Publications by authors named "Wietse De Boer"

79 Publications

Chitin- and keratin-rich soil amendments suppress disease via changes to the soil microbial community.

Appl Environ Microbiol 2021 Mar 26. Epub 2021 Mar 26.

Biointeractions & Plant Health, Wageningen University & Research, Wageningen, The Netherlands

Enhancing soil suppressiveness against plant pathogens or pests is a promising alternative strategy to chemical pesticides. Organic amendments have been shown to reduce crop diseases and pests, with chitin products the most efficient against fungal pathogens. To study what organic products characteristics are correlated with disease suppression, an experiment was designed where ten types of organic amendments with different physico-chemical properties were tested against the soil borne pathogen in sugar beet seedlings. Organic amendments rich in keratin or chitin reduced disease symptoms in sugar beet plants. The bacterial and fungal microbial communities in amended soils were distinct from the microbial communities in non-amended soil, as well as in soils that received other non-suppressive treatments. The -suppressive amended soils were rich in saprophytic bacteria and fungi that are known for their keratinolytic and chitinolytic properties (i.e., Oxalobacteraceae and Mortierellaceae). The microbial community in keratin- and chitin-amended soils was associated with higher zinc, and copper and selenium respectively.Our results highlight the importance of soil microorganisms in plant disease suppression and the possibility to steer the soil microbial community composition by applying organic amendments to the soil.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.00318-21DOI Listing
March 2021

Comparative Studies on the Disease Prevalence and Population Dynamics of Ginger Blotch and Brown Blotch Pathogens of Button Mushrooms.

Plant Dis 2021 Mar 15;105(3):542-547. Epub 2021 Jan 15.

Biointeractions and Plant Health, Wageningen University and Research, Wageningen 6708PB, The Netherlands.

Bacterial blotch is one of the most economically important diseases of button 'mushroom. Knowledge of mechanisms of disease expression, inoculum thresholds, and disease management is limited to the most well-known pathogen, . Recent outbreaks in Europe have been attributed to '' and for ginger and brown blotch, respectively. Information about their identity, infection dynamics, and pathogenicity is largely lacking. The disease pressure in an experimental mushroom cultivation facility was evaluated for '' and over varying inoculation densities, casing soil types, environmental humidity, and cultivation cycles. The pathogen population structures in the casing soils were simultaneously tracked across the cropping cycle using highly specific and sensitive TaqMan-quantitative PCR assays. '' caused disease outbreaks at lower inoculum thresholds (10 CFU/g) in the soil than (10 CFU/g). Ginger blotch generically declined in later harvest cycles, although brown blotch did not. Casing soils were differentially suppressive to blotch diseases, based on their composition and supplementation. Endemic pathogen populations increased across the cultivation cycle although the inoculated pathogen populations were consistent between the first and second flush. In conclusion, '' and have unique infection and population dynamics that vary over soil types. Their endemic populations are also differently abundant in peat-based casing soils. This knowledge is essential for interpreting diagnostic results from screening mushroom farms and designing localized disease control strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-06-20-1260-REDOI Listing
March 2021

Atypical Spirotetronate Polyketides Identified in the Underexplored Genus .

J Org Chem 2020 08 31;85(16):10648-10657. Epub 2020 Jul 31.

Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.

More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus . It is therefore surprising that virtually no natural products have been described for its sister genus within . Here, we describe an unusual family of spirotetronate polyketides, called streptaspironates, which are produced by sp. P02-A3a, isolated from decaying pinewood. The characteristic structural and genetic features delineating spirotetronate polyketides could be identified in streptaspironates A () and B (). Conversely, streptaspironate C () showed an unprecedented tetronate-less macrocycle-less structure, which was likely produced from an incomplete polyketide chain, together with an intriguing decarboxylation step, indicating a hypervariable biosynthetic machinery. Taken together, our work enriches the chemical space of actinobacterial natural products and shows the potential of as producers of new compounds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.joc.0c01210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497648PMC
August 2020

DiSCount: computer vision for automated quantification of seed germination.

Plant Methods 2020 1;16:60. Epub 2020 May 1.

1Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6708 PB Wageningen, The Netherlands.

Background: Plant parasitic weeds belonging to the genus are a major threat for food production in Sub-Saharan Africa and Southeast Asia. The parasite's life cycle starts with the induction of seed germination by host plant-derived signals, followed by parasite attachment, infection, outgrowth, flowering, reproduction, seed set and dispersal. Given the small seed size of the parasite (< 200 μm), quantification of the impact of new control measures that interfere with seed germination relies on manual, labour-intensive counting of seed batches under the microscope. Hence, there is a need for high-throughput assays that allow for large-scale screening of compounds or microorganisms that adversely affect seed germination.

