Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata

Abstract

Background Corals, which form the foundation of biodiverse reef ecosystems, are under threat from warming oceans. Reefs provide essential ecological services, including food, income from tourism, nutrient cycling, waste removal, and the absorption of wave energy to mitigate erosion. Here, we studied the coral thermal stress response using network methods to analyze transcriptomic and polar metabolomic data generated from the Hawaiian rice coral Montipora capitata. Coral nubbins were exposed to ambient or thermal stress conditions over a 5-week period, coinciding with a mass spawning event of this species. The major goal of our study was to expand the inventory of thermal stress-related genes and metabolites present in M. capitata and to study gene-metabolite interactions. These interactions provide the foundation for functional or genetic analysis of key coral genes as well as provide potentially diagnostic markers of pre-bleaching stress. A secondary goal of our study was to analyze the accumulation of sex hormones prior to and during mass spawning to understand how thermal stress may impact reproductive success in M. capitata. Methods M. capitata was exposed to thermal stress during its spawning cycle over the course of 5 weeks, during which time transcriptomic and polar metabolomic data were collected. We analyzed these data streams individually, and then integrated both data sets using MAGI (Metabolite Annotation and Gene Integration) to investigate molecular transitions and biochemical reactions. Results Our results reveal the complexity of the thermal stress phenome in M. capitata, which includes many genes involved in redox regulation, biomineralization, and reproduction. The size and number of modules in the gene co-expression networks expanded from the initial stress response to the onset of bleaching. The later stages involved the suppression of metabolite transport by the coral host, including a variety of sodium-coupled transporters and a putative ammonium transporter, possibly as a response to reduction in algal productivity. The gene-metabolite integration data suggest that thermal treatment results in the activation of animal redox stress pathways involved in quenching molecular oxygen to prevent an overabundance of reactive oxygen species. Lastly, evidence that thermal stress affects reproductive activity was provided by the downregulation of CYP-like genes and the irregular production of sex hormones during the mass spawning cycle. Overall, redox regulation and metabolite transport are key components of the coral animal thermal stress phenome. Mass spawning was highly attenuated under thermal stress, suggesting that global climate change may negatively impact reproductive behavior in this species.

Development of a portable toolkit to diagnose coral thermal stress

“…Additional research needs to be done to understand the cause of this response. Nonetheless, the results are consistent with the widely accepted hypothesis that M. capitata adapts well to bleaching conditions 12 . PCA of the M. capitata test strip results shows a clear separation of the T1-HT coral data from the T3-HT and T5-HT values, with the ambient and field samples intermixed among the latter two timepoints (Fig.…”

“…Bleaching in corals which are incapable of obtaining adequate energy stores through heterotrophy results in diminished growth rates, degraded reproductive capacity, amplified susceptibility to disease, and elevated mortality rates for the entire colony 20 . Although ketosis has not been explored in cnidarians, transcriptomic data generated from the M. capitata samples measured in this study 12 demonstrate expression of the KEGG pathway for degradation of ketone bodies (Fig. S1 ).…”

“…Samples from three different coral experiments (two bleaching experiments and one environmental survey) were used to assess the response and utility of the different tests on each strip. The first bleaching experiments was done in 2019 on two Hawaiian species: Montipora capitata (stress resistant) and Pocillopora acuta (stress sensitive); this research has been previously described in detail 11 , 12 . Briefly, three M. capitata colonies (different genotypes) were selected, with samples collected from each in triplicate at three timepoints (referred to as T1, T3, and T5) that span a period of prolonged thermal stress (16 days).…”

“…Healthy corals are expected to exhibit a broad array of natural biological responses under normal conditions, and only when they are stressed for prolonged periods due to local heating events or other insults do we expect stress markers to rise above the background "noise" inherent in complex systems 11 , 12 . Achieving the level of sensitivity required to assess coral stress prior to bleaching is the gold standard for field applications and recent data suggest that gene expression, proteomic, and metabolomic markers are promising in this regard 12 – 15 . These measures of stress however require specialized equipment and may prove costly or challenging to apply at remote reef sites that lack lab facilities or other needed infrastructure (these issues can, of course, be addressed over time).…”

Expression plasticity regulates intraspecific variation in the acclimatization potential of a reef-building coral

“…Raw reads were de-duplicated using tagseq_clipper.pl ( https://github.com/z0on ) and trimmed with Cutadapt 3.7 70 to remove poly-A tails and low quality bases. We quantified filtered reads using Salmon 1.8 71 (--validateMappings, --gcBias, --seqBias) against a transcriptome prepared from 72 . To prepare the reference and isolate host sequences, we used bwa-mem 0.7.17 73 to align the metatranscriptome against the M. capitata genome 74 and excluded unmapped contigs before clustering similar sequences using cd-hit-est 4.8.1 (-c 0.95 -G 0 -aL 0.3 -aS 0.3) 75 .…”