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

Abstract

Global warming has caused elevated seawater temperature and coral bleaching, including events on shallow reefs in the upper Gulf of Thailand (uGoT). Previous studies have reported an association between loss of zooxanthellae and coral bleaching. However, studies on the microbial diversity of prokaryotes and eukaryotes (microbiome) as coral holobionts are also important and this information is still limited in the uGoT. To address this shortcoming, this report provided baseline information on the prokaryotic (bacteria and archaea) and eukaryotic microbes of healthy and bleached colonies of four prevalent corals Acropora humilis, Acropora millepora, Platygyra sinensis, and Porites lutea and surrounding seawater and sediments, using 16S and 18S rRNA gene next-generation sequencing. Both prokaryotic and eukaryotic microbes showed isolated community profiles among sample types (corals, sediment, and seawater) (ANOSIM: P < 0.001, R = 0.51 for prokaryotic profiles and P < 0.001, R = 0.985 for eukaryotic microbe profiles). Among coral species, P. sinensis showed the most diverse prokaryotic community compared with the others (ANOSIM: P < 0.001, R = 0.636), and P. lutea showed the most diverse eukaryotic microbes (P = 0.014, R = 0.346). Healthy and bleached corals had some different microbiomes in species and their prevalences. For instance, the significant increase of Alphaproteobacteria in P. sinensis resulted in reduced prokaryotic community evenness and altered potential metabolic profiles (i.e., increased amino acid metabolism and genetic information processing and transcription, but decreased prokaryotic functions in cell motility, signaling, and transduction). For eukaryotic microbes, the loss of the algal Symbiodinium (colloquially known as zooxanthellae) in bleached corals such as P. lutea resulted in increased Chromista and Protista and, hence, clearly distinct eukaryotic microbe (including fungi) communities in healthy vs. bleached colonies of corals. Bleached corals were enriched in bacterial pathogens (e.g., Acinetobacter, Helicobacter, Malassesia, and Aspergillus) and decreased coral-beneficial prokaryotic and eukaryotic microbes (e.g., Rhizobiales and Symbiodinium). Additionally, this study identified microbiome species in bleached P. lutea that might help bleaching recovery (e.g., high abundance of Rhizobiales, Oceanospirillales, Flavobacteriales, and Alteromonadales). Overall, our coral-associated microbiome analyses identified altered diversity patterns of bacteria, archaea, fungi, and eukaryotic microbes between healthy and bleached coral species that are prevalent in the uGoT. This knowledge supports our ongoing efforts to manipulate microbial diversity as a means of reducing the negative impacts of thermal bleaching events in corals inhabiting the uGoT.

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

“…Three independent replicates were collected for each sample. Healthy (H) and bleached (B) coral colonies were determined via their appearance [healthy coral colony appeared light or dark brown color (natural color, 0% sign of bleaching), and bleached coral colony appeared white color by on-site marine scientist divers (S. Chavanich, S. Jandang, and V. Viyakarn) (Bulan et al, 2018a,b;Kusdianto et al, 2021)]. The four coral genera had an identical bleached appearance, and the bleached sample was collected in the bleached area (completely white area) of coral color that bleached more than 50%.…”

“…For seawater, 2.5 L was filtered through a sterile 0.22-µm filter membrane (Merck Millipore, MA, United States) and the filtered membrane was used. Metagenomic DNA was extracted using Power Soil DNA Isolation Kit for coral and sediment samples, and Power Water DNA Isolation Kit for seawater samples (MoBio, Carlsbad, CA, United States), following the instructions of the manufacturer and previous works of literature (Bulan et al, 2018a,b;Kusdianto et al, 2021). The quantity and quality of the extracted DNA were analyzed by NanoDrop TM 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States) and agarose gel electrophoresis (0.55% agarose gel w/v).…”

“…Then, these data samples for 16S and 18S rRNA genes sequences were normalized at 9,045 and 38,429 sequences per sample to prevent a bias from various sequencing depth across samples when comparisons among samples and groups were performed; noted a data sample with fewer sequences than the normalization (samples CAH2-3, CCH1-3, and CRH1-3) was pooled with other independently replicate sample followed by subsampling to normalization or using all those sequences. Venn diagram, alpha diversity (Chao1 richness, and Shannon diversity indices), and beta diversity [thetaYC dissimilarity index and non-metric multidimensional scaling (NMDS)], with default parameters, were determined using Mothur (Schloss et al, 2009;Kusdianto et al, 2021).…”

“…(25-49%), in which scientists had suggested to be associated with the different Symbiodinium clades between Acropora and Porites (C3 and C15, respectively) (Fisher et al, 2012;Phongsuwan and Chansang, 2012;Gardner et al, 2019). Additionally, a shift of Symbiodinium clades from type C in healthy Acropora millepora to type D in bleached A. millepora (Berkelmans and van Oppen, 2006;Oliver and Palumbi, 2011) and the higher abundance of coral pathogens had been reported in bleached Acropora (Roder et al, 2014;Kusdianto et al, 2021).…”

“…Following the aforementioned reports that successfully utilized universal 16S and 18S rRNA genes to analyze coral associated prokaryote and eukaryote diversities (Hadziavdic et al, 2014;Wang et al, 2014;Banos et al, 2018;Kusdianto et al, 2021), this report, therefore, utilized similar methods [16S and 18S rRNA genes next-generation sequencing (NGS)] to describe prokaryotic and eukaryotic microbiomes in healthy and bleached corals Acropora humilis, Platygyra sp., Pocillopora damicornis, and Porites lutea, in the Andaman Sea around Racha Yai Island, Phuket province, along with the microbiomes of the surrounding seawater and sediments, during a thermal bleaching event in 2016. Previously, the coral-associated microbiome of prokaryotes during the 2016 bleaching event in the Andaman Sea had been investigated (Pootakham et al, 2018); however, that study only reported on P. lutea leaving other three coral genera that are prevalent in the studied locations and also did not include analyses of the eukaryote microbiomes.…”