Subsurface metagenomes uncover a vast repertoire of hypervariable proteins encoded by genetic elements in uncultivated organisms and viruses
Abstract
Uncultivated microorganisms primarily account for the remarkable diversity harbored in subsurface environments and represent an expansive subset of the current Tree of Life. Recent metagenomic efforts to investigate subsurface biomes have unveiled an array of bacterial and archaeal candidate phyla, whose members have minimal genomes and an apparent host-dependent existence. Still, little is known about the adaptive strategies that mediate host interactions in these organisms or their viruses. Genomic features known as diversity-generating retroelements (DGRs), which guide variability into targeted genes, were recently discovered in two single-cell genomes of uncultivated nanoarchaea, and independently in the genome of a marine virus from methane seep sediments. These prodigious drivers of protein hypervariability were first identified as the key force behind phage tail fiber diversification for binding different host receptors. Since their discovery, approximately 500 new DGRs have been found across a wide range of bacterial genomes representing various niches. We identified an unexpected 1136 distinct diversifiers from a single groundwater environment in reconstructed microbial genomes and genome fragments. The newly detected DGRs - predominantly linked to members of the candidate phyla radiation (CPR) - appear to target genes associated with cell-cell attachment, signaling, and transcription regulation. These findings suggest that targeted protein diversification may have an important role in regulating symbiotic or parasitic associations in groundwater microbiomes.
- Publication:
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AGU Fall Meeting Abstracts
- Pub Date:
- December 2016
- Bibcode:
- 2016AGUFM.B13J..04P
- Keywords:
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- 0414 Biogeochemical cycles;
- processes;
- and modeling;
- BIOGEOSCIENCESDE: 0439 Ecosystems;
- structure and dynamics;
- BIOGEOSCIENCESDE: 0465 Microbiology: ecology;
- physiology and genomics;
- BIOGEOSCIENCESDE: 0470 Nutrients and nutrient cycling;
- BIOGEOSCIENCES