Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome

Abstract

The Sorcerer II Global Ocean Sampling (GOS) sequencing effort has vastly expanded the landscape of metagenomics, providing an opportunity to study the genetic potential of surface ocean water bacterioplankton on a global scale. Here we describe the habitat-based microbial diversity, both taxon evenness and taxon richness, for each GOS site and estimate genome characteristics of a typical free-living, surface ocean water bacterium. While Alphaproteobacteria and particularly SAR11 dominate the 0.1- to 0.8-mum size fraction of surface ocean water bacteria (43% and 31%, respectively), the proportions of other taxa varied with ocean habitat type. Within each habitat type, lower-bound estimates of phylum richness ranged between 18 and 59 operational taxonomic units (OTUs). However, OTU richness was relatively low in the hypersaline lagoon community at every taxonomic level, and open-ocean communities had much more microdiversity than any other habitat. Based on the abundance of single-copy eubacterial genes from the same data set, we estimate that the genome of an average free-living surface ocean water bacterium (sized between 0.1 and 0.8 mum) contains approximately 1,019 genes and 1.8 copies of the 16S rRNA gene, suggesting that these bacteria have relatively streamlined genomes in comparison to those of cultured bacteria and bacteria from other habitats (e.g., soil or acid mine drainage).

FIG. 1.

Microbial diversity (16S rRNA) for all GOS samples. Dotted lines connect taxonomic data to sample locations (filled circles). Numbers within taxonomic plots indicate the sample identification numbers (preceded by “GS” as described by Rusch et al. [41]). The border color surrounding each taxonomic plot indicates the habitat type. The habitats classified as “Other” include the following: 5, embayment; 16, coastal sea; 20, fresh water; 25, fringing reef; 30, warm seep; 31, coastal upwelling; 32, mangrove; 51, coral reef atoll. All samples were collected from the 0.1- to 0.8-μm size fraction, unless indicated otherwise by the following symbols: *, from the 0.22- to 0.8-μm size fraction; †, from the 3- to 20-μm size fraction; and ‡, from the 0.8- to 3-μm size fraction.

FIG. 2.

Diversity, evenness, and richness indices for GOS habitats, as calculated by DOTUR. (A) Diversity indices were estimated using the Shannon-Weaver index of diversity. (B) Evenness scores were estimated from Shannon-Weaver indices of diversity as well as richness. (C) Lower bounds of richness were calculated using the Chao1 estimator. Error bars indicate 95% confidence intervals.