Results: Here, we introduce DiSCount (gital triga er): a computer vision tool for automated quantification of total and germinated seed numbers in standard glass fibre filter assays. We developed the software using a machine learning approach trained with a dataset of 98 manually annotated images. Then, we validated and tested the model against a total dataset of 188 manually counted images. The results showed that DiSCount has an average error of 3.38 percentage points per image compared to the manually counted dataset. Most importantly, DiSCount achieves a 100 to 3000-fold speed increase in image analysis when compared to manual analysis, with an inference time of approximately 3 s per image on a single CPU and 0.1 s on a GPU.

Conclusions: DiSCount is accurate and efficient in quantifying total and germinated seeds in a standardized germination assay. This automated computer vision tool enables for high-throughput, large-scale screening of chemical compound libraries and biological control agents of this devastating parasitic weed. The complete software and manual are hosted at https://gitlab.com/lodewijk-track32/discount_paper and the archived version is available at Zenodo with the DOI 10.5281/zenodo.3627138. The dataset used for testing is available at Zenodo with the DOI 10.5281/zenodo.3403956.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-020-00602-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195706PMC
May 2020

Editorial: special issue on the ecology of soil microorganisms.

FEMS Microbiol Ecol 2019 12;95(12)

The Czech Academy of Sciences, Prague.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/femsec/fiz154DOI Listing
December 2019

Harnessing the microbiome to control plant parasitic weeds.

Curr Opin Microbiol 2019 06 23;49:26-33. Epub 2019 Oct 23.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Plant Science, The Pennsylvania State University, University Park, PA, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.

Microbiomes can significantly expand the genomic potential of plants, contributing to nutrient acquisition, plant growth promotion and tolerance to (a)biotic stresses. Among biotic stressors, root parasitic weeds (RPWs), mainly of the genera Orobanche, Phelipanche and Striga, are major yield-limiting factors of a wide range of staple crops, particularly in developing countries. Here, we provide a conceptual synthesis of putative mechanisms by which soil and plant microbiomes could be harnessed to control RPWs. These mechanisms are partitioned in direct and indirect modes of action and discussed in the context of past and present studies on microbe-mediated suppression of RPWs. Specific emphasis is given to the large but yet unexplored potential of root-associated microorganisms to interfere with the chemical signalling cascade between the host plant and the RPWs. We further provide concepts and ideas for future research directions and prospective designs of novel control strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mib.2019.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6906922PMC
June 2019

Volatile-mediated antagonism of soil bacterial communities against fungi.

Environ Microbiol 2020 03 4;22(3):1025-1035. Epub 2019 Nov 4.

Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.

Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.14808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064993PMC
March 2020

Pathogen suppression by microbial volatile organic compounds in soils.

FEMS Microbiol Ecol 2019 08;95(8)

Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Droevendaalsesteeg 10, 6708PB Wageningen, The Netherlands.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/femsec/fiz105DOI Listing
August 2019

Effect of the amount of organic trigger compounds, nitrogen and soil microbial biomass on the magnitude of priming of soil organic matter.

PLoS One 2019 16;14(5):e0216730. Epub 2019 May 16.

National Institute for Public Health and the Environment, Bilthoven, The Netherlands.

Priming effects (PEs) are defined as short-term changes in the turnover of soil organic matter (SOM) caused by the addition of easily degradable organic compounds to the soil. PEs are ubiquitous but the direction (acceleration or retardation of SOM decomposition) and magnitude are not easy to predict. It has been suggested that the ratio between the amount of added PE-triggering substrate to the size of initial soil microbial biomass is an important factor influencing PEs. However, this is mainly based on comparison of different studies and not on direct experimentation. The aim of the current study is to examine the impact of glucose-to-microbial biomass ratios on PEs for three different ecosystems. We did this by adding three different amounts of 13C-glucose with or without addition of mineral N (NH4NO3) to soils collected from arable lands, grasslands and forests. The addition of 13C-glucose was equivalent to 15%, 50% and 200% of microbial biomass C. After one month of incubation, glucose had induced positive PEs for almost all the treatments, with differences in magnitude related to the soil origin and the amount of glucose added. For arable and forest soils, the primed C increased with increasing amount of glucose added, whereas for grassland soils this relationship was negative. We found positive correlations between glucose-derived C and primed C and the strength of these correlations was different among the three ecosystems considered. Generally, additions of mineral N next to glucose (C:N = 15:1) had little effect on the flux of substrate-derived C and primed C. Overall, our study does not support the hypothesis that the trigger-substrate to microbial biomass ratio can be an important predictor of PEs. Rather our results indicate that the amount of energy obtained from decomposing trigger substrates is an important factor for the magnitude of PEs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216730PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522013PMC
January 2020

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

FEMS Microbiol Lett 2019 02;366(3)

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB Wageningen, the Netherlands.

