Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.

Chaetopterid tubes from vent and seep sites: Implications for fossil record and evolutionary history of vent and seep annelids

Vestimentiferan tube worms living at deep-sea hydrothermal vents and cold seeps have been considered as a clade with a long and continuing evolutionary history in these ecosystems. Whereas the fossil record appears to support this view, molecular age estimates do not. The two main features that are used to identify vestimentiferan tubes in the fossil record are longitudinal ridges on the tube's surface and a tube wall constructed of multiple layers. It is shown here that chaetopterid tubes from modern vents and seeps—as well as a number of fossil tubes from shallow-water environments—also show these two features. This calls for a more cautious interpretation of tubular fossils from ancient vent and seep deposits. We suggest that: current estimates for a relatively young evolutionary age based on molecular clock methods may be more reliable than the inferences of ancient “vestimentiferans” based on putative fossils of these worms; not all of these putative fossils actually belong to this group; and that tubes from fossil seeps should be investigated for chitinous remains to substantiate claims of their potential siboglinid affinities.