Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome.
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).
Biers
Erin J
EJ
Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA. ejbiers@mailbox.sc.edu
Sun
Shulei
S
Howard
Erinn C
EC
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D017753:Ecosystem; D005838:Genotype; D009792:Oceans and Seas; D010802:Phylogeny; D021521:Ribotyping; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D004275:DNA, Ribosomal