Estimates show that 50% of the world’s corals have already been lost with as much as 90% loss projected by 2050. Consensus is building that even the strongest corals will struggle to withstand more frequent and more severe stressors in the future. But there is hope! Several recent research advances have demonstrated the potential for new tools in the study and engineering of corals. We created the Advanced Coral Toolkit program to promote the development and fielding of new biotechnologies that have the potential to greatly benefit coral resilience and restoration efforts. Below are the current and completed projects and their principal investigators.


Dr. Iliana Baums, Pennsylvania State University and Dr. Kirsty McFarland, Draper

A critical need for coral restoration planning is genotype identification to promote genotypic and species diversity within nurseries and outplanting sites. While technically feasible, genotyping in the field is too resource-intensive to be performed in the remote locations where most corals are found. This is problematic because many coral species reproduce through fragmentation, which makes it difficult to distinguish large clonal stands from genetically diverse communities. Furthermore, coral species are often difficult to identify in the field without genetic information. The Charles Stark Draper Laboratory (“Draper”), a high-tech engineering firm based in Cambridge, Massachusetts, has developed a customizable fieldable miniature microarray device originally made for the identification of genetically engineered organisms. The Baum lab will work with Draper to adapt this fieldable device for genotyping corals in low resource environments.

Photo, right: Drs. Baums and McFarland will develop and demonstrate the device for the genotyping of Acropora coral, many of which are seen here. (Courtesy Baums Lab)

Coral Probiotics

Dr. Blake Ushijima, University of North Carolina Wilmington

Stony coral tissue loss disease (SCTLD) is now one of the greatest threats to Caribbean coral reefs, having spread from Florida into the greater Caribbean in just the past seven years. Unidentified pathogenic bacteria are believed to be involved with SCTLD. Currently, the only effective treatment is an antibiotic, which poses its own dangers to the marine environment. The objective of this project is two-fold: First, biomedical technologies and advanced robotics will be applied in the development of a high throughput system for isolating, culturing, and testing potentially effective probiotics as a treatment for SCTLD. Secondly, synthetic molecules called peptide-conjugated morpholino oligomers (or PPMOs) will be used to remove specific groups within the microbial communities on corals to help identify pathogenic strains responsible for SCTLD, a novel use for PPMOs. The long-term implication of this work is the development of new technologies that have the potential to revolutionize the field of environmental microbiology for studying and fighting diseases.

Photo, left: Here, