Chemical grazing defence of bacterial populations in the ocean

• Applicant: Dr. Stefan Thiele
• Subject Area: Microbial Ecology and Applied Microbiology
• Term: from 2015 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 275177774

Within the ocean, the second biggest carbon reservoir on Earth, microbial interactions lead to substantial carbon cycling in a process called the microbial loop. Within the microbial loop carbon is channelled between different trophic levels and retained in the surface layer where most primary productivity happens. Therefore, interactions between the trophic levels, mainly between the bacterial and archaeal community and their nano- and picoplankton grazers are of tremendous importance for understanding the global carbon cycle. In particular, predator-prey interactions, such as prey choice or grazing defence, are of importance but are often neglected in studies addressing microbial communities. Several grazing defence mechanisms have been described recently, like morphological adaptations, biofilm formation, performance of motility patterns, and chemical defence mechanisms, e.g. changes in cell surface structures and excretion of secondary metabolites as defensive compounds. These mechanisms have remained poorly understood and will be the focus of the proposed projects. I will first build an interaction matrix using different Vibrio strains and natural grazers and then explore mechanisms of grazing resistance by a combination of genomic, molecular genetic and chemical approaches. The genus Vibrio represents an excellent model due to the high physiological diversity among closely related species and strains, and availability of genomic and genetic resources. To date, ~10,000 strains are available, of which ~1,000 will be fully genome sequenced by the start of the project, in the lab of my host Prof. Dr. Martin Polz at the Massachusetts Institute of Technology. I will test 100 of these strains by co-incubating them with different mixotrophic and heterotrophic nano- and picoplankton grazers, available in the lab of Dr. Matthew Johnson at the Woods Hole Oceanographic Institute, to score differences in grazing efficiency. Results from this experiment will help to find potential candidates for genome analyses, aiming to find the pathways for the production of secondary metabolites used as grazing defence mechanisms, and to inform novel pathways for secondary metabolites potentially used as chemorepellents for grazing defence. Candidate genes and pathways responsible for defence mechanisms will be identified by creating transposon mutant libraries of different strains and challenging these with predators. This will identify mutants with transposon disruptions in relevant genes by detection of their decreased frequency post predation. When necessary, these genes and pathways can be further tested by specific gene knockouts. These experiments will be complemented by chemical analyses of exudates from strains which potentially use compounds for chemical grazing defence in the lab of Dr. Tracy Mincer at the Woods Hole Oceanographic Institute. From these results I also aim to deduce possible effects of the pathways on the formation of the microdiversity.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Professor Martin Polz, Ph.D.