Global biogeography of Prochlorococcus genome diversity in the surface ocean

Abstract

Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.

Meta‐omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation

“…Notably, the most abundant aquatic picocyanobacterial genus worldwide, Prochlorococcus, is not present in the Baltic Sea cyanobacterial community (no cyanobacterial 16S rRNA amplicon reads and a minute percentage of all metagenomics cyanobacterial reads annotated). This finding is naturally explained by their inability to thrive outside marine oligotrophic and warm water habitats (Partensky et al, 1999;Kent et al, 2016). Instead, strains of Synechococcus, another globally highly abundant genus, dominate brackish Baltic Sea waters, which stresses its high adaptability in relation to environmental conditions in the Baltic Sea (steep gradients in salinities, temperature and nutritional status/ Fig.…”

Distinct ecological niches of marine symbiotic N2‐fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages

“…Sublineages of marine microorganisms may occupy different ecological niches and their functions may be shaped by environmental factors ( Prochlorococcus for example; Kent et al. ); however, our understanding of the distribution of these UCYN‐A sublineages is limited. UCYN‐A1 and UCYN‐A2 both have greatly reduced genomes and live symbiotically with genetically distinct prymnesiophyte hosts (Tripp et al.…”

Microdiversity shapes the traits, niche space, and biogeography of microbial taxa

“…In some cases this may be due to the fact that no whole genome sequencing and comparisons have taken place. In other cases, such as Prochlorococcus, despite extensive sequencing no gene related to temperature has been shown to differentiate clades with distinct thermal growth optima (Kettler et al, 2007;Zinser et al, 2007), though a small number of genes have been putatively associated with low temperature Prochlorococcus in the field (Kent et al, 2016). The variability in temperature growth optima may be associated with subtle differences in chaperonin activity, enzymatic optima, and heat shock protein activity that are driven by allelic variation or differences in gene copy number (Zinser et al, 2009;Yung et al, 2015).…”