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Microorganisms (i.e. Archaea, Bacteria and Fungi) represent the dominant life forms in soil both in terms of biomass and biodiversity and build complex functional interaction networks. These microbial communities are therefore often referred to as “soil microbiome”. They provide important ecosystem services, such as soil formation, element cycling, plant nutrition, detoxification, as well as the exchange of gas and matter with atmosphere and ground water. These key roles rely on complex trans-kingdom interactions between the soil microorganisms themselves but also between microorganisms and the below and aboveground plant and animal communities.

In addition to site-specific properties such as soil type and local climate, the types of land use and land use intensity can also be important drivers of soil microbial diversity. So far, the functional relationships between environmental factors and microbial diversity in soil are not sufficiently understood.

Thanks to the development of high throughput sequencing and powerful bioinformatics methods, it has become possible to analyse the biodiversity of soil microorganisms at large scales. Since the start of the Biodiversity Exploratories in 2006, Core project 8 has been in charge of monitoring the biodiversity of soil microorganisms.

While the initial focus was on soil and arbuscular mycorrhizal fungi, Core 8 in its current phase encompasses the study of all relevant microorganisms, including fungi, bacteria and archaea.


The main objectives of the Microorganisms Core Project are:

  • Organization of coordinated soil sampling campaigns (in cooperation with Core project 9). The next campaign is planned for spring 2023.
  • Long-term archive of soil samples und extracted nucleic acids.
  • Long term monitoring on biodiversity of soil bacteria, archaea and fungi in all 300 EPs as well as in the newly established field experiments (FOX, REX I+II, LUX).
  • Identification and characterization of microbial key stone species employing co-occurrence network analyses, followed by selected metagenomics analyses using shot gun sequencing. This will provide better insights into functional microbial diversity.
  • Identification and assessment of the small but functionally relevant proportion of active bacteria, through analysis of rRNA/rDNA ratios. This is of relevance, since the majority of soil bacteria is inactive or dormant and hence does not contribute to ecosystem functions.
  • Establishment of adequate primers and quantification of key organisms using quantitative PCR (qPCR).
  • Functional fingerprinting and reconstruction of microbial genomes from representative grassland areas (metagenomes).
  • Participation in several synthesis activities within the Biodiversity Exploratories community.
  • Interaction and data exchange with projects on an international level.

All core projects provide important basic information on land use, diversity and ecosystem processes (long-term monitoring). These are made available to the sub-projects in each phase for researching more in-depth questions.

Services provided in the current phase

In the 6th phase (2020-2023) the core project 8 provides the following services / basic examinations:

  • Organization, in cooperation with Core project 9, of the coordinated soil sampling campaigns of 2021 (under Corona restrictions) and 2023.
  • Deposit and long-term storage (-80°C) of soil samples from coordinated soil sampling campaigns and new experiments (FOX, REX I+II, LUX) for subsequent analysis. Subsamples can be provided for future work in the contributing projects (targeted at molecular work – small quantities).
  • Standardization of nucleic acid extraction techniques as well as up and downstream bioinformatics after next generation sequencing. Optimized standards can be shared with contributing projects.
  • Extraction and storage of nucleic acids (both DNA and RNA) from all EP plot samples from coordinated soil sampling campaigns and new experiments (FOX, REX I+II, LUX), which can be provided to demanding contributing projects.
  • Provision of diversity data on soil microorganisms (Archaea, Bacteria and Fungi).
  • Sequencing (Illumina, PacBio) for contributing projects.
  • Training and assistance to members of contributing projects on molecular techniques and bioinformatics after next generation sequencing.

Services provided in past phases

  • Provision of diversity data on soil Fungi. We already uploaded lists of amplicon sequence variants (ASVs) or operational taxonomic units (OTUs) of soil and arbuscular mycorrhizal fungi for the sampling campaigns 2011, 2014 and 2017 in all EPs. This data has been used in numerous synthesis publications on the relationship between land use intensity, below and above ground biodiversity and multi-functionality of ecosystems.
  • Provision of DNA extracts from soil samples of coordinated soil sampling campaigns (2008-2017) to all interested contribution projects.
  • Quantification of key organisms using quantitative PCR (qPCR) (2008-2017).

Core 8 data were used to:

  • analyse the distance decay of forest soil microbial communities across Germany and how tree species modulate it in the soil rooting zone (Goldmann et al. 2016. Scientific reports, 6(1), 1-10).
  • unravel the spatiotemporal variability of arbuscular mycorrhizal fungi grasslands (Goldmann et al. 2020. Environmental Microbiology, 22(3), 873-888).
  • unravel the spatiotemporal variability of nitrifying organisms and their interactions (Stempfhuber et al. 2017).
  • reveal that in grasslands, belowground biodiversity reacts opposite to aboveground biodiversity with increase of land use intensity (Goßner et al. 2016. Nature, 540(7632), 266-269).
  • demonstrate that biodiversity at multiple levels is needed for ecosystem multifunctionality (Soliveres et al. 2016. Nature, 536(7617), 456-45) and rare species influence grassland multifunctionality (Soliveres et al. 2016. Nature, 536, 456-459).
  • identify via rRNA/rDNA ratios and analyse the fraction of active soil bacteria and their contribution to soil function (in preparation).

