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Rimicaris exoculata digestive tract dual symbiosis revealed through metagenomics

ABSTRACT: Metagenomic analyses of the hydrothermal shrimp Rimicaris exoculata digestive tract symbiosis.

PROVIDER: PRJEB50056 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR7998031_1.fastq.gz	Fastqsanger.gz
	ERR7998031_2.fastq.gz	Fastqsanger.gz
	ERR7998032_1.fastq.gz	Fastqsanger.gz
	ERR7998032_2.fastq.gz	Fastqsanger.gz
	ERR7998033_1.fastq.gz	Fastqsanger.gz

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Rimicaris exoculata

Project description:Rimicaris exoculata overview

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Rimicaris exoculata

Project description:Rimicaris exoculata Raw sequence reads

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Rimicaris exoculata

Project description:The transcriptome of Rimicaris exoculata

| PRJNA646342 | ENA

A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

Project description:BackgroundIn deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential.ResultsWe reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this.ConclusionOverall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.

| S-EPMC9636832 | biostudies-literature

Project description:Metagenomic analyses of the hydrothermal shrimp Rimicaris exoculata symbiosis

| PRJEB37577 | ENA

Rimicaris

Project description:Rimicaris sp. Raw sequence reads

| PRJNA345278 | ENA

Rimicaris kairei

Project description:Rimicaris kairei overview

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Gill chamber R. exoculata metagenome

Project description:Metagenomics of the gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata and discovery of zetaproteobacterial epibionts

| PRJEB3061 | ENA

Project description:Rimicaris exoculata egg microbiome

| PRJNA509116 | ENA

Investigation of bacterial communities within the digestive organs of the hydrothermal vent shrimp Rimicaris exoculata provide insights into holobiont geographic clustering.

Project description:Prokaryotic communities forming symbiotic relationships with the vent shrimp, Rimicaris exoculata, are well studied components of hydrothermal ecosystems at the Mid-Atlantic Ridge (MAR). Despite the tight link between host and symbiont, the observed lack of spatial genetic structure seen in R. exoculata contrasts with the geographic differentiation detected in specific bacterial ectosymbionts. The geographic clustering of bacterial lineages within a seemingly panmictic host suggests either the presence of finer scale restriction to gene flow not yet detected in the host, horizontal transmission (environmental selection) of its endosymbionts as a consequence of unique vent geochemistry, or vertically transmitted endosymbionts that exhibit genetic differentiation. To identify which hypothesis best fits, we tested whether bacterial assemblages exhibit differentiation across sites or host populations by performing a 16S rRNA metabarcoding survey on R. exoculata digestive prokaryote samples (n = 31) taken from three geochemically distinct vents across MAR: Rainbow, Trans-Atlantic Geotraverse (TAG) and Logatchev. Analysis of communities across two organs (digestive tract, stomach), three molt colors (white, red, black) and three life stages (eggs, juveniles, adults) also provided insights into symbiont transmission mode. Examining both whole communities and operational taxonomic units (OTUs) confirmed the presence of three main epibionts: Epsilonproteobacteria, Mollicutes and Deferribacteres. With these findings, we identified a clear pattern of geographic segregation by vent in OTUs assigned to Epsilonproteobacteria. Additionally, we detected evidence for differentiation among all communities associated to vents and life stages. Overall, results suggest a combination of environmental selection and vertical inheritance of some of the symbiotic lineages.

| S-EPMC5351989 | biostudies-literature

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