• Hollie Putnam, University of Rhode Island, United States

Reef-building corals form massive calcium carbonate structures that are visible from space and support invaluable reef goods and services. These corals are metaorganisms whose functionality comes from the holobiont integration of the cnidarian host, its primary dinoflagellate endosymbionts (family Symbiodinaceae), and a multitude of bacteria, archaea, viruses, and fungi that are surface, tissue, and skeletal dwelling symbionts. The study of this symbiotic system as a fascinating functional puzzle has intensified with the rapid decline in coral cover and growing threat of reef extinction due to climate change factors, such as increasing seawater temperatures and ocean acidification. In particular, the high frequency of mass bleaching events, where thermal stress causes dysbiosis and loss or expulsion the Symbiodinaceae and mass coral mortality, has sharpened our focus on these threatened organisms. Technological advances have allowed a rapid expansion of coral and symbiont sequence data for studies of coral response to stress, but bioinformatic challenges remain in analyzing and interpreting this wealth of metaorganism data.

• Cheong Xin Chan, University of Queensland, Australia

Coral reefs are hotspots of marine biodiversity. The ecological success of corals in nutrient-poor waters relies on photosynthetic algal symbionts (Symbiodiniaceae) for supply of fixed carbon as energy, and nutrients. However, the implication of the evolution of these algae and its implications on coral evolution is poorly understood. Genomes of Symbiodiniaceae present a bioinformatics challenge, because of their immense sizes (1-3 Gbp) and highly idiosyncratic genome features. In this talk, I will present our recent effort to generate 12 de novo genome assemblies from diverse Symbiodiniaceae species and their free-living relative, and how we developed a customised computational workflow for predicting genes from these genomes. Comparative analysis reveals unexpectedly high sequence and structural divergence, and conserved lineage-specific gene families of unknown function. Many genes are encoded in unidirectional clusters, and some critical functions are encoded in tandemly repeated single-exon genes. Our results underscore the rapid evolution of coral symbionts that comprise a massive, undiscovered phylogenetic diversity, and elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation, e.g. by enhancing transcriptional responses. These outcomes provide an important reference for research of coral holobionts and their resilience in changing environments.

• Judith Klein-Seetharaman, Colorado School of Mines, United States

Mining of the large coral and symbiont sequence data is a challenge but also provides an opportunity for understanding functionality and evolution of these and other non-model organisms. Much more information than for any other eukaryotic species is available for human, especially related to signal transduction and diseases. However, the coral cnidarian host and human have diverged over 700 million years ago and homologies between proteins are therefore often in the gray zone or undetectable with traditional Blast searches. Through remote homology detection using hidden markov models we can identify putative candidate human homologues in the cnidarian genome. However, for many proteins, the human genome alone contains multiple family members with similar or more divergence in sequence. To illustrate and address this challenge, we developed a pipeline for mapping membrane receptors in human to membrane receptors in corals. We will discuss functional implications for the presence and absence of membrane receptor homologues for communication across different cell types of the cnidarian host and across the microbiome. This pipeline may prove generally useful, e.g. for other protein families or types of functions important to both corals and humans, such as wound healing and biomineralization, and for other non-model organisms including plants where discovery of human homologues can open novel avenues for agricultural applications.

• Mónica Medina, Pennsylvania State University, United States

Coral holobiont members – which include the coral host, the algal symbiont and a poorly characterized consortium of diverse microbial taxa – have different generation times and effective population sizes. These differences can have pronounced evolutionary and ecological consequences for holobiont members, especially under a rapidly changing climate. Corals tend to have slow generation times relative to their microbes, on the order of decades. Algal symbionts with different physiological adaptations to temperature are known to shift in abundance within a host in response to perturbations (e.g., global warming) over months to years. Coral associated prokaryotic microbial assemblages not only have very fast generation times, but their community composition can shift rapidly under changing environmental conditions.

Metabolic complementary analysis has revealed a keystone role for the coral microbiome in holobiont homeostasis. We performed temperature stress experiments on three Caribbean coral holobionts and examined their response via metatranscriptome sequencing. Our data have uncovered genes with lineage-specific expression level adaptation in both host and photosymbiont taxa as well as the potential roles for bacterial associates.

We have only scratched the surface of complex holobiont dynamics, yet these studies highlight the need for additional data and a comprehensive theoretical framework that integrates ecological and evolutionary time scales.

• Debashish Bhattacharya, Rutgers University, United States

Coral reef systems are under threat globally due to anthropomorphic climate change. Understanding the response of the coral holobiont to abiotic and biotic stress is therefore crucial to aid conservation efforts. The most pressing problem is “coral bleaching”, usually precipitated by prolonged thermal stress that disrupts the algal symbiosis sustaining the holobiont. Here we used metabolomics to address the following questions: how does the coral holobiont metabolome respond to heat stress, and can we find diagnostic markers of that stress prior to the onset of bleaching? We studied the heat tolerant Montipora capitata and heat sensitive Pocillopora acuta coral species from the Hawaiian reef system. Untargeted LC-MS analysis uncovered a suite of known and novel metabolites that accumulate under heat stress, including a variety of dipeptides, some of which occupy hub positions in metabolite networks, and are present in both coral species. The structures of four of these were determined (Arginine-Glutamine, Alanine-Arginine, Valine-Arginine, Lysine-Glutamine). These dipeptides show differential accumulation in symbiotic and aposymbiotic (alga free) individuals of the sea anemone Aiptasia, suggesting their animal derivation and algal symbiont related function. We have identified a suite of metabolites associated with thermal stress in corals that provide tools to diagnose coral health in the wild.