Paolina Garbeva

Dr. Paolina Garbeva

Senior Researcher


Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands


Microbial communities are largely shaped by chemical interaction networks mediated by specialized water-soluble and/or volatile metabolites


The focus of my current research is to understand the fundamental mechanisms of microbial chemical interactions and communication. Secondary metabolites (both volatile and water-soluble) play an important role in microbial interactions, e.g. as signalling compounds for communication or as suppressive agents in interference competition.
Using omics-based tools, advanced analytical chemistry and novel imaging techniques, my research aims to decipher, explore and exploit the so far unknown belowground microbe-microbe and plant-microbe chemical interactions and communication. Understanding the belowground inter-kingdom (bacteria, protists, fungi, plants) interactions is crucial for assessing the functioning of soil ecosystems, which underpins soil and plant health.




  • 2015–Present
    Senior Scientist and Researcher group leader at NIOO-KNAW
  • 2013–2015
    Tenure track position within the Department of Microbial Ecology, NIOO-KNAW, VIDI personal grant (NWO)
  • 2013–2006
    Postdoctoral researcher within the Department of Microbial Ecology, VENI and MEERVOUD personal grants (NWO)


PhD degree Leiden University, the Netherlands



Peer-reviewed publicaties

  • Applied Soil Ecology

    The nitrification inhibitor nitrapyrin has non-target effects on the soil microbial community structure, composition and functions

    Ruth Schmidt, Xiao-Bo Wang, Paolina Garbeva, E. Yergeau
    Nitrapyrin is a nitrification inhibitor used to retain ammonia-N in soil to improve crop yields and quality. Nitrapyrin targets specifically the ammonia oxidizers, but it is not known if it has non-target effects on the soil microbial communities. Here, we tested the hypothesis that nitrapyrin also leads to large shifts in soil microbial community structure, composition, diversity and functions. To test this hypothesis, we set-up a field experiment where wheat (Triticum aestivum cv. AC Walton) was fertilized with ammonium nitrate (NH4NO3) and supplemented or not with nitrapyrin. Rhizosphere and bulk soils were sampled twice (at grain filling and harvest), the 16S rRNA gene and ITS region were amplified and sequenced to follow the changes in archaeal, bacterial and fungal community structure, composition and diversity. To assess microbial functions, several genes involved in the nitrogen cycle were quantified by real-time qPCR, and volatile organic compounds (VOCs) were trapped in the rhizosphere at the moment of sampling. Sampling dates and soil compartments had overwhelming effects on the microbial communities. However, nitrapyrin still significantly affected the relative abundance of Thaumarchaeota, Proteobacteria, Nitrospirae and Basidiomycota, and several genera. Nitrapyrin also significantly affected bacterial and fungal community structure, and the abundance of all the N-cycle gene tested, but always in interaction with the sampling date. In contrast, nitrapyrin had no significant effect on the emission of VOCs, where only sampling dates significantly influenced the profiles observed. Our results show that nitrapyrin influences non-target soil- and plant-associated microbial communities. In the longer term, these shifts might counteract the positive effect of nitrapyrin on crop nutrition and greenhouse gas emissions.
  • Molecules

    Exploring the Volatiles Released from Roots of Wild and Domesticated Tomato Plants under Insect Attack

    Ana Shein Lee Diaz, Muhammad Syamsu Rizaludin, Hans Zweers, Jos M. Raaijmakers, Paolina Garbeva

    Plants produce volatile organic compounds that are important in communication and defense. While studies have largely focused on volatiles emitted from aboveground plant parts upon exposure to biotic or abiotic stresses, volatile emissions from roots upon aboveground stress are less studied. Here, we investigated if tomato plants under insect herbivore attack exhibited a different root volatilome than non-stressed plants, and whether this was influenced by the plant’s genetic background. To this end, we analyzed one domesticated and one wild tomato species, i.e., Solanum lycopersicum cv Moneymaker and Solanum pimpinellifolium, respectively, exposed to leaf herbivory by the insect Spodoptera exigua. Root volatiles were trapped with two sorbent materials, HiSorb and PDMS, at 24 h after exposure to insect stress. Our results revealed that differences in root volatilome were species-, stress-, and material-dependent. Upon leaf herbivory, the domesticated and wild tomato species showed different root volatile profiles. The wild species presented the largest change in root volatile compounds with an overall reduction in monoterpene emission under stress. Similarly, the domesticated species presented a slight reduction in monoterpene emission and an increased production of fatty-acid-derived volatiles under stress. Volatile profiles differed between the two sorbent materials, and both were required to obtain a more comprehensive characterization of the root volatilome. Collectively, these results provide a strong basis to further unravel the impact of herbivory stress on systemic volatile emissions.
  • Natural Product Reports

    Biosynthesis, Evolution and Ecology of Microbial Terpenoids

    Mariana Avalos Garcia, Paolina Garbeva, L. Vader, Gilles van Wezel, Jeroen Dickschat, D. Ulanova
    Terpenoids are the largest class of natural products recognised to date. While mostly known to humans as bioactive plant metabolites and part of essential oils, structurally diverse terpenoids are increasingly reported to be produced by microorganisms. For many of the compounds biological functions are yet unknown, but during the past years significant insights have been obtained for the role of terpenoids in microbial chemical ecology. Their functions include stress alleviation, maintenance of cell membrane integrity, photoprotection, attraction or repulsion of organisms, host growth promotion and defense. In this review we discuss the current knowledge of the biosynthesis and evolution of microbial terpenoids, and their ecological and biological roles in aquatic and terrestrial environments. Perspectives on their biotechnological applications, knowledge gaps and questions for future studies are discussed.
  • Antibiotics

    Air Ambulance: The Antimicrobial Power of Bacterial Volatiles

    Alexander Lammers, M. Lalk, Paolina Garbeva
    We are currently facing an antimicrobial resistance crisis, which means that a lot of bacterial pathogens have developed resistance to common antibiotics. Hence, novel and innovative solutions are urgently needed to combat resistant human pathogens. A new source of antimicrobial compounds could be bacterial volatiles. Volatiles are ubiquitous produced, chemically divers and playing essential roles in intra- and interspecies interactions like communication and antimicrobial defense. In the last years, an increasing number of studies showed bioactivities of bacterial volatiles, including antibacterial, antifungal and anti-oomycete activities, indicating bacterial volatiles as an exciting source for novel antimicrobial compounds. In this review we introduce the chemical diversity of bacterial volatiles, their antimicrobial activities and methods for testing this activity. Concluding, we discuss the possibility of using antimicrobial volatiles to antagonize the antimicrobial resistance crisis.
  • Harmful Algae

    Intraspecific variation in multiple trait responses of Alexandrium ostenfeldii towards elevated pCO2

    Karen M. Brandenburg, Bernd Krock, Helena C.L. Klip, Appy Sluijs, Paolina Garbeva, Dedmer Van de Waal

    Dissolved oceanic CO2 concentrations are rising as result of increasing atmospheric partial pressure of CO2 (pCO2), which has large consequences for phytoplankton. To test how higher CO2 availability affects different traits of the toxic dinoflagellate Alexandrium ostenfeldii, we exposed three strains of the same population to 400 and 1,000 µatm CO2, and measured traits including growth rate, cell volume, elemental composition, 13C fractionation, toxin content, and volatile organic compounds (VOCs). Strains largely increased their growth rates and particulate organic carbon and nitrogen production with higher pCO2 and showed significant changes in their VOC profile. One strain showed a significant decrease in both PSP and cyclic imine content and thereby in cellular toxicity. Fractionation against 13C increased in response to elevated pCO2, which may point towards enhanced CO2 acquisition and/or a downscaling of the carbon concentrating mechanisms. Besides consistent responses in some traits, other traits showed large variation in both direction and strength of responses towards elevated pCO2. The observed intraspecific variation in phenotypic plasticity of important functional traits within the same population may help A. ostenfeldii to negate the effects of immediate environmental fluctuations and allow populations to adapt more quickly to changing environments.
  • Metabolites

    The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots

    Muhammad Syamsu Rizaludin, Nejc Stopnisek, Jos M. Raaijmakers, Paolina Garbeva
    Plants are faced with various biotic and abiotic stresses during their life cycle. To withstand these stresses, plants have evolved adaptive strategies including the production of a wide array of primary and secondary metabolites. Some of these metabolites can have direct defensive effects, while others act as chemical cues attracting beneficial (micro)organisms for protection. Similar to aboveground plant tissues, plant roots also appear to have evolved “a cry for help” response upon exposure to stress, leading to the recruitment of beneficial microorganisms to help minimize the damage caused by the stress. Furthermore, emerging evidence indicates that microbial recruitment to the plant roots is, at least in part, mediated by quantitative and/or qualitative changes in root exudate composition. Both volatile and water-soluble compounds have been implicated as important signals for the recruitment and activation of beneficial root-associated microbes. Here we provide an overview of our current understanding of belowground chemical communication, particularly how stressed plants shape its protective root microbiome.
  • Environmental Microbiology Reports