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Goldmann K., Ammerschubert S., Pena R., Polle A., Wu B.-W., Wubet T., Buscot F. (2020): Early stage root-associated fungi show a high temporal turnover, but are independent of beech progeny. Microorganisms 8 (2), 210. doi: 10.3390/microorganisms8020210
More information:  doi.org
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Goldmann K., Boeddinghaus R. S., Klemmer S., Regan K. M., Heintz-Buschart A., Fischer M., Prati D., Piepho H.-P., Berner D., Marhan S., Kandeler E., Buscot F., Wubet T. (2020): Unraveling spatio‐temporal variability of arbuscular mycorrhiza fungi in a temperate grassland plot. Environmental Microbiology 22 (3), 873-888. doi: 10.1111/1462-2920.14653
More information:  doi.org
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Auswirkung von pflanzlichen Nachbarschaftseffekten auf die pilzliche Diversität und Gemeinschaftszusammensetzung in der Rhizosphäre
Lohmaier A. (2018): Auswirkung von pflanzlichen Nachbarschaftseffekten auf die pilzliche Diversität und Gemeinschaftszusammensetzung in der Rhizosphäre. Master thesis, University Halle-Wittenberg
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Der Einfluss von Borkenkäfern (Curculionidae, Scolytinae) auf das Mykobiom der Gemeinen Fichte (Picea abies (L.) H. Karst., Pinaceae) im Biodiversitäts-Exploratorium Hainich-Dün
Masch D. (2020): Der Einfluss von Borkenkäfern (Curculionidae, Scolytinae) auf das Mykobiom der Gemeinen Fichte (Picea abies (L.) H. Karst., Pinaceae) im Biodiversitäts-Exploratorium Hainich-Dün. Bachelor thesis, FU Berlin
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Belowground plant microbiome diversity and community composition in grassland ecosystems along land-use gradients in the German Biodiversity Exploratories
Unterirdische Pflanzenmikrobiomvielfalt und Gemeinschaftszusammensetzung in Grünlandökosystemen entlang von Landnutzungsgradienten in den deutschen Biodiversitäts-Exploratorien
Schöps R. (2020): Belowground plant microbiome diversity and community composition in grassland ecosystems along land-use gradients in the German Biodiversity Exploratories, Dissertation, Leipzig University
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Landnutzungsintsität anstatt von funktionellen Pflanzengruppen beeinflussen die bakterielle und pilzliche Rhizosphärengemeinschaft
Schöps R., Goldmann K., Herz K., Lentendu G., Schöning I., Bruelheide H., Wubet T., Buscot F. (2018): Land-use intensity rather than plant functional identity shapes bacterial and fungal rhizosphere communities. Frontiers in Microbiology 9:2711. doi: 10.3389/fmicb.2018.02711
More information:  doi.org
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Vergleichbare Pilzgemeinschaften in der Rhizosphäre von ansässigen Pflanzen und Phytometerpflanzen in bewirtschafteten Grünlandökosystemen
Schöps R., Goldmann K., Korell L., Bruelheide H., Wubet T., Buscot F. (2020): Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems. Scientific Reports 10: 919. doi: 10.1038/s41598-020-57760-x
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Weißbecker C., Buscot F., Wubet T. (2017): Preservation of nucleic acids by freeze-drying for next generation sequencing analyses of soil microbial communities. Journal of Plant Ecology 10 (1), 81-90. doi: 10.1093/jpe/rtw042
More information:  doi.org
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Verbreitung von medizinisch relevanten Antibiotikaresistenzgenen und mobilen genetischen Elementen in Wald- und Grünlandböden
Willms I. M., Yuan J., Penone C., Goldmann K., Vogt J., Wubet T., Schöning I., Schrumpf M., Buscot F., Nacke H. (2020): Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use. Genes 11 (2), 150. doi: 10.3390/genes11020150
More information:  doi.org

The so-called core projects of the BE emerged from the site selection project and the establishment of the exploratories (2006-2008). Since 2008, they have been providing the infrastructure and collecting important basic information on land use, diversity and ecosystem processes (long-term monitoring) for all projects. In addition, they coordinate project-wide activities such as various large-scale experiments.

Project in other funding periods

Scientific assistants

Prof. Dr. Francois Buscot
Project manager
Prof. Dr. Francois Buscot
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Prof. Dr. Jörg Overmann
Project manager
Prof. Dr. Jörg Overmann
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
Prof. Dr. Michael Schloter
Project manager
Prof. Dr. Michael Schloter
Technische Universität München (TUM)
Dr. Stefanie Schulz
Employee
Dr. Stefanie Schulz
Helmholtz Zentrum München
Dr. Kezia Goldmann
Employee
Dr. Kezia Goldmann
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Dr. Johannes Sikorski
Employee
Dr. Johannes Sikorski
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
Dr. Selma Gomes Vieira
Employee
Dr. Selma Gomes Vieira
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
Julia Kurth
Employee
Julia Kurth
Technische Universität München (TUM)
Luis Daniel Prada Salcedo
Employee
Luis Daniel Prada Salcedo
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Beatrix Schnabel
Employee
Beatrix Schnabel
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Franziska Burkart
Employee
Franziska Burkart
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
Dr. Gisle Alberg Vestergaard
Employee
Dr. Gisle Alberg Vestergaard
Technical University of Denmark
Trine Zachariasen
Employee
Trine Zachariasen
Technical University of Denmark
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