Publications by authors named "François Buscot"

136 Publications

Above- and belowground biodiversity jointly tighten the P cycle in agricultural grasslands.

Nat Commun 2021 07 21;12(1):4431. Epub 2021 Jul 21.

Department of Evolutionary Ecology and Environmental Studies, University of Zürich, Zürich, Switzerland.

Experiments showed that biodiversity increases grassland productivity and nutrient exploitation, potentially reducing fertiliser needs. Enhancing biodiversity could improve P-use efficiency of grasslands, which is beneficial given that rock-derived P fertilisers are expected to become scarce in the future. Here, we show in a biodiversity experiment that more diverse plant communities were able to exploit P resources more completely than less diverse ones. In the agricultural grasslands that we studied, management effects either overruled or modified the driving role of plant diversity observed in the biodiversity experiment. Nevertheless, we show that greater above- (plants) and belowground (mycorrhizal fungi) biodiversity contributed to tightening the P cycle in agricultural grasslands, as reduced management intensity and the associated increased biodiversity fostered the exploitation of P resources. Our results demonstrate that promoting a high above- and belowground biodiversity has ecological (biodiversity protection) and economical (fertiliser savings) benefits. Such win-win situations for farmers and biodiversity are crucial to convince farmers of the benefits of biodiversity and thus counteract global biodiversity loss.
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http://dx.doi.org/10.1038/s41467-021-24714-4DOI Listing
July 2021

Contrasting responses of above- and belowground diversity to multiple components of land-use intensity.

Nat Commun 2021 06 24;12(1):3918. Epub 2021 Jun 24.

Institute of Zoology, Terrestrial Ecology, University of Cologne, Köln, Germany.

Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.
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http://dx.doi.org/10.1038/s41467-021-23931-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8225671PMC
June 2021

Interactions between soil properties, agricultural management and cultivar type drive structural and functional adaptations of the wheat rhizosphere microbiome to drought.

Environ Microbiol 2021 May 24. Epub 2021 May 24.

Soil Ecology Department, UFZ - Helmholtz-Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle, 06120, Germany.

Rhizosphere microbial communities adapt their structural and functional compositions to water scarcity and have the potential to substantially mitigate drought stress of crops. To unlock this potential, it is crucial to understand community responses to drought in the complex interplay between soil properties, agricultural management and crop species. Two winter wheat cultivars, demanding and non-demanding, were exposed to drought stress in loamy Chernozem and sandy Luvisol soils under conventional or organic farming management. Structural and functional adaptations of the rhizosphere bacteria were assessed by 16S amplicon sequencing, the predicted abundance of drought-related functional genes in the bacterial community based on 16S amplicon sequences (Tax4Fun) and the activity potentials of extracellular enzymes involved in the carbon cycle. Bacterial community composition was strongly driven by drought and soil type. Under drought conditions, Gram-positive phyla became relatively more abundant, but either less or more diverse in Luvisol and Chernozem soil respectively. Enzyme activities and functional gene abundances related to carbon degradation were increased under drought in the rhizosphere of the demanding wheat cultivar in organic farming. We demonstrate that soil type, farming system and wheat cultivar each constitute important factors during the structural and/or functional adaptation of rhizobacterial communities in response to drought.
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http://dx.doi.org/10.1111/1462-2920.15607DOI Listing
May 2021

Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners.

Ecol Evol 2021 May 2;11(10):5424-5440. Epub 2021 Apr 2.

Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.

Recent studies found that the majority of shrub and tree species are associated with both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. However, our knowledge on how different mycorrhizal types interact with each other is still limited. We asked whether the combination of hosts with a preferred association with either AM or EM fungi increases the host tree roots' mycorrhization rate and affects AM and EM fungal richness and community composition.We established a tree diversity experiment, where five tree species of each of the two mycorrhiza types were planted in monocultures, two-species and four-species mixtures. We applied morphological assessment to estimate mycorrhization rates and next-generation molecular sequencing to quantify mycobiont richness.Both the morphological and molecular assessment revealed dual-mycorrhizal colonization in 79% and 100% of the samples, respectively. OTU community composition strongly differed between AM and EM trees. While host tree species richness did not affect mycorrhization rates, we observed significant effects of mixing AM- and EM-associated hosts in AM mycorrhization rate. Glomeromycota richness was larger in monotypic AM tree combinations than in AM-EM mixtures, pointing to a dilution or suppression effect of AM by EM trees. We found a strong match between morphological quantification of AM mycorrhization rate and Glomeromycota richness. . We provide evidence that the combination of hosts differing in their preferred mycorrhiza association affects the host's fungal community composition, thus revealing important biotic interactions among trees and their associated fungi.
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http://dx.doi.org/10.1002/ece3.7437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131788PMC
May 2021

Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand.

PLoS One 2021 8;16(4):e0248806. Epub 2021 Apr 8.

Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0248806PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8031335PMC
April 2021

Organic agricultural practice enhances arbuscular mycorrhizal symbiosis in correspondence to soil warming and altered precipitation patterns.

Environ Microbiol 2021 Mar 29. Epub 2021 Mar 29.

Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany.

Climate and agricultural practice interact to influence both crop production and soil microbes in agroecosystems. Here, we carried out a unique experiment in Central Germany to simultaneously investigate the effects of climates (ambient climate vs. future climate expected in 50-70 years), agricultural practices (conventional vs. organic farming), and their interaction on arbuscular mycorrhizal fungi (AMF) inside wheat (Triticum aestivum L.) roots. AMF communities were characterized using Illumina sequencing of 18S rRNA gene amplicons. We showed that climatic conditions and agricultural practices significantly altered total AMF community composition. Conventional farming significantly affected the AMF community and caused a decline in AMF richness. Factors shaping AMF community composition and richness at family level differed greatly among Glomeraceae, Gigasporaceae and Diversisporaceae. An interactive impact of climate and agricultural practices was detected in the community composition of Diversisporaceae. Organic farming mitigated the negative effect of future climate and promoted total AMF and Gigasporaceae richness. AMF richness was significantly linked with nutrient content of wheat grains under both agricultural practices.
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http://dx.doi.org/10.1111/1462-2920.15492DOI Listing
March 2021

The multidimensionality of soil macroecology.

Glob Ecol Biogeogr 2021 Jan 11;30(1):4-10. Epub 2020 Nov 11.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.

The recent past has seen a tremendous surge in soil macroecological studies and new insights into the global drivers of one-quarter of the biodiversity of the Earth. Building on these important developments, a recent paper in outlined promising methods and approaches to advance soil macroecology. Among other recommendations, White and colleagues introduced the concept of a spatial three-dimensionality in soil macroecology by considering the different spheres of influence and scales, as soil organism size ranges vary from bacteria to macro- and megafauna. Here, we extend this concept by discussing three additional dimensions (biological, physical, and societal) that are crucial to steer soil macroecology from pattern description towards better mechanistic understanding. In our view, these are the requirements to establish it as a predictive science that can inform policy about relevant nature and management conservation actions. We highlight the need to explore temporal dynamics of soil biodiversity and functions across multiple temporal scales, integrating different facets of biodiversity (i.e., variability in body size, life-history traits, species identities, and groups of taxa) and their relationships to multiple ecosystem functions, in addition to the feedback effects between humans and soil biodiversity. We also argue that future research needs to consider effective soil conservation policy and management in combination with higher awareness of the contributions of soil-based nature's contributions to people. To verify causal relationships, soil macroecology should be paired with local and globally distributed experiments. The present paper expands the multidimensional perspective on soil macroecology to guide future research contents and funding. We recommend considering these multiple dimensions in projected global soil biodiversity monitoring initiatives.
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http://dx.doi.org/10.1111/geb.13211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116881PMC
January 2021

Soil Texture, Sampling Depth and Root Hairs Shape the Structure of ACC Deaminase Bacterial Community Composition in Maize Rhizosphere.

Front Microbiol 2021 4;12:616828. Epub 2021 Feb 4.

Helmholtz Centre for Environmental Research, Halle, Germany.

Preservation of the phytostimulatory functions of plant growth-promoting bacteria relies on the adaptation of their community to the rhizosphere environment. Here, an amplicon sequencing approach was implemented to specifically target microorganisms with 1-aminocyclopropane-1-carboxylate deaminase activity, carrying the gene. We stated the hypothesis that the relative phylogenetic distribution of carrying microorganisms is affected by the presence or absence of root hairs, soil type, and depth. To this end, a standardized soil column experiment was conducted with maize wild type and root hair defective mutant in the substrates loam and sand, and harvest was implemented from three depths. Most sequences (99%) were affiliated to Actinobacteria and Proteobacteria, and the strongest influence on the relative abundances of sequences were exerted by the substrate. , and sequences dominated in loam, whereas and were more abundant in sand. Soil depth caused strong variations in sequence distribution, with differential levels in the relative abundances of sequences affiliated to , and in loam, but , , and in sand. Maize genotype influenced the distribution of sequences mainly in loam and only in the uppermost depth. Variovorax sequences were more abundant in WT, but , and in rhizosphere. Substrate and soil depth were strong and plant genotype a further significant single and interacting drivers of carrying microbial community composition in the rhizosphere of maize. This suggests that maize rhizosphere carrying bacterial community establishes according to the environmental constraints, and that root hairs possess a minor but significant impact on carrying bacterial populations.
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http://dx.doi.org/10.3389/fmicb.2021.616828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7891401PMC
February 2021

Targeting the Active Rhizosphere Microbiome of in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link.

Front Microbiol 2021 1;12:629169. Epub 2021 Feb 1.

Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.

The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of . Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.
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http://dx.doi.org/10.3389/fmicb.2021.629169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7882529PMC
February 2021

Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect.

Environ Microbiol 2021 Apr 24;23(4):2274-2292. Epub 2021 Feb 24.

Department Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle, Germany.

Tree root-associated microbiomes are shaped by geographic, soil physico-chemical, and host tree parameters. However, their respective impacts on microbiome variations in soils across larger spatial scales remain weakly studied. We out-planted saplings of oak clone DF159 (Quercus robur L.) as phytometer in four grassland field sites along a European North-South transect. After four years, we first compared the soil microbiomes of the tree root zone (RZ) and the tree root-free zone (RFZ). Then, we separately considered the total microbiomes of both zones, besides the microbiome with significant affinity to the RZ and compared their variability along the transect. Variations within the microbiome of the tree RFZ were shaped by geographic and soil physico-chemical changes, whereby bacteria responded more than fungi. Variations within both microbiomes of the tree RZ depended on the host tree and abiotic parameters. Based on perMANOVA and Mantel correlation tests, impacts of site specificities and geographic distance strongly decreased for the tree RZ affine microbiome. This pattern was more pronounced for fungi than bacteria. Shaping the microbiome of the soil zones in root proximity might be a mechanism mediating the acclimation of oaks to a wide range of environmental conditions across geographic regions.
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http://dx.doi.org/10.1111/1462-2920.15433DOI Listing
April 2021

Amplicon Sequencing-Based Bipartite Network Analysis Confirms a High Degree of Specialization and Modularity for Fungi and Prokaryotes in Deadwood.

mSphere 2021 01 13;6(1). Epub 2021 Jan 13.

Institute for National and International Plant Health, Julius Kühn-Institut, Braunschweig, Germany.

Fungi and prokaryotes are dominant colonizers of wood and mediate its decomposition. Much progress has been achieved to unravel these communities and link them to specific wood properties. However, comparative studies considering both groups of organisms and assessing their relationships to wood resources are largely missing. Bipartite interaction networks provide an opportunity to investigate this colonizer-resource relationship more in detail and aim to directly compare results between different biotic groups. The main questions were as follows. Are network structures reflecting the trophic relationship between fungal and prokaryotic colonizers and their resources? If so, do they reflect the critical role of these groups, especially that of fungi, during decomposition? We used amplicon sequencing data to analyze fungal and prokaryotic interaction networks from deadwood of 13 temperate tree species at an early to middle stage of decomposition. Several diversity- and specialization-related indices were determined and the observed network structures were related to intrinsic wood traits. We hypothesized nonrandom bipartite networks for both groups and a higher degree of specialization for fungi, as they are the key players in wood decomposition. The results reveal highly modular and specialized interaction networks for both groups of organisms, demonstrating that many fungi and prokaryotes are resource-specific colonizers. However, as the level of specialization of fungi significantly surpassed that of prokaryotes, our findings reflect the strong association between fungi and their host. Our novel approach shows that the application of bipartite interaction networks is a useful tool to explore, quantify, and compare the deadwood-colonizers relationship based on sequencing data. Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling. The aim of this study was to explore and quantify the relationship between these two main wood-inhabiting organism groups and their corresponding host trees. Two independent DNA-based amplicon sequencing data sets (fungi and prokaryotes) were analyzed via bipartite interaction networks. The links in the networks represent the interactions between the deadwood colonizers and their deadwood hosts. The networks allowed us to analyze whether many colonizing species interact mostly with a restricted number of deadwood tree species, so-called specialization. Our results demonstrate that many prokaryotes and fungi are resource-specific colonizers. The direct comparison between both groups revealed significantly higher specialization values for fungi, emphasizing their strong association to respective host trees, which reflects their dominant role in exploiting this resource.
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http://dx.doi.org/10.1128/mSphere.00856-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7845612PMC
January 2021

Fungal guilds and soil functionality respond to tree community traits rather than to tree diversity in European forests.

Mol Ecol 2021 01 14;30(2):572-591. Epub 2020 Dec 14.

Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Germany.

At the global scale, most forest research on biodiversity focuses on aboveground organisms. However, understanding the structural associations between aboveground and belowground communities provides relevant information about important functions linked to biogeochemical cycles. Microorganisms such as soil fungi are known to be closely coupled to the dominant tree vegetation, and we hypothesize that tree traits affect fungal guilds and soil functionality in multiple ways. By analysing fungal diversity of 64 plots from four European forest types using Illumina DNA sequencing, we show that soil fungal communities respond to tree community traits rather than to tree species diversity. To explain changes in fungal community structure and measured soil enzymatic activities, we used a trait-based ecological approach and community-weighted means of tree traits to define 'fast' (acquisitive) versus 'slow' (conservative) tree communities. We found specific tree trait effects on different soil fungal guilds and soil enzymatic activities: tree traits associated with litter and absorptive roots correlated with fungal, especially pathogen diversity, and influenced community composition of soil fungi. Relative abundance of the symbiotrophic and saprotrophic guilds mirrored the litter quality, while the root traits of fast tree communities enhanced symbiotrophic abundance. We found that forest types of higher latitudes, which are dominated by fast tree communities, correlated with high carbon-cycling enzymatic activities. In contrast, Mediterranean forests with slow tree communities showed high enzymatic activities related to nitrogen and phosphorous. Our findings highlight that tree trait effects of either 'fast' or 'slow' tree communities drive different fungal guilds and influence biogeochemical cycles.
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http://dx.doi.org/10.1111/mec.15749DOI Listing
January 2021

Land-use intensity alters networks between biodiversity, ecosystem functions, and services.

Proc Natl Acad Sci U S A 2020 11 22;117(45):28140-28149. Epub 2020 Oct 22.

Institute of Geography and Geoecology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.

Land-use intensification can increase provisioning ecosystem services, such as food and timber production, but it also drives changes in ecosystem functioning and biodiversity loss, which may ultimately compromise human wellbeing. To understand how changes in land-use intensity affect the relationships between biodiversity, ecosystem functions, and services, we built networks from correlations between the species richness of 16 trophic groups, 10 ecosystem functions, and 15 ecosystem services. We evaluated how the properties of these networks varied across land-use intensity gradients for 150 forests and 150 grasslands. Land-use intensity significantly affected network structure in both habitats. Changes in connectance were larger in forests, while changes in modularity and evenness were more evident in grasslands. Our results show that increasing land-use intensity leads to more homogeneous networks with less integration within modules in both habitats, driven by the belowground compartment in grasslands, while forest responses to land management were more complex. Land-use intensity strongly altered hub identity and module composition in both habitats, showing that the positive correlations of provisioning services with biodiversity and ecosystem functions found at low land-use intensity levels, decline at higher intensity levels. Our approach provides a comprehensive view of the relationships between multiple components of biodiversity, ecosystem functions, and ecosystem services and how they respond to land use. This can be used to identify overall changes in the ecosystem, to derive mechanistic hypotheses, and it can be readily applied to further global change drivers.
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http://dx.doi.org/10.1073/pnas.2016210117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668166PMC
November 2020

Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils.

Environ Microbiol 2021 Apr 12;23(4):1889-1906. Epub 2020 Oct 12.

Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany.

Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.
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http://dx.doi.org/10.1111/1462-2920.15244DOI Listing
April 2021

Blind spots in global soil biodiversity and ecosystem function research.

Nat Commun 2020 08 3;11(1):3870. Epub 2020 Aug 3.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.

Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
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http://dx.doi.org/10.1038/s41467-020-17688-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400591PMC
August 2020

Future Climate Significantly Alters Fungal Plant Pathogen Dynamics during the Early Phase of Wheat Litter Decomposition.

Microorganisms 2020 Jun 16;8(6). Epub 2020 Jun 16.

Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany.

Returning wheat residues to the soil is a common practice in modern agricultural systems and is considered to be a sustainable practice. However, the negative contribution of these residues in the form of "residue-borne pathogens" is recognized. Here, we aimed to investigate the structure and ecological functions of fungal communities colonizing wheat residues during the early phase of decomposition in a conventional farming system. The experiment was conducted under both ambient conditions and a future climate scenario expected in 50-70 years from now. Using MiSeq Illumina sequencing of the fungal internal transcribed spacer 2 (ITS2), we found that plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome. Destructive wheat fungal pathogens such as , and were detected under ambient and future climates. Moreover, future climate enhanced the appearance of new plant pathogenic fungi in the plant residues. Our results based on the bromodeoxyuridine (BrdU) immunocapture technique demonstrated that almost all detected pathogens are active at the early stage of decomposition under both climate scenarios. In addition, future climate significantly changed both the richness patterns and the community dynamics of the total, plant pathogenic and saprotrophic fungi in wheat residues as compared with the current ambient climate. We conclude that the return of wheat residues can increase the pathogen load, and therefore have negative consequences for wheat production in the future.
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http://dx.doi.org/10.3390/microorganisms8060908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356542PMC
June 2020

Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi.

BMC Genomics 2020 Jun 12;21(1):399. Epub 2020 Jun 12.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany.

Background: Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis.

Results: The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed.

Conclusions: Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.
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http://dx.doi.org/10.1186/s12864-020-06806-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291512PMC
June 2020

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact.

Front Microbiol 2020 23;11:749. Epub 2020 Apr 23.

Department of Soil Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle, Germany.

Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings ( L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.
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http://dx.doi.org/10.3389/fmicb.2020.00749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190799PMC
April 2020

Diversity and geographic distribution of soil streptomycetes with antagonistic potential against actinomycetoma-causing Streptomyces sudanensis in Sudan and South Sudan.

BMC Microbiol 2020 02 12;20(1):33. Epub 2020 Feb 12.

Department of Soil Ecology, Helmholtz-Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Str. 4, 06120, Halle, Germany.

Background: Production of antibiotics to inhibit competitors affects soil microbial community composition and contributes to disease suppression. In this work, we characterized whether Streptomyces bacteria, prolific antibiotics producers, inhibit a soil borne human pathogenic microorganism, Streptomyces sudanensis. S. sudanensis represents the major causal agent of actinomycetoma - a largely under-studied and dreadful subcutaneous disease of humans in the tropics and subtropics. The objective of this study was to evaluate the in vitro S. sudanensis inhibitory potential of soil streptomycetes isolated from different sites in Sudan, including areas with frequent (mycetoma belt) and rare actinomycetoma cases of illness.

Results: Using selective media, 173 Streptomyces isolates were recovered from 17 sites representing three ecoregions and different vegetation and ecological subdivisions in Sudan. In total, 115 strains of the 173 (66.5%) displayed antagonism against S. sudanensis with different levels of inhibition. Strains isolated from the South Saharan steppe and woodlands ecoregion (Northern Sudan) exhibited higher inhibitory potential than those strains isolated from the East Sudanian savanna ecoregion located in the south and southeastern Sudan, or the strains isolated from the Sahelian Acacia savanna ecoregion located in central and western Sudan. According to 16S rRNA gene sequence analysis, isolates were predominantly related to Streptomyces werraensis, S. enissocaesilis, S. griseostramineus and S. prasinosporus. Three clusters of isolates were related to strains that have previously been isolated from human and animal actinomycetoma cases: SD524 (Streptomyces sp. subclade 6), SD528 (Streptomyces griseostramineus) and SD552 (Streptomyces werraensis).

