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Microbial Symbionts in Deep-Sea Vents Have Diverse Metabolic Functions, Metagenomics Study Finds

NEW YORK (GenomeWeb News) – A new metagenomic study is helping to illuminate the adaptation and metabolic strategies used by a group of microbial symbionts in deep-sea, hydrothermal vents.
Researchers from the US and New Zealand used environmental genome sequencing to characterize the bacteria living on hair-like surfaces on the backs of polychaete worms called Alvinella pompejana, which live on the walls of high-temperature vents deep below the sea. Their results, scheduled to appear online this week in the Proceedings of the National Academies of Sciences, suggest that a class of bacteria called Epsilonproteobacteria have adapted to their role as episymbionts through a host of metabolic functions — including some functions normally associated with parasites.
“The episymbionts have characteristics of pathogens and biofilms that facilitate their success,” senior author Stephen Craig Cary, a marine biosciences researcher at the University of Delaware, and his colleagues wrote. “They are armed with many characteristics of their pathogenic Epsilonproteobacteria relatives, harboring the genetic armory required to evade a host response — through cell-surface modifications, mobile DNA, and other flexible gene pool features.”
Deep-sea hydrothermal vents or “black smoker chimneys” in the East Pacific Rise are characterized by high, fluctuating temperatures, anoxia, variable pH, and chemical gradients. Communities of small A. pompejana worms live along the walls of these vents and are exposed to temperature fluctuations from around 30°C to 84°C as well as variable chemical conditions and pH that ranges from slightly acidic to neutral.
The worms also establish symbiotic relationships with bacteria, which assemble along hair-like projections found on the mucus glands on the worms’ backs. These episymbionts — which form a dense biofilm of bacterial species — typically belong to Epsilonproteobacteria, which are also found as free-living bugs in this environment.
Cary and his team employed environmental genomics in an effort to understand just how Epsilonproteobacteria species thrive as episymbionts in the hostile hydrothermal vent environment. Specifically, they collected worm samples from hydrothermal vents in the East Pacific Rise at 9°N latitude using the deep submergence research vehicle Alvin.
Using a combination of BAC shotgun library sequencing and rRNA sequencing, the researchers began determining which bacteria were associated with the worms as well as the genes these bacteria contained. The team constructed a main metagenomic library that came from one worm, as well as two additional genomic libraries based on the bacterial sequences associated with three and four worms, respectively.
Their results suggest that the A. pompejana episymbiont metagenome contains at least 27 different bacterial strains. This community appears to be dominated by two ribotypes called 5A and 13B, which make up 35 percent and 30 percent of the consortium, respectively.
The researchers also found sequence data predicting 103,371 proteins. By clustering amino acid sequences with 40 percent identity, the researchers came up with a non-redundant, core episymbiont metagenome.
By comparing this core metagenome with both free-living Epsilonproteobacteria such as Sulfurovum sp. NBC37-1 and Sulfurimonas denitrificans and pathogenic Epsilonproteobacteria such as Helicobacter pylori and Campylobacter jejuni, the researchers began gaining insights into the metabolic and other functions within the episymbiont community.
Their results suggest that the episymbiont bacteria share strategies with both pathogenic and free-living bacteria. And, the researchers noted, the species appear to be fine-tuned to thrive in their habitat on A. pompejana, adapting to changes in temperature, chemical composition in the water, and so on.
The microbial community also has a suite of genes necessary for processes such as sulfur oxidation, denitrification, and more. That suggests that the microbes are relatively self-sufficient and may provide nutritional benefits to their host, A. pompejana.
“The success of Epsilonproteobacteria as episymbionts in hydrothermal vent ecosystems is a product of adaptive capabilities, broad metabolic capacity, strain variance, and virulent traits in common with pathogens,” the authors wrote.

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