Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima

Isis Guibert,Gergely Torda,Gael Lecellier,Xavier Pochon,Véronique Berteaux-Lecellier

doi:10.1186/s40168-020-00835-8

Abstract

BackgroundGiant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics.ResultsOur results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima.ConclusionsAltogether, our results suggest that at least three microbiotypes naturally exist in the studied clam populations, regardless of water temperature. These microbiotypes plausibly provide similar functions to the clam host via alternate molecular pathways as well as microbiotype-specific functions. This redundancy in functions among microbiotypes together with their specificities provides hope that giant clam populations can tolerate some levels of environmental variation such as increased temperature. Importantly, the composition of the benthic assemblage could make clams susceptible to infections by Vibrionaceae, especially when water temperature increases.Dmya7RRvZemunHrBwHskoDVideo abstract.

Highlights

Giant clams and scleractinian corals are keystone species of coral reef ecosystems
Mortality of giant clams Some mortality of T. maxima was observed during the experiments (Fig. 1; Additional file 1)
Sample numbers differ among experimental conditions (number of analyzed giant clams: n = 8 in T at the end of acclimation (T0) and n = 3 in AT.L, n = 3 in AT.S, n = 6 in PAT.L, n = 4 in PAT.S, n = 6 in T.L, and n = 6 in T.S at day 17 (T1))

Summary

Introduction

Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. Like some other marine bivalves, giant clams live in close partnership with unicellular dinoflagellate algae from the family Symbiodiniaceae [3, 4] that satisfy the majority of the clams’ carbon and energy needs [5, 6]. Microbiome profiling studies using the ITS2 and/or the LSU nuclear and chloroplast markers have recorded clade A (genus Symbiodinium), C (genus Cladocopium), D (genus Durusdinium), and G (genus Gerakladium) in giant clams [10,11,12] These genera are found in cnidarians [13, 14], but in contrast to the typically intracellular symbiosis with corals, algae reside in the clams’ siphonal mantle extracellularly [7]

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Conclusion