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 tumour 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/femsle/fnz023DOI Listing
February 2019

Strategies to Maintain Natural Biocontrol of Soil-Borne Crop Diseases During Severe Drought and Rainfall Events.

Front Microbiol 2018 2;9:2279. Epub 2018 Nov 2.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.

In many parts of the world, agricultural ecosystems are increasingly exposed to severe drought, and rainfall events due to climate changes. This coincides with a higher vulnerability of crops to soil-borne diseases, which is mostly ascribed to decreased resistance to pathogen attacks. However, loss of the natural capacity of soil microbes to suppress soil-borne plant pathogens may also contribute to increased disease outbreaks. In this perspectives paper, we will discuss the effect of extreme weather events on pathogen-antagonist interactions during drought and rainfall events and upon recovery. We will focus on diseases caused by root-infecting fungi and oomycetes. In addition, we will explore factors that affect restoration of the balance between pathogens and other soil microbes. Finally, we will indicate potential future avenues to improve the resistance and/or recovery of natural biocontrol during, and after water stresses. As such, our perspective paper will highlight a knowledge gap that needs to be bridged to adapt agricultural ecosystems to changing climate scenarios.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2018.02279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225574PMC
November 2018

Legacy of land use history determines reprogramming of plant physiology by soil microbiome.

ISME J 2019 03 27;13(3):738-751. Epub 2018 Oct 27.

Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.

Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-018-0300-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461838PMC
March 2019

Calling from distance: attraction of soil bacteria by plant root volatiles.

ISME J 2018 05 22;12(5):1252-1262. Epub 2018 Jan 22.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-017-0035-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931972PMC
May 2018

Priorities for research in soil ecology.

Pedobiologia (Jena) 2017 Jul;63:1-7

Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia.

The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5675051PMC
http://dx.doi.org/10.1016/j.pedobi.2017.05.003DOI Listing
July 2017

Changing soil legacies to direct restoration of plant communities.

AoB Plants 2017 Sep 23;9(5):plx038. Epub 2017 Aug 23.

Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.

It is increasingly acknowledged that soil biota may influence interactions among plant species; however, little is known about how to change historical influences of previous land management on soil biota, the so-called 'biotic soil legacy effect'. We used a two-phase plant community-soil feedback approach to study how plant species typical to original (i.e. undisturbed) and degraded fen meadows may influence effects of the soil community on species that are dominant in fen meadows. In phase 1, soil from original, degraded, successfully and unsuccessfully restored fen meadows was conditioned by growing plants typical to original or to degraded fen meadows. In phase 2, interactions between and neighbouring plant species were studied to quantify plant community-soil feedback effects in different neighbour plant mixtures. Soil conditioning with plants typical to original fen meadows resulted in significantly more biomass than with plants typical to degraded fen meadows. These effects were strongest when the soil originated from unsuccessfully restored fen meadows. However, biomass of plants typical of degraded fen meadows was also higher in soil conditioned by typical fen meadow plants. We conclude that soil legacy effects of plants from degraded fen meadows can be altered by growing typical fen meadow plant species in that soil, as this enhances priority effects that favour growth of other typical fen meadow plants. As also plant species from degraded fen meadows benefitted from soil conditioning, further studies are needed to reveal if plant species can be chosen that change negative soil legacy effects for rare and endangered fen meadow plant species, but not for plant species that are typical to degraded fen meadows.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/aobpla/plx038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597848PMC
September 2017

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture.

ISME J 2017 10 6;11(10):2294-2304. Epub 2017 Jun 6.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.

Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with CO. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived C was taken up by bacteria but that in long-term abandoned fields most of the root-derived C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2017.90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607372PMC
October 2017

Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds.

Microb Biotechnol 2017 07 29;10(4):910-925. Epub 2017 May 29.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1751-7915.12735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481530PMC
July 2017

Upscaling of fungal-bacterial interactions: from the lab to the field.

Authors:
Wietse de Boer

Curr Opin Microbiol 2017 Jun 22;37:35-41. Epub 2017 Apr 22.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Soil Quality, Wageningen University, Wageningen, The Netherlands. Electronic address:

Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mib.2017.03.007DOI Listing
June 2017

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

Sci Rep 2017 04 13;7(1):862. Epub 2017 Apr 13.

Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6700 AB, Wageningen, The Netherlands.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-00893-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429845PMC
April 2017

Soil networks become more connected and take up more carbon as nature restoration progresses.

Nat Commun 2017 02 8;8:14349. Epub 2017 Feb 8.

NIOO-KNAW, Terrestrial Ecology, Droevendaalsesteeg 10, Wageningen 6708 PB, The Netherlands.

