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.

Keywords: Hawaii; Metabolomics; Montipora capitata; Multi-omics analysis; Network analysis; Stony coral; Stress biology; Thermal stress; Transcriptomics.

Figure 1. Analysis of the rice coral Montipora capitata.

(A) M. capitata photographed in waters near the Hawaiʻi Institute of Marine Biology (HIMB) in O‘ahu, HI. Photo credit: Debashish Bhattacharya. (B) Color scores and their standard errors for the ambient (green line) and high temperature (red line) treated M. capitata nubbins that were cultured in tanks at HIMB. Low color scores indicate the bleaching phenotype in coral holobionts. The omics data sampling points are shown with the white lines at T1 (5/22/19), T3 (6/03/19), and T5 (6/07/19) (for details, see Williams et al. (2021)). The date of the New Moon in June 2019 is also shown.

Figure 2. Gene co-expression analysis of M. capitata.

Network of differentially expressed genes in M. capitata at TP1 (the early thermal stress phenome) showing the different gene modules and their interactions. Purple nodes are up-regulated and green nodes are down-regulated. All dark genes are marked with DG with M. capitata gene IDs shown. The down-regulated genes in M6 that are dominated by members of the small cysteine-rich protein family, often involved in signaling and protein interactions, are annotated. Only selected genes are annotated in this network and module annotations provide a representation of overall function(s). The annotations of all genes (when known) in each module in this, and all networks generated by this study, are available in File S1 (Cytoscape file).

Figure 3. M. capitata TP5 module M1 of significantly down-regulated genes that includes many transporters.

The legend for level of downregulation is shown. Dark genes are identified with DG and genes encoding sodium-coupled transporters are marked with ST.

Figure 4. M. capitata TP5 module M4 of significantly upregulated genes.

(A) The legend for level of upregulation is shown. Dark genes are identified with DG. (B) Maximum likelihood (IQ-Tree; Trifinopoulos et al., 2016) phylogenetic analysis of paralogous coral dark genes g59122 and g59133 and related homologs inferred using default parameters and 1,000 ultrafast bootstrap replicates. The results of the bootstrap analysis are shown on the branches when >60%. The legend shows the expected substitution rate for the protein dataset. Complex and robust coral species are shown in brown and blue text, respectively.

Figure 5. Analysis of sex steroids in M. capitata.

Accumulation of a variety of predicted sex steroids in M. capitata nubbins over the duration of the ambient and thermal stress treatments as well as from wild populations collected after T5 from the same colonies used in the tank experiments (FS; for details, see Williams et al., 2021). Each dot represents a single nubbin measurement from four different genotypes (2–4 nubbins (usually 3)/genotype were sampled). The pattern of metabolite accumulation suggests that these steroid levels increased at T5 (Fig. 1B), which preceded the expected mass spawning event (arrow labeled with “New Moon” between T3 and T5) for this species in June 2019. The putative functions of these steroids are as follows: 17a-hydroxypregnenolone–a neuromodulator generated by the action of mitochondrial cytochrome P450 enzyme 17α-hydroxylase (CYP17A1) that is an intermediate in the delta-5 pathway of biosynthesis of gonadal steroid hormones and adrenal corticosteroids; 17a-hydroxyprogesterone–progestogen that is a chemical intermediate in the biosynthesis of androgens, estrogens, glucocorticoids, and mineralocorticoids; estriol–female sex hormone (weak estrogen), with a large amount produced in humans by the placenta; estrone–another female sex hormone (weak estrogen), binds to the estrogen response element and promotes transcription of genes involved in the female reproductive system functions; androstenedione-weak androgen steroid hormone, precursor of testosterone and other androgens; testosterone-primary male sex hormone involved in development of male reproductive tissues.