assay enabling the detection of neutrophilic iron oxidizers in wetland habitats. Gradient tubes were used to enrich FeOB. From these enrichments, a clone library was established on the basis of the almost complete 16S rRNA gene using the universal bacterial primers 27f and 1492r. This clone library consisted of mainly - and -Proteobacteria, among which two major clusters were closely related to Gallionella spp. Specific probes and primers were developed on the basis of this 16S rRNA gene clone library. The newly designed Gallionella-specific 16S rRNA gene primer set 122f/998r was applied to community DNA obtained from three contrasting wetland environments, followed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis. A second 16S rRNA gene clone library was constructed using the PCR products from one of our sampling sites amplified with the newly developed primer set 122f/998r. The cloned 16S rRNA gene sequences all represented novel culturable iron oxidizers most closely related to Gallionella sp. On the basis of their nucleotide sequences, four groups could be identified that were comparable to the DGGE banding pattern obtained before with the same PCR products as used for the second clone library. Using these Gallionella-specific 16S rRNA gene-based primers, in combination with DGGE, first insights into the diversity and distribution of these bacteria in wetland soils were obtained.
  • Global Change Biology

    Soil type links microbial colonization of rice roots to methane emission

    R. Conrad, M. Klose, M. Noll, D. Kemnitz, Paul Bodelier
    Most of the methane (CH4) emission from rice fields is derived from plant photosynthates, which are converted to CH4. Rice cluster I (RC-1) archaea colonizing the rhizosphere were found to be the methanogens responsible for this process. Hence, RC-1 methanogens seem to play a crucial role in emission of the greenhouse gas CH4. We determined the community composition and activity of methanogens colonizing the roots of eight different rice cultivars after growth on both Italian rice soil and river bank soil, which contained different communities of methanogenic archaea. The community composition was analyzed by terminal restriction fragment length polymorphism and cloning/sequencing of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase. When grown on rice field soil, the methanogenic community of the different rice cultivars was always dominated by RC-1 methanogens. In contrast, roots were colonized by Methanomicrobiales when grown on river bank soil, in which RC-1 methanogens were initially not detectable. Roots colonized with Methanomicrobiales compared with RC-1 exhibited lower CH4 production and CH4 emission rates. The results show that the type of methanogens colonizing rice roots has a potentially important impact on the global CH4 cycle.
  • Applied and Environmental Microbiology

    Epiphyton as a niche for ammonia-oxidizing bacteria: detailed comparison with benthic and pelagic compartments in shallow freshwater lakes

    Manuela Coci, Paul Bodelier, (Riks) H.J. Laanbroek
    Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated.
  • FEMS Microbiology Ecology

    Biogeography of sulfate-reducing prokaryotes in river floodplains

    M. Miletto, A. Loy, A.M. Antheunisse, R. Loeb, Paul Bodelier, (Riks) H.J. Laanbroek
    In this study, a large-scale field survey was conducted to describe the biogeography of sulfate-reducing prokaryotes (SRPs) in river floodplains. Fingerprints obtained with three methods, i.e. 16S rRNA gene-based oligonucleotide microarray, dsrB-based denaturing gradient gel electrophoresis (DGGE) and polar lipid-derived fatty acid (PLFA) analyses, were used as a proxy to describe the SRPs community diversity. Each set of profiles was subjected to a combined multivariate/correlation analysis in order to compare SRP community profiles and to highlight the environmental variables influencing the SRPs distribution along environmental gradients. Floodplain soils harbored distinct SRP communities displaying biogeographic patterns. Nearly all profiles from the tidal sites consistently separated from the nontidal sites, independently from the screening method and the multivariate statistics used. The distribution of the microarray/DGGE/PLFA-based fingerprints in the principal component plots could be correlated to eight soil variables, i.e. soil organic matter, total nitrogen, total phosphorous and total potassium, and extractable ammonium, nitrate, phosphate and sulfate, as well as seven pore water variables, i.e. phosphate, sulfate, sulfide, chloride, sodium, potassium and magnesium ions. Indication of a salinity- and plant nutrient-dependent distribution of SRPs related to Desulfosarcina, Desulfomonile and Desulfobacter was suggested by microarray, DGGE and PLFA analyses.
  • International Journal of Systematic and Evolutionary Microbiology

    Singulisphaera acidiphila gen. nov., sp. nov., a non-filamentous, Isosphaera-like planctomycete from acidic northern wetlands

    I.S. Kulichevskaya, A.O. Ivanova, O.I. Baulina, Paul Bodelier, J.S. Sinninghe Damsté, S.N. Dedysh
    Four novel strains of budding bacteria, designated MOB10T, PO2, MPL1015 and BG32, were isolated from acidic wetlands of northern Russia. Cells of these four strains were aerobic, non-motile spheres that occurred singly or in shapeless aggregates and attached to surfaces by means of a holdfast material. The isolates were moderately acidophilic, mesophilic organisms capable of growth between pH 4.2 and 7.5 (optimum growth at pH 5.0–6.2) and at temperatures between 4 and 33 °C (optimum growth at 20–26 °C). The strains possessed a complex intracellular membrane system that compartmentalized the cells. The major fatty acids were C16 : 0, C18 : 19c and C18 : 26c,12c. The major quinone was menaquinone-6 (MK-6). The G+C content of the DNA was 57.8–59.9 mol%. 16S rRNA gene sequence analysis showed that strains MOB10T, PO2, MPL1015 and BG32 were members of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Isosphaera, exhibiting 90 % sequence similarity to the type strain of the thermophilic planctomycete Isosphaera pallida and 95–95.5 % sequence similarity to a taxonomically uncharacterized group of filamentous bacteria from activated sludge, ‘Nostocoida limicola’ III. However, compared with ‘Nostocoida limicola’ III and Isosphaera pallida, the new isolates from acidic wetlands were non-filamentous, unpigmented bacteria, which possessed highly distinctive phospholipid fatty acid profiles and were capable of growth and of degrading several biopolymers under acidic, microaerobic and cold conditions. The data suggest that the four isolates should be considered as representing a novel species of a new genus of the order Planctomycetales, for which the name Singulisphaera acidiphila gen. nov., sp. nov. is proposed. The type strain of Singulisphaera acidiphila is MOB10T (=ATCC BAA-1392T =VKM B-2454T =DSM 18658T).
  • Water Research

    Limitations of the use of group-specific primers in real-time PCR as appear from quantitative analyses of closely related ammonia-oxidising species

    T. Sekido, Paul Bodelier, T. Shoji, Y. Suwa, (Riks) H.J. Laanbroek
    To study the ecology of ammonia-oxidising bacteria (AOB), quantitative techniques are essential. Real-time PCR assays based on the 16S rRNA or on the structural amoA gene are routinely used. The CTO primer set rooted on the 16S rRNA gene has a number of mismatches with some of the cultures of AOB. To examine if these mismatches have an effect on the outcome of real-time PCR assays, the assay was tested with DNA from a number of closely related isolates of AOB. Standard curves of known amounts of initial DNA were similar among most of the tested cultures of AOB, except for the standard curves of Nitrosomonas strain AL212 and Nitrosospira strain NpAV. Nitrosomonas strain AL212 had 3 mismatches with the CTO primer set. Adaptation of the CTO primer set in order to perfectly match the Nitrosomonas strain AL212 gave a standard curve similar to the majority of the AOB tested. As Nitrosospira strain NpAV has no mismatches with the original CTO primer set, there must be another reason for the less efficient amplification than the sequence itself. Application of an existing sigmoidal mathematical model gave no other results with respect to the standard curves of Nitrosomonas europaea and Nitrosomonas strain AL212, but also demonstrated that primer mismatches can seriously underestimate the initial target concentration. It was concluded that in general correct interpretation of real-time PCR results requires knowledge of the target community composition, in particular of the target sequences of the dominant community members.
  • International Journal of Systematic and Evolutionary Microbiology

    Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands

    I.S. Kulichevskaya, A.O. Ivanaova, S.E. Belova, O.I. Baulina, Paul Bodelier, W.I.C. Rijpstra, J.S. Sinninghe-Damsté, G.A. Zavarin, S.N. Dedysh
    Three strains of budding, ellipsoid-shaped and rosette-forming bacteria were isolated from acidic Sphagnum-dominated boreal wetlands of northern Russia and were designated strains MPL7T, MOB77 and SB2. The presence of crateriform pits and numerous fibrillar appendages on the cell surface and an unusual spur-like projection on one pole of the cell indicated a planctomycete morphotype. These isolates are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4.2 and 7.5 (with an optimum at pH 5.0–6.2) and at temperatures between 4 and 32 °C (optimum 15–26 °C). The major fatty acids are C16 : 0 and C16 : 17c; the major quinone is MK-6. The G+C content of the DNA is 54.4–56.5 mol%. Strains MPL7T, MOB77 and SB2 possess nearly identical 16S rRNA gene sequences and belong to the planctomycete lineage defined by the genus Planctomyces, being most closely related to Planctomyces limnophilus DSM 3776T (86.9–87.1 % sequence similarity). However, strain MPL7T showed only 28 % DNA–DNA hybridization with P. limnophilus DSM 3776T. Compared with currently described members of the genus Planctomyces, the isolates from northern wetlands do not form long and distinctive stalks, have greater tolerance of acidic conditions and low temperatures, are more sensitive to NaCl, lack pigmentation and degrade a wider range of biopolymers. The data therefore suggest that strains MPL7T, MOB77 and SB2 represent a novel genus and species, for which the name Schlesneria paludicola gen. nov., sp. nov., is proposed. Strain MPL7T (=ATCC BAA-1393T =VKM B-2452T) is the type strain of Schlesneria paludicola.
  • FEMS Microbiology Ecology

    Effect of temperature on composition of the methanotrophic community in rice field and forest soil

    S.R. Mohanty, Paul Bodelier, R. Conrad
    Temperature change affects methane consumption in soil. However, there is no information on possible temperature control of methanotrophic bacterial populations. Therefore, we studied CH4 consumption and populations of methanotrophs in an upland forest soil and a rice field soil incubated at different temperatures between 5 and 45°C for up to 40 days. Potential methane consumption was measured at 4% CH4. The temporal progress of CH4 consumption indicated growth of methanotrophs. Both soils showed maximum CH4 consumption at 25–35°C, but no activity at >40°C. In forest soil CH4 was also consumed at 5°C, but in rice soil only at 15°C. Methanotroph populations were assessed by terminal restriction fragment length polymorphism (T-RFLP) targeting particulate methane monooxygenase (pmoA) genes. Eight T-RFs with relative abundance >1% were retrieved from both forest and rice soil. The individual T-RFs were tentatively assigned to different methanotrophic populations (e.g. Methylococcus/Methylocaldum, Methylomicrobium, Methylobacter, Methylocystis/Methylosinus) according to published sequence data. Two T-RFs were assigned to ammonium monooxygenase (amoA) gene sequences. Statistical tests showed that temperature affected the relative abundance of most T-RFs. Furthermore, the relative abundance of individual T-RFs differed between the two soils, and also exhibited different temperature dependence. We conclude that temperature can be an important factor regulating the community composition of methanotrophs in soil.
  • Journal of Microbiological Methods

    Improved PCR-DGGE for high resolution diversity screening of complex sulfate-reducing prokaryotic communities in soils and sediments

    M. Miletto, Paul Bodelier, (Riks) H.J. Laanbroek
    In this study we evaluated a high resolution PCR-DGGE strategy for the characterization of complex sulfate-reducing microbial communities inhabiting natural environments. dsrB fragments were amplified with a two-step nested PCR protocol using combinations of primers targeting the dissimilatory (bi)sulfite reductase genes. The PCR-DGGE conditions were initially optimized using a dsrAB clone library obtained from a vegetated intertidal riparian soil along the river Rhine (Rozenburg, the Netherlands). Partial dsrB were successfully amplified from the same environmental DNA extracts used to construct the library, DGGE-separated and directly sequenced. The two approaches were in good agreement: the phylogenetic distribution of clones and DGGE-separated dsrB was comparable, suggesting the presence of sulfate-reducing prokaryotes (SRP) belonging to the families ‘Desulfobacteraceae,' ‘Desulfobulbaceae’ and ‘Syntrophobacteraceae,' and to the Desulfomonile tiedjei- and Desulfobacterium anilini-groups. The nested PCR-DGGE was also used to analyze sediment samples (Appels, Belgium) from a series of microcosms subjected to a tidal flooding regime with water of different salinity, and proved to be a valid tool also to monitor the SRP community variation over time and space as a consequence of environmental changes.
  • International Journal of Systematic and Evolutionary Microbiology

    Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing signature fatty acids of type I methanotrophs

    S.N. Dedysh, S.E. Belova, Paul Bodelier, K.V. Smirnova, A. Khmelenina, A. Chidthaisong, Y.A. Trotsenko, W. Liesack, P.F. Dunfield
    A novel species is proposed for two strains of methanotrophic bacteria (H2T and Sakb1) isolated from an acidic (pH 4.3) Sphagnum peat bog lake (Teufelssee, Germany) and an acidic (pH 4.2) tropical forest soil (Thailand), respectively. Cells of strains H2T and Sakb1 were aerobic, Gram-negative, non-motile, straight or curved rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type II methanotrophs. They possessed both a particulate and a soluble methane monooxygenase and utilized the serine pathway for carbon assimilation. They were moderately acidophilic organisms capable of growth between pH 4.4 and 7.5 (optimum 5.8–6.2). The most unique characteristic of these strains was the phospholipid fatty acid profile. In addition to the signature fatty acid of type II methanotrophs (18 : 18c), the cells also contained large amounts of what was previously considered to be a signature fatty acid of type I methanotrophs, 16 : 18c. The DNA G+C contents of strains H2T and Sakb1 were 61.5 and 62.1 mol%, respectively. The 16S rRNA gene sequences possessed 96–98 % similarity to sequences of other type II methanotrophs in the genera Methylosinus and Methylocystis. 16S rRNA gene sequence and pmoA phylogeny demonstrated that the strains form a novel lineage within the genus Methylocystis. DNA–DNA hybridization values of strain H2T with Methylocystis parvus OBBPT and Methylocystis echinoides IMET 10491T were 18 and 25 %, respectively. Thus, it is proposed that these two strains represent a novel species, Methylocystis heyeri sp. nov. Strain H2T (=DSM 16984T=VKM B-2426T) is the type strain.
  • Environmental Microbiology

    Methane-derived carbon flows through methane-oxidizing bacteria to higher trophic levels in aquatic systems

    P. Deines, Paul Bodelier, G. Eller
    Recent investigations have shown that biogenic methane can be a carbon source for macro invertebrates in freshwater food webs. Stable carbon isotopic signatures, used to infer an organism's food source, indicated that methane can play a major role in the nutrition of chironomid larvae. However, the pathway of methane-derived carbon into invertebrate biomass is still not confirmed. It has been proposed that chironomid larvae ingest methane-oxidizing bacteria (MOB), but this has not been experimentally demonstrated to date. Using 13C-labelled methane we could show for the first time that chironomid larvae assimilate methane-derived carbon through MOB. Chironomid larval biomass was significantly 13C-enriched after dwelling for 10 days in lake sediment enriched with labelled methane. Moreover, phospholipid fatty acids diagnostic for MOB were detected in larval tissue and were significantly 13C-enriched, which encompasses the 13C-uptake predicted for a methane-based nutrition. Additionally, chironomid larvae fed on sediment and water-column derived MOB biomass.
  • Nature

    Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia

    P.F. Dunfield, A.Q. Yurgey, P. Senin, A.V. Smirnova, M.B. Stott, S. Hou, B. Ly, J.H. Saw, Z. Zhou, Y. Ren, Jianmei Wang, B.W. Mountain, M.A. Crowe, T.M. Weatherby, Paul Bodelier, W. Liesack, L. Feng, L. Wang, M. Alam
    Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment1. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows optimally below pH 5, but some environments with active methane cycles are very acidic2, 3. Here we describe an extremely acidophilic methanotroph that grows optimally at pH 2.0–2.5. Unlike the known methanotrophs, it does not belong to the phylum Proteobacteria but rather to the Verrucomicrobia, a widespread and diverse bacterial phylum that primarily comprises uncultivated species with unknown genotypes. Analysis of its draft genome detected genes encoding particulate methane monooxygenase that were homologous to genes found in methanotrophic proteobacteria. However, known genetic modules for methanol and formaldehyde oxidation were incomplete or missing, suggesting that the bacterium uses some novel methylotrophic pathways. Phylogenetic analysis of its three pmoA genes (encoding a subunit of particulate methane monooxygenase) placed them into a distinct cluster from proteobacterial homologues. This indicates an ancient divergence of Verrucomicrobia and Proteobacteria methanotrophs rather than a recent horizontal gene transfer of methanotrophic ability. The findings show that methanotrophy in the Bacteria is more taxonomically, ecologically and genetically diverse than previously thought, and that previous studies have failed to assess the full diversity of methanotrophs in acidic environments.
  • Environmental Microbiology

    The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration

    C. Knief, S. Kolb, Paul Bodelier, A. Lipski, P.F. Dunfield
    Methanotrophic communities were studied in several periodically water-saturated gleyic soils. When sampled, each soil had an oxic upper layer and consumed methane from the atmosphere (at 1.75 ppmv). In most gleyic soils the Km(app) values for methane were between 70 and 800 ppmv. These are higher than most values observed in dry upland soils, but lower than those measured in wetlands. Based on cultivation-independent retrieval of the pmoA-gene and quantification of partial pmoA gene sequences, type II (Alphaproteobacteria) methanotrophs of the genus Methylocystis spp. were abundant (> 107pmoA target molecules per gram of dry soil). Type I (Gammaproteobacteria) methanotrophs related to the genera Methylobacter and Methylocaldum/Methylococcus were detected in some soils. Six pmoA sequence types not closely related to sequences from cultivated methanotrophs were detected as well, indicating that diverse uncultivated methanotrophs were present. Three Gleysols were incubated under different mixing ratios of 13C-labelled methane to examine 13C incorporation into phospholipid fatty acids (PLFAs). Phospholipid fatty acids typical of type II methanotrophs, 16:0 and 18:17c, were labelled with 13C in all soils after incubation under an atmosphere containing 30 ppmv of methane. Incubation under 500 ppmv of methane resulted in labelling of additional PLFAs besides 16:0 and 18:17c, suggesting that the composition of the active methanotrophic community changed in response to increased methane supply. In two soils, 16:1 PLFAs typical of type I methanotrophs were strongly labelled after incubation under the high methane mixing ratio only. Type II methanotrophs are most likely responsible for atmospheric methane uptake in these soils, while type I methanotrophs become active when methane is produced in the soil.
  • Applied and Environmental Microbiology

    Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soil

    S.R. Mohanty, Paul Bodelier, V. Floris, R. Conrad
    The impact of environmental perturbation (e.g., nitrogenous fertilizers) on the dynamics of methane fluxes from soils and wetland systems is poorly understood. Results of fertilizer studies are often contradictory, even within similar ecosystems. In the present study the hypothesis of whether these contradictory results may be explained by the composition of the methane-consuming microbial community and hence whether methanotrophic diversity affects methane fluxes was investigated. To this end, rice field and forest soils were incubated in microcosms and supplemented with different nitrogenous fertilizers and methane concentrations. By labeling the methane with 13C, diversity and function could be coupled by analyses of phospholipid-derived fatty acids (PLFA) extracted from the soils at different time points during incubation. In both rice field and forest soils, the activity as well as the growth rate of methane-consuming bacteria was affected differentially. For type I methanotrophs, fertilizer application stimulated the consumption of methane and the subsequent growth, while type II methanotrophs were generally inhibited. Terminal restriction fragment length polymorphism analyses of the pmoA gene supported the PLFA results. Multivariate analyses of stable-isotope-probing PLFA profiles indicated that in forest and rice field soils, Methylocystis (type II) species were affected by fertilization. The type I methanotrophs active in forest soils (Methylomicrobium/Methylosarcina related) differed from the active species in rice field soils (Methylobacter/Methylomonas related). Our results provide a case example showing that microbial community structure indeed matters, especially when assessing and predicting the impact of environmental change on biodiversity loss and ecosystem functioning.
  • Current Microbiology

    Validation of the correct start codon of norX/nxrX and universality of the norAXB/nxrAXB gene cluster in Nitrobacter species

    B. Vanparys, Paul Bodelier, P. De Vos
    The complete norX/nxrX sequence of five Nitrobacter strains was determined showing that the norAXB/nxrAXB gene cluster is present in all hitherto described Nitrobacter species. Evidence is provided that the previously published sequence of norX in N. hamburgensis X14T contains an invalid base “insertion,” which resulted in a frameshift and a misidentified start codon.
  • Oecologia

    Animal-plant-microbe interactions: direct and indirect effects of swan foraging behavior modulate methane cycling in temperate shallow wetlands

    Paul Bodelier, M. Stomp, L. Santamaria, M.R.J. Klaassen, (Riks) H.J. Laanbroek
    Wetlands are among the most important ecosystems on Earth both in terms of productivity and biodiversity, but also as a source of the greenhouse gas CH4. Microbial processes catalyzing nutrient recycling and CH4 production are controlled by sediment physico-chemistry, which is in turn affected by plant activity and the foraging behaviour of herbivores. We performed field and laboratory experiments to evaluate the direct effect of herbivores on soil microbial activity and their indirect effects as the consequence of reduced macrophyte density, using migratory Bewick’s swans (Cygnus columbianus bewickii Yarrell) feeding on fennel pondweed (Potamogeton pectinatus L.) tubers as a model system. A controlled foraging experiment using field enclosures indicated that swan bioturbation decreases CH4 production, through a decrease in the activity of methanogenic Archaea and an increased rate of CH4 oxidation in the bioturbated sediment. We also found a positive correlation between tuber density (a surrogate of plant density during the previous growth season) and CH4 production activity. A laboratory experiment showed that sediment sterilization enhances pondweed growth, probably due to elimination of the negative effects of microbial activity on plant growth. In summary, the bioturbation caused by swan grazing modulates CH4 cycling by means of both direct and indirect (i.e. plant-mediated) effects with potential consequences for CH4 emission from wetland systems. [KEYWORDS: Multitrophic interactions ; Methane cycling ; Shallow lakes ; Bewick’s swans ; Fennel pondweed]
  • 2006

    Ecological Aspects of Microbes and Microbial Communities Inhabiting the Rhizosphere of Wetland Plants

    Paul Bodelier, P. Frenzel, H. Drake, T. Hurek, K. Küsel, C. Lovell, P. Megonigal, B. Reinhold-Hurek, B. Sorrell
  • FEMS Microbiology Ecology

    New DGGE strategies for the analyses of methanotrophic microbial communities using different combinations of existing 16S rRNA-based primers

    Paul Bodelier, Marion Meima-Franke, G. Zwart, (Riks) H.J. Laanbroek
    Methane-oxidising microbial communities are studied intensively because of their importance for global methane cycling. A suite of molecular microbial techniques has been applied to the study of these communities. Denaturing gradient gel electrophoresis (DGGE) is a diversity screening tool combining high sample throughput with phylogenetic information of high resolution. The existing 16S rRNA-based DGGE assays available for methane-oxidising bacteria suffer from low-specificity, low phylogentic information due to the length of the amplified fragments and/or from lack of resolving power. In the present study we developed new combinations of existing primers and applied these on methane-oxidising microbial communities in a freshwater wetland marsh. The designed strategies comprised nested as well as direct amplification of environmental DNA. Successful application of direct amplification using combinations of universal and specific primers circumvents the nested designs currently used. All developed assays resulted in identical community profiles in wetland soil cores with Methylobacter sp. and Methylocystis sp.-related sequences. Changes in the occurrence of Methylobacter-related sequences with depth in the soil profile may be related to the decrease in methane-oxidizing activity. [KEYWORDS: DGGE ; 16S rRNA ; Methanotrophs ; Methane oxidation ; Wetland soil]
  • FEMS Microbiology Ecology

    Effect of salinity on temporal and spatial dynamics of ammonia-oxidising bacteria from intertidal freshwater sediment

