Population genetics

Bacteria and archaea are genetically, phylogenetically and physiologically very diverse. Beyond typical hospital strains, little is known about the evolutionary mechanisms that lead to discrete lineages, their niche separation and genetic isolation within natural bacterial communities. The marine Roseobacter-group and the human pathogen Clostridioides difficile (CDiff) have been selected as models for our studies of bacterial population structure. Extrachromosomal elements are crucial for the speciation of the surface-associated marine genus Phaeobacter, which is exemplified by the stable recruitment of a plasmid by P. gallaeciensis. The comparison with the phylogenetically more diverse genus Sulfitobacter will allow to draw general conclusions about the underlying mechanisms shaping the population structure of these marine Alphaproteobacteria. Comparative analyses of the Gram-positive pathogen CDiff propose transposable elements as main evolutionary drivers.

Projects

  • ŸProject 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.

Plasmid biology

A multipartite genome architecture with a chromosome and several extrachromosomal elements (ECRs) is characteristic for many Proteobacteria. The stable maintenance of up to 14 low copy number replicons in a single bacterium is reminscent of the complexity in eukaryotes. ECRs serve as life style determinants and our investigations indicate that their stable recruitment triggers bacterial speciation. We systematically investigate the sequence data bases for plasmids to identify novel replication systems and to retrace the molecular mechanisms of their stability. Our phylogeny-based plasmid classification systems allow to predict plasmid compatibility without laborious wet lab 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 in the colloborative research centre Roseobacter and beyond. 

Projects

  • ŸProject A5, TRR51-Roseobacter

Selected References

  1. ŸBartling P, Brinkmann H, Bunk B, Overmann J, Göker M, Petersen J (2017).  The composite 259-kb plasmid of Martelella mediterraneaDSM 17316T - A natural replicon with functional RepABC modules from Rhodobacteraceaeand Rhizobiaceae. Front. Microbiol. 8: 1787. 
  2. ŸMichael 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. ŸTrautwein K, Will SE, Hulsch R, …, Petersen J, Schomburg D, Rabus R (2016). Native plasmids restrict growth of Phaeobacter inhibensDSM 17395. Energetic costs of plasmids assessed by quantitative physiological analyses. Environ. Microbiol. 18: 4817–4829. 
  4. ŸFrank O, Göker M, Pradella S, Petersen J. (2015). Ocean’s Twelve: flagellar and biofilm chromids in the multipartite genome of Marinovum algicolaDG898 exemplify functional compartmentalization. Environ. Microbiol. 17: 4019–4034. 
  5. ŸEbert M, Laaß S, Burghartz M, Petersen J, Koßmehl S, Wöhlbrand L, Rabus R, Wittmann C, Tielen P, Jahn D (2013). Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibaeto anaerobic conditions. J Bacteriol. 195: 4769-4777.
  6. ŸPetersen J, Frank O, Göker M, Pradella S (2013). Extrachromosomal, extraordinary and essential--the plasmids of the Roseobacter clade. Appl Microbiol Biotechnol. 97: 2805-2815.
  7. ŸPetersen J, Brinkmann H, Berger M, Brinkhoff T, Päuker O, Pradella S (2011). Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacteraceae. Mol. Biol. Evol. 28: 1229–1240.
  8. ŸPetersen J, Brinkmann H, Pradella S (2009). Diversity and evolution of repABC-type plasmids in Rhodobacterales. Environ Microbiol 11: 1627-2638.

Horizontal gene transfer

Darwin´s concept of a 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 case example is the capacity of aerobic anoxygenic photosynthesis (AAnP) that is encoded by a compact photosynthesis gene cluster (PGC) of 45-kb and that was transferred at least seven times in the evolution of Rhodobacteraceae(Brinkmann et al. 2018). Analogous plasmid transfers can also explain the occassional 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 simulate 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. ŸMichael 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
  4. 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.
  5. ŸPetersen J, Brinkmann H, Bunk B, Michael V, Päuker O, Pradella S (2012). Think pink: photosynthesis, plasmids and the Roseobacter clade. Env. Microbiol. 14: 2661–2672.