Conclusion: The in vitro inhibitory potential against S. sudanensis was proven for more than half of the soil streptomycetes isolates in this study and this potential may contribute to suppressing the abundance and virulence of S. sudanensis. The streptomycetes isolated from the mycetoma free South Saharan steppe ecoregion show the highest average inhibitory potential. Further analyses suggest that mainly soil properties and rainfall modulate the structure and function of Streptomyces species, including their antagonistic activity against S. sudanensis.
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http://dx.doi.org/10.1186/s12866-020-1717-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017484PMC
February 2020

Shifts Between and Among Populations of Wheat Rhizosphere , and Suggest Consistent Phosphate Mobilization at Different Wheat Growth Stages Under Abiotic Stress.

Front Microbiol 2019 22;10:3109. Epub 2020 Jan 22.

Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany.

Climate change models predict more frequent and prolonged drought events in Central Europe, which will exert extraordinary pressure on agroecosystems. One of the consequences is drought-related nutrient limitations for crops negatively affecting agricultural productivity. These effects can be mitigated by beneficial plant growth promoting rhizobacteria. In this study, we investigated the potential of cultivable bacterial species for phosphate solubilization in the rhizosphere of winter wheat at two relevant growth stages - stem elongation and grain filling stages. Rhizosphere samples were collected in the Global Change Experimental Facility in Central Germany, which comprises plots with conventional and organic farming systems under ambient and future climate. Phosphate-solubilizing bacteria were selectively isolated on Pikovskaya medium, phylogenetically classified by sequencing, and tested for mineral phosphate solubilization and drought tolerance using plate assays. The culture isolates were dominated by members of the genera and Cultivation-derived species richness and abundance of dominant taxa, especially within the genera and , as well as composition of species were affected by wheat growth stage. was found to be more abundant at stem elongation than at grain filling, while for the opposite pattern was observed. The abundance of isolates remained stable throughout the studied growth stages. The temporal shifts in the cultivable fraction of the community along with considerable P solubilization potentials of and species suggest functional redundancy between and among genera at different wheat growth stages. Phosphate-solubilizing species were assigned to and It is the first time that phosphate solubilization potential is described for these species. Since species showed the highest drought tolerance along all isolates, they may play an increasingly important role in phosphate solubilization in a future dryer climate.
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http://dx.doi.org/10.3389/fmicb.2019.03109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6987145PMC
January 2020

Early stage root-Associated fungi show a high temporal turnover, but Are independent of beech progeny.

Microorganisms 2020 Feb 4;8(2). Epub 2020 Feb 4.

UFZ-Helmholtz-Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Straße 4, 06120 Halle (Saale), Germany.

The relationship between trees and root-associated fungal communities is complex. By specific root deposits and other signal cues, different tree species are able to attract divergent sets of fungal species. Plant intraspecific differences can lead to variable fungal patterns in the root's proximity. Therefore, within the , we analyzed the impact of three different European beech ecotypes on the fungal communities in roots and the surrounding rhizosphere soil at two time points. Beech nuts were collected in three German sites in 2011. After one year, seedlings of the different progenies were out-planted on one site and eventually re-sampled in 2014 and 2017. We applied high-throughput sequencing of the fungal ITS2 to determine the correlation between tree progeny, a possible home-field advantage, plant development and root-associated fungal guilds under field conditions. Our result showed no effect of beech progeny on either fungal OTU richness or fungal community structure. However, over time the fungal OTU richness in roots increased and the fungal communities changed significantly, also in rhizosphere. In both plant compartments, the fungal communities displayed a high temporal turnover, indicating a permanent development and functional adaption of the root mycobiome of young beeches.
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http://dx.doi.org/10.3390/microorganisms8020210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074820PMC
February 2020

Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use.

Genes (Basel) 2020 01 30;11(2). Epub 2020 Jan 30.

Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, Germany.

Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene as well as the sulfonamide resistance gene was positively correlated with organic fertilization and the abundance of , conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except and , the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.
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http://dx.doi.org/10.3390/genes11020150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073645PMC
January 2020

Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems.

Sci Rep 2020 01 22;10(1):919. Epub 2020 Jan 22.

UFZ - Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Straße 4, 06120, Halle/Saale, Germany.

