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Symbiosis is a complex and ecologically integrated interaction between organisms that provides emergent properties key to their survival. Such is the case for the relationship between reef-building corals and their microbiome, a meta-organism, where nutritional and biogeochemical recycling provide the necessary benefits that fuel high reef productivity and calcification. The rapid warming and acidification of our oceans threatens this symbiosis.

This project addresses how relatively stress resistant and stress sensitive corals react to the environmental perturbations of increased temperature and reduced pH. It utilizes transcriptomic, epigenetic, and microbial profiling approaches, to elucidate how corals respond to environmental challenges. In addition to this profiling, work by the BSF Israeli partner will implement powerful analytical techniques such as network theory to detect key transcriptional hubs in meta-organisms and quantify biological integration.

This work will generate a stress gene inventory for two ecologically important coral species and a (epi)genome and microbiome level of understanding of how they respond to the physical environment. Acknowledgment of a role for epigenetic mechanisms in corals overturns the paradigm of hardwired genetic control and highlights the interplay of genetic and epigenetic variation that may result in emergent evolutionary and ecologically relevant properties with implications for the future of reefs. Furthermore, clarifying the joint contribution of the microbiome and host in response to abiotic change will provide an important model in metazoan host-microbiome biotic interactions.

Coral Hospital: Developing a Coral Reef Health Data Hub

Coral reefs sustain sea life in many parts of the world and are essential to the health of the planet and humanity, providing goods and services worth ca. 99 trillion USD globally. The ongoing decline and impending loss of tropical reef systems due to climate change calls out for comprehensive and centralized approaches. We propose that adaptation of modern analysis and diagnostic tools as well as remediation approaches pioneered in the field of human medicine can be consolidated and implemented to accelerate discovery of threatened reefs and provide avenues to prevent further degradation. Like humans, marine species such as corals are meta-organisms (holobionts), in which hosts partner with microbiomes that provide defense against disease and hostile microbes, fungi, and viruses, recycle nutrients, and acquire/produce metabolites, thereby shaping holobiont biology. In the case of corals, the microbiome also regulates redox responses to the photosynthetic algal symbionts that sustain reefs. The specific nature and control of secondary metabolite production by the coral or its symbionts, how these molecules shape the coral microbiome, and how agonistic/ antagonistic chemicals or signaling molecules influence the response to climate change such as “bleaching” is poorly understood. Bleaching, or the expulsion or loss of algal symbionts leading to a white, bleached appearance is one of the most important and widespread threats to corals and is driven primarily by warming oceans. Our research goal is to generate a mechanistic understanding of bleaching (based on holobiont metatranscriptomic and metabolomics data) and to build a portable tool for its early diagnosis (via a “dipstick” nanodevice) to provide the opportunity for early management interventions. These data and tools will create an innovative virtual “coral hospital”, analogous to the NIH translational medicine model that focuses on the role of environmental change leading to coral symbiotic breakdown and mortality.

The proposed research aims to:

  1. Determine the coral holobiont response to abiotic (thermal, pH) stress using metatranscriptomics and characterize the prokaryotic contribution to identify stress marker genes, identify affected pathways, and/or unique metabolite production.
  2. Analyze the metabolic fluxes and identify the active members of the coral microbiome via stable isotope tracing and probing (SIP), and link these active microbes to re-constructed microbial metagenomes.
  3. Build a hand-held nanodevice to monitor expression of stress marker genes and/or metabolites to determine their “state of health” under normal and bleaching conditions. This device will be made available to the public at the cost of production.
  4. Utilize the omics data to build a transferrable, model coral conservation program based on selection, breeding, and outplanting of resilient genotypes with broad species applicability.
  5. Generate a publically available open source data platform, the Coral Reef Health Data Hub, to provide significant tools to aid coral reef management on a global scale.