    Manuela Coci, D. Riechmann, Paul Bodelier, S. Stefani, G. Zwart, (Riks) H.J. Laanbroek
    Temporal and spatial dynamics within an ammonia-oxidising community from intertidal, freshwater sediments were studied in microcosms simulating flooding twice a day with fresh, brackish and marine waters. The microcosms had been filled with the upper 5 cm of intertidal freshwater sediment from the river Scheldt. Changes in community composition were examined by denaturing gradient gel electrophoresis of amplified DNA from the community. In the first week of incubation the initially present members of the Nitrosomonas oligotropha lineage were replaced by other members of the same lineage in the top layer of the sediment subjected to flooding with freshwater. Prolonged incubation extended niche differentiation to a depth of 5 cm. In the microcosms flooded with saline media, the initially present members of the N. oligotropha lineage were replaced by strains belonging to the Nitrosomonas marina lineage, but only in the top 1 cm. Shift in community composition occurred earlier in the marine microcosm than in the brackish microcosms and was slower than the change in the freshwater microcosms. Irrespective of the nature of the flooding medium, shifts in community composition were always consistent among replicate microcosms. We conclude that salinity is an important steering factor in niche differentiation among ammonia-oxidising bacteria and also that changes within the community of this functional group of bacteria may occur at different rates. [KEYWORDS: Ammonia-oxidising bacteria ; Freshwater sediment ; Salt stress ; Microcosms ; Niche differentiation ; Spatial and temporal community change]
  • Aquatic Ecology

    The impact of climate change on lakes in the Netherlands: a review

    Wolf M. Mooij, S. Hülsmann, Lisette de Senerpont Domis, Bart A. Nolet, Paul Bodelier, P. Boers, L.M. Dionisio Pires, H.J. Gons, Bas Ibelings, R. Noordhuis, R. Portielje, K. Wolfstein, R. Wolfstein, E.H.R.R. Lammens
    Climate change will alter freshwater ecosystems but specific effects will vary among regions and the type of water body. Here, we give an integrative review of the observed and predicted impacts of climate change on shallow lakes in the Netherlands and put these impacts in an international perspective. Most of these lakes are man-made and have preset water levels and poorly developed littoral zones. Relevant climatic factors for these ecosystems are temperature, ice-cover and wind. Secondary factors affected by climate include nutrient loading, residence time and water levels. We reviewed the relevant literature in order to assess the impact of climate change on these lakes. We focussed on six management objectives as bioindicators for the functioning of these ecosystems: target species, nuisance species, invading species, transparency, carrying capacity and biodiversity. We conclude that climate change will likely (i) reduce the numbers of several target species of birds; (ii) favour and stabilize cyanobacterial dominance in phytoplankton communities; (iii) cause more serious incidents of botulism among waterfowl and enhance the spreading of mosquito borne diseases; (iv) benefit invaders originating from the Ponto-Caspian region; (v) stabilize turbid, phytoplankton-dominated systems, thus counteracting restoration measures; (vi) destabilize macrophyte-dominated clear-water lakes; (vii) increase the carrying capacity of primary producers, especially phytoplankton, thus mimicking eutrophication; (viii) affect higher trophic levels as a result of enhanced primary production; (ix) have a negative impact on biodiversity which is linked to the clear water state; (x) affect biodiversity by changing the disturbance regime. Water managers can counteract these developments by reduction of nutrient loading, development of the littoral zone, compartmentalization of lakes and fisheries management. [KEYWORDS: Biodiversity ; Carrying capacity ; Invading species ; Nuisance species ; Temperature ; Transparency]
  • Environmental Microbiology

    Community analysis of methanogenic archaea within a riparian flooding gradient

    D. Kemnitz, K-J. Chin, Paul Bodelier, R. Conrad
    Anoxic soils in river floodplains (or riparian soils) are a source of methane emission. However, little is known about the ecology and community structure of archaeal methanogenic microbes, which are a crucial component of methane flux in those habitats. We studied the archaeal community in the vertical profile of four different sites along the River Waal in the Netherlands. These sites differ in their annual flooding regime ranging from never or seldom to permanently flooded. The archaeal community structure has been characterized by terminal restriction fragment length polymorphism (T-RFLP) and comparative sequence analysis of the archaeal SSU rRNA gene and the mcrA gene. The latter gene codes for the -subunit of methyl-coenzyme M reductase. Additionally, the potential methanogenic activity was determined by incubation of soil slurries under anoxic conditions. The community composition differed only slightly with the depth of the soil (0-20 cm). However, the diversity of archaeal SSU rRNA genes increased with the frequency of flooding. Terminal restriction fragment length polymorphism analysis of mcrA gene amplicons confirmed the results concerning methanogenic archaea. In the never and rarely flooded soils, crenarchaeotal sequences were the dominant group. In the frequently and permanently flooded soils, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae and the uncultured Rice Clusters IV and VI (Crenarchaeota) were detectable independently from duration of anoxic conditions. Methanosaetaceae, on the other hand, were only found in the permanently and frequently flooded soils under conditions where concentrations of acetate were <30 µM. The results indicate that methanogens as well as other archaea occupy characteristic niches according to the flooding conditions in the field. Methanosaetaceae, in particular, seem to be adapted (or proliferate at) to low acetate concentrations
  • FEMS Microbiology Ecology

    Nitrogen as a regulatory factor of methane oxidation in soils and sediments

    Paul Bodelier, (Riks) H.J. Laanbroek
    The oxidation of methane by methane-oxidising microorganisms is an important link in the global methane budget. Oxic soils are a net sink while wetland soils are a net source of atmospheric methane. It has generally been accepted that the consumption of methane in upland as well as lowland systems is inhibited by nitrogenous fertiliser additions. Hence, mineral nitrogen (i.e. ammonium/nitrate) has conceptually been treated as a component with the potential to enhance emission of methane from soils and sediments to the atmosphere, and results from numerous studies have been interpreted as such. Recently, ammonium-based fertilisation was demonstrated to stimulate methane consumption in rice paddies. Growth and activity of methane-consuming bacteria in microcosms as well as in natural rice paddies was N limited. Analysing the available literature revealed that indications for N limitation of methane consumption have been reported in a variety of lowland soils, upland soils, and sediments. Obviously, depriving methane-oxidising bacteria of a suitable source of N hampers their growth and activity. However, an almost instantaneous link between the presence of mineral nitrogen (i.e. ammonium, nitrate) and methane-oxidising activity, as found in rice soils and culture experiments, requires an alternative explanation. We propose that switching from mineral N assimilation to the fixation of molecular nitrogen may explain this phenomenon. However, there is as yet no experimental evidence for any mechanism of instantaneous stimulation, since most studies have assumed that nitrogenous fertiliser is inhibitory of methane oxidation in soils and have focused only on this aspect. Nitrogen as essential factor on the sink side of the global methane budget has been neglected, leading to erroneous interpretation of methane emission dynamics, especially from wetland environments. The purpose of this minireview is to summarise and balance the data on the regulatory role of nitrogen in the consumption of methane by soils and sediments, and thereby stimulate the scientific community to embark on experiments to close the existing gap in knowledge. [KEYWORDS: Methane oxidation; Fertilization; Inhibition; Ammonia oxidation; Wetland; Soil; Sediment; Methane emission]
  • Nature

    Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots

    Paul Bodelier, P. Roslev, T. Henckel, P. Frenzel
    Methane is involved in a number of chemical and physical processes in the Earths atmosphere, including global warming(1), Atmospheric methane originates mainly from biogenic sources, such as rice paddies and natural wetlands; the former account for at least 30% of the global annual emission of methane to the atmosphere(2). As an increase of rice production by 60% is the most appropriate way to sustain the estimated increase of the human population during the next three decades(3), intensified global fertilizer application will be necessary(3): but it is known that an increase of the commonly used ammonium-based fertilizers can enhance methane emission from rice agriculture. Approximately 10-30% of the methane produced by methanogens in rice paddies is consumed by methane- oxidizing bacteria associated with the roots of rice(4,5); these bacteria are generally thought to be inhibited by ammonium-based fertilizers, as tvas demonstrated for soils(6-8) and sediments(9,10). In contrast, we show here that the activity and growth of such bacteria in the root zone of rice plants are stimulated after fertilization. Using a combination of radioactive fingerprinting(11) and molecular biology(12) techniques, we identify the bacteria responsible for this effect. We expect that our results will make necessary a re- evaluation of the link between fertilizer use and methane emissions, with effects on global warming studies. [KEYWORDS: Methanotrophic bacteria; oryza-sativa; forest soils inhibition; consumption; kinetics; plants]
  • Biogeochemistry

    Effects of ammonium-based fertilisation on microbial processes involved in methane emission from soils planted with rice

    Paul Bodelier, A.P. Hahn, I.R. Arth, P. Frenzel
    The emission of the greenhouse gas CH4 from rice paddies is strongly influenced by management practices such as the input of ammonium-based fertilisers. We assessed the impact of different levels (200 and 400 kgN.ha(-1)) of urea and (NH4)(2)HPO4 on the microbial processes involved in production and consumption of CH4 in rice field soil. We used compartmented microcosms which received fertiliser twice weekly. Potential CH4 production rates were substantially higher in the rice rhizosphere than in unrooted soil, but were not affected by fertilisation. However, CH4 emission was reduced by the addition of fertiliser and was negatively correlated with pore water NH4+ concentration, probably as the consequence of elevated CH4 oxidation due to fertilisation. CH4 oxidation as well as numbers of methanotrophs was distinctly stimulated by the addition of fertiliser and by the presence of the rice plant. Without fertiliser addition, nitrogen- limitation of the methanotrophs will restrict the consumption of CH4. This may have a major impact on the global CH4 budget, as nitrogen-limiting conditions will be the normal situation in the rice rhizosphere. Elevated potential nitrifying activities and numbers were only detected in microcosms fertilised with urea. However, a substantial part of the nitrification potential in the rhizosphere of rice was attributed to the activity of methanotrophs, as was demonstrated using the inhibitors CH3F and C2H2. [KEYWORDS: fertiliser; methane emission; methane oxidation; microcosm; rice Atmospheric methane; oxidizing bacteria; ch4 oxidation; nitrous-oxide; flooded rice; sparganium-eurycarpum; nitrosococcus-oceanus; nitrosomonas-europaea; water management; glyceria-maxima]
  • Applied and Environmental Microbiology

    Contribution of methanotrophic and nitrifying bacteria to CH4 and NH4+ oxidation in the rhizosphere of rice plants as determined by new methods of discrimination

    Paul Bodelier, Peter Frenzel

    Methanotrophic and nitrifying bacteria are both able to oxidize CH4 as well as NH4+. To date it is not possible to estimate the relative contribution of methanotrophs to nitrification and that of nitrifiers to CH4 oxidation and thus to assess their roles in N and C cycling in soils and sediments. This study presents new options for discrimination between the activities of methanotrophs and nitrifiers, based on the competitive inhibitor CH3F and on recovery after inhibition with C2H2. By using rice plant soil as a model system, it was possible to selectively inactivate methanotrophs in soil slurries at a CH4/CH3F/NH4+ molar ratio of 0.1:1:18. This ratio of CH3F to NH4+ did not affect ammonia oxidation, but methane oxidation was inhibited completely. By using the same model system, it could be shown that after 24 h of exposure to C2H2 (1,000 parts per million volume), methanotrophs recovered within 24 h while nitrifiers stayed inactive for at least 3 days. This gave an 'assay window' of 48 h when only methanotrophs were active. Applying both assays to model microcosms planted with rice plants demonstrated a major contribution of methanotrophs to nitrification in the rhizosphere, while the contribution of nitrifiers to CH4 oxidation was insignificant.
  • FEMS Microbiology Ecology

    Community analysis of ammonia-oxidising bacteria, in relation to oxygen availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation

    George Kowalchuk, Paul Bodelier, G.H.J. Heilig, J.R. Stephen, (Riks) H.J. Laanbroek
    The rhizosphere of oxygen-releasing wetland plants provides a niche for oxygen-consuming microorganisms such as chemolithotrophic ammonia-oxidising bacteria. These bacteria are adapted to oxygen limitation with respect to their affinity for oxygen, ability to survive periods of anoxia, and immediate response to the appearance of oxygen. In this study the techniques of specific amplification of ammonia oxidiser 16S rDNA fragments by PCR, separation of mixed PCR samples by denaturing gradient gel electrophoresis (DGGE), and band identification by specific hybridisation with oligonucleotide probes were combined to allow for the comparison of the community composition of multiple samples over space and time. DGGE bands of interest were also excised for DNA isolation, reamplification, sequence determination and phylogenetic analysis. We compared monthly samples from both the root zone and the bare sediment of a shallow lake inhabited by the emergent macrophyte Glyceria maxima to determine the seasonal effects that the plant roots and the oxygen availability might have on the beta-subgroup ammonia-oxidiser populations present. Similarly, five soil or sediment samples, varying in oxygen availability, from different locations in the Netherlands were compared. Although the presence of two previously defined Nitrosospira sequence clusters could be differentially detected in the samples examined, there was no evidence for a particular group which was specific to periodically anoxic environments. [KEYWORDS: Nitrosospira; Nitrosomonas; diversity; nitrification; biogeography; oxygen limitation 16s ribosomal-rna; gradient gel-electrophoresis; polymerase chain-reaction; oxidizing bacteria; nitrifying bacteria; gene-sequences; class proteobacteria; dna fragments; plants; nitrification]
  • FEMS Microbiology Ecology

