Ocean Genomics Horizon Scan

Marine Threat: Climate Change

See also 

The impact of human development and increased ocean temperatures are causing frequent and widespread global coral bleaching events and die-offs. Coral reefs are declining at an average global rate of 1 – 2.5 percent per year, but some reefs are declining at considerably faster rates. Fifty percent of the planet’s corals have been lost already, according to the most recent estimates, and models predict around 90 percent will be lost by 2050. Even more worrisome – there is no global plan to deal with the failure of biotic reef infrastructure and maintain coral reefs beyond 2050.

Pictured Above: Bleached coral on the Great Barrier Reef. As average sea surface temperatures around the world continue to increase, so too do the frequency and extent of global bleaching events. 

Based on interviews with coral biologists pursing the development of state-of-the-art technologies for coral resilience and restoration, our Key Findings below highlight seven essential innovations for coral conservation. Several teams around the world are focused on the science mechanics of coral restoration, while others are working to understand and harness elements of resilience that occur or develop naturally within threatened coral species. These efforts are helping to guide the preservation of resilient coral genotypes remaining on reefs, the translocation of more resilient strains within a reef area, and the ex situ efforts to preserve and grow corals in aquariums.

Scroll down the page to review these Key Findings; each highlighted area provides background information on the current challenge, the potential areas for innovation, identifies the leading scientists and initiatives underway in the field, and flags some of the risks and challenges.

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Cryopreservation and Coral Sperm Banking

As mature coral populations continue to die off due to a combination of stressors hurting reefs around the world, coral reproductive capabilities are diminishing. Simply put, not only are there fewer corals today, there are fewer healthy sperm and eggs to sample and preserve, and there will be even fewer in the years to come. With dying populations and declining fertility, affected corals are on the road to extinction.

As corals become further endangered or even extinct in the wild, cryopreserved coral samples will serve as enormously valuable resources for both scientific and restoration efforts. However, at the present time, coral cryopreservation is enormously limited in scope: only a small fraction of reefs around the world have been sampled and there is very little experience and knowledge in the field outside the few originator laboratories.

Cryopreservation serves as an extremely reliable insurance policy for coral biotechnology because it allows coral cells to be put on ice until later breakthroughs can be applied to corals for research or restoration purposes.

While the cryopreservation of eggs remains challenging, significant advances have made freezing coral sperm and larvae. Coral larvae cryopreservation )the preservation of corals shortly after the point of conception) produces an essential resource for future conservation of reefs. The recently developed ability to successfully preserve coral larvae means researchers no longer must rely on the annual natural spawning events. With frozen larvae, researchers can work with coral larvae on a weekly basis, which has speed up research to grown and achieve coral settlement by a factor of fifty or more.  

Dr. Mary Hagdorn
Dr. Kristen Marhaver

The Hagedorn group at the Smithsonian Institution has established genetic banks for coral conservation, successfully frozen embryonic coral cells and sperm, and successfully thawed sperm to fertilize coral eggs, which subsequently grew into coral larvae and settled. Dr. Mary Hagedorn’s recent work with Dr. Kristen Marhaver at the Caribbean Marine Biological Institute (CARMABI) demonstrated the successful use of cryopreserved sperm to fertilize and develop 4700 juvenile corals, the largest living wildlife population ever created with cryopreserved material.

The largest collection of frozen coral cells is at Australia-based Taronga Conservation Society’s “Frozen Zoo”, which has enough frozen material to generate approximately 200 million coral colonies.

The key remaining technical challenge for coral cryopreservation is the inability to preserve coral eggs (ova). At this time, only coral sperm and larvae have been successfully frozen. Frozen sperm still represents a highly valuable resource that may be used to bank alleles and genotypes on a reef. But without a supply of frozen ova, cryopreserved sperm can only be paired with fresh ova.

Improved methods for freezing coral sperm are also essential. Current methods require highly concentrated sperm (not easy to obtain in open water) and are limited in throughput.

Since many coral species spawn only once a year, more trained divers and collectors are needed at the most vulnerable sites.

Best practices for collection and cryopreservation techniques need to be established and training materials disseminated before significant scale can be reached.

At this time, it appears that there is no single dedicated coral cryopreservation facility available, nor is there a network that can coordinate the redundant sampling and banking required to provide long-term confidence that corals are banked in perpetuity.

Regulatory challenges: The Convention on the International Trade of Endangered Species (CITES) and the Nagoya Protocol require extensive licensing and permitting, which restricts the collection and transporting of biological materials.

Inducible Captive Spawning

Corals are almost entirely sourced using three approaches:

  1. by directly collecting adult corals from the wild,
  2. by collecting larvae from remote reefs during seasonal broadcast spawning events, or
  3. by fragmenting live corals.

These three approaches cannot be universally applied to all corals. These techniques are also unsustainable. They rely on collecting or propagating fragile wild genotypes that are being lost at alarming rates. Compounding these issues is the problem that corals cannot be easily bred in laboratory or aquarium settings without highly specialized equipment and training. Ultimately these issues translate to a major problem for coral researchers and conservationists: there is no truly reliable or convenient way to source corals or their larvae.

Emerging inducible spawning methods allow new corals to be sourced in a laboratory environment. Inducing spawning depends on an accurate simulation of corals’ natural environments in aquaria, including photoperiod, seasonal insolation, lunar cycles, and seasonal sea surface temperatures found in nature. 

The new spawning methods have successfully induced the captive broadcast spawning of at least 18 Acroporid species in a completely closed environment. Twenty-nine to 100 percent of colonies were shown to produce sperm and oocytes (egg cells).  

Coral eggs generated from inducible spawning have since been fertilized with sperm of corals of the same species via IVF procedures, demonstrating that the technique can be used to generate offspring corals with parents from different locations that would not naturally occur. Inducible spawning thus provides a reliable source of eggs that could be paired with a coral sperm banking program to support a large breeding program focused on developing novel genetic diversity. In particular, the technique potentially could be applied to corals that have survived stressor events in the wild, allowing new strains of thermally-tolerant corals to be produced.

Jamie Craggs

Since 2012, the Project Coral team headed by Jamie Craggs at the Horniman Museum Aquarium in London has been pioneering the inducible spawning technique to predictably induce broadcast coral spawning events in closed system aquariums. The group has established collaborations with Florida Aquarium and the California Academy of Sciences, both of which are now scaling up the approach for use in additional species. The team in Florida, led by Keri O’Neil, is focused on scaling up coral production for restoration activities in in the Gulf, Atlantic, and Caribbean, while the Cal Academy team led by Dr. Rebecca Albright is focused on ocean acidification research.

Inducible spawning remains a niche technique, and its nascent state has been severely limited to date by the intensive training required, which is currently 12 months per person/team. 

The Project Coral team has noted the challenge in training as the technique must be learned tacitly, on location, or over great distances using one-on-one support.

Moreover, large aquariums are needed set up and operate these systems with substantial cost for materials and staffing.

Stem Cell Technology Development

Coral stem cells have never been isolated or propagated in a laboratory setting, and experts have identified this capability as the most important priority for achieving genetic resilience in corals before even more corals are lost due to climate change. Stem cells have two important properties:

    1. Self-renewal, the ability to undergo numerous cycles of cell division without aging, and
    2. Potency, the capacity to differentiate into specialized cells and give rise to individual tissues or organisms.

Stem cells derived from adult tissues can be kept in culture and used for experimentation or to clone and propagate an individual organism without the use of sexual reproduction, and are therefore a useful and versatile new tool for restoration programs and research.

Putative stem cells have recently been isolated from corals, using mechanical dissociation of soft tissues from their skeletons and a technique known as subsequent fluorescent activated cell sorting.

Recent work has demonstrated the value of “coral tissue plugs,” in which a recipient coral from one reef has received a donor plug from another reef and subsequently exhibited improved fitness. The convergence of these two areas of research are likely to give rise to a stem cell therapy approach for corals.

The ability to manipulate coral stem cells and reconstitute colonies opens up the possibility of cryopreservation of coral genotypes from adult tissues, eliminating the difficult sourcing of gametes. An incoming generation of coral stem cell experiments and the development of protocols to isolate stem cells from wild coral tissues could lay the groundwork for coral stem cell applications to rescue dying corals at scale.

Dr. Nikki Traylor-Knowles

Dr. Nikki Traylor-Knowles at the University of Miami and Dr. Benyamin Rosental at Ben Gurion University have proposed research to further characterize and purify putative stem cells and refine methods for their isolation; investigate their functionality and location in the holobiont using already developed cell tracking and transplantation methods; develop methods for in vitro stem cell propagation; and demonstrate the feasibility of stem cell transplantation as a therapeutic approach for saving corals.

Identifying totipotency – the ability of a cell to become any other – in coral stem cells may prove challenging. The divergence of cell surface markers between coral species means that the successful identification of stem cells could require challenging experimentation and fine-tuning of protocols on a species-by-species basis.

It is also unclear how effective the use of stem cell therapy for restoration will be. Success will generally depend on the precise way in which stem cells are to be used in each application, as well as the desired scale and production capacity of each group. 

There is also the challenge of assembling operating stem cell hardware-software-wetware systems, the living and automated tools needed to manipulate coral stem cells with precision. While there have been promising innovations that partially bring elements of this platform together, such as the coral-on-a-chip system, these have not been used for significant R&D beyond the originator lab.

Lastly, there remain unanswered questions about the viability of deploying stem cells on a wild reef; proponents will have to demonstrate that stem cell therapies are an appropriate and scalable tool for coral restoration in the wild. Permission for stem cell transplantation, even without the use of genetic engineering, will likely require lengthy examination by public institutions, as there is no precedent for this in conservation science or biotechnology enterprise to date.

Functional Genomics of Coral Bleaching & Assisted Evolution

Coral bleaching is a phenomenon involving the expulsion of photosynthetic symbiodinium from coral polyps. It is thought that the departure of one or more dominant or co-dominant symbiodinium species during a period of stress leads to the invasion of another more appropriate species that can maintain photosynthesis function and resolve the stress response. Therefore, bleaching is typically a temporary event that lasts only a few days or weeks, and is a healthy coral’s reaction to changing conditions.

However, when the period of stress becomes protracted, bleaching can become chronic, and the loss of the algal source of nourishment can cause the polyps to starve and die. The precise mechanism of coral bleaching remains unknown and is complicated in that the breakdown of the endosymbiotic relationship between corals and symbiodinium can be triggered by a large number of stressors, including high or low temperature, UV radiation, reduced salinity, microbial infection, marine pollutants, and even an absence of light. Taken together, this implies a complex set of genetic circuits is involved in the maintenance of this critical relationship between coral and symbiodinium. The lack of knowledge about basic functional genomics in coral symbiont homeostasis is a major impediment to the development of safe and effective coral reef intervention and restoration strategies.

While the genomic mechanisms underlying bleaching is not yet understood, the photo-inhibition model posits that high temperature leads to alterations in light capture, light utilization, and heat dissipation, as well as a build-up of reactive oxygen species (ROS), or free radicals. ROS-scavenging enzymes become over-encumbered and denatured, and the cellular outcomes are analogous to the mammalian inflammatory response: beneficial in short bursts, but harmful in chronic conditions as they inappropriately destroy healthy tissues. Multiple groups are working on the characterization of these protein responses in corals. 

Lower-cost genome and transcriptome sequencing and analysis techniques make possible population-based assessments on corals that have survived or died in bleaching events, and this data could enable the identification of adaptive (and maladaptive) mutations in wild stocks and inform novel hypotheses about genotype-phenotype interactions and bleaching resolution. Moreover, the recent demonstration of the CRISPR genome engineering technique in corals allows researchers to investigate those hypotheses by way of targeted genetic engineering. Such techniques are crucial to advancing coral genomics to a level that useful therapies can be developed, as with human cells and mouse models.

Several labs working on functional coral genomics are searching for adaptive traits using comparative methods to develop actionable insight into natural selection in corals. Many of these labs employ widely used genomics tools and techniques from human biomedicine and functional genomics. The availability and maturity of analogous tools in coral-specific formats has only recently emerged, or has yet to emerge.

Elkhorn Coral

The Reef Genomics group, funded by the Great Barrier Reef Foundation, is coordinating the sequencing and publication of the genomes of 20+ key reef species found across the world, which will form the foundations for functional genomics projects and likely yield other important additive benefits as they are published. For example, the current lack of coral reference genomes leaves functional genomics projects dependent on genomes from close-related model organisms that do not reflect the complexity of a coral genome.

The Baums lab at Pennsylvania State University has conducted a genome-wide SNP analysis for signatures of natural selection in the threatened Caribbean elkhorn coral, Acropora palmata. The team revealed fine-scale population structure and inferred a major physical barrier to gene flow. Scans detected 13 candidate genomic loci under positive selection; however, there was no correlation between available environmental parameters and genetic distance. Given this result, the team has highlighted a critical barrier facing all coral functional genomics actors: the absence of fine-scale environmental and coral life history data, with which the putative adaptations may be correlated.

The Van Oppen lab at Australian Institute of Marine Sciences, and the Gates lab at Hawai’i Institute of Marine Biology are both conducting functional genomics experiments on coral and their symbionts, as a core component of more involved projects pioneering assisted evolution and assisted gene flows. By investigating adaptations in corals found across the Indo-Pacific, from Australia to Hawai’i, the Van Oppen and Gates labs are working to identify a large set of potentially adaptive mutations across a broad geographic range in many coral species and environment types.

The Palumbi lab at Stanford University’s Hopkins Marine Station uses molecular and physical approaches to understand complex traits, such as heat resilience, which appear to have hundreds of mutations driving hundreds of genes, each with small effects that combine to have large outcomes. In order to determine the role of each gene, the Palumbi lab is experimenting with functionally blocking gene expression by applying pharmaceutical agents known to disrupt particular genes and pathways. The goal is to uncover which genes or pathways are involved in adaptation to warmer waters.

The collaboration between the Pringle lab at Stanford University and the Bay lab at the Australian Institute of Marine Science have demonstrated that CRISPR/Cas9 genome editing can be used to functionally disrupt a single gene family in a coral species. This is an essential first step in advancing gene editing technologies for coral so that individual adaptive or maladaptive mutations found in wild species can eventually be edited into a coral genome for genetic rescue.

The lack of reference genomes presents a significant challenge to researchers. Although, there are ongoing efforts to establish reference genome sequences for specific coral species, the work is slow and often produced using data sourced from only a handful of individual organisms.

The scale of computational and intellectual work requires the focus of numerous bioinformaticians to effectively sequence, assemble, and annotate coral genomes. But there are few coral scientists with the requisite skills to execute these projects in a timely manner.

Because corals are categorized as a meta-organism, functional genomics often includes the microbes that inhabit coral, adding further complexity.

Epigenetic Adaptation & Conditioning

Corals from environmentally variable locations are generally better able to withstand stress through phenotypic plasticity and have greater adaptive potential compared to those that live in more stable environments. For example, corals endemic to the Persian Gulf survive temperatures that are too extreme for coral species elsewhere, and certain coral species naturally tolerate water with lower pH.

The thermal tolerance of corals generally reflects their local temperature environment, meaning that corals in warmer waters bleach at higher temperatures than those in cooler waters. Most interestingly, there is mounting evidence that corals can adapt to different conditions, such that two genetically identical corals can exhibit different responses to the same conditions, with these adaptations being “learned” over time as a coral is exposed to a novel environment.

Understanding the epigenetic mechanisms by which corals are able to adapt to their environments by modifying gene expression, rather than by modifying their genomes, could provide a reliable means to intervene in the coral crisis without the need for breeding programs or genetic engineering.

Evidence of phenotypic plasticity across a range of coral life history stages and traits is growing, highlighting the significant capacity for corals to respond to altered environmental conditions. It has been shown that some corals can modulate their growth form to optimize light environments for photosynthesizing symbionts and to physiologically acclimatize to resist elevated temperatures. 

The revolution in -omics approaches, in particular ChIP-seq and other means of detecting and measuring epigenetic modifications, provide innovative opportunities for exploring different epigenetic components in coral adaptive response. Moreover, CRISPR has recently been used to artificially modify epigenetic states in a predictable manner, creating an opportunity for meaningful experimentation.

Holly Putnam

The Putnam lab at the University of Rhode Island is a leader in applying epigenetics to coral acclimatization, and a key goal is understanding how the abiotic environment and biotic interactions drive organism phenotype, ecological patterning, and evolutionary processes through the interaction of symbiosis, genetics, and epigenetics.

