Population structure and divergence in the Roseobacter group (J. Overmann)

Bacteria and archaea are genetically, phylogenetically and physiologically very diverse. Beyond well-studied pathogens, little is known about the evolutionary mechanisms that lead to discrete bacterial lineages, niche separation and genetic isolation within natural bacterial communities. The marine Roseobacter-group has been selected as a model for our studies of bacterial population structure because of its cosmopolitan distribution and environmental relevance.

Within the surface-associated genus Phaeobacter (project DFG Transregio 51 Roseobacter), there are genetically-defined subpopulations that have identical 16S rRNA gene sequences, but significantly different genome sequences. Through our work, we have shown that genomically discrete Phaeobacter populations in the open ocean are not the result of geographical isolation, but rather have specificly adapted to different ecological niches. The comprehensive characterization of the mobilome of the entire Roseobacter group has shown an unexpectedly high diversity of different plasmids (up to 13 replicons per cell). Mobile plasmids have evolved into stable inherited extrachromosomal replicons with essential genes. The multipartite genome organization of many Proteobacteria indicates that the stable acquisition of plasmids in this phase plays a crucial role in the development of new genera and species.

New comparisons of Phaeobacter with the phylogenetically more diverse genus Sulfitobacter will allow us to draw general conclusions about the underlying mechanisms shaping the population structure of these marine Alphaproteobacteria.

Projects

  • Project A7, TRR51-Roseobacter


Selected References

  1. Freese HM, Sikorski J, Bunk B, Scheuner C, Meier-Kolthoff JP, Spröer C, Gram L, Overmann J (2017). Trajectories and drivers of genome evolution in surface-associated marine Phaeobacter. Genome Biol. Evol. 9: 3297-3311.
  2. Freese HM, Methner A, Overmann J (2017) Adaptation of biofilm bacteria to the open ocean: A genomically distinct subpopulation of Phaeobacter gallaeciensis colonizes Pacific mesozooplankton. Front Microbiol 8, 1659
  3. Sonnenschein EC, Broughton C, Phippen W, Nielsen KF, Mateiu RV, Melchiorsen J, Gram L, Overmann J, Freese HM (2017) Phaeobacter piscinae sp. nov., a novel species of the Roseobacter group and potential aquaculture probiont. Int J Syst Evol Microbiol 67, 4559-4564

Population genomics of emerging bacterial pathogens (J. Overmann)

The Gram-positive human pathogen Clostridioides difficile (formerly Clostridium difficile) is a leading cause of hospital-acquired diarrhea with a high morbidity and mortality especially in the elderly. As part of the interdisciplinary research group CDInfect (funded by the Volkswagen Foundation) that includes institutions in Braunschweig (DSMZ, HZI, TU Braunschweig), Göttingen (University and UMG), Hannover (MHH) and Greifswald (University), we have characterized and genome-sequenced 230 strains from Germany, Ghana, Indonesia and Latin America to study C. difficile genome space and diversification. Genome analyses of C. difficile revealed a significant contribution of mobile elements such as plasmids, prophages and conjugative transposons to C. difficile genome size and diversity, and an acquisition and exchange of infection relevant traits. As the epidemiological situation in low-income countries is unclear, Latin American strains are being investigated in detail in a subsequent project togethr with the Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica and the University Greifswald (GEnoMICd_LA). Here, a pipeline for the development of C. difficile diagnostic methods capable of distinguishing classical and Clade C-I isolates is being established that matches the infrastructure and technical expertise available in the developing world.

In a second part of the project, the bacterial fish pathogen, Piscirickettsia salmonis, is of considerable economic importance in salmon aquaculture, but the biology and epidemiology of this pathogen has not yet been clarified. In close cooperation with the Pontificia Universidad Católica de Valparaíso and Universidad Austral de Chile (funded by Sernapesca and Intesal-Chile), genome comparisons showed that the fish pathogen has evolved into three different species and has coexisted stably in the environment ever since. These findings are of direct relevance for the prevention, diagnosis and legal classification of the pathogen.

Although pathogens have obvious health and economic implications, no public facilities in Germany existed that were able to safeguard and distribute quality-controlled clinical strains of human pathogens. As member of the German Centre of Infection research (Deutsches Zentrum für Infektionsforschung, DZIF), DSMZ collects and maintains the translational infrastructure TI Pathogen Repository -- a highly diverse collection of 2,332 authenticated strains of bacterial pathogens from >150 different genera. Since 2011, this collection has served to maintain and distribute well-characterized clinical strains from DZIF studies, is continuously growing, and provides in-depth documentation of strain-associated information.

