Combination Analysis of Metatranscriptome and Metagenome Reveal the Composition and Functional Response of Coral Symbionts to Bleaching During an El Niño Event

Abstract

With the abnormal rise in ocean temperatures globally in recent years, coral bleaching is becoming common and serious. However, the response mechanisms and processes of coral symbionts to bleaching are not well understood. In this study, metagenomics and metatranscriptomics were used to explore the composition of coral symbionts and their functions in response to coral bleaching. All four bleaching coral species displayed a significant reduction of the abundance and function of Dinophyceae-like eukaryotes at the DNA and RNA levels. However, different species of bleaching coral have their own characteristic symbiotic components. Bleaching Acropora tenuis and Goniastrea minuta corals exhibited a very high abundance of prokaryotes and associated gene functions, especially for opportunistic bacteria. In contrast, algae and fungi were identified as the main microbial associate components and had relatively high RNA abundance in bleaching Pocillopora verrucosa and Pocillopora meandrina. Different coral species, whether unbleached or bleaching, have the same symbiotic taxa that perform the same biological functions in vivo. Different stages of bleaching, or transitional states, were identified by different genome content and functional gene abundance among bleaching corals. These stages should be considered in future coral bleaching studies to accurately determine symbiont structure and function. An implicit hypothesis is that there is a causal relationship between the stability of eukaryotic communities and coral bleaching.

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Upper Gulf of Thailand

“…Gardner et al (2019) previously reported that Acropora muricata and Acropora gemmifera are more bleaching sensitive than P. lutea, and raised a hypothesis that the high bacterial diversity found in Acropora may negatively affect bleaching resistance. In general, our results support this hypothesis, as we found that bleached corals exhibited a higher degree of both prokaryotic and eukaryotic microbe Shannon indices (which include both OTU richness and evenness) than healthy corals, consistent with previous reports that claimed an association between increased community diversity and corals undergoing a bleaching event (McDevitt-Irwin et al, 2017;Gardner et al, 2019;Sun et al, 2020).…”

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Andaman Sea of Thailand

“…Nevertheless, it is hypothesized that the specific interaction put by these bacterial species and their host which was unique for each coral genus could be the underlining reason. Moreover, these specific community shifts for each coral genus were also evidenced in previous studies where specific bacterial taxa (e.g., Vibrionales, Rhodobacterales, Alteromonadales, Rhizobiales, Rhodospirillales, and Oceanospirillales) were found to be dominant in a healthy state of certain coral species but were also more abundant in a bleached state of other coral species (Bourne and Munn, 2005;McDevitt-Irwin et al, 2017;Sun et al, 2020).…”

“…Interestingly, when bleached these coral genera, they demonstrated the unique dysbiosis to their prokaryotic and microbial eukaryotic biodiversity (Figure 1 and Supplementary Figure 1). This species alteration could be due to the specific microbial composition and unique coral genus host-bacterial interaction Carlos et al, 2013;McDevitt-Irwin et al, 2017;Osman et al, 2020;Sun et al, 2020). Venn diagrams showed that bleached corals had relatively fewer number of genus OTUs than healthy corals in approximately half the number (Figure 1E; Pollock et al, 2019); nonetheless, this lower alpha diversity was not held true to every coral species, in part highlighting the report that the alpha diversity of the stressed corals, regardless of the stressor, could carry the more alpha diversity (McDevitt-Irwin et al, 2017), and these differences might be associated with coral species and their associated microbiome (Kusdianto et al, 2021).…”

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

“…When applied to marine systems, it may offer information on the biogeochemical and ecological roles of community members across ecosystems and environmental conditions. Marine metatranscriptomic studies to date have been conducted across spatial and temporal scales (e.g., Sun et al, 2020;Becker et al, 2021;Cohen et al, 2021;Coesel et al, 2021;Groussman et al, 2021;Harke et al, 2021;Muratore et al, 2022), and in concert with experimental incubations/microcosms in which key biological, chemical and/or physical parameters are manipulated (e.g., Alexander et al, 2015b;Bertrand et al, 2015;Lampe et al, 2018). Such metatranscriptomic investigations into marine protists have expanded our understanding of their nutrient physiology (Alexander et al, 2015a;Pearson et al, 2015;Lampe et al, 2018;Caputi et al, 2019;Kolody et al, 2019), nutritional modes (Hu et al, 2018;Lambert et al, 2021), coastal bloom dynamics (Gong et al, 2017;Ji et al, 2018;Metegnier et al, 2020), and contributions to ocean biogeochemistry (Carradec et al, 2018;Cohen et al, 2021).…”