Paul Bodelier

Nanomaterials are increasingly recognized for their potential in soil remediation. However, their impact on soil microbial communities in contaminated soil remains poorly understood. In this study, we investigated the dynamic effects of sulfonated graphene (SG) following one-time or repeated applications on heavy metal availability and soil microbial communities in long-term heavy metal-contaminated soil over 180 days. Our findings revealed that one-time SG application at 30 mg kg⁻¹ significantly increased the bioavailable cadmium (Cd) and copper (Cu) contents by approximately 30 %–40 % after 2 and 180 days. Repeated SG applications, however, displayed no significant influence on heavy metal availability. One-time SG application, coupled with the increased available Cd, induced significant enrichment of some specific functional bacterial genera involved in glycan biosynthesis metabolism and biosynthesis of other secondary metabolites, thereby decreasing the available contents of heavy metals after 90 days. However, the shifts in bacterial community structure and function were subsequently partially recovered after 180 days. Conversely, repeated SG treatments led to minimal alterations after 90 days while leading to similar shifts in the bacterial community at 60 mg kg⁻¹ after 180 days. The fungal community structure remained largely unaltered across all SG treatments. Intriguingly, SG treatments substantially stimulated fungal biomass, with the stimulation degree dependent on SG dosage. These results provide valuable insights for developing phytoremediation strategies, suggesting tailored SG applications during specific growth phases to optimize remediation efficiency.

As a recurrent climatic phenomenon in the context of climate change, extreme rainstorms induce vertical translocation of organic matter and increase moisture content in terrestrial ecosystems. However, it remains unclear whether heavy rainstorms can impact microbial communities in the deep biosphere by modulating organic matter input. In this study, we present findings on the different responses of bacterial and fungal communities in a subsurface cave to rainstorms and moisture variations through field surveys and microcosm experiments. During periods of rainstorms, the influx of dissolved organic matter (DOM) from soil overlying the cave into cave sediments significantly enhanced the correlation between core bacteria and environmental factors, particularly fluorescence spectral indices. The resource utilization of core bacteria was diminished, while the functional diversity of core fungi remained relatively unaltered. We also performed simulated experiments with restricted external DOM inputs, in which DOM content was observed to decrease and microbial diversity increase in response to artificially increased moisture content (MC). The niche breadth of core bacteria decreased and became more closely associated with DOM as the MC increased, while the niche breadth of core fungi remained predominantly unchanged. Compared to fungi, cave bacteria exhibited higher sensitivity towards variations in DOM. The core microbiome can efficiently utilize the available organic matter and participate in nitrogen- and sulfur-related metabolic processes. The study systematically revealed distinct microbial responses to rainstorm events, thereby providing valuable insights for future investigations into energy utilization within deep biospheres.

Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH₄) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH₄ oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and ¹³CH₄-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH₄ oxidation in supporting denitrification. Our results reveal positive relationships between CH₄ oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH₄ and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, ¹³CH₄-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating ¹³C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of ¹³C-metagenome-assembled genomes and ¹³C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH₄ oxidation, for the coupling of CH₄ oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH₄ oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.

Asbestos poses a substantial environmental health risk, and biological treatment offers a promising approach to mitigate its impact by altering its chemical composition. However, the dynamics of microbial co-inoculation in asbestos bioremediation remain poorly understood. This study investigates the effect of microbial single cultures and co-cultures on modifying crocidolite and chrysotile fibers, focusing on the extraction of iron and magnesium. Seventy bacterial and eighty-three fungal strains were isolated from five diverse sites, characterized phylogenetically using the 16S rRNA gene and ITS region, respectively, and assessed for siderophore and organic acid production. Most bacterial strains were identified as Pseudomonas, while Penicillium predominated among fungal strains. Ten bacterial and 25 fungal strains were found to produce both organic compounds. Four microbial co-cultures (one bacterium-bacterium, two fungus-bacterium, and one fungus-fungus) exhibiting synergistic effects in plate assays, alongside their respective single cultures, were incubated with crocidolite and chrysotile. ICP-OES analysis revealed that in crocidolite, the co-culture HRF19–HRB12 removed more iron than their single cultures, while Penicillium TPF36 showed the highest iron removal. The co-culture of two Pseudomonas strains (HRB12–RB5) exhibited the highest magnesium concentration in the supernatant. In chrysotile, the co-culture HRB12–RB5 removed more iron than their individual cultures, with Penicillium TFSF27 exhibiting the highest iron concentration in the solution. Penicillium TFSF27 and the co-culture TFSF27–TPF36 demonstrated the highest magnesium removal. SEM-XRMA analysis showed a significant reduction in iron and magnesium content, confirming elemental extraction from the fibers' structure. This study significantly broadens the range of microbial strains capable of modifying asbestos fibers and underscores the potential of microbial co-cultures in asbestos remediation.

Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methylomonas as model organism. Our study unambiguously shows how methanotrophy can be influenced by other organisms without direct physical contact. This influence is mediated by VOCs (e.g. dimethyl-polysulphides) or/and CO₂ emitted during respiration, which can inhibit growth and methane uptake of the methanotroph, while other VOCs had a stimulating effect on methanotroph activity. Depending on whether the methanotroph was exposed to the volatolome of the heterotroph or to CO₂, proteomics revealed differential protein expression patterns with the soluble methane monooxygenase being the most affected enzyme. The interaction between methanotrophs and heterotrophs can have strong positive or negative effects on methane consumption, depending on the species interacting with the methanotroph. We identified potential VOCs involved in the inhibition while positive effects may be triggered by CO₂ released by heterotrophic respiration. Our experimental proof of methanotroph–heterotroph interactions clearly calls for detailed research into strategies on how to mitigate methane emissions.

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.

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.

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.

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.

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, LF4-65^T (=CCUG 56422^T=DSM 107630^T) and MWH-P2sevCIIIb^T (=CCUG 56420^T=DSM 107629^T), 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 LF4-65^T and the new genus Jezberella gen. nov. and the new species J. montanila-cus sp. nov. to harbour strain MWH-P2sevCIIIb^T. 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.

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.

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.

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.

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.

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)/N_org.), 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)/N_org. 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.

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.