Projects

  • CDInfect, funded by VW-Vorab
  • GEnoMICd_LA, EU-LAC Health joint call
  • Programa para la Gestión Sanitaria de la Acuicultura, funded by Sernapesca, Intesal-Chile
  • Deutsches Zentrum für Infektionsforschung (DZIF), Translational Infrastructure TI Pathogen Repository, BMBF


Selected References

  1. Riedel T, Neumann-Schaal M, Wittmann J, Schober I, Hofmann JD, Lu C-W, Dannheim A, Zimmermann O, Lochner M, Groß U, Overmann J (2020) Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ phenotype from a late recurrent colonization. Genome Biol Evol (accepted)
  2. Ramirez-Vargas G, López-Ureña D, Badilla A, Orozco-Aguilar J, Murillo T, Riedel T, Overmann J, Gonzalez G, Chaves-Olarte E, Quesada-Gómez C, Rodríguez C (2018) Novel Clostridium difficile strains from the Clade C-I escape common diagnostics tests, differ in their pathogenicity potential, and carry their toxins on extrachromosomal elements. Sci Rep 8, 13951
  3. Riedel T, Wittmann J, Bunk B, Schober I, Spröer C, Gronow S, Overmann J (2017) A Clostridioides difficile bacteriophage genome encodes functional binary toxin-associated genes. J Biotechnol 250, 23-28

Plasmid biology (J. Petersen)

A multipartite genome architecture with a chromosome and several extrachromosomal elements (ECRs) is characteristic of many Proteobacteria. The stable maintenance of up to 14 low copy number replicons in a single bacterium is reminiscent of the chromosomal complexity in eukaryotes. ECRs serve as life style determinants and our investigations indicate that their stable recruitment triggers bacterial speciation. We systematically investigated the public sequence databases for plasmids to identify novel replication systems and to retrace the molecular mechanisms of their stability. Our phylogeny-based plasmid classification systems allows us to predict plasmid compatibility without in vitro (lab-based) tests. Based on the most abundant group of RepABC-type plasmids we are currently establishing a set of versatile molecular tools that can be used for basic research and biotechnological applications. Our established methods of plasmid curing, directed gene knock-out and conjugation beyond species borders provides the basis to investigate the functional role of extrachromosomal elements in depth. Systems biological analyses are performed with various cooperation partners within the collaborative research centre Roseobacter and beyond.

Projects

  • ŸProject A5, TRR51-Roseobacter


Selected References

  1. Bartling P, Brinkmann H, Bunk B, Overmann J, Göker M, Petersen J (2017).  The composite 259-kb plasmid of Martelella mediterranea DSM 17316T - A natural replicon with functional RepABC modules from Rhodobacteraceae and Rhizobiaceae. Front. Microbiol. 8: 1787.
  2. Michael V, Frank O, Bartling P, Scheuner C, Göker M, Brinkmann H, Petersen J (2016).  Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick’ lifestyle in roseobacters. ISME J. 10: 2498–2513
  3. Frank O, Göker M, Pradella S, Petersen J. (2015). Ocean’s Twelve: flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization. Environ. Microbiol. 17: 4019–4034.

Horizontal gene transfer (J. Petersen)

Darwin´s concept of strict vertical evolution was expanded by the discovery of horizontal gene transfers in microorganisms. Our comparative genome analyses revealed the plasmid-mediated transfer of crucial metabolic and physiological functions. A prime example is the 45-kb compact photosynthesis gene cluster (PGC) which enable aerobic anoxygenic photosynthesis (AAnP) that was transferred at least seven times in the evolution of Rhodobacteraceae.
Another interesting example of plasmid transfer explains the occasional presence of two functional flagellar gene clusters (FGCs), which are indispensable for swimming motility, in one bacterium. Our work indicates that the horizontal acquisition of new traits is crucial for the conquest of novel ecological niches at least for Proteobacteria. We are currently investigating the role of plasmids for the scattered distribution of the denitrification pathway in roseobacters and simulating natural adaptation processes via conjugation experiments.

Project

  • ŸProject A5, TRR51-Roseobacter

Selected References

  1. ŸBrinkmann H, Göker M, Koblížek M, Wagner-Döbler I, Petersen J (2018). Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae. ISME J. 12: 1994–2010.
  2. ŸPetersen J, Wagner-Döbler I (2017). Plasmid transfer in the ocean - A case study from the roseobacter group. Front. Microbiol. 8: 1350.
  3. ŸSimon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M (2017). Phylogenomics of Rhodobacteraceaereveals evolutionary adaptation to marine and non-marine habitats. ISME J. 11: 1483–1499.