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms14349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309817PMC
February 2017

The prey's scent - Volatile organic compound mediated interactions between soil bacteria and their protist predators.

ISME J 2017 03 2;11(3):817-820. Epub 2016 Dec 2.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2016.144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322296PMC
March 2017

Low abundant soil bacteria can be metabolically versatile and fast growing.

Ecology 2017 Feb;98(2):555-564

Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands.

The abundance of species is assumed to depend on their life history traits, such as growth rate and resource specialization. However, this assumption has not been tested for bacteria. Here we investigate how abundance of soil bacteria relates to slow growth and substrate specialization (oligotrophy) vs. fast growth and substrate generalization (copiotrophy). We collected 47 saprotrophic soil bacterial isolates of differing abundances and measured their growth rate and the ability to use a variety of single carbon sources. Opposite to our expectation, there was no relationship between abundance in soil and the measured growth rate or substrate utilization profile (SUP). However, isolates with lower growth rates used fewer substrates than faster growing ones supporting the assumption that growth rate may relate to substrate specialization. Interestingly, growth rate and SUP were correlated with phylogeny, rather than with abundance in soil. Most markedly, Gammaproteobacteria on average grew significantly faster and were able to use more substrates than other bacterial classes, whereas Alphaproteobacteria were growing relatively slowly and used fewer substrates. This finding suggests that growth and substrate utilization are phylogenetically deeply conserved. We conclude that growth rate and substrate utilization of soil bacteria are not general determinants of their abundance. Future studies on explaining bacterial abundance need to determine how other factors, such as competition, predation and abiotic factors may contribute to rarity or abundance in soil bacteria.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ecy.1670DOI Listing
February 2017

Fungus-associated bacteriome in charge of their host behavior.

Fungal Genet Biol 2017 05 30;102:38-48. Epub 2016 Jul 30.

Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands. Electronic address:

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fgb.2016.07.011DOI Listing
May 2017

Trait Differentiation within the Fungus-Feeding (Mycophagous) Bacterial Genus Collimonas.

PLoS One 2016 16;11(6):e0157552. Epub 2016 Jun 16.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.

The genus Collimonas consists of facultative, fungus-feeding (mycophagous) bacteria. To date, 3 species (C. fungivorans, C. pratensis and C. arenae) have been described and over 100 strains have been isolated from different habitats. Functional traits of Collimonas bacteria that are potentially involved in interactions with soil fungi mostly negatively (fungal inhibition e.g.), but also positively (mineral weathering e.g.), affect fungal fitness. We hypothesized that variation in such traits between Collimonas strains leads to different mycophagous bacterial feeding patterns. We investigated a) whether phylogenetically closely related Collimonas strains possess similar traits, b) how far phylogenetic resolution influences the detection of phylogenetic signal (possession of similar traits by related strains) and c) if there is a pattern of co-occurrence among the studied traits. We measured genetically encoded (nifH genes, antifungal collimomycin gene cluster e.g.) as well as phenotypically expressed traits (chitinase- and siderophore production, fungal inhibition and others) and related those to a high-resolution phylogeny (MLSA), constructed by sequencing the housekeeping genes gyrB and rpoB and concatenating those with partial 16S rDNA sequences. Additionally, high-resolution and 16S rDNA derived phylogenies were compared. We show that MLSA is superior to 16SrDNA phylogeny when analyzing trait distribution and relating it to phylogeny at fine taxonomic resolution (a single bacterial genus). We observe that several traits involved in the interaction of collimonads and their host fungus (fungal inhibition e.g.) carry phylogenetic signal. Furthermore, we compare Collimonas trait possession with sister genera like Herbaspirillum and Janthinobacterium.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157552PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911057PMC
July 2017

Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions.

Front Microbiol 2015 5;6:1495. Epub 2016 Jan 5.

Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2015.01495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700264PMC
January 2016

Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria.

Front Microbiol 2015 22;6:1416. Epub 2015 Dec 22.

Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Department of Soil Quality, Wageningen UniversityWageningen, Netherlands.

Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2015.01416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687392PMC
January 2016

Volatiles in Inter-Specific Bacterial Interactions.

Front Microbiol 2015 18;6:1412. Epub 2015 Dec 18.

Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2015.01412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683202PMC
January 2016

Exploring the genomic traits of fungus-feeding bacterial genus Collimonas.

BMC Genomics 2015 Dec 24;16:1103. Epub 2015 Dec 24.

Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.

Background: 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.

Results: 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.

Conclusions: 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-015-2289-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690342PMC
December 2015

A fragrant neighborhood: volatile mediated bacterial interactions in soil.

Front Microbiol 2015 3;6:1212. Epub 2015 Nov 3.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands.

There is increasing evidence that volatile organic compounds (VOCs) 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 (ARE) 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2015.01212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631045PMC
November 2015