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1. Specific and soil dominant species of acidobacteria and actinobacteria are responsible for the degradation of poorly degradable organic carbon and plant litter.

2. Specifically adapted alphaproteobacteria are a dominant part of the plant rhizosphere and control the food chain of organic carbon from plants to microorganisms.

3. Different types of acidobacteria, actinobacteria and alphaproteobacteria are adapted to different soil conditions.


ProFunD focuses on the study of bacterial species involved in the degradation of root exudates and plant litter in different soil compartments. The aim is to understand the relationship between functional bacterial biodiversity, plant diversity and productivity, soil parameters and land use.

Bacteria account for up to 60-80% of all soil organisms and therefore represent important control points of the biogeochemical nutrient cycle, soil fertility and pest control. The specific composition of the bacterial community therefore controls key ecosystem processes. It has been shown that acidobacteria, actinobacteria and alphaproteobacteria are not randomly distributed in the soil but preferentially colonise different soil compartments. Differences in bacterial community composition drive organic carbon sequestration, nutrient regeneration and the bacterial food chain. Nevertheless, the distribution of different species of these bacterial groups, their influence by biotic and abiotic parameters, and the functional consequences of these parameters on nutrient cycling is still under-researched.

In this project we will examine the partitioning of active members of Acidobacteria, Actinobacteria and Alphaproteobacteria between the rhizosphere of different dominant plant species and the surrounding soil particles, as well as the function of these dominant groups on carbon cycling under different ecological conditions.

  • We will look at the spatial distribution of Acidobacteria, Actinobacteria and Alphaproteobacteria between rhizosphere and soil particles at the taxonomic level of species using Illumina high-throughput sequencing of 16S rRNA and correlate species abundances with the specific composition of plant exudates, other plant properties, soil physicochemical parameters and land-use gradients.
  • We will analyse the contribution of different bacteria to carbon and nitrogen transfer from plant roots (respectively plant litter) to soil in functional mesocosms. To do this, we will use a combination of different isotope labels in techniques such as 13C/ 15N-RNA Stable Isotope Probing (SIP) and 13C-RNA Captured RNA Isotope Probing (CARIP).
  • In addition, we will determine the relative abundance of Acidobacteria, Actinobacteria and Alphaproteobacteria at different taxonomic resolution levels (species, genus, family, order, class, phylum) using Illumina high-throughput sequencing of 16S rRNA. This will provide a deeper understanding of the relationship between bacterial diversity, functional bacterial biodiversity, plant diversity and productivity, soil parameters and land use.

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Die erste vollständige Genomsequenz eines Subgruppe 6 Acidobacteriums
Huang S., Vieira V., Bunk B., Riedel T., Spröer C., Overmann J. (2016): First Complete Genome Sequence of a Subdivision 6 Acidobacterium. Genome Announcements 4(3):e00469-16. doi: 10.1128/genomeA.00469-16
More information:  doi.org
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Wie verändern sich bakterielle Gemeinschaften auf verwesenden Tierkadavern und welche mögliche Auswirkung auf das Ökosystem hat dies?
Pascual J., von Hoermann C., Rottler-Hoermann A.-M., Nevo O., Geppert A., Sikorski J., Huber K. J. , Steiger S., Ayasse M., Overmann J. (2017): Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition. Environmental Microbiology 19 (8), 3310-3322. doi: 10.1111/1462-2920.13828
More information:  doi.org
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Richter-Heitmann T. (2016): (Acido)bacterial diversity in space and time. Dissertation, University Bremen
More information:  elib.suub.uni-bremen.de
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Bakterielle Anpassungsstrategien und Interaktionen in unterschiedlichen Bodenhabitaten
Vieira S. G. (2019): Bacterial adaptation strategies and interactions in different soil habitats. Dissertation, TU Braunschweig. doi: 10.24355/dbbs.084-201904101116-0
More information:  doi.org
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Vieira S., Huber K. J., Neumann-Schaal M., Geppert A., Luckner M., Wanner G., Overmann J. (2021): Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil. International Journal of Systematic and Evolutionary Microbiology 71 (2). doi: 10.1099/ijsem.0.004631
More information:  doi.org
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Vieira S., Luckner M., Wanner G., Overmann J. (2017): Lutitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil. International Journal of Systematic and Evolutionary Microbiology 67, 1408-1414. doi: 10.1099/ijsem.0.001827
More information:  doi.org
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Vieira S., Pascual J., Boedeker C., Geppert A., Riedel T., Rohde M., Overmann J. (2020): Terricaulis silvestris gen. nov., sp. nov., a novel prosthecate, budding member of the family Caulobacteraceae isolated from forest soil. International Journal of Systematic and Evolutionary Microbiology 70 (9): 4966-4977. doi: 10.1099/ijsem.0.004367
More information:  doi.org
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Was bestimmt die Zusammensetzung der mikrobielGemeinschaft auf den Wurzeln von Pflanzen?
Vieira S., Sikorski J., Dietz S., Herz K., Schrumpf M., Bruelheide H., Scheel D., Friedrich M. W., Overmann J. (2020): Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. The ISME Journal 14, 463–475. doi: 10.1038/s41396-019-0543-4
More information:  doi.org
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Nach welchen Regeln besiedeln Bakterien den Boden?
Vieira S., Sikorski J., Gebala A., Boeddinghaus R. S., Marhan S., Rennert T., Kandeler E., Overmann J. (2020): Bacterial colonization of minerals in grassland soils is selective and highly dynamic. Environmental Microbiology 22 (3), 917-933. doi: 10.1111/1462-2920.14751
More information:  doi.org

This project will be done in close collaboration with other microbiology and plant- and soil-related projects to allow integration of data and their synthesis.

Scientific assistants

Prof. Dr. Michael Friedrich
Project manager
Prof. Dr. Michael Friedrich
Universität Bremen
Prof. Dr. Jörg Overmann
Project manager
Prof. Dr. Jörg Overmann
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
Dr. Johannes Sikorski
Employee
Dr. Johannes Sikorski
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
Dr. Tim Richter-Heitmann
Employee
Dr. Tim Richter-Heitmann
Universität Bremen
Dr. Selma Gomes Vieira
Employee
Dr. Selma Gomes Vieira
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen
Shreya Tilve
Employee
Shreya Tilve
Universität Bremen
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