Drivers of bacterial community assembly

Within the DFG-funded German Biodiversity Exploratories projects, we focus on the composition and activity patterns of bacterial communities and systematically elucidate the environmental factors that influence community assembly in soils including mineral surfaces, plant roots, and animal organic matter. To date, the majority of rhizobiome studies focus on model or crop plants grown in microcosms or monospecific plant cultures. Using the Biodiversity Exploratories allows us to study a more complex environment, natural temperate grasslands, and attempt to tease apart the influence of plant species, soil conditions, and root exudate composition on the assembly of rhizosphere bacterial communities under different edaphic and climatic conditions along a land use gradient.
For the first time, we have shown that, in this complex environment, the composition of the plant rhizobiome is controlled by soil properties and not by the plant species. Moving beyond this well-characterized soil environment within Gemany, we have analyzed, for comparison, bacterial communities in soils and endemic plants of (sub)tropical ecosystems in Ethiopia and Colombia that have not yet or barely been studied by microbial ecologists (BMBF-WTZ project BiCFAM; project DiSeMiNation, funded by the Leibniz Competition, together with the Leibniz institutes ZMT, IPB and IÖR).

Projects

  • Core project Microorganisms, DFG SPP 1374 Biodiversity Exploratories
  • German-Colombian Bilateral Consortium for functional and applied microbiological diversity research (BiCFAM), BMBF-WTZ
  • DiSeMiNation - Digging into Sediments and Microbes for Nature conservation: Identifying the drivers of ecosystem processes for spatial conservation planning, Leibniz-SAW

Selected References

  1. Vieira S, Sikorski J, Dietz S, Herz K, Schrumpf M, Bruelheide H, Scheel D, Friedrich MW, Overmann J (2020) Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. ISME J 14, 463-475
  2. Vieira S, Sikorski J, Gebala A, Boeddinghaus R, Marhan S, Rennert T, Kandeler E, Overmann J (2020) Bacterial colonization of reactive minerals in grassland soils is selective and highly dynamic. Environ Microbiol 22, 917-933
  3. Soliveres S, van der Plas F, Manning P, Prati D, Gossner MM, Renner SC, Alt F, Arndt H, Baumgartner V, Binkenstein J, Birkhofer K, Blaser S, Blüthgen N, Boch S, Böhm S, Börschig C, Buscot F, Diekötter T, Heinze J, Hölzel N, Jung K, Klaus VH, Kleinebecker T, Klemmer S, Krauss J, Lange M, Morris K, Müller J, Oelmann Y, Overmann J, Pašalić E, Rillig MC, Schaefer HM, Schloter M, Schmitt B, Schöning I, Schrumpf M, Sikorski J, Socher SA, Solly EF, Sonnemann I, Sorkau E, Steckel J, Steffan-Dewenter I, Stempfhuber B, Tschapka M, Türke M, Venter P, Weiner CN, Weisser WW, Werner M, Westphal C, Wilcke W, Wolters V, Wubet T, Wurst S, Fischer M, Allan E (2016) Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality. Nature 536, 456-459
     

Insights into bacterial functions and adaptations through advanced statistics and modeling

Soil microbial communities are highly diverse environments for prokaryotes with up to 104 different species per gram of soil. Soil microbiomes are also highly dynamic in time and space. But precisely because of this rich diversity and complexity, understanding the soil community was limited to rough estimates and crude snapshots. However, advances in molecular and high-throughput sequencing techniques and falling costs over the last decade have enabled the exploration of entire complex soil microbiomes at increasingly high resolution. Even still, the sheer numbers of taxa in hundreds of datasets generated by high-throughput sequencing pose computational challenges and require novel bioinformatics analysis pipelines. We have developed an advanced method for determining the state of activity for individual types of bacteria which is based on the ratio of rRNA to rDNA for individual bacterial phylotypes. Structural equation modeling is then used to identify major drivers of changes in microbial diversity.
Unraveling the interactions between different species and identifying keystone species is an additional challenge in the soil environment and we have developed novel computational approaches for inferring interactions and their change along environmental gradients. We also employ state-of-the-art network analyses to generate novel hypotheses on biotic interactions and to identify microbial keystone species with central functions. Most recently, these approaches have been complemented by a combination of single cell genomics and metabolic modeling which has been applied to elucidate the adaptations of selected target bacteria.

