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

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.

FIGURE 1

(A) Alvinocaridids shrimps on the wall of an active vent chimney at Pacmanus (Manus basin). (B) Alvinocaridids shrimps around assemblages of barnacles and at La Scala (Woodlark Basin). (C) Sampling localities of alvinocaridid shrimps from Southwest Pacific basins. Colour dots depict hydrothermal vent field locations. Shapes depict shrimp species collected at a given sampling field.

FIGURE 2

Scanning Electron Microscopy (SEM) observations of microbial communities on the surface of Rimicaris variabilis branchiostegites and mouthparts. (A) Overview of the branchiostegite inner side. scale = 1 mm. (B) Enlargement of the branchiostegite inner side devoid of bacterial colonisation; scale = 500 μm. (C) Filamentous bacteria colonising the ventral setae along the external side of the branchiostegite. scale = 100 μm. (D) Single‐layered bacterial mats colonising inner side of R. variabilis branchiostegite. scale = 10 μm. (E) Overview of a scaphognathite dorsal side. scale = 1.5 mm. (F) Dense aggregations of filamentous bacteria covering plumose setae of the scaphognathite margin. scale = 200 μm. (G) Filamentous bacteria colonising the scaphognathite surface. scale = 50 μm. (H) Small cocci and rod‐shaped bacteria colonising the scaphognathite surface. scale = 50 μm.

FIGURE 3

Scanning Electron Microscopy (SEM) observations of microbial communities on the surface of Nautilocaris saintlaurentae and Manuscaris sp. branchiostegites and mouthparts. (A) Overview (composite image) of the inner side of N. saintlaurentae branchiostegite. scale = 1 mm. (B) Single‐layered bacterial mats colonising the inner side of Manuscaris sp. branchiostegite. scale = 50 μm. (C) Spot of filamentous bacteria colonising the most anterior part of the Manuscaris sp. branchiostegite. scale = 50 μm. (D) Dense aggregations of filamentous bacteria covering plumose setae of N. saintlaurentae scaphognathite margin. scale = 50 μm.

FIGURE 4

Isotopic niches of alvinocaridid shrimps from southwest Pacific basins. (A) Carbon and sulphur isotopic niches. (B) Carbon and nitrogen isotopic niches. (A,B) Each dot corresponds to the isotopic ratios of a shrimp individual; colours depict hydrothermal vent field locations and shapes depict different alvinocaridid species. (C) Model‐estimated bivariate standard area (SEA_B) for carbon and sulphur ellipses. (D) Model‐estimated bivariate standard area (SEA_B) for carbon and sulphur ellipses. (C,D) Boxes in dark grey, medium grey and light grey correspond, respectively, to the 50%, 75% and 95% credibility intervals of probability density function distributions of the model solutions, and black dots are the modes of these distributions. Red dots are the standard ellipse areas computed using a frequentist algorithm adapted for small sample sizes (SEA_C).

FIGURE 5

Constrained ordinations of 16S rRNA bacterial diversity by stable isotope ratios using canonical analysis on the principal coordinates (CAP) for each hosting organs. (A) Mouthparts bacterial communities; (B) Foreguts bacterial communities; (C) Midguts bacterial communities. Results from ANOVA‐like permutation tests for CAP are displayed on each plot panel. Stable isotopic ratios that significantly contributed to CAP results are marked with an asterisk (p < 0.01, see Table S3). Points are coloured by hydrothermal vent field locations with shapes depicting distinct alvinocaridid species.

FIGURE 6

Relative abundances of 16S rRNA gene sequence reads from bacterial communities associated with southwest Pacific alvinocaridids according to their classification at the phylum level (Silva 138 database). *Bacteria unaffiliated at the phylum level according to the Silva 138 database include also some ASVs belonging to the Deferribacterota phylum (see Figure 7). (A) Mouthparts bacterial communities; (B) Foreguts bacterial communities; (C) Midguts bacterial communities.

FIGURE 7

Phylogenetic trees of (A) Deferribacterota and unaffiliated bacterial ASVs and (B) Firmicutes ASVs agglomerated by similarity (h = 0.1). Panel A: Bacterial ASVs without phylum affiliation with the Silva 138 database are marked with an asterisk. All panels: Trees were constructed with the Maximum Likelihood method, based on the General Time Reversible model with Gamma distribution and allowing for some sites to be invariable (GTR + I + G). Prop: Relative abundance of the ASV among total sequence reads within the dataset. %Sim: % of similarity with the ASV best BLAST hit (R. exoculata or R. chacei digestive epibiont; details on Table S5). Each dot represents the occurrence of the lineage in an individual with shapes depicting alvinocaridid species (circle: R. variabilis; triangle: N. saintlaurentae; square: Manuscaris sp.) and colours depicting the hosting organ (red: mouthpart; green: stomach; blue: digestive tube).