Ecogenomics of genome-streamlined freshwater methylotrophs

Project leader: Michaela Salcher

The most abundant planktonic microbes have reduced genomes and streamlining theory predicts that gene loss is caused by evolutionary selection driven by environmental factors. Yet the evolutionary path of streamlining remains unknown because of obstacles in establishing axenic cultures of such microbes. We developed a targeted isolation technique for abundant genome-streamlined freshwater methylotrophs: ‘Ca. Methylopumilus planktonicus’ (Betaproteobacteria, 1.3 Mbp genome size), that are ideal model organisms for studying microdiversification patterns and the evolution of genome-streamlining per se. The closest relatives of ‘Ca. M. planktonicus’ inhabit lake sediments and the pelagial of oceans, and we propose that the evolutionary origin of the family can be traced back to sediment microbes with medium-sized genomes. Whole genome sequencing of 150 strains and deep sequencing of metagenomes will allow comparative population genomics with the aim to disentangle the underlying ecological reasons for the widespread but yet enigmatic phenomenon of genomestreamlining in aquatic microbes.

The aim of the project is using targeted isolation and whole-genome-sequencing of oligotrophic freshwater ‘Ca. Methylopumilus planktonicus’ (Betaproteobacteria) together with metagenomics to study the evolution of genome-streamlining in planktonic microbes. Identifying microdiversification patterns in closely related taxa.

Financial support: Czech Science Foundation; Project No.: 19-23469S, duration: 2019 - 2021