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

Area of Science:

• Marine microbiology
• Genomics
• Oceanography

Background:

• SAR11 clade bacteria are the most abundant microorganisms in marine ecosystems, comprising over 25% of global seawater bacterial cells.
• SAR11 is diverse, with distinct ecotypes adapted to various marine environments, including some specific to the deep ocean.

Purpose of the Study:

• To investigate the genomic basis for the deep ocean distribution of SAR11 subclade Ic, a specific bathytype.
• To compare the genomes of deep-sea subclade Ic with surface SAR11 ecotypes to identify adaptation mechanisms.

Main Methods:

• Isolation and sequencing of four single-cell genomes from SAR11 subclade Ic at 770 m depth.
• Comparative genomic analysis of Ic genomes against eight SAR11 surface genomes.
• Analysis of metagenomic datasets to assess the prevalence of subclade Ic below the euphotic zone.

Main Results:

• Subclade Ic genomes were dominant in deep ocean metagenomic data, confirming their bathytype status.
• Ic genomes shared high similarity (69% orthologous clusters) with surface SAR11 but were distinct phylogenetically and at the amino-acid level.
• Adaptations include enrichment in membrane biosynthesis genes, unique phage defenses, and subtle genomic differences like larger genome and coding regions.

Conclusions:

• SAR11 subclade Ic's adaptation to the deep ocean involves subtle genomic modifications rather than large-scale gene content changes.
• These adaptations, including preferential amino-acid substitutions and altered genomic architecture, facilitate niche differentiation in deep marine environments.
• Hypothetical genes in subclade Ic may play roles in deep-sea survival and niche adaptation, warranting further investigation.