Illuminating Microbial Dark Matter by Single Cell Genomics- Shedding Light on the Phylum Chloroflexi

• Applicant: Professorin Dr. Anne-Kristin Kaster
• Subject Area: Microbial Ecology and Applied Microbiology ; Metabolism, Biochemistry and Genetics of Microorganisms
• Term: from 2016 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 320579085

Chloroflexi are a ubiquitous phylum, thriving in many types of environments with a high diversity of phenotypes and a wide range of metabolic activities. However, these microorganisms have so far often evaded cultivation attempts in the laboratory, therefore obscuring our knowledge of their biochemical potentials, eco-physiology and evolutionary histories. Although culture-independent methodologies like metagenomics and 16S rRNA gene analysis revealed the abundance and importance of Chloroflexi in ecological processes, they are still vastly under-studied. It is therefore proposed to conduct single cell genomic studies in combination with binning of environmental omics data to obtain multiple novel complete and draft Chloroflexi genomes. This research aims at filling gaps in the tree of life and re- shaping it by finding novel Chloroflexi species or even classes. It is hypothesized that this additional genomic information will prove that the eight Chloroflexi classes do not consistently form a monophyletic clade and have to be split up in two or more phyla. Furthermore, the roles of Chloroflexi in the environment and their metabolism will be elucidated. The integration of different technologies and methods will provide unprecedented insights into the diversity of Chloroflexi that could not be detected by any of the individual techniques alone. In addition, it is proposed to work on significant technical and conceptual challenges in order to improve the success of genome recovery by single cell- and metagenomics. Though method development will not be the major focus of this research proposal, it will co-develop by exploring novel microorganisms from different interesting environments.

• DFG Programme: Research Grants