    Interactions between nitrifying and denitrifying bacteria in gnotobiotic microcosms planted with the emergent macrophyte Glyceria maxima

    Paul Bodelier, Henk Duyts, Cornelis Blom, (Riks) H.J. Laanbroek
    The population dynamics of the chemolithoautotrophic nitrifiers Nitrosomonas europaea and Nitrobacter winogradskyi were studied in gnotobiotic microcosms fed with ammonium in response to the presence or absence of the emergent macrophyte Glyceria maxima and the heterotrophic denitrifying bacterium Pseudomonas chlororaphis. By subjecting the plants to different day lengths, the effect of possibly limiting factors (i.e. oxygen and ammonium) on the interactions between the nitrifiers and denitrifying bacterium could be analysed. The presence of the plant had no effect on the growth of nitrifiers suggesting that, in addition to radial oxygen loss from the roots, other non-plant sources of oxygen (e.g. diffusion from the water layer) were important for nitrification. Potential nitrifying activities were suppressed by G. maxima due to ammonium uptake by the plants. Elongation of the day length in combination with the presence of G. maxima led to an increase in the number of P. chlororaphis. The presence of P. chlororaphis suppressed the growth of N. winogradskyi, but the growth of N. europaea and the potential nitrifying activities were not significantly affected. Potential denitrifying activities were stimulated by the plant, but showed no correlations with nitrifier activities or numbers. Apparently ammonium, and not oxygen, was the limiting factor for nitrification in the root zone of G. maxima. However, when the plant did not deplete the ammonium pool, P. chlororaphis could repress the nitrifiers indicating the latter's poor competitive status with respect to oxygen when the presence of root exudates allows for heterotrophic oxygen consumption. [KEYWORDS: nitrification; denitrification; microcosm; oxygen ammonium; root Heterotrophic bacteria; wetland plants; nitrification; competition; oxygen; soil; denitrification; ammonium; nitrate; nitrifiers]
  • Archives of Microbiology

    Oxygen uptake kinetics of Pseudomonas chlororaphis grown in glucose- or glutamate-limited continuous cultures

    Paul Bodelier, (Riks) H.J. Laanbroek
    Oxygen uptake and glucose and glutamate oxidation kinetics of the heterotrophic bacterium Pseudomonas chlororaphis grown in glucose- or glutamate-limited cultures under oxygen-saturating or oxygen-limiting conditions were determined. K-m values for oxygen were 1.4-5.6 mu M Only in the case of glucose were significantly lower K-m values and enhanced specific oxygen affinity (V-max/K-m) per cell found under oxygen-limiting conditions. Both K-m and specific affinity values for glucose and glutamate oxidation were apparently affected by oxygen concentration, although a statistically significant enhancement of the oxidation kinetics was found only for glutamate. The kinetic data found for P. chlororaphis support the conclusion that the outcome of competition for oxygen with Niti europaea europaea in the rhizosphere of oxygen-releasing macrophytes will primarily be determined by oxidation kinetics of the electron donor instead of the oxygen uptake kinetics of the respective organisms. [KEYWORDS: oxygen kinetics; K-m; Pseudomonas chlororaphis; Nitrosomonas europaea; chemostat; competition Mixed continuous cultures; nitrosomonas-europaea; competition; bacteria; nitrification; ammonium; roots]
  • Plant and Soil

    Effects of photoperiod on growth of and denitrification by Pseudomonas chlororaphis in the root zone of Glyceria maxima, studied in a gnotobiotic microcosm

    Paul Bodelier, A.G. Wijlhuizen, Cornelis Blom, (Riks) H.J. Laanbroek
    The emergent macrophyte Glyceria maxima was subjected to different photoperiods and grown with ammonium or nitrate as nitrogen source in presterilized microcosms with spatially separated root and non-root compartments. The microcosms were inoculated with the denitrifying bacterium Pseudomonas chlororaphis. The effect of the plant and the photoperiod on growth and denitrification by P. chlororaphis was assessed. The plant had a strong positive effect on the growth of the bacteria. The bacterial numbers in the root compartment of the planted microcosms were 19-32 times higher than found in the non-root sediment of the unplanted systems. Lengthening the photoperiod resulted in elevated bacterial numbers due to the higher carbon exudation of the plant. This effect was greater still with the nitrate-fed plants, where additional P. chlororaphis growth could proceed via denitrification, indicating oxygen-limiting conditions in the microcosms. Higher porewater N2O concentrations in the root compartments as compared to the non-root compartments, which were highest for the long photoperiod, were also indicative of a plant-induced stimulation of denitrification. An effect of a diurnal oxygen release pattern of G. maxima on denitrification could not be detected. The gnotobiotic microcosm used in this study represents st potential system for the study of the behaviour and interactions of important bacterial groups, such as nitrifying and denitrifying bacteria where plant roots drive bacterial activity. [KEYWORDS: denitrification; exudates; Glyceria maxima; microcosm; Pseudomonas chlororaphis; rhizosphere Nitrogen transformations; cereal plants; model system; soil; rhizosphere; nitrate; barley; seedlings; ammonium; wheat]
  • Applied and Environmental Microbiology

    Dynamics of nitrification and denitrification in root- oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats

    Paul Bodelier, J.A. Libochant, Cornelis Blom, (Riks) H.J. Laanbroek
    Oxygen-releasing plants may provide aerobic niches in anoxic sediments and soils for ammonia-oxidizing bacteria, The oxygen- releasing, aerenchymatous emergent macrophyte Glycerin maxima had a strong positive effect on numbers and activities of the nitrifying bacteria in its root zone in spring and early summer, The stimulation of the aerobic nitrifying bacteria in the freshwater sediment, ascribed to oxygen release by the roots of G. maxima, disappeared in late summer, Numbers and activities of the nitrifying bacteria were positively correlated, and a positive relationship with denitrification activities also was found, To assess possible adaptations of ammonia-oxidizing bacteria to low oxygen or anoxic habitats, a comparison was made between the freshwater lake sediment and three soils differing in oxicity profiles. Oxygen kinetics and tolerance to anoxia of the ammonia-oxidizing communities from these habitats were determined, The apparent K-m values for oxygen of the ammonia-oxidizing community in the lake sediment were in the range of 5 to 15 mu M, which was substantially lower than the range of K-m values for oxygen of the ammonia- oxidizing community from a permanently oxic dune location, Upon anoxic incubation, the ammonia-oxidizing communities of dune, chalk grassland, and calcareous grassland soils lost 99, 95, and 92% of their initial nitrifying capacity, respectively, In contrast, the ammonia-oxidizing community in the lake sediment started to nitrify within 1 h upon exposure to oxygen at the level of the initial capacity, It is argued that the conservation of the nitrifying capacity during anoxic periods and the ability to react instantaneously to the presence of oxygen are important traits of nitrifiers in fluctuating oxic- anoxic environments such as the root zone of aerenchymatous plant species. [KEYWORDS: Mixed continuous cultures; nitrosomonas-europaea; greenhouse conditions; flood-tolerance; wetland plants; rice plants; water; competition; transport; nitrogen]
  • FEMS Microbiology Letters

    Nitrification in the rhizosphere of a flooding-resistant and a flooding-non-resistant Rumex species under drained and waterlogged conditions

    W.M.H.G. Engelaar, Paul Bodelier, (Riks) H.J. Laanbroek, Cornelis Blom

    The effects of the flooding-resistant plant species Rumex palustris and the non-flooding-resistant plant species Rumex acetosa on nitrification were compared. The plants were grown under drained and waterlogged conditions on a mixture of calcareous riversand and sieved grassland soil with a high potential nitrifying activity. In the shoots of R. acetosa, but not in those of R. palustris, the ratio between the amounts of accumulated carboxylates and organic nitrogen, ((CA-A)/Norg.), appeared to be a useful indicator of ammonium or nitrate consumption by tghe plant. In both plant species, the inorganic nitrogen source had no observed effect on the (C-A)/Norg. ratio in the roots. The growth of R. acetosa, but not that of R. palustris was inhibited by waterlogging of the soil. Both the activity and the growth of the ammonium-oxidizing bacteria were repressed under drained and waterlogged conditions in soils with R. palustris, a condition that was attributed to a competitive ammonium uptake by its relatively fast growing roots. In the presence of R. acetosa, the activity and growth of the ammonium-oxidizing bacteria were inhibited under waterlogged, but not under drained, conditions. he growth and activity of nitrite-oxidizing bacteria in the absence of actively ammonium-oxidizing, nitrite-producing bacteria was likely due to organotrophic growth.
  • Aquatic Botany

    Preliminary investigations into the background levels of various metals and boron in the aquatic liverwort Scapania uliginosa (Sw.) Dum.

    A. Samecka-Cymerman, A.J. Kempers, Paul Bodelier

    Studies were made of the aquatic liverwort Scapania uliginosa (Sw.)Dum. originating from Sudeten streams in Poland and from Ardennes streams in Belgium and West Germany. These populations were exposed in various degrees to metal and boron concentrations, mainly of natural origin. It was found that S. uliginosa contains up to a maximum of (in mg kg-1 dry plant weight) 518 B, 418 Ba, 16 Cd, 180 Co, 119 Cr, 292 Cu, 11 Li, 10 700 Mn, 694 Mo, 243 Ni, 464 Pb, 955 Sr, 123 V and 2067 Zn. The highest concentrations are indicative for bryophytes growing in low to moderately contaminated environments.

Projects & collaborations


  • Soil biodiversity analysis for sustainable production systems (SoilProS)

    Project 2022–Present
    SoilProS will interpret big data on soil biodiversity, soil chemical and physical characteristics with respect to current and desired soil functions, and how to use this information in order to help farmers predicting which crop varieties, seed mixtures, (organic) fertilizers, soil inocula, and organic substrates enhance the environmental sustainability of their activities.
    microscopic soil organisms
  • PhyloFunDB

    Project 2020–Present
    PhyloFunDB. This project aims at creating and maintaining phylogenetically validated reference databases of various microbial functional genes and creating the tools to make the databases available for the scientific community
    Pipeline for analyses of functional genes.
  • Fiber2Fiber

    Project 2018
    This project aims at degrading asbestos fibers using a combination of plants, fungi and bacteria.
    Fungi and bacteria with asbestos fibers
  • ClipsMicro: Climate proof soils by steering soil and residue microbiomes

    Project 2022–2028
    To mitigate climate change, global agricultural soils needs to store more carbon and emit less greenhouse gasses (GHG). In ClipsMicro, together with partners in agro-business, this is realised by steering soil microbes by application of novel, refined compost and crops that can reduce emissions of GHG.
    Soil from 70 year composting trial
  • SmartResidue

    Project 2019–2023
    This project will investigate residue-stimulated atmospheric methane oxidation, and aims to elucidate its occurrence in field conditions, responsible microorganisms, underlying mechanisms and controlling factors.
    Sampling compost
  • Volatile mediated interactions between methanotrophs and heterotrophs

    Project 2016–Present
    Methanotrophic bacteria are crucial in the regulation of methane concentration in the atmosphere and therefore for regulating our climate.
    Approaches for studying
  • Clever Cover cropping. Synergistic Mixtures for Sustainable Soils

    Project 2015–2020
    Since recently, Dutch farmers are required to grow cover crops in mixtures of at least two plant species.
    In the Clever Cropping Project we investigated whether mixtures of cover crops have beneficial effects on soil microbiology and associated functions.
    In long-term field experiments and laboratory incubations, we assessed emissions of greenhouse gasses and the diversity, abundance, and activity of microbial groups involved in environmentally relevant processes.
    While in laboratory incubations we could clearly find increased beneficial microbial functioning associated with mixtures of cover crop residues, we could not observe this in a 5-year field experiment.
    Overall, the use of cover crop mixtures did not have significant beneficial effects on soil microbial functioning but also no negative effects on for example greenhouse gas emissions.
    Gas flux measurements in Cover crops
  • The zooplankton-microbiome (MicroZoo): beyond microbe-host associations

    Project 2016–Present
    Zooplankton is a crucial component of aquatic food webs
    Collection of approaches taken in MicroZoo