#Microorganisms & Fungi #2017 – 2020 #Fungi #Sequencing #Interaction #Genetic diversity #Mycorrhiza fungi #Species biodiversity #Archaea #Bacteria #Plant - fungus interaction #Soil microorganisms #Functional diversity #Microbial community #Nitrogen cycle #Forest #Land use #Species communities #Soil organisms #Soil sample

Microorganisms (Core project)

Species diversity and community composition of soil microorganisms in grassland and forest ecosystems along land use gradients

Core project 8

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, especially fungi and bacteria, play an essential role in soil, including as destructors in the decomposition of organic matter and as symbionts for the growth and health of plant partners. In addition to these interactions with plants, soil microorganisms are influenced by environmental changes such as land use and forest management. However, the degree to which individual factors affect microbial diversity and composition is not yet fully understood.

Hypotheses

The main task of the Core Project Microorganisms is the collection and monitoring, especially of the fungal community, on all 300 grassland and forest experimental plots (EPs). In addition to coordinated sampling in May 2011 and 2014, the core project will also be responsible for organising the sampling of all 100 EPs of the Hainich exploratory in 2017.

Furthermore, synthesis activities are taking place between the core project and various projects: e.g., with Norbert Hölzel, University of Münster or Ellen Kandeler and Sven Marhan, University of Hohenheim.

Picture: The photo shows a meadow on which three objects are standing and lying: first, a bucket with small stones in it; second, a yellow bowl containing soil samples with a folding ruler lying on its corner; and third, a clipboard with a form on which a pencil and a knife lie.

Goals

The objectives in the phase (2017-2020) are:

1. Monitoring of soil microorganisms to determine temporal effects of land use and forest management (soil samples from 2011, 2014 and 2017).
2. Record the diversity of arbuscular mycorrhizal fungi (AMF) in all EPs.
3. Study the influence of topsoil disturbance and additional seed placement on the adaptability of soil microorganisms in grasslands (SADE).
4. Analysis of the fungal community under different land use intensity and disturbance within one year (TIMEMIC).

Methods

DNA extraction and quantification from soil, creation of a fungal amplicon library and next-generation sequencing with the Illumina MiSeq platform, bioinformatics (MOTHUR & QIIME) and multivariate statistics.

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

Datasets

Non-public datasets

16S rRNA gene (V3 region) DNA-based analysis of bacterial soil communities at sequence variant level in all reduced land-use intensity experiment (REX) and land-use experiment (LUX) plots, using QIIME2-based bioinformatics, 2021

Overmann, Jörg; Vieira, Selma (2024): 16S rRNA gene (V3 region) DNA-based analysis of bacterial soil communities at sequence variant level in all reduced land-use intensity experiment (REX) and land-use experiment (LUX) plots, using QIIME2-based bioinformatics, 2021. Version 4. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de. Dataset ID= 31936

Forest Gap Experiment (FOX): DNA-based analysis of soil fungal communities (Illumina MiSeq) – ASV abundances

Buscot, Francois; Goldmann, Kezia (2024): Forest Gap Experiment (FOX): DNA-based analysis of soil fungal communities (Illumina MiSeq) - ASV abundances. Version 7. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de. Dataset ID= 31838

Forest Gap Experiment (FOX): DNA-based analysis of soil fungal communities (Illumina MiSeq) – ASV taxonomic look-up table

Buscot, Francois; Goldmann, Kezia (2024): Forest Gap Experiment (FOX): DNA-based analysis of soil fungal communities (Illumina MiSeq) - ASV taxonomic look-up table. Version 5. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de. Dataset ID= 31839

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.