Biology Centre CAS, Institute of Hydrobiology, Czech Republic

Small is beautiful: genome streamlining in planktonic freshwater microbes


Michaela M. Salcher


Biology Centre CAS, Institute of Hydrobiology, Czech Republic


The most abundant taxa of planktonic freshwater microbes have minute cell sizes and highly reduced genomes. Streamlining theory predicts that gene loss is caused by evolutionary selection driven by environmental factors, making these organisms superior competitors under oligotrophic conditions. Although such microbes numerically dominate in freshwaters, potential auxotrophies and dependencies amongst co-occurring organisms frequently preclude the establishment of axenic cultures. This has hampered an in-depth ecological assessment of the reasons for their success in nature. In my talk, I will present data on the first axenic strains from two lineages of abundant and ubiquitous ultra-small freshwater bacteria: ‘Ca. Methylopumilus spp.’ (Betaproteobacteria, genome sizes: 1.3-1.7 Mb) and acI Actinobacteria (genome sizes: 1.2-1.4 Mb). Both groups display characteristic features of most abundant pelagic microbes, i.e. photoheterotrophy and streamlined genomes with low genomic GC content and short intergenic spacers. Remarkably, the betaproteobacterial genomes capture the gradual process of genome reduction of freshwater sediment-dwelling methylotrophs towards a planktonic lifestyle both in freshwater and marine habitats. The genomes of acI Actinobacteria show a high degree of ecotype diversity with major differences in e.g., sugar, amino sugar, and polyamine metabolism, hinting at possible niche-specific adaptations to seasonally changing environmental conditions. The availability of axenic cultures of such successful microbes is a major step forward towards understanding their interactions amongst themselves and with the ecosystem at large.

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