#Microorganisms & Fungi #BEF #Soil Ecology #REX/LUX #FOX #2023 – 2026 #2020 – 2023 #Species biodiversity #Bacteria #Soil microorganisms #Functional diversity #Microbial community #Nitrogen cycle #Land use #Species communities #Fungi #Sequencing #Genetic diversity #Mycorrhiza fungi #Archaea #Mikrobiom

Microorganisms (Core project)

Soil microbial diversity and community composition of grassland and forest ecosystems along land-use gradients

Core project 8

Living organisms that are smaller than 50µm are classified as microorganisms. These include bacteria, archaea, fungi, but also unicellular smaller eukaryotes such as protists.

Picture: The collage contains six photographs of steps in molecular analyses in a laboratory, performed by a scientist. Photo 1 shows a sample standardization device. Photo 2 shows the scientist working on a polymerase chain reaction device. Photo 3 shows the scientist using an electronic pipette to fill a sample into a micro-reaction tube. Photo 4 shows an Illumina MiSeq sequencer. Photo 5 shows the scientist working on a bioinformatics quality control device. Photo 6 shows the scientist at a desk in front of a computer making inputs for assignment.

Background

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.

Goals

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.

Picture: The photo shows a core drill stick lying on a forest floor and next to it the removed inner container, which is half open lengthwise and contains the drill core. Above the container one can see the gloved hands of a scientist shortly before the core is removed. To the right of the scientist is a transparent sample bag

Impressions of the joint soil sampling in the Hainich-Dün, May 2017

Picture: The photograph shows a deserted room lit by a fluorescent tube on the ceiling. on the left in the background against the wall are canisters, gas bottles, sieves and rucksacks. directly next to it is an open passage to a courtyard. on the right in the background are ladders against the wall. next to them can be seen a metal cupboard and three tall refrigerators or freezers, two of them out of order. in the middle of the room are two long folding tables with wooden table tops. in front of one table is a wheelbarrow, in front of the other a bench. on both tables are various working materials as well as transparent bags with samples in them. in the foreground of the picture can be seen on a table on the left a large heap of bags with samples in them.

Zero sampling of the forest gap experiment (FOX) in December 2019 at the Schorfheide-Chorin exploratory

Services

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).

Results

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).

Publications

The influence of forest gaps and their subsequent closure on the diversity of soil fungi

Der Einfluss von Waldlücken auf Bodenpilze

Wöltjen J. (2023): The influence of forest gaps and their subsequent closure on the diversity of soil fungi. Master thesis, University Koblenz-Landau

Influence of land use on the temporal dynamics of fungal communities across the German Biodiversity Exploratories (BE)

Einfluss von Landnutzung auf die zeitlichen Dynamiken von Bodenpilze in den Deutschen Biodiversitätexploratorien (BE)

Rivera Cerquera D. F. (2023): Influence of land use on the temporal dynamics of fungal communities across the German Biodiversity Exploratories (BE). Bachelor thesis, University of Leipzig

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

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

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

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

Early stage root-associated fungi show a high temporal turnover, but are independent of beech progeny

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

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

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

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

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

Land-use intensity rather than plant functional identity shapes bacterial and fungal rhizosphere communities

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

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

Preservation of nucleic acids by freeze-drying for next generation sequencing analyses of soil microbial communities

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

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.