Symbioses of alvinocaridid shrimps from the South West Pacific: No chemosymbiotic diets but conserved gut microbiomes

Type Article
Date 2023-12
Language English
Author(s) Methou PierreORCID1, Cueff-Gauchard ValerieORCID2, Michel LoïcORCID2, 3, Gayet Nicolas2, Pradillon FlorenceORCID2, Cambon-Bonavita Marie-AnneORCID2
Affiliation(s) 1 : X‐STAR Japan Agency for Marine‐Earth Science and Technology (JAMSTEC) Yokosuka, Japan
2 : Univ Brest Ifremer, CNRS, Unité Biologie des Environnements Extrêmes marins Profonds Plouzané France
3 : Laboratory of Oceanology, Freshwater, and Oceanic Sciences Unit of reSearch (FOCUS) University of Liège Liège ,Belgium
Source Environmental Microbiology Reports (1758-2229) (Wiley), 2023-12 , Vol. 15 , N. 6 , P. 614-630
DOI 10.1111/1758-2229.13201
WOS© Times Cited 1
Abstract

Rimicaris exoculata shrimps from hydrothermal vent ecosystems are known to host dense epibiotic communities inside their enlarged heads and digestive systems. Conversely, other shrimps from the family, described as opportunistic feeders have received less attention. We examined the nutrition and bacterial communities colonising ‘head’ chambers and digestive systems of three other alvinocaridids—Rimicaris variabilis, Nautilocaris saintlaurentae and Manuscaris sp.—using a combination of electron microscopy, stable isotopes and sequencing approaches. Our observations inside ‘head’ cavities and on mouthparts showed only a really low coverage of bacterial epibionts. In addition, no clear correlation between isotopic ratios and relative abundance of epibionts on mouthparts could be established among shrimp individuals. Altogether, these results suggest that none of these alvinocaridids rely on chemosynthetic epibionts as their main source of nutrition. Our analyses also revealed a substantial presence of several Firmicutes and Deferribacterota lineages within the foreguts and midguts of these shrimps, which closest known lineages were systematically digestive symbionts associated with alvinocaridids, and more broadly for Firmicutes from digestive systems of other crustaceans from marine and terrestrial ecosystems. Overall, our study opens new perspectives not only about chemosynthetic symbioses of vent shrimps but more largely about digestive microbiomes with potential ancient and evolutionarily conserved bacterial partnerships among crustaceans.

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Publisher's official version 17 5 MB Open access
Figures S1-S2 2 273 KB Open access
Table S1. Summary of alvinocaridid shrimp sampling and conducted analyses with individual GenBank Identifier. 18 KB Open access
Table S2. p values of Dunn tests used for isotopic ratio comparisons (δ13C, δ15N δ34S) among alvinocaridid species and vent fields. 12 KB Open access
Table S3. Results from ANOVA-like permutation tests for RDA by term with 999 permutations for each hosting organs. 9 KB Open access
Table S4. Results from PERMANOVA tests of isotopic ratios with 999 permutations for each hosting organs. 10 KB Open access
Table S5. Best Blast hit results of Firmicutes ASVs from hosting organs of SW Pacific alvinocaridid shrimps 10 KB Open access
Preprint - 10.1101/2023.02.08.527621 26 1 MB Open access
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How to cite 

Methou Pierre, Cueff-Gauchard Valerie, Michel Loïc, Gayet Nicolas, Pradillon Florence, Cambon-Bonavita Marie-Anne (2023). Symbioses of alvinocaridid shrimps from the South West Pacific: No chemosymbiotic diets but conserved gut microbiomes. Environmental Microbiology Reports, 15(6), 614-630. Publisher's official version : https://doi.org/10.1111/1758-2229.13201 , Open Access version : https://archimer.ifremer.fr/doc/00855/96672/