Projects

  • Core project Microorganisms, DFG SPP 1374 Biodiversity Exploratories

Selected References

  1. Dedysh SN, Henke P, Ivanova AA, Kulichevskaya IS, Philippov DA, Meier-Kolthoff JP, Göker M, Huang S, Overmann J (2020) 100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii. Environ Microbiol 22, 198-211
  2. Shang Y, Sikorski J, Bonkowski M, Fiore-Donno A-M, Kandeler E, Boeddinghaus R, Marhan S, Solly E, Schrumpf M, Schöning I, Tesfaye W, Buscot F, Overmann J (2017) Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters. PLoS One 12, e0173765
  3. Coolen MJL, Cypionka H, Smock A, Sass H, Overmann J (2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296, 2407-2410

Targeted cultivation and isolation of so-far-uncultured bacteria

The highly limited culturability of microbes is now well known (and the oft-cited 99% unculturability rate in some systems) but yet systematic studies to explore and improve the culturability of bacteria, although highly promising and called for by the community, are rarely conducted. Our culture-independent studies (sequencing and bioinformatics) give insight into the patterns and drivers of bacterial activity and the potential adaptations of so-far-uncultured bacteria. We use these “hints” from genomic data to guide our subsequent cultivation attempts. Here we employ an automated, multifactorial approach, exposing bacteria to different types and concentrations of growth substrates, nutrients and salts, supplements, signal compounds, liquid or solid incubation medium, and accompanying bacteria (co-cultivation). Parallel analyses of thousands of cultivation trials by high-throughput amplicon sequencing of 16S rRNA genes allows the identification and isolation of numerous, previously unculturable target bacteria for subsequent studies. 

One focus here over the past decade or so has been on the acidobacteria, a dominant group of bacteria in soils, as their functional importance, for example for soil fertility, is still poorly understood. For the first time, representatives of  two classes of previously uncultivated Acidobacteria that dominate in soils were isolated and comprehensively characterized. In cooperation with natural product chemists, the potential of novel bacteria for future biotechnological applications and products is also being assessed.

Selected References

  1. Overmann J, Abt B, Sikorski J (2017) Present and future of cultivating bacteria. Annu Rev Microbiol 71, 711–730
  2. Lagkouvardos I, Pukall R, Abt B, Foesel B, Meier-Kolthoff J, Kumar N, Bresciani A, Martínez I, Just S., Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui T, Wang J, Hugenholtz F, Plugge C, Peterson D, Hornef M, Baines J, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B, Clavel T (2016) A mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiol 1, 16131
  3. Huber KJ, Geppert AM, Wanner G, Foesel BU, Wüst PK, Overmann J (2016) Vicinamibacter silvestris-The first representative of the globally widespread subdivision 6 Acidobacteria isolated from subtropical savannah soil. Int J Syst Evol Microbiol 66, 2971-2979
  4. Pascual J, Wüst PK, Geppert A, Foesel BU, Huber KJ, Overmann J (2015) Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 38, 534–544

Establishing and expanding microbial biodiversity databases

Drawing from its expertise in biodiversity research, cultivation, and systematics, the Leibniz Institute DSMZ participates in three joint database initiatives, contributing towards the mobilization, standardization, and curation of microbial (meta)data. The Global Biodiversity Information Facility (GBIF) facilitates free and open access to biodiversity data worldwide via the Internet. Within GBIF, DSMZ maintains the German Node on Bacteria & Archaea to create a common access point for the microbiological collection databases in Germany and establish links to GBIF International construction of universal virtual collections, support the digitalization of data and harmonization of data capture in German collections of prokaryotes and viruses, and closely cooperate with the other national GBIF nodes, with GBIF International and other regional and international organizations.

The second initiative is the German Federation of Biological Data (GFBio), a DFG funded network of experts for research data management. GFBio is the authoritative, national contact point for issues concerning the management and standardisation of biological and environmental research data. DSMZ represents one of nine GFBio Data Centers, responsible for the data archiving and curation of microbial and cell culture data. Moreover the DSMZ contributes to the GFBio terminology services with its taxonomy service LPSN/PNU and provides internal culture collection data to the GFBio database.

The third project is within the German Network for Bioinformatics Infrastructure (de.NBI), a BMBF funded network of bioinformatic experts offering state-of-art services and training. It fosters the cooperation of the German bioinformatics community and provides access to computing resources in the de.NBI cloud. The DSMZ database BacDive is one of four flagship databases (core data resources) within the de.NBI BioData node and offers services and training for researchers all over the world. de.NBI also constitutes the German Node of Elixir, a European intergovernmental organization for life science. Thereby, the DSMZ is partner institute of the Elixir network (Horizon 2020) and involved in developments in the European life science data community.

Projects 

  • GBIF-D, Erschließung organismenbezogener prokaryotischer Daten für Biodiversitätsanalysen der nächsten Generation, BMBF
  • GFBio, German Federation for Biological Data, DFG
  • de.NBI, Deutsches Netzwerk für Bioinformatik, BMBF

Selected References

  1. Reimer LC, Vetcininova A, Sardà Carbasse J, Söhngen C, Gleim D, Ebeling C, Overmann J (2019) BacDive in 2019: Bacterial phenotypic data for high-throughput biodiversity analysis. Nucl Acids Res 47(D1), D631-D636
  2. Reimer LC, Söhngen C, Vetcininova A, Overmann J (2017) Mobilization and integration of bacterial phenotypic data - enabling next generation biodiversity analysis through the BacDive Metadatabase. J Biotechnol 261, 187-193