Sea Simulator

Researchers at AIMS are conducting experiments to measure epigenetic changes and genetic adaptations and the conditions under which they can be promoted, using long-term “stress-conditioning” experiments at AIMS’s National Sea Simulator to acclimatize corals to future thermal and pH conditions.

For the van Oppen lab, these findings will inform efforts to use synthetic biology techniques to engineer or breed coral resilience. Specifically, researchers are examining how conditioning occurs in corals, the condition under which it can be optimized, and whether it can prepare offspring for further ocean warming and acidification.

Manuel Aranda

The Aranda Group at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia has discovered extensive DNA methylation in the genome of a Red Sea Coral and identified specific patterns of epigenetic marks which emerge when corals are stressed for prolonged periods. Their research currently focuses on understanding the exact ways these mechanisms work and to what extent they allow corals to adapt, alongside the impact of microbial changes on these systems.

The mechanisms and impacts of epigenetic adaptation in corals are difficult to separate from genetic adaptations and other adaptations or parameters in an organism’s genome or general life history. Understanding the difference will prove especially challenging given the limited experimental capacity and epigenetic toolkits available to marine biologists.

Epigenetic changes in corals themselves are only one piece of a more complex puzzle, with extreme complexity emerging from the entire coral holobiont, which may consist of many thousands of distinct organisms.

Characterizing and Manipulating the Holobiont

Corals transcend the typical definition of a species, and therefore, are better referred to as “holobionts,” metaorganism communities in which a single “individual” is composed of: the specific host coral animal, one or more species of symbiodinium, and a collection of bacteria, viruses, fungi, archaea, protists, and other microorganisms. The holobiont has been shown to serve as a metabolically complete system, where genes from multiple organisms act together to cycle essential nutrients from one organism to another. Each coral species plays host to more than 100 unique bacterial species, and more than 100 million microbes occupy each square centimeter of coral surface alone. Furthermore, the holobiont composition shifts in response to changing environmental conditions.

Adaptation to distinct reef habitats occurs in the wild through natural selection on at least three members of the coral holobiont: the coral host, its symbiodinium and the tissue-associated bacteria.

Engineering the microbiome has been proposed by several groups. Studies have already examined the preference of corals with particular microbiomes for a particular substrate to guide initial larval settlement; documented the ability of coral-associated viruses to augment the coral immune system; and investigated how  various surface microorganism species engage in nutrient cycling. It is posited that information about the reef microbiome can be used to assess the suitability of a location for a particular restoration approach and unlock new directions in engineering the coral holobiont itself. Symbiodinium species have received particular attention as they are one of the ubiquitous constituents of the coral microbiome and could potentially be manipulated to be resilient to disturbed conditions.

Forest Rohwer

The Rohwer-Wegley Kelly group at San Diego State University is a pioneering developer of fundamental microbial reef genomics and metagenomics. The group currently uses metabolomics to understand the relatedness of unknown coral holobiont molecules based on their molecular fingerprints, and this research is explaining how and why specific molecules are created by coral holobionts in response to various stimuli.

Linda Blackall

The Marine Microbial Symbiosis (MMS) group, led by Dr. Madeleine van Oppen and Dr. Linda Blackall at the University of Melbourne, is investigating the fundamentals of coral-microbe symbiosis using experimental evolution, genome editing, and epigenetic alteration via stress conditioning, and projects focused on symbiodinium physiology, engineering, and metagenomics are underway.

Red Sea Research Center

The Coral Symbiomics group run by Dr. Aranda at KAUST is examining the evolutionary history of the relationships between coral, microbe, and symbiont. The group has demonstrated that corals and related organisms share a common core set of thermal stress response pathways for dealing with protein-(mis)folding and reactive oxygen species observed in bleaching and known to be important to the homeostasis of symbionts. The group has observed enhanced resilience in Red Sea coral holobiont organisms, likely through association with specific strains of Red Sea symbiont not found anywhere else.

Raquel Peixoto

In collaboration with researchers at the Federal University of Rio de Janeiro, Dr. Raquel Peixoto, at the University of California at Davis has studied how increasing beneficial coral microorganisms might partially mitigate coral bleaching. Peixoto and her colleagues have proposed that “beneficial coral microorganisms” play a role in coral holobiont health similar to the plant growth promoting rhizosphere, a soil bacteria living around/on the root surface that are directly or indirectly involved in promoting plant growth and development. Their research is developing strategies for using this knowledge to manipulate the microbiome, reverse dysbiosis (bleaching and other effects of a breakdown of the symbioses), and restore and protect coral reefs.