Plants are known to modulate their own rhizosphere mycobiome. However, field studies that use resident plants to relate the microbiome assemblage to environmental factors such as land-use suffer from the problem that confounding factors such as plant age and performance may override the targeted effects. In contrast, the use of even-aged phytometer plants pre-cultivated under uniform conditions helps to reduce such random variation. We investigated the rhizosphere mycobiomes of phytometer and resident plants of two common grassland species, Dactylis glomerata L. s. str. and Plantago lanceolata L. along a land-use intensity gradient using ITS rRNA Illumina amplicon sequencing. Remarkably, we did not detect effects of the plant types (resident vs. phytometer plant, even though some fungal taxa exhibited plant species specificity), indicating that phytometer plants hosted a comparable rhizosphere mycobiome as resident plants. Our data indicate that the plant species harbor distinct fungal communities, with fungal richness in the rhizosphere of P. lanceolata being substantially higher than that of D. glomerata. Land-use intensity had a clear impact on the mycobiome of both plant species, with specific fungal genera showing differential tolerance to high intensities. Overall, the phytometer approach has a high potential to reveal environmental impacts on rhizosphere communities.
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http://dx.doi.org/10.1038/s41598-020-57760-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976665PMC
January 2020

A multitrophic perspective on biodiversity-ecosystem functioning research.

Adv Ecol Res 2019 23;61:1-54. Epub 2019 Jul 23.

Department of Biology, Marquette University, Milwaukee, WI USA.

Concern about the functional consequences of unprecedented loss in biodiversity has prompted biodiversity-ecosystem functioning (BEF) research to become one of the most active fields of ecological research in the past 25 years. Hundreds of experiments have manipulated biodiversity as an independent variable and found compelling support that the functioning of ecosystems increases with the diversity of their ecological communities. This research has also identified some of the mechanisms underlying BEF relationships, some context-dependencies of the strength of relationships, as well as implications for various ecosystem services that mankind depends upon. In this paper, we argue that a multitrophic perspective of biotic interactions in random and non-random biodiversity change scenarios is key to advance future BEF research and to address some of its most important remaining challenges. We discuss that the study and the quantification of multitrophic interactions in space and time facilitates scaling up from small-scale biodiversity manipulations and ecosystem function assessments to management-relevant spatial scales across ecosystem boundaries. We specifically consider multitrophic conceptual frameworks to understand and predict the context-dependency of BEF relationships. Moreover, we highlight the importance of the eco-evolutionary underpinnings of multitrophic BEF relationships. We outline that FAIR data (meeting the standards of findability, accessibility, interoperability, and reusability) and reproducible processing will be key to advance this field of research by making it more integrative. Finally, we show how these BEF insights may be implemented for ecosystem management, society, and policy. Given that human well-being critically depends on the multiple services provided by diverse, multitrophic communities, integrating the approaches of evolutionary ecology, community ecology, and ecosystem ecology in future BEF research will be key to refine conservation targets and develop sustainable management strategies.
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http://dx.doi.org/10.1016/bs.aecr.2019.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944504PMC
July 2019

First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments.

Microorganisms 2019 Nov 20;7(12). Epub 2019 Nov 20.

Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, 06120 Halle(Saale), Germany.

Mangrove forest trees play important ecological functions at the interface between terrestrial and marine ecosystems. However, despite playing crucial roles in plant health and productivity, there is little information on microbiomes of the tree species in mangrove ecosystems. Thus, in this study we aimed to characterize the microbiome in soil (rhizosphere) and plant (root, stem, and leaf endosphere) compartments of the widely distributed mangrove tree . Surprisingly, bacterial operational taxonomic units (OTUs) were only confidently detected in rhizosphere soil, while fungal OTUs were detected in all soil and plant compartments. The major detected bacterial phyla were affiliated to Proteobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Several nitrogen-fixing bacterial OTUs were detected, and the presence of nitrogen-fixing bacteria was confirmed by gene based-PCR in all rhizosphere soil samples, indicating their involvement in N acquisition in the focal mangrove ecosystem. We detected taxonomically (54 families, 83 genera) and functionally diverse fungi in the mycobiome. Ascomycota (mainly Dothideomycetes, Eurotiomycetes, Sordariomycetes) were most diverse in the mycobiome, accounting for 86% of total detected fungal OTUs. We found significant differences in fungal taxonomic and functional community composition among the soil and plant compartments. We also detected significant differences in fungal OTU richness ( < 0.002) and community composition ( < 0.001) among plant compartments. The results provide the first information on the microbiome of rhizosphere soil to leaf compartments of mangrove trees and associated indications of ecological functions in mangrove ecosystems.
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http://dx.doi.org/10.3390/microorganisms7120585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955992PMC
November 2019

Linking Soil Fungal Generality to Tree Richness in Young Subtropical Chinese Forests.