    Disentangling soil microbiome functions by perturbation

    Soil biota contribute to diverse soil ecosystem services such as greenhouse gas mitigation, carbon sequestration, pollutant degradation, plant disease suppression and nutrient acquisition for plant growth. Here, we provide detailed insight into different perturbation approaches to disentangle soil microbiome functions and to reveal the underlying mechanisms. By applying perturbation, one can generate compositional and functional shifts of complex microbial communities in a controlled way. Perturbations can reduce microbial diversity, diminish the abundance of specific microbial taxa and thereby disturb the interactions within the microbial consortia and with their eukaryotic hosts. Four different microbiome perturbation approaches, namely selective heat, specific biocides, dilution-to-extinction and genome editing are the focus of this mini-review. We also discuss the potential of perturbation approaches to reveal the tipping point at which specific soil functions are lost and to link this change to key microbial taxa involved in specific microbiome-associated phenotypes.
  • Frontiers in Microbiology

    Antimicrobial Compounds in the Volatilome of Social Spider Communities

    Alexander Lammers, Hans Zweers, T. Sandfeld, T. Bilde, Paolina Garbeva, A. Schramm, M. Lalk
    Social arthropods such as termites, ants, and bees are among others the most successful animal groups on earth. However, social arthropods face an elevated risk of infections due to the dense colony structure, which facilitates pathogen transmission. An interesting hypothesis is that social arthropods are protected by chemical compounds produced by the arthropods themselves, microbial symbionts, or plants they associate with. Stegodyphus dumicola is an African social spider species, inhabiting communal silk nests. Because of the complex three-dimensional structure of the spider nest antimicrobial volatile organic compounds (VOCs) are a promising protection against pathogens, because of their ability to diffuse through air-filled pores. We analyzed the volatilomes of S. dumicola, their nests, and capture webs in three locations in Namibia and assessed their antimicrobial potential. Volatilomes were collected using polydimethylsiloxane (PDMS) tubes and analyzed using GC/Q-TOF. We showed the presence of 199 VOCs and tentatively identified 53 VOCs. More than 40% of the tentatively identified VOCs are known for their antimicrobial activity. Here, six VOCs were confirmed by analyzing pure compounds namely acetophenone, 1,3-benzothiazole, 1-decanal, 2-decanone, 1-tetradecene, and docosane and for five of these compounds the antimicrobial activity were proven. The nest and web volatilomes had many VOCs in common, whereas the spider volatilomes were more differentiated. Clear differences were identified between the volatilomes from the different sampling sites which is likely justified by differences in the microbiomes of the spiders and nests, the plants, and the different climatic conditions. The results indicate the potential relevance of the volatilomes for the ecological success of S. dumicola.
  • mSystems

    Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10X metagenomics

    Vittorio Tracanna, Adam Ossowicki, M.L.C. Petrus, S. Overduin, B. Terlouw, G. Lund, S. Robinson, Sven Warris, E. Schijlen, Gilles van Wezel, Jos M. Raaijmakers, Paolina Garbeva, M. Medema
    Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10x metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype.
  • Nature Reviews Microbiology

    Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions

    Laure Weisskopf, S. Schulz, Paolina Garbeva
    Microorganisms produce and excrete a versatile array of metabolites with different physico-chemical properties and biological activities. However, the ability of microorganisms to release volatile compounds has only attracted research attention in the past decade. Recent research has revealed that microbial volatiles are chemically very diverse and have important roles in distant interactions and communication. Microbial volatiles can diffuse fast in both gas and water phases, and thus can mediate swift chemical interactions. As well as constitutively emitted volatiles, microorganisms can emit induced volatiles that are triggered by biological interactions or environmental cues. In this Review, we highlight recent discoveries concerning microbial volatile compounds and their roles in intra-kingdom microbial interactions and inter-kingdom interactions with plants and insects. Furthermore, we indicate the potential biotechnological applications of microbial volatiles and discuss challenges and perspectives in this emerging research field.
  • Journal of Hazardous Materials

    Effects of plastic mulch film residues on wheat rhizosphere and soil properties

    Yueling Qi, Adam Ossowicki, X. Yang, E. Huerta Lwanga, Francisco Dini-Andreote, V. Geissen, Paolina Garbeva
    Plastic residues could accumulate in soils as a consequence of using plastic mulching, which results in a serious environmental concern for agroecosystems. As an alternative, biodegradable plastic films stand as promising products to minimize plastic debris accumulation and reduce soil pollution. However, the effects of residues from traditional and biodegradable plastic films on the soil-plant system are not well studied. In this study, we used a controlled pot experiment to investigate the effects of macro- and micro- sized residues of low-density polyethylene and biodegradable plastic mulch films on the rhizosphere bacterial communities, rhizosphere volatile profiles and soil chemical properties. Interestingly, we identified significant effects of biodegradable plastic residues on the rhizosphere bacterial communities and on the blend of volatiles emitted in the rhizosphere. For example, in treatments with biodegradable plastics, bacteria genera like Bacillus and Variovorax were present in higher relative abundances and volatile compounds like dodecanal were exclusively produced in treatment with biodegradable microplastics. Furthermore, significant differences in soil pH, electrical conductivity and C:N ratio were observed across treatments. Our study provides evidence for both biotic and abiotic impacts of plastic residues on the soil-plant system, suggesting the urgent need for more research examining their environmental impacts on agroecosystems.
  • Scientific Reports

    A non-invasive soil based setup to study tomato root volatiles released by healthy and infected roots

    S. Gulati, M-B. Ballhausen, Purva Kulkarni, R. Grosch, Paolina Garbeva
    The role of root exudates in mediating plant–microbe interactions has been well documented. However, the function of volatile organic compounds (VOCs) emitted by plant roots has only recently begun to attract attention. This newly recognized relevance of belowground VOCs has so far mostly been tested using systems limited to a two-compartment Petri-dish design. Furthermore, many of the plant–microbe interaction studies have only investigated the effects of microbial VOCs on plant growth. Here, we go two steps further. First we investigated the volatile profile of healthy and pathogen (Fusarium oxysporum) infected tomato roots grown in soil. We then used a unique soil-based olfactometer-choice assay to compare the migration pattern of four beneficial bacteria (Bacillus spp.) towards the roots of the tomato plants. We demonstrate that the blend of root-emitted VOCs differs between healthy and diseased plants. Our results show that VOCs are involved in attracting bacteria to plant roots.
  • New Phytologist

    Airborne medicine - Bacterial volatiles and their influence on plant health

    Paolina Garbeva, Laure Weisskopf
    Like most other eukaryotes, plants do not live alone but in close association with a diverse microflora. These plant‐associated microbes contribute to plant health in many different ways, ranging from modulation of hormonal pathways to direct antibiosis of plant pathogens. Over the last 15 yr, the importance of volatile organic compounds as mediators of mutualistic interactions between plant‐associated bacteria and their hosts has become evident. This review summarizes current knowledge concerning bacterial volatile‐mediated plant protection against abiotic and biotic stresses. It then discusses the translational potential of such metabolites or of their emitters for sustainable crop protection, the possible ways to harness this potential, and the major challenges still preventing us from doing so. Finally, the review concludes with highlighting the most pressing scientific gaps that need to be filled in order to enable a better understanding of: the molecular mechanisms underlying the biosynthesis of bacterial volatiles; the complex regulation of bacterial volatile emission in natural communities; the perception of bacterial volatiles by plants; and the modes of actions of bacterial volatiles on their host.
  • ISME Journal

    Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces

    Mariana Avalos, Paolina Garbeva, Jos M. Raaijmakers, Gilles van Wezel
    Soil-inhabiting streptomycetes are Nature’s medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatile compounds, and research into these molecules and their role in soil ecology is rapidly gaining momentum. Here we show that streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile antimicrobial ammonia, which travels over long distances and antagonises both Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system annihilated air-borne antibiosis. As a resistance strategy, E. coli cells acquired mutations resulting in reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ, which was just enough to allow them to survive. We further show that ammonia enhances the activity of the more costly canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis over longer distances.
  • Journal of Plant Interactions

    Investigating the effect of belowground microbial volatiles on plant nutrient status: perspective and limitations

    Lara Martín Sánchez, C. Ariotti, Paolina Garbeva, G. Vigani
    Volatile organic compounds displayed biological activities on a wide range of organisms, including plants and microbes. Investigating their role in the plant-microbe interaction processes occurring in the soil is challenging. By simulating belowground communication conditions between plant and microbes, in this study, we aimed to investigate the effects of the volatiles emitted by Serratia plymuthica and Fusarium culmorum on the nutrient status of maize plants. Plants were grown in potting soil and exposed to volatiles emitted by microbes inoculated in Petri dishes at the bottom of a jar. Nutrients content of plant tissues as well as soil volatiles were analyzed by ICP-MS and GC-MS, respectively. Our results showed that volatiles emitted belowground by Serratia plymuthica and Fusarium culmorum, in monoculture or interaction, differentially impacted on the content of some nutrient in plants, indicating that microbial volatiles-emitted belowground can affect the nutritional status of plants from a distance.
  • Environmental Microbiology

