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

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.

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S1 Fig. 16S Maximum Likelihood (ML) consensus boostrap tree for Epsilonproteobacteria.
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S2 Fig. 16S Maximum Likelihood (ML) consensus boostrap tree for Gammaproteobacteria.
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S3 Fig. 16S Maximum Likelihood (ML) consensus boostrap tree for Mollicutes.
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S4 Fig. 16S Maximum Likelihood (ML) consensus boostrap tree for Deferribacteres.
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S5 Fig. Multidimensional Scaling (MDS) analyses for Rimicaris exoculata bacterial communities, including unidentified bacteria.
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S6 Fig. Frequencies of identified bacterial classes for the three life stages at Logatchev, including unidentified bacteria.
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S7 Fig. Species count and species richness for molt colors at Rainbow (A) and life stages at Logatchev (B).
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S8 Fig. Geographic network for Operational Taxonomic Unit (OTU) assigned to Gammaproteobacteria.
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S1 File. QIIME workflows and commands.
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S2 File. ANOVA testing of OTU frequency among groups, performed using the group_significance.py script in QIIME [29].
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S1 Table. Geographic coordinates, depth, year(s) and number of samples sequenced for Rimicaris exoculata collections from three vents along the Mid-Atlantic Ridge (MAR)
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S2 Table. Rimicaris exoculata sample counts by organs, molts and life stage categories.
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S3 Table. Metadata for each sample.
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S4 Table. Strategy for statistically testing the rejection of the null hypothesis of homogeneity of bacterial communities across molt stages, organs, life stages and vents.
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S5 Table. Counts and percentages of OTUs that were described only to domain level ‘bacteria’ for each sample (unclassified bacteria).
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S6 Table. ANOSIM test results for dataset including unclassified bacteria.
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S7 Table. Alpha diversity indices, species count and species richness (Chao1 and standard error) for dataset including unclassified bacteria.
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S8 Table. Frequency of OTUs assigned to class for each vent, including unclassified bacteria.
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S9 Table. ANOSIM and PERMANOVA results excluding unclassified bacteria.
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S10 Table. Frequency of OTUs assigned to class for each vent, excluding unclassified bacteria.
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S11 Table. Qualitative results of the most common haplotypes.
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How to cite
Cowart Dominique, Durand Lucile, Cambon-Bonavita Marie-Anne, Arnaud-Haond Sophie (2017). Investigation of bacterial communities within the digestive organs of the hydrothermal vent shrimp Rimicaris exoculata provide insights into holobiont geographic clustering. Plos One. 12 (3). e0172543 (1-22). https://doi.org/10.1371/journal.pone.0172543, https://archimer.ifremer.fr/doc/00376/48705/

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