Microorganisms 2019 Nov 10;7(11). Epub 2019 Nov 10.

Helmholtz-Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Straße 4, 06120 Halle, Germany.

Soil fungi are a highly diverse group of microorganisms that provide many ecosystem services. The mechanisms of soil fungal community assembly must therefore be understood to reliably predict how global changes such as climate warming and biodiversity loss will affect ecosystem functioning. To this end, we assessed fungal communities in experimental subtropical forests by pyrosequencing of the internal transcribed spacer 2 (ITS2) region, and constructed tree-fungal bipartite networks based on the co-occurrence of fungal operational taxonomic units (OTUs) and tree species. The characteristics of the networks and the observed degree of fungal specialization were then analyzed in relation to the level of tree species diversity. Unexpectedly, plots containing two tree species had higher and values than those with higher tree diversity. Most of the frequent fungal OTUs were saprotrophs. The degree of fungal specialization was highest in tree monocultures. Ectomycorrhizal fungi had higher specialization coefficients than saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi. High tree species diversity plots with 4 to 16 different tree species sustained the greatest number of fungal species, which is assumed to be beneficial for ecosystem services because it leads to more effective resource exploitation and greater resilience due to functional redundancy.
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http://dx.doi.org/10.3390/microorganisms7110547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6921041PMC
November 2019

DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors.

Microorganisms 2019 Sep 11;7(9). Epub 2019 Sep 11.

Helmholtz Centre for Environmental Research-UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany.

Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the "total" and "active" fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the "total" and "active" fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%-40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems.
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http://dx.doi.org/10.3390/microorganisms7090341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780912PMC
September 2019

Potential links between wood-inhabiting and soil fungal communities: Evidence from high-throughput sequencing.

Microbiologyopen 2019 09 27;8(9):e00856. Epub 2019 May 27.

Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.

Wood-inhabiting fungi (WIF) are pivotal to wood decomposition, which in turn strongly influences nutrient dynamics in forest soils. However, their dispersal mechanisms remain unclear. We hypothesized that the majority of WIF are soil-borne. For this reason, the presented research aimed to quantify the contribution of soil as a source and medium for the dispersal of WIF to deadwood using high-throughput sequencing. We tested effects of tree species (specifically Schima superba and Pinus massoniana) on the percentage of WIF shared between soil and deadwood in a Chinese subtropical forest ecosystem. We also assessed the taxonomic and ecological functional group affiliations of the fungal community shared between soil and deadwood. Our results indicate that soil is a major route for WIF colonization as 12%-15% (depending on the tree species) of soil fungi were simultaneously detected in deadwood. We also demonstrate that tree species (p < 0.01) significantly shapes the composition of the shared soil and deadwood fungal community. The pH of decomposing wood was shown to significantly correspond (p < 0.01) with the shared community of wood-inhabiting (of both studied tree species) and soil fungi. Furthermore, our data suggest that a wide range of fungal taxonomic (Rozellida, Zygomycota, Ascomycota, and Basidiomycota) and ecological functional groups (saprotrophs, ectomycorrhizal, mycoparasites, and plant pathogens) may use soil as a source and medium for transport to deadwood in subtropical forest ecosystem. While 12%-62% of saprotrophic, ectomycorrhizal, and mycoparasitic WIF may utilize soil to colonize deadwood, only 5% of the detected plant pathogens were detected in both soil and deadwood, implying that these fungi use other dispersal routes. Animal endosymbionts and lichenized WIF were not detected in the soil samples. Future studies should consider assessing the relative contributions of other possible dispersal mechanisms (e.g. wind, water splash, water dispersal, animal dispersal, and mycelial network) in the colonization of deadwood by soil fungi.
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http://dx.doi.org/10.1002/mbo3.856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6741142PMC
September 2019

Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot.

Environ Microbiol 2020 03 27;22(3):873-888. Epub 2019 Jun 27.

Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Straße 4, 06120, Halle (Saale), Germany.

Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha- and beta-diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta-diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome.
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http://dx.doi.org/10.1111/1462-2920.14653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7065148PMC
March 2020