Size of the coral holobiont: The scale of work involved in decoding coral microbiomes is huge. With over 1000 species of soft and hard coral, there may be as many as 100,000 unique bacterial species directly partnered with corals, not to mention the non-specialist bacteria and other microorganisms that may be more casually associated with corals.

Culturing Microorganisms: Many microorganisms cannot be cultured directly, so researchers must rely on the use of -omics tools and measurement approaches to assess their presence and function. Other microorganisms that may be suitable for culture could be very challenging to genetically engineer; symbiodinium, thought to be the keystone for microbial manipulation, is particularly difficult to “genetically transform.”

Fitness Tradeoffs: Although some host-associated microbes might facilitate adaptive responses in corals, there are fitness tradeoffs between each adaptation. The impact of those fitness tradeoffs on desired adaptations remains unclear at the present time, and microbial/holobiont manipulations could prove harmful to corals by stimulating, rather than resolving, dysbiosis.

Translocation and Designer Reefs

Natural recombination and breeding have given rise to resilient corals in the past and could give rise to new resilient corals in the future, often referred to as “super corals.”

However, declining environmental conditions across most reef sites has destroyed reefs and is reducing connectivity between reef meta-populations. This will likely grow worse in the coming years, minimizing the ability of corals to naturally encounter one another, hybridize during breeding events, and subsequently create more resilient subspecies in the wild.

Currently, the only practical approach to improving reef resilience is to harness and foster the adaptive genetic diversity that is already present in coral populations.

Severe and frequent mortality events have already exerted strong selection pressure on coral populations and have selected for wild alleles that are more likely to spawn a new generation of better-adapted corals.

The goal of translocation and designer reefs is to establish self-sustaining populations of sexually reproducing corals that have sufficient genetic variation and demonstrated an ability to adapt to changing environments. Genomic data is an essential tool for guiding this restoration.

There are early stage proposals to develop large scale “coral arks” that consist of modular sub-arks that can each be submerged to capture the broad range of coral reef diversity onto a fixed structure over an extended period.

Current proposals integrate advanced technologies, such as routine genotyping of propagated stock, trait-based assessment of genotype performance, jump-starting genetic admixture by producing first-generation offspring in the lab for out-planting, and promoting long-range genetic exchange (“assisted gene flow”). 

Physically relocating corals en masse would benefit significantly from advances in cryopreservation, as well as the use of larval rearing and freezing programs, which will significantly reduce the volume and complexity of coral relocation efforts.

The Coral Restoration Consortium shares technology and best practices between participants and facilitates scientific and practical ingenuity needed to demonstrate that restoration can achieve meaningful results at scales that will allow reefs to continue protecting coastlines, supporting fisheries, and serving as economic engines for coastal communities. Key members of the group specialize in different aspects of designer reef development, and include the NOAA Restoration Center, NOAA Fisheries Office of Science and Technology, Mote Marine Laboratories, UN Environment-Caribbean Environment Programme, SECORE, The Nature Conservancy, and Seascape Caribbean.

There are promising precedents for coral translocation, with a good deal of work having been conducted over many decades. But the use of genetic insight to guide translocation efforts remains untested and unclear, meaning a self-sustaining super-reef may not yet be possible. 

Current understanding of genotype-phenotype relationships is rudimentary, making it difficult to rationally select corals for use in translocation programs.

The nascent state of coral functional genomics and genome engineering have yet to produce actionable data, and there are few reliable biomarkers that can be used to facilitate the identification of candidate corals for translocation or breeding. Current translocation approaches depend on phenotypic traits.

While the Coral Restoration Consortium’s Genetics Working Group has concluded that capturing only four unique coral genotypes per reef type will generally be enough to capture more than 50% of common alleles in a population, without targeted identification and collection system, only the most common genotypes are likely to be well-represented. 

Translocated coral must be able to successfully reproduce and generate novel combinations with sustained hybrid vigor over subsequent generations; otherwise, ongoing interventions through continued sexual propagation and breeding programs may be necessary.