Daniel Mende: Patterns of genomic architecture, distribution, and diversity of bacterioplankton populations in the North Pacific Subtropical Gyre

Microbial communities are of central importance to marine ecosystems. Current perspectives on microbial community structure and variability have advanced greatly via comparative studies of cultivar genes and genomes, and more recently, single-cell genomes, and metagenomic analyses. To better define community structure and microdiversity of bacteria and archaea in the North Pacific Subtropical Gyre (NPSG), we analyzed their genomic features as well as their fine-scale phyloge netic affiliations, abundances, and distributions using single-copy, universally conserved protein-coding gene markers derived from Station ALOHA metagenomic datasets.

We could show the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift in genome size, genomic GC content, and protein nitrogen and carbon content. These community-wide changes in genome features appear to be driven by gradients in the surrounding environmental energy and nutrient fields. Comprehensive cross-clade analyses of species-level taxa revealed a specific relationship between persistence and abundance, with implications for interpreting near species-level distributions and diversity patterns among disparate microbial clades. Within any given clade, a smaller number of abundant, persistent core populations appeared to form the foundation for a much larger variety of more ephemeral variants, that together contributed to overall microdiversity. 

Our analyses also revealed two novel SAR11 subclades, one of which was dominant in themesopelagic representing a large, mesopelagic SAR11 subpopulation. Additionally, we observed Prochlorococcus distributional signatures that implicated the export and persistence of specific populations from surface waters into the mesopelagic. In total, our results highlight the utility of metagenome-derived, protein-coding phylogenetic markers for revealing population-specific habitat origins, diversity patterns, and niche differentiation among diverse bacterial and archaeal subclades.