The gill chamber epibiosis of deep‐sea shrimp Rimicaris exoculata: an in‐depth metagenomic investigation and discovery of Zetaproteobacteria

Abstract

The gill chamber of deep-sea hydrothermal vent shrimp Rimicaris exoculata hosts a dense community of epibiotic bacteria dominated by filamentous Epsilonproteobacteria and Gammaproteobacteria. Using metagenomics on shrimp from the Rainbow hydrothermal vent field, we showed that both epibiont groups have the potential to grow autotrophically and oxidize reduced sulfur compounds or hydrogen with oxygen or nitrate. For carbon fixation, the Epsilonproteobacteria use the reductive tricarboxylic acid cycle, whereas the Gammaproteobacteria use the Calvin-Benson-Bassham cycle. Only the epsilonproteobacterial epibionts had the genes necessary for producing ammonium. This ability likely minimizes direct competition between epibionts and also broadens the spectrum of environmental conditions that the shrimp may successfully inhabit. We identified genes likely to be involved in shrimp-epibiont interactions, as well as genes for nutritional and detoxification processes that might benefit the host. Shrimp epibionts at Rainbow are often coated with iron oxyhydroxides, whose origin is intensely debated. We identified 16S rRNA sequences and functional genes affiliated with iron-oxidizing Zetaproteobacteria, which indicates that biological iron oxidation might play a role in forming these deposits. Fluorescence in situ hybridizations confirmed the presence of active Zetaproteobacteria in the R. exoculata gill chamber, thus providing the first evidence for a Zetaproteobacteria-invertebrate association.

Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

“…Gill chamber samples were collected from R. exoculata specimens found at locations in the western flank of the Rainbow Ridge in the Atlantic Ocean (36°14=N, 33°54=W; 2,320 m depth; MAR site), where the average seawater temperature is 8.7°C (ranging from 3 to 25°C) ( Fig. 1) (19). Total DNA was extracted from the gill chambers of the collected specimens as previously described (19); from this DNA, a large-insert pCCFOS1 fosmid library was generated using the Escherichia coli EPI300-T1 R strain (Epicentre Biotechnologies; Madison, WI, USA), and the library was scored for the ability to hydrolyze ␣-naphthyl acetate and tributyrin (27,30).…”

“…1) (19). Total DNA was extracted from the gill chambers of the collected specimens as previously described (19); from this DNA, a large-insert pCCFOS1 fosmid library was generated using the Escherichia coli EPI300-T1 R strain (Epicentre Biotechnologies; Madison, WI, USA), and the library was scored for the ability to hydrolyze ␣-naphthyl acetate and tributyrin (27,30). Positive clones were selected, and their DNA inserts were sequenced using a Roche 454 GS FLX Ti sequencer (454 Life Sciences, Branford, CT, USA) at Life Sequencing SL (Valencia, Spain) or were completely Sanger sequenced using universal primers and subsequent primer walking.…”

“…Hydrochemistry data for the Mid-Atlantic Ridge (19,20) preparations, allowed us to infer habitat-specific features of the gill-associated bacterial enzymes as well as to evaluate their specificities and reactivities. Note that two of the enzymes reported in this study originate from an unknown species or possibly from genera related to Thiothrix and/or Leucothrix, a group of organisms largely neglected with respect to enzyme discovery; only a small number of isolates from these genera are available, and no enzymes from these genera have been characterized.…”

“…R. exoculata thrives along deep chimney walls in the gradient between hydrothermal fluids and cold, oxygenated, and slightly saline ambient waters (19). Based on functional gene surveys, it was found that shrimp specimens, including adult R. exoculata, host a dense bacterial community within their gill chambers (12).…”

Current Advances in Functional Genomics in Aquaculture

“…Whole genome shotgun sequencing has also been widely used in the study of environmental microbial communities and pathogens infecting diferent aquatic organisms. The major advantage with this approach is that it can be used to sequence whole genomes of known or unknown organisms using de novo assemblies unlike guided marker assemblies that are dependent on a reference gene [93][94][95][96].…”