    Volatile-mediated antagonism of soil bacterial communities against fungi

    Xiogang Li, Paolina Garbeva, Xiaojiao Liu, P.J.A. Klein Gunnewiek, Anna Clocchiatti, M.P.J. Hundscheid, Xingxiang Wang, Wietse de Boer
  • Proceedings of the Royal Society B-Biological Sciences

    Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat

    Adam Ossowicki, Vittorio Tracanna, M.L.C. Petrus, Gilles van Wezel, Jos M. Raaijmakers, Marnix H Medema, Paolina Garbeva
  • FEMS Microbiology Ecology

    Pathogen suppression by microbial volatile organic compounds in soils

    Wietse de Boer, Xiogang Li, Annelein Meisner, Paolina Garbeva
    There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions
    between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of
    plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in
    soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence
    the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities,
    community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC
    blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such
    as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil
    environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on
    artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil
    atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and
    predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the
    chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management
    strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of
    soil-borne pathogens are discussed.
  • Beilstein Journal of Organic Chemistry

    Phylogenomic analyses and distribution of terpene synthases among Streptomyces

    Lara Martín Sánchez, K Saurabh Singh, Mariana Avalos Garcia, Gilles van Wezel, Jeroen Dickschat, Paolina Garbeva
    Terpene synthases are widely distributed among microorganisms and have been mainly studied in members of the genus Streptomyces. However, little is known about the distribution and evolution of the genes for terpene synthases. Here, we performed whole-genome based phylogenetic analysis of Streptomyces species, and compared the distribution of terpene synthase genes among them. Overall, our study revealed that ten major types of terpene synthases are present within the genus Streptomyces, namely those for geosmin, 2-methylisoborneol, epi-isozizaene, 7-epi-α-eudesmol, epi-cubenol, caryolan-1-ol, cyclooctat-9-en-7-ol, isoafricanol, pentalenene and α-amorphene. The Streptomyces species divide in three phylogenetic groups based on their whole genomes for which the distribution of the ten terpene synthases was analysed. Geosmin synthases were the most widely distributed and were found to be evolutionary positively selected. Other terpene synthases were found to be specific for one of the three clades or a subclade within the genus Streptomyces. A phylogenetic analysis of the most widely distributed classes of Streptomyces terpene synthases in comparison to the phylogenomic analysis of this genus is discussed.
  • Nature Communications

    Root traits and belowground herbivores relate to plant-soil feedback variation among congeners

    Rutger Wilschut, Wim H. van der Putten, Paolina Garbeva, Paula Harkes, Wouter Konings, Purva Kulkarni, Henk Martens, Stefan Geisen
    Plant–soil feedbacks contribute to vegetation dynamics by species-specific interactions between plants and soil biota. Variation in plant–soil feedbacks can be predicted by root traits, successional position, and plant nativeness. However, it is unknown whether closely related plant species develop more similar plant–soil feedbacks than more distantly related species. Where previous comparisons included plant species from distant phylogenetic positions, we studied plant–soil feedbacks of congeneric species. Using eight intra-continentally range-expanding and native Geranium species, we tested relations between phylogenetic distances, chemical and structural root traits, root microbiomes, and plant–soil feedbacks. We show that root chemistry and specific root length better predict bacterial and fungal community composition than phylogenetic distance. Negative plant–soil feedback strength correlates with root-feeding nematode numbers, whereas microbiome dissimilarity, nativeness, or phylogeny does not predict plant–soil feedbacks. We conclude that root microbiome variation among congeners is best explained by root traits, and that root-feeding nematode abundances predict plant–soil feedbacks.
  • FEMS Microbiology Letters

    Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine

    Thierry K.S. Janssens, Olaf Tyc, Harrie Besselink, Wietse de Boer, Paolina Garbeva
    Pyrazines are 1,4- diazabenzene based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp. AD24. In addition, we were using transcriptional reporter assays in E. coli and mammalian cells to decipher the possible mode of action. Bacterial and mammalian luciferase reporter strains were deployed to elucidate antimicrobial and toxicological effects of 2,5-bis(1-methylethyl)-pyrazine. At high levels of exposure, 2,5-bis(1-methylethyl)-pyrazine exerted strong DNA damage response. At lower concentrations, cell-wall damage response was observed. The activity was corroborated by a general toxicity reporter assay in E. coli ΔampD, defective in peptidoglycan turnover. The maximum E. coli cell-wall stress activity was measured at a concentration close to the onset of the mammalian cytotoxicity, while other adverse outcome pathways, such as the activation of aryl hydrocarbon and estrogenic receptor, the p53 tumor suppressor, and the oxidative stress related Nrf2 transcription factor, were induced at elevated concentrations compared to the response of mammalian cells. Because of its broad-spectrum antimicrobial activity at lower concentrations and the relatively low mammalian toxicity, 2,5-bis(1-methylethyl)-pyrazine is a potential bio-based fumigant with possible applications in food industry, agriculture or logistics.
  • ISME Journal

    Microbe-driven chemical ecology – past, present and future

    Ruth Schmidt, D. Ulanova, L.Y. Wick, Helge B Bode, Paolina Garbeva
    In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.
  • FEMS Microbiology Letters

    The effect of isabelin, a sesquiterpene lactone from Ambrosia artemisiifolia on soil microorganisms and human pathogens

    F. Molinaro, Olaf Tyc, J. Beekwilder, Katarina Cankar, C.M. Bertea, M. Negre, Paolina Garbeva
    Ambrosia artemisiifolia L. (common ragweed) is an invasive weed, well-known for the strong allergenic effect of its pollen, as well as for its invasiveness and impact in crop fields (e.g. causing yield losses). This species produces a broad range of sesquiterpenoids. In recent years, new bioactive molecules have been discovered in this plant, e.g. isabelin, a sesquiterpene dilactone. The bioactivity of isabelin has been already demonstrated on allergy-related receptors and its inhibitory effect on seeds of various plant species. Isabelin was tested for potential antimicrobial effects by using a selection of soil-borne bacteria and fungi and three human pathogens as model organisms. For the majority of microorganisms tested, no antimicrobial activity of isabelin was observed. However, isabelin revealed strong antimicrobial activity against the Gram-positive soil bacterium Paenibacillus sp. and against the Gram-positive, multi-drug-resistant Staphylococcus aureus (MRSA). The observed inhibitory activity of isabelin can enlighten the importance to study similar compounds for their effect on human pathogens and on soil and rhizosphere microorganisms.
  • FEMS Microbiology Ecology

    Growth Promotion and Inhibition Induced by Interactions of Groundwater Bacteria

    P. Geesink, Olaf Tyc, K. Küsel, Marco Taubert, Charlotte van de Velde, S. Kumar, Paolina Garbeva
    Microorganisms can produce a plethora of secondary metabolites, some acting as signaling compounds, and others as suppressing agents. As yet, the potential of groundwater microbes to produce antimicrobial compounds to increase their competitiveness against other bacteria has not been examined. In this study, we developed an AlamarBlue® based high-throughput screening method that allowed for a fast and highly standardized evaluation of both growth inhibiting and promoting metabolites. With this technique, 149 screened bacterial isolates were grown in monocultures and in 1402 co-cultures. Co-cultivation did not increase the frequency of growth inhibition against the two tested model organisms (S. aureus 533R4 and E. coli WA321) compared to monocultures. Mainly co-cultivation of Proteobacteria induced growth inhibition of both model organisms. Only slightly increased growth promotion of S. aureus 533R4 was observed. Growth promoting effects on E. coli WA321 were observed by supernatants from co-cultures between Bacteroidetes and Firmicutes. With the standardized screening for both, growth inhibiting and promoting effects, this method will enable further studies to elaborate and better understand complex interspecific interactions and networks in aquatic communities as well as in other environments.
  • FEMS Microbiology Ecology

    Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum

    Ruth Schmidt, M. Durling, Victor de Jager, R. C. Menezes, E. Nordkvist, A. Svatos, Mohit Dubey, L. Lauterbach, J.S. Dikschat, M. Karlsson, Paolina Garbeva
    Fusarium culmorum is one of the most important fungal plant pathogens that causes diseases on a wide diversity of cereal and non-cereal crops. We report herein for the first time the genome sequence of F. culmorum strain PV and its associated secondary metabolome that plays a role in the interaction with other microorganisms and contributes to its pathogenicity on plants. The genome revealed the presence of two terpene synthases, trichodiene and longiborneol synthase, which generate an array of volatile terpenes. Furthermore, we identified two gene clusters, deoxynivalenol and zearalenone, which encode for the production of mycotoxins. Linking the production of mycotoxins with in vitro bioassays, we found high virulence of F. culmorum PV on maize, barley and wheat. By using ultra-performance liquid chromatography–mass spectrometry, we confirmed several compounds important for the behaviour and lifestyle of F. culmorum. This research sets the basis for future studies in microbe–plant interactions.
  • Science of the Total Environment

    Decay of low-density polyethylene by bacteria extracted from earthworm’s guts: a potential for soil restoration

    E. Huerta Lwanga, B. Thapa, X. Yang, H. Gertsen, T. Salánki, V. Geissen, Paolina Garbeva
    Low-density polyethylene (LDPE) is the most abundant source of microplastic pollution worldwide. A recent
    study found that LDPE decay was increased and the size of the plastic was decreased after passing through the
    gut of the earthworm Lumbricus terrestris (Oligochaeta). Here, we investigated the involvement of earthworm
    gut bacteria in the microplastic decay. The bacteria isolated from the earthworm's gut were Gram-positive, belonging
    to phylum Actinobacteria and Firmicutes. These bacteria were used in a short-term microcosm experiment
    performed with gamma-sterilized soil with or without LDPE microplastics (MP). We observed that the
    LDPE-MP particle size was significantly reduced in the presence of bacteria. In addition, the volatile profiles of
    the treatments were compared and clear differences were detected. Several volatile compounds such as
    octadecane, eicosane, docosane and tricosane were measured only in the treatments containing both bacteria
    and LDPE-MP, indicating that these long-chain alkanes are byproducts of bacterial LDPE-MP decay.
  • ISME Journal

    Calling from distance: Attraction of soil bacteria by plant root volatiles

    Kristin Bohm, Saskia Gerards, M.P.J. Hundscheid, Jasper Melenhorst, Wietse de Boer, Paolina Garbeva
    Plants release a wide set of secondary metabolites including volatile organic compounds (VOCs). Many of those compounds are considered to function as defense against herbivory, pests, and pathogens. However, little knowledge exists about the role of belowground plant VOCs for attracting beneficial soil microorganisms. We developed an olfactometer system to test the attraction of soil bacteria by VOCs emitted by Carex arenaria roots. Moreover, we tested whether infection of C. arenaria with the fungal pathogen Fusarium culmorum modifies the VOCs profile and bacterial attraction. The results revealed that migration of distant bacteria in soil towards roots can be stimulated by plant VOCs. Upon fungal infection, the blend of root VOCs changed and specific bacteria with antifungal properties were attracted. Tests with various pure VOCs indicated that those compounds can diffuse over long distance but with different diffusion abilities. Overall, this work highlights the importance of plant VOCs in belowground long-distance plant–microbe interactions.
  • Science of the Total Environment

    Macro- and micro- plastics in soil-plant system: effects of plastic mulch film residues on wheat (Triticum aestivum) growth.

    Yueling Qi, X. Yang, A.M. Pelaez, E. Huerta Lwanga, N. Beriot, H. Gertsen, Paolina Garbeva, V. Geissen
    Plastic residues have become a serious environmental problem in the regions with intensive use of plastic mulching. Even though plastic mulch is widely used, the effects of macro- and micro- plastic residues on the soil-plant system and the agroecosystem are largely unknown. In this study, low density polyethylene and one type of starch-based biodegradable plastic mulch film were selected and used as examples of macro- and micro- sized plastic residues. A pot experiment was performed in a climate chamber to determine what effect mixing 1% concentration of residues of these plastics with sandy soil would have on wheat growth in the presence and absence of earthworms. The results showed that macro- and micro- plastic residues affected both above-ground and below-ground parts of the wheat plant during both vegetative and reproductive growth. The type of plastic mulch films used had a strong effect on wheat growth with the biodegradable plastic mulch showing stronger negative effects as compared to polyethylene. The presence of earthworms had an overall positive effect on the wheat growth and chiefly alleviated the impairments made by plastic residues.
  • Current Opinion in Microbiology

    Healthy scents: microbial volatiles as new frontier in antibiotic research?

    Mariana Avalos Garcia, Gilles van Wezel, Jos M. Raaijmakers, Paolina Garbeva
    Microorganisms represent a large and still resourceful pool for the discovery of novel compounds to combat antibiotic resistance in human and animal pathogens. The ability of microorganisms to produce structurally diverse volatile compounds has been known for decades, yet their biological functions and antimicrobial activities have only recently attracted attention. Various studies revealed that microbial volatiles can act as infochemicals in long-distance cross-kingdom communication as well as antimicrobials in competition and predation. Here, we review recent insights into the natural functions and modes of action of microbial volatiles and discuss their potential as a new class of antimicrobials and modulators of antibiotic resistance.
  • ISME Journal

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

    Annelies Veraart, Paolina Garbeva, Femke van Beersum, Adrian Ho, Cees Hordijk, M. 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.
  • Planta

    LAESI mass spectrometry imaging as a tool to differentiate the root metabolome of native and range-expanding plant species

    Purva Kulkarni, Rutger Wilschut, Koen Verhoeven, Wim H. van der Putten, Paolina Garbeva
    Our understanding of chemical diversity in biological samples has greatly improved through recent advances in mass spectrometry (MS). MS-based-imaging (MSI) techniques have further enhanced this by providing spatial information on the distribution of metabolites and their relative abundance. This study aims to employ laser-assisted electrospray ionization (LAESI) MSI as a tool to profile and compare the root metabolome of two pairs of native and range expanding plant species. It has been proposed that successful range-expanding plant species, like introduced exotic invaders, have a novel, or a more diverse secondary chemistry. Although some tests have been made using aboveground plant materials, tests using root materials are rare. We tested the hypothesis that range-expanding plants possess more diverse root chemistries than native plant species. To examine the root chemistry of the selected plant species, LAESI-MSI was performed in positive ion mode and data was acquired in a mass range of m/z 50-1200 with a spatial resolution of 100 μm. The acquired data was analyzed using in-house scripts, and differences in the spatial profiles were studied for discriminatory mass features. The results revealed clear differences in the metabolite profiles amongst and within both pairs of congeneric plant species, in the form of distinct metabolic fingerprints. The use of ambient conditions and the fact that no sample preparation was required, established LAESI-MSI as an ideal technique for untargeted metabolomics and for direct correlation of the acquired data to the underlying metabolomic complexity present in intact plant samples.
  • PLoS One

    The Antimicrobial Volatile Power of the Rhizospheric Isolate Pseudomonas donghuensis P482.

    Adam Ossowicki, S. Jafra, Paolina Garbeva
    Soil and rhizosphere bacteria produce an array of secondary metabolites including a wide range of volatile organic compounds (VOCs). These compounds play an important role in the long-distance interactions and communication between (micro)organisms. Furthermore, bacterial VOCs are involved in plant pathogens inhibition and induction of soil fungistasis and suppressivenes. In the present study, we analysed the volatile blend emitted by the rhizospheric isolate Pseudomonas donghuensis P482 and evaluated the volatile effect on the plant pathogenic fungi and bacteria as well as one oomycete. Moreover, we investigated the role of the GacS/GacA system on VOCs production in P. donghuensis P482. The results obtained demonstrated that VOCs emitted by P. donghuensis P482 have strong antifungal and antioomycete, but not antibacterial activity. The production of certain volatiles such as dimethyl sulfide, S-methyl thioacetate, methyl thiocyanate, dimethyl trisulfide, 1-undecan and HCN is depended on the GacS/GacA two-component regulatory system. Apparently, these compounds play an important role in the pathogens suppression as the gacA mutant entirely lost the ability to inhibit via volatiles the growth of tested plant pathogens.
  • Trends in Microbiology

    The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria

    Olaf Tyc, Chunxu Song, Jeroen Dickschat, M. Vos, Paolina Garbeva
    The rich diversity of secondary metabolites produced by soil bacteria has been appreciated for over a century, and advances in chemical analysis and genome sequencing continue to greatly advance our understanding of this biochemical complexity. However, we are just at the beginning of understanding the physicochemical properties of bacterial metabolites, the factors that govern their production and ecological roles. Interspecific interactions and competitor sensing are among the main biotic factors affecting the production of bacterial secondary metabolites. Many soil bacteria produce both volatile and soluble compounds. In contrast to soluble compounds, volatile organic compounds can diffuse easily through air- and gas-filled pores in the soil and likely play an important role in long-distance microbial interactions. In this review we provide an overview of the most important soluble and volatile classes of secondary metabolites produced by soil bacteria, their ecological roles, and their possible synergistic effects.
  • Frontiers in Microbiology

    Microbial volatiles: Small molecules with an important role in intra- and inter-kingdom interactions

    Kristin Bohm, Lara Martín Sánchez, Paolina Garbeva
    During the last decades, research on the function of volatile organic compounds focused primarily on the interactions between plants and insects. However, microorganisms can also release a plethora of volatiles and it appears that microbial volatile organic compounds (mVOCs) can play an important role in intra- and inter-kingdom interactions. So far, most studies are focused on aboveground volatile-mediated interactions and much less information is available about the function of volatiles belowground. This minireview summarizes the current knowledge on the biological functions of mVOCs with the focus on mVOCs-mediated interactions belowground. We pinpointed mVOCs involved in microbe-microbe and microbe–plant interactions, and highlighted the ecological importance of microbial terpenes as a largely underexplored group of mVOCs. We indicated challenges in studying belowground mVOCs-mediated interactions and opportunities for further studies and practical applications.
  • ISME Journal

    The prey’s scent – volatile organic compound mediated interactions between soil bacteria and their protist predators

    Kristin Bohm, Stefan Geisen, Jasper Wubs, Chunxu Song, Wietse de Boer, Paolina Garbeva
    Protists are major predators of bacteria in soils. However, it remains unknown how protists sense their prey in this highly complex environment. Here, we investigated whether volatile organic compounds (VOCs) of six phylogenetic distinct soil bacteria affect the performance of three different soil protists and how that relates to direct feeding interactions. We observed that most bacteria affected protist activity by VOCs. However, the response of protists to the VOCs was strongly dependent on both the bacterial and protist interacting partner. Stimulation of protist activity by volatiles and in direct trophic interaction assays often coincided, suggesting that VOCs serve as signals for protists to sense suitable prey. Furthermore, bacterial terpene synthase mutants lost the ability to affect protists, indicating that terpenes represent key components of VOC-mediated communication. Overall, we demonstrate that volatiles are directly involved in protist−bacterial predator−prey interactions.
  • Scientific Reports

    Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C

    Ruth Schmidt, Victor de Jager, D. Zühlke, C. Wolff, J. Bernhardt, Katarina Cankar, J. Beekwilder, Wilfried F.J. van IJcken, Frank Sleutels, Wietse de Boer, K. Riedel, Paolina Garbeva
    The ability of bacteria and fungi to communicate with each other is a remarkable aspect of the microbial world. It is recognized that volatile organic compounds (VOCs) act as communication signals, however the molecular responses by bacteria to fungal VOCs remain unknown. Here we perform transcriptomics and proteomics analyses of Serratia plymuthica PRI-2C exposed to VOCs emitted by the fungal pathogen Fusarium culmorum. We find that the bacterium responds to fungal VOCs with changes in gene and protein expression related to motility, signal transduction, energy metabolism, cell envelope biogenesis, and secondary metabolite production. Metabolomic analysis of the bacterium exposed to the fungal VOCs, gene cluster comparison, and heterologous co-expression of a terpene synthase and a methyltransferase revealed the production of the unusual terpene sodorifen in response to fungal VOCs. These results strongly suggest that VOCs are not only a metabolic waste but important compounds in the long-distance communication between fungi and bacteria
  • Frontiers in Plant Science

    Belowground plant-herbivore interactions vary among climate-driven range-expanding plant species with different degrees of novel chemistry

    Rutger Wilschut, J.C. Pereira da Silva, Paolina Garbeva, Wim H. van der Putten
    An increasing number of studies reports plant range expansions to higher latitudes and altitudes in response to global warming. However, consequences for interactions with other species in the novel ranges are poorly understood. Here, we examine how range-expanding plant species interact with root-feeding nematodes from the new range. Root-feeding nematodes are ubiquitous belowground herbivores that may impact the structure and composition of natural vegetation. Because of their ecological novelty, we hypothesized that range-expanding plant species will be less suitable hosts for root-feeding nematodes than native congeneric plant species. In greenhouse and lab trials we compared nematode preference and performance of two root-feeding nematode species between range-expanding plant species and their congeneric natives. In order to understand differences in nematode preferences, we compared root volatile profiles of all range expanders and congeneric natives. Nematode preferences and performances differed substantially among the pairs of range-expanders and natives. The range-expander that had the most unique volatile profile compared to its related native was unattractive and a poor host for nematodes. Other range-expanding plant species that differed less in root chemistry from native congeners, also differed less in nematode attraction and performance. We conclude that the three climate-driven range-expanding plant species studied varied considerably in their chemical novelty compared to their congeneric natives, and therefore affected native root-feeding nematodes in species-specific ways. Our data suggest that through variation in chemical novelty, range-expanding plant species may vary in their impacts on belowground herbivores in the new range.
  • Fungal Genetics and Biology

    Fungus-associated bacteriome in charge of their host behaviour

    Kristin Bohm, Olaf Tyc, Wietse de Boer, Nils Peereboom, Fons Debets, Niels Zaagman, Thierry K.S. Janssens, Paolina Garbeva
    Abstract Bacterial-fungal interactions are widespread in nature and there is a growing number of studies reporting distinct fungus-associated bacteria. However, little is known so far about how shifts in the fungus-associated bacteriome will affect the fungal host’s lifestyle. In the present study, we describe for the first time the bacterial community associated with the saprotrophic fungus Mucor hiemalis, commonly found in soil and rhizosphere. Two broad-spectrum antibiotics that strongly altered the bacterial community associated with the fungus were applied. Our results revealed that the antibiotic treatment did not significantly reduce the amount of bacteria associated to the fungus but rather changed the community composition by shifting from initially dominating Alpha-Proteobacteria to dominance of Gamma-Proteobacteria. A novel approach was applied for the isolation of fungal-associated bacteria which also revealed differences between bacterial isolates obtained from the original and the antibiotic-treated M. hiemalis. The shift in the composition of the fungal-associated bacterial community led to significantly reduced fungal growth, changes in fungal morphology, behavior and secondary-metabolites production. Furthermore, our results showed that the antibiotic-treated isolate was more attractive and susceptible to mycophagous bacteria as compared to the original isolate. Overall, our study highlights the importance of the fungus-associated bacteriome for the host’s lifestyle and interactions and indicate that isolation with antibacterials is not sufficient to eradicate the associated bacteria.
  • Microbial Biotechnology

    Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds

    Olaf Tyc, Victor de Jager, M. Van den Berg, Saskia Gerards, Thierry Janssens, Niels Zaagman, Marco Kai, A. Svatos, Hans Zweers, Cees Hordijk, Harrie Besselink, Wietse de Boer, Paolina Garbeva
    Recent studies indicated that the production of secondary metabolites by soil bacteria can be triggered by interspecific interactions. However, little is known to date about interspecific interactions between Gram-positive and Gram-negative bacteria. In this study, we aimed to understand how the interspecific interaction between the Gram-positive Paenibacillus sp. AD87 and the Gram-negative Burkholderia sp. AD24 affects the fitness, gene expression and the production of soluble and volatile secondary metabolites of both bacteria. To obtain better insight into this interaction, transcriptome and metabolome analyses were performed. Our results revealed that the interaction between the two bacteria affected their fitness, gene expression and the production of secondary metabolites. During interaction, the growth of Paenibacillus was not affected, whereas the growth of Burkholderia was inhibited at 48 and 72 h. Transcriptome analysis revealed that the interaction between Burkholderia and Paenibacillus caused significant transcriptional changes in both bacteria as compared to the monocultures. The metabolomic analysis revealed that the interaction increased the production of specific volatile and soluble antimicrobial compounds such as 2,5-bis(1-methylethyl)-pyrazine and an unknown Pederin-like compound. The pyrazine volatile compound produced by Paenibacillus was subjected to bioassays and showed strong inhibitory activity against Burkholderia and a range of plant and human pathogens. Moreover, strong additive antimicrobial effects were observed when soluble extracts from the interacting bacteria were combined with the pure 2,5-bis(1-methylethyl)-pyrazine. The results obtained in this study highlight the importance to explore bacterial interspecific interactions to discover novel secondary metabolites and to perform simultaneously metabolomics of both, soluble and volatile compounds.
  • Frontiers in Microbiology

    Editorial: Smelly fumes: volatile-mediated communication between bacteria and other organisms

    Laure Weisskopf, Paolina Garbeva, Choo-Min Ryu, Jos M. Raaijmakers
    Volatiles are small (<300 Da), smelly molecules emitted by all organisms. They have very diverse roles for the producing organism (e.g., as infochemicals or antimicrobial compounds) and fulfill important ecosystem functions. While the importance of plant volatiles has been recognized for more than 30 years, research on microbial volatiles attracted attention only in the last decades. This special issue focuses on several new findings and recent developments in the field of microbial (fungal and bacterial) volatiles, their biological functions and chemical identification, which are highlighted in this editorial.
  • Frontiers in Microbiology

    Microbial small talk: volatiles in fungal-bacterial interactions

    Ruth Schmidt, Desalegn Etalo, Victor de Jager, Saskia Gerards, Hans Zweers, Wietse de Boer, Paolina Garbeva
    There is increasing evidence that volatile organic compounds (VOCs) play an important role in the interactions between fungi and bacteria, two major groups of soil inhabiting microorganisms. Yet, most of the research has been focused on effects of bacterial volatiles on suppression of plant pathogenic fungi whereas little is known about the responses of bacteria to fungal volatiles. In the current study we performed a metabolomics analysis of volatiles emitted by several fungal and oomycetal soil strains under different nutrient conditions and growth stages. The metabolomics analysis of the tested fungal and oomycetal strains revealed different volatile profiles dependent on the age of the strains and nutrient conditions. Furthermore, we screened the phenotypic responses of soil bacterial strains to volatiles emitted by fungi. Two bacteria, Collimonas pratensis Ter291 and Serratia plymuthica PRI-2C, showed significant changes in their motility, in particular to volatiles emitted by Fusarium culmorum. This fungus produced a unique volatile blend, including several terpenes. Four of these terpenes were selected for further tests to investigate if they influence bacterial motility. Indeed, these terpenes induced or reduced swimming and swarming motility of S. plymuthica PRI-2C and swarming motility of C. pratensis Ter291, partly in a concentration-dependent manner. Overall the results of this work revealed that bacteria are able to sense and respond to fungal volatiles giving further evidence to the suggested importance of volatiles as signaling molecules in fungal–bacterial interactions.
  • PLoS One

    Validation of the AlamarBlue® assay as a fast screening method to determine the antimicrobial activity of botanical extracts

    Olaf Tyc, L. Tomás-Menor, Paolina Garbeva, E. Barrajón-Catalán, V. Micol
    Plant compounds are a potential source of new antimicrobial molecules against a variety of infections. Plant extracts suppose complex phytochemical libraries that may be used for the first stages of the screening process for antimicrobials. However, their large variability and complexity require fast and inexpensive methods that allow a rapid and adequate screening for antimicrobial activity against a variety of bacteria and fungi. In this study, a multi-well plate assay using the AlamarBlue® fluorescent dye was applied to screen for antimicrobial activity of several botanical extracts and the data were correlated with microbial colony forming units (CFU). This correlation was performed for three pathogenic model microorganisms: Escherichia coli (Gram negative bacteria), Staphylococcus aureus (Gram positive bacteria) and for the yeast-like fungi Candida albicans. A total of ten plant extracts from different Mediterranean plants, including several Cistus and Hibiscus species, were successfully tested. HPLC-DAD-ESI-MS/MS analysis was utilized for the characterization of the extracts in order to establish structure-activity correlations. The results show that extracts enriched in ellagitannins and flavonols are promising antibacterial agents against both Gram positive and Gram negative bacteria. In contrast, phenolic acids, anthocyanidins and flavonols may be related to the observed antifungal activity.
  • Angewandte Chemie

    Lessons from 1,3-Hydride Shifts in Sesquiterpene Cyclizations

    J. Rinkel, P. Rabe, Paolina Garbeva, Jeroen Dickschat
    Stereospecifically labelled precursors were subjected to conversion by seven bacterial sesquiterpene cyclases to investigate the stereochemistry of their initial 1,10-cyclisation-1,3-hydride shift cascades. Enzymes with products of known absolute configuration showed a coherent stereochemical course, except for (−)-α-amorphene synthase, for which the obtained results are better explained by an initial 1,6-cyclisation. The link between the absolute configuration of the product and the stereochemical course of the 1,3-hydride shifts enabled assignment of the absolute configurations of three enzyme products, which were confirmed independently through the absolute configuration of the common byproduct germacrene D-4-ol.
  • ISME Journal

    Volatile affairs in microbial interactions

    Ruth Schmidt, Viviane Cordovez da Cunha, Wietse de Boer, Jos M. Raaijmakers, Paolina Garbeva
    Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe–microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance.
  • Ecology

    Non-random species loss in bacterial communities reduces antifungal volatile production

    (Gera) W.H.G. Hol, Paolina Garbeva, Cees Hordijk, M.P.J. Hundscheid, P.J.A. Klein Gunnewiek, Maaike Van Agtmaal, Eiko Kuramae, Wietse de Boer
    The contribution of low-abundance microbial species to soil ecosystems is easily overlooked because there is considerable overlap between metabolic abilities (functional redundancy) of dominant and subordinate microbial species. Here we studied how loss of less abundant soil bacteria affected the production of antifungal volatiles, an important factor in the natural control of soil-borne pathogenic fungi. We provide novel empirical evidence that the loss of soil bacterial species leads to a decline in the production of volatiles that suppress root pathogens. By using dilution-to-extinction for seven different soils we created bacterial communities with a decreasing number of species and grew them under carbon-limited conditions. Communities with high bacterial species richness produced volatiles that strongly reduced the hyphal growth of the pathogen Fusarium oxysporum. For most soil origins loss of bacterial species resulted in loss of antifungal volatile production. Analysis of the volatiles revealed that several known antifungal compounds were only produced in the more diverse bacterial communities. Our results suggest that less abundant bacterial species play an important role in antifungal volatile production by soil bacterial communities and, consequently, in the natural suppression of soil-borne pathogens.

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  • Frontiers in Microbiology

    A fragrant neighborhood: Volatile mediated bacterial interactions in soil

    Kristin Bohm, Hans Zweers, Wietse de Boer, Paolina Garbeva
    BACKGROUND: There is increasing evidence that volatile organic compounds play essential roles in communication and competition between soil microorganisms. Here we assessed volatile-mediated interactions of a synthetic microbial community in a model system that mimics the natural conditions in the heterogeneous soil environment along the rhizosphere. Phylogenetic different soil bacterial isolates (Burkholderia sp., Dyella sp., Janthinobacterium sp., Pseudomonas sp., and Paenibacillus sp.) were inoculated as mixtures or monoculture in organic-poor, sandy soil containing artificial root exudates and the volatile profile and growth were analyzed. Additionally, a two-compartment system was used to test if volatiles produced by inter-specific interactions in the rhizosphere can stimulate the activity of starving bacteria in the surrounding, nutrient-depleted soil. The obtained results revealed that both microbial interactions and shifts in microbial community composition had a strong effect on the volatile emission. Interestingly, the presence of a slow-growing, low abundant Paenibacillus strain significantly affected the volatile production by the other abundant members of the bacterial community as well as the growth of the interacting strains. Furthermore, volatiles released by mixtures of root-exudates consuming bacteria stimulated the activity and growth of starved bacteria. Besides growth stimulation, also an inhibition in growth was observed for starving bacteria exposed to microbial volatiles. The current work suggests that volatiles produced during microbial interactions in the rhizosphere have a significant long distance effect on microorganisms in the surrounding, nutrient-depleted soil.
  • PLoS One

    The effect of phylogenetically different bacteria on the fitness of Pseudomonas fluorescens in sand microcosms

    Olaf Tyc, Alexandra Wolf, Paolina Garbeva
    n most environments many microorganisms live in close vicinity and can interact in various ways. Recent studies suggest that bacteria are able to sense and respond to the presence of neighbouring bacteria in the environment and alter their response accordingly. This ability might be an important strategy in complex habitats such as soils, with great implications for shaping the microbial community structure. Here, we used a sand microcosm approach to
    investigate how Pseudomonas fluorescens Pf0-1 responds to the presence of monocultures or mixtures of two phylogenetically different bacteria, a Gram-negative (Pedobacter sp. V48) and a Gram-positive (Bacillus sp. V102) under two nutrient conditions. Results revealed that under both nutrient poor and nutrient rich conditions confrontation with the Gram-positive Bacillus sp. V102 strain led to significant lower cell numbers of Pseudomonas fluorescens Pf0-1, whereas confrontation with the Gram-negative Pedobacter sp. V48 strain did not affect the growth of Pseudomonas fluorescens Pf0-1. However, when Pseudomonas fluorescens Pf0-1 was confronted with the mixture of both strains, no significant effect on the growth of Pseudomonas fluorescens Pf0-1 was observed. Quantitative realtime PCR data showed up-regulation of genes involved in the production of a broad-spectrum antibiotic in Pseudomonas fluorescens Pf0-1 when confronted with Pedobacter sp. V48, but not in the presence of Bacillus sp. V102. The results provide evidence that the performance of bacteria in soil depends strongly on the identity of neighbouring bacteria and that inter-specific interactions are an important factor in determining microbial community structure.
  • Frontiers in Microbiology

    Volatiles in inter-specific bacterial interactions

    Olaf Tyc, Hans Zweers, Wietse de Boer, Paolina Garbeva
    The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal and bacterial model organisms.
    Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.
  • BMC Genomics

    Exploring the genomic traits of fungus-feeding bacterial genus Collimonas

    Chunxu Song, Ruth Schmidt, Victor de Jager, Dorota Krzyzanowska, Esmer Jongedijk, Katarina Cankar, J. Beekwilder, Anouk van Veen, Wietse de Boer, Hans van Veen, Paolina Garbeva
    Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities.

    In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7 % of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities.

    Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.
  • Frontiers in Microbiology

    Volatile-mediated interactions between phylogenetically different soil bacteria

    Paolina Garbeva, Cees Hordijk, Saskia Gerards, Wietse de Boer
    There is increasing evidence that organic volatiles play an important role in interactions between micro-organisms in the porous soil matrix. Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0–1. We applied a novel cultivation approach that mimics the natural nutritional heterogeneity in soil in which P. fluorescens grown on nutrient-limited agar was exposed to volatiles produced by 4 phylogenetically different bacterial isolates (Collimonas pratensis, Serratia plymuthica, Paenibacillus sp., and Pedobacter sp.) growing in sand containing artificial root exudates. Contrary to our expectation, the produced volatiles stimulated rather than inhibited the growth of P. fluorescens. A genome-wide, microarray-based analysis revealed that volatiles of all four bacterial strains affected gene expression of P. fluorescens, but with a different pattern of gene expression for each strain. Based on the annotation of the differently expressed genes, bacterial volatiles appear to induce a chemotactic motility response in P. fluorescens, but also an oxidative stress response. A more detailed study revealed that volatiles produced by C. pratensis triggered, antimicrobial secondary metabolite production in P. fluorescens. Our results indicate that bacterial volatiles can have an important role in communication, trophic - and antagonistic interactions within the soil bacterial community.
  • FEMS Microbiology Ecology

    Volatiles produced by the mycophagous soil bacterium Collimonas

    Paolina Garbeva, Cees Hordijk, Saskia Gerards, Wietse de Boer
    It is increasingly recognized that volatile organic compounds play an import role during interactions between soil microorganisms. Here, we examined the possible involvement of volatiles in the interaction of Collimonas bacteria with soil fungi. The genus Collimonas is known for its ability to grow at the expense of living fungi (mycophagy), and antifungal volatiles may contribute to the attack of fungi by these bacteria. We analyzed the composition of volatiles produced by Collimonas on agar under different nutrient conditions and studied the effect on fungal growth. The volatiles had a negative effect on the growth of a broad spectrum of fungal species. Collimonas bacteria did also produce volatiles in sand microcosms supplied with artificial root exudates. The production of volatiles in sand microcosms was enhanced by the presence of fungi. The overall picture that we get from our study is that antifungal volatiles produced by Collimonas could play an important role in realizing its mycophagous lifestyle. The current work is also interesting for understanding the ecological relevance of volatile production by soil bacteria in general as we found strong influences of root exudates composition and incubation conditions on the spectrum of volatiles produced.
  • Genome Announcements

    Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand Dune in the Netherlands

    A.S. Bitzer, Paolina Garbeva, M.W. Silby
    Pedobacter sp. strain V48 participates in an interaction with Pseudomonas fluorescens which elicits interaction-induced phenotypes. We report the draft genome sequence of Pedobacter sp. V48, consisting of 6.46 Mbp. The sequence will contribute to improved understanding of the genus and facilitate genomic analysis of the model interspecies interaction with P. fluorescens.
  • FEMS Microbiology Reviews

    The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

    Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.
  • ISME Journal

    Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors

    Paolina Garbeva, M.W. Silby, Jos M. Raaijmakers, S. Levy, Wietse de Boer
    The ability of soil bacteria to successfully compete with a range of other microbial species is crucial for their growth and survival in the nutrient-limited soil environment. In the present work, we studied the behavior and transcriptional responses of soil-inhabiting Pseudomonas fluorescens strain Pf0-1 on nutrient-poor agar to confrontation with strains of three phylogenetically different bacterial genera, that is, Bacillus, Brevundimonas and Pedobacter. Competition for nutrients was apparent as all three bacterial genera had a negative effect on the density of P. fluorescens Pf0-1; this effect was most strong during the interaction with Bacillus. Microarray-based analyses indicated strong differences in the transcriptional responses of Pf0-1 to the different competitors. There was higher similarity in the gene expression response of P. fluorescens Pf0-1 to the Gram-negative bacteria as compared with the Gram-positive strain. The Gram-negative strains did also trigger the production of an unknown broad-spectrum antibiotic in Pf0-1. More detailed analysis indicated that expression of specific Pf0-1 genes involved in signal transduction and secondary metabolite production was strongly affected by the competitors’ identity, suggesting that Pf0-1 can distinguish among different competitors and fine-tune its competitive strategies. The results presented here demonstrate that P. fluorescens Pf0-1 shows a species-specific transcriptional and metabolic response to bacterial competitors and provide new leads in the identification of specific cues in bacteria–bacteria interactions and of novel competitive strategies, antimicrobial traits and genes.
  • Soil Biology & Biochemistry

    Fungistasis and general soil biostasis - A new synthesis.

    Paolina Garbeva, (Gera) W.H.G. Hol, Aad J Termorshuizen, George Kowalchuk, Wietse de Boer
    In most soils, fungal propagules are restricted to a certain extent in their ability to grow or germinate. This phenomenon, known as soil fungistasis, has received considerable attention for more than five decades, mostly due to its association with the general suppression of soil-borne fungal diseases. Here, we review major breakthroughs in understanding the mechanisms of fungistasis. Integration of older fungistasis research and more recent findings from different biological and chemical disciplines has lead to the consensus opinion that fungistasis is most likely caused by a combination of microbial activities, namely withdrawal of nutrients from fungal propagules and production of fungistatic compounds. In addition, recent findings indicate that there are mechanistic links between these activities leading towards an integrated theory of fungistasis. Among the potentially fungistatic compounds volatiles have received particular attention. Whereas it has long been assumed that fungistasis is the result of the metabolic activity of the total soil microbial biomass, more recent research points at the importance of activities of specific components of the microbial community. These insights into fungistasis have also formed the basis for strategies to increase general soil suppression. Besides these basic and practical aspects of fungistasis, its impact on fungal ecology, in particular on fungal exploration strategies, is discussed. Finally, we take a closer look at plant–soil feedback experiments to demonstrate the occurrence of fungistasis-like phenomena and to suggest that fungistasis may be part of a much wider phenomenon: general soil biostasis.
  • PLoS One

    No apparent costs for facultative antibiotic production by the soil bacterium Pseudomonas fluorescens Pf0-1

    Paolina Garbeva, Olaf Tyc, Mitja Remus-Emsermann, Annemieke van der Wal, M. Vos, M.W. Silby, Wietse de Boer
    Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures. Methodology and Principal Findings: We measured the possible cost of antibiotic production for Pseudomonas fluorescens Pf0-1 by monitoring changes in growth rate with and without induction of antibiotic production by supernatant of a bacterial competitor, namely Pedobacter sp.. Experiments were performed in liquid as well as on semi-solid media under nutrient-limited conditions that are expected to most clearly reveal fitness costs. Our results did not reveal any significant costs for production of antibiotics by Pseudomonas fluorescens Pf0-1. Comparison of growth rates of the antibioticproducing wild-type cells with those of non-antibiotic producing mutants did not reveal costs of antibiotic production either. Significance: Based on our findings we propose that the facultative production of antibiotics might not be selected to mitigate metabolic costs, but instead might be advantageous because it limits the risk of competitors evolving resistance, or even the risk of competitors feeding on the compounds produced.
  • Microbial Ecology

    Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression

    Paolina Garbeva, Wietse de Boer
    Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other’s behavior and gene expression patterns when growing together under carbon-limited conditions on agar. The most pronounced observed visual changes in mixed cultures as compared to monocultures were (1) strong inhibition of a bioindicator fungus, suggesting the production of a broad-spectrum antibiotic, and (2) the occurrence of gliding-like movement of Pedobacter cells. Two independent techniques, namely random arbitrary primed-PCR (RAP-PCR) and suppressive subtractive hybridization (SSH), identified in total 24 genes that had higher expression in mixed cultures compared to monocultures. Microbial interactions were clearly bidirectional, as differentially expressed genes were detected for both bacteria in mixed cultures. Sequence analysis of the differentially expressed genes indicated that several of them were most related to genes involved in motility and chemotaxis, secondary metabolite production and two-component signal transduction systems. The gene expression patterns suggest an interference competition strategy by the Pseudomonas strain and an escape/explorative strategy by the Pedobacter strain during confrontation with each other. Our results show that the bacterial strains can distinguish between intra- and inter-specific carbon competition.
  • Plant and Soil

    Rhizosphere microbial community and its response to plant species and soil history

    Paolina Garbeva, J.D. Van Elsas, Hans van Veen
    The plant rhizosphere is a dynamic environment in which many parameters may influence the population structure, diversity and activity of the microbial community. Two important factors determining the structure of microbial community present in the vicinity of plant roots are plant species and soil type. In the present study we assessed the structure of microbial communities in response to four plant species (i.e. maize (Zea mays L.), oat (Avena sativa L.), barley (Hordeum vulgare L.) and commercial grass mix) planted in soil with different land use history (i.e. arable land under crop rotation, maize monoculture and permanent grassland). Both factors, plant species and land use history, showed clear effects on microbial community and diversity as determined by PCR-DGGE fingerprinting with universal and group-specific bacterial primers. Moreover, we explored the rhizosphere effect of these plant species on the abundance of bacterial antagonists of the potato pathogen Rhizoct! onia solani AG3. The data showed that the abundance and taxonomic composition of antagonists differed clearly between the different plants. The highest percentages of antagonists were found in maize and grass rhizosphere. When antagonistic Pseudomonas populations were compared, the highest, abundance and diversity of antagonists were detected in barley and oat rhizospheres, as compared to maize and grass rhizosphere. The results obtained in our study demonstrate clearly that plant species and soil type are two important factors affecting the structure of total bacterial, Pseudomonas and Bacillus community.
  • Environmental Microbiology

    Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3

    Paolina Garbeva, J. Postma, Hans van Veen, J.D. Van Elsas
    The extent of soil microbial diversity is seen to be critical to the maintenance of soil health and quality. Different agricultural practices are able to affect soil microbial diversity and thus the level of suppressiveness of plant diseases. In a 4-year field experiment, we investigated the microbial diversity of soil under different agricultural regimes. We studied permanent grassland, grassland turned into arable land, long-term arable land and arable land turned into grassland. The diversity of microbial communities was described by using cultivation-based and cultivation-independent methods. Both types of methods revealed differences in the diversities of soil microbial communities between different treatments. The treatments with higher above-ground biodiversity generally maintained higher levels of microbial diversity. Moreover, a positive correlation between suppression of Rhizoctonia solani AG3 and microbial diversity was observed. Permanent (species-rich) grassland and grassland turned into maize stimulated higher microbial diversities and higher levels of suppressiveness of R. solani AG3 compared with the long-term arable land. Effects of agricultural practices on Bacillus and Pseudomonas communities were also observed and clear correlations between the levels of suppressiveness and the diversities of these bacterial groups were found. This study highlighted the importance of agricultural management regime for soil microbial community structure and diversity as well as the level of soil suppressiveness.
  • FEMS Microbiology Ecology

    Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes

    Paolina Garbeva, Hans van Veen, J.D. Van Elsas
    The genus Pseudomonas is one of the best-studied bacterial groups in soil, and includes numerous species of environmental interest. Pseudomonas species play key roles in soil, for instance in biological control of soil-borne plant pathogens and in bioremediation of pollutants. A polymerase chain reaction-denaturing gradient gel electrophoresis system that specifically describes the diversity of Pseudomonas spp. in soil was developed. On the basis of this molecular method as well as cultivation-based approaches, the diversity of Pseudomonas species in soil under different agricultural regimes (permanent grassland, arable land either under rotation or under monoculture of maize) was studied. Both types of approaches revealed differences in the composition of Pseudomonas populations between the treatments. Differences between the treatments were also found based on the frequency of isolation of Pseudomonas strains with antagonistic properties against the soil-borne pathogen Rhizoctonia solani AG3. Higher relative numbers of isolates either with antagonistic activity toward this pathogen or with chitinolytic activity were obtained from permanent grassland or from the short-term arable land than from the arable land. The results obtained in this study strongly indicate that agricultural regimes influence the structure of Pseudomonas populations in soil, with specific antagonistic subpopulations being stimulated in grassland as compared to arable land. [KEYWORDS: Pseudomonas; Bacterial diversity; Soil; Polymerase chain reaction-denaturing gradient gel electrophoresis; Antifungal activity]
  • Annual Review of Phytopathology

    Microbail diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness

    Paolina Garbeva, Hans van Veen, J.D. Van Elsas
    An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil functions. This review focuses on recent data relating how plant type, soil type, and soil management regime affect the microbial diversity of soil and the implication for the soil's disease suppressiveness. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. We propose that the fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to the complexity of the microbial interactions in soil, including interactions between microorganisms and soil and microorganisms and plants. A conceptual framework, based on the relative strengths of the shaping forces exerted by plant and soil versus the ecological behavior of microorganisms, is proposed. [KEYWORDS: soil microbial diversity and community; plant effect; soil type; management regimes; soil suppressiveness]
  • Soil Biology & Biochemistry

    Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments

    Paolina Garbeva, K. Voesenek, J.D. Van Elsas
    The prevalence of antibiotic production loci in soil is a key issue of current research aimed to unravel the mechanisms underlying the suppressiveness of soil to plant pathogens. Pyrrolnitrin (PRN) is a key antibiotic involved in the suppression of a range of phytopathogenic fungi. Therefore, field soils from different agricultural regimes, including permanent grassland, arable land under common agricultural rotation and arable land under maize monoculture, were investigated in respect of the prevalence of pyrrolnitrin biosynthetic loci. Primers for detection of the prnD gene were used for initial PCR/hybridisation-based assessments. By this method, evidence was obtained for the contention that PRN production loci were most prevalent in grasslands, however, robust quantitative data were not achieved. To quantify the prevalence of PRN biosynthetic loci, we designed a TaqMan PCR system based on the prnD gene for the real-time quantitative detection of this production locus in soil. The system was found to be specific for prnD sequences from Pseudomonas, Serratia and Burkholderia species. Using pure culture DNA, the prnD gene was detectable down to a level of 60 fg, or approximately 10 gene copies, per amplification reaction. Application of the system to soil DNA spiked with different levels of Field soil samples obtained from the different agricultural regimes were then screened for the prevalence of prnD with the real-time PCR system. The quantitative data obtained suggested a strongly enhanced presence of prnD genes in grassland or grassland-derived plots, as compared to the prevalence of this biosynthetic locus in the arable land plots. The implications of these findings are placed in the context of the suppressiveness of soil to phytopathogens, notably Rhizoctonia solani AG3. [KEYWORDS: Pyrrolnitrin biosynthetic locus; Detection; Real-time PCR; Diversity; Soil]
  • Microbial Ecology

    Predominant Bacillus spp. in agricultural soil under different management regimes detected via PCR-DGGE

    Paolina Garbeva, Hans van Veen, J.D. Van Elsas
    A PCR system for studying the diversity of species of Bacillus and related taxa directly from soil was developed. For this purpose, a specific 24-bp forward primer located around position 110 of the 16S ribosomal RNA gene was designed and combined with a reverse bacterial primer located at the end of the gene. The specificity of this PCR system for bacilli and related taxons was confirmed on the basis of tests with diverse strains as well as with soil DNA. Analysis of a soil DNA derived clone library showed that the amplified fragments affiliated exclusively with sequences of gram-positive bacteria, with up to 95% of the sequences originating from putative Bacillus species. In particular, sequences affiliated to those of B. mycoides, B. pumilus, B. megaterium, B. thuringiensis, and B. firmus, as well as to related taxa such as Paenibacillus, were obtained. A minority, i.e., less than 6%, of the clones affiliated with other gram-positive bacteria, such as Arthrobacter spp., Frankia spp., and uncultured gram-positives. The amplified fragments were used as templates for a second PCR using bacterial 16S rDNA primers, yielding PCR products of about 410 bp, which were separated by denaturing gradient gel electrophoresis (DGGE). Amplicons indicating Bacillus spp. were found in the gel between 45% and roughly 60% denaturant, whereas those representing other, high-G+C% bacteria, were localized in gel regions with denaturant concentrations exceeding about 60%, thus allowing the distinction between these two groups of sequences. We applied this system to compare the group-specific diversity in bacterial communities in an agricultural soil under different regimes, i.e., permanent grassland, grassland recently turned to arable land, and arable land under agricultural rotation. Differences in the Bacillus-related community structures between the treatments were clearly detected. Higher diversities, as judged by Shannon–Weaver indices calculated on the basis of the molecular profiles, were consistently observed in the permanent grassland and the grassland turned into arable land, as compared to the arable land
  • Biodegradation

    Effects of agronomical measures on the microbial deversity of soils as related to the suppression of soil-borne plant pathogens

    J.D. Van Elsas, Paolina Garbeva, Joanna Salles
    The diversity of soil microbial communities can be key to the capacity of soils to suppress soil-borne plant diseases. As agricultural practice, as well as directed agronomical measures, are known to be able to affect soil microbial diversity, it is plausible that the soil microflora can be geared towards a greater suppressivity of soil-borne diseases as a result of the selection of suitable soil management regimes. In the context of a programme aimed at investigating the microbial diversity of soils under different agricultural regimes, including permanent grassland versus arable land under agricultural rotation, we assessed how soil microbial diversity is affected in relation to the suppression of the soil-borne potato pathogen Rhizoctonia solani AG3. The diversity in the microbial communities over about a growing season was described by using cultivation-based – plating on different media – and cultivation-independent – soil DNA-based PCR followed by denaturing gradient gel electrophoresis (DGGE) community fingerprinting – methods. The results showed great diversity in the soil microbiota at both the culturable and cultivation-independent detection levels. Using cultivation methods, various differences between treatments with respect to sizes of bacterial and fungal populations were detected, with highest population sizes generally found in rhizospheres. In addition, the evenness of eco-physiologically differing bacterial types was higher in grassland than in arable land under rotation. At the cultivation-independent level, clear differences in the diversities of several microbial groups between permanent grassland and arable land under rotation were apparent. Bio-assays that assessed the growth of R. solani AG3 hyphae through soil indicated a greater growth suppression in grassland than in arable land soils. Similarly, an experiment performed in the glasshouse showed clear differences in both microbial diversities and suppressiveness of R. solani growth in soil, depending on the presence of either maize or oats as the crop. The significance of these findings for designing soil management strategies is discussed. [KEYWORDS: microbial diversity, soil, pathogen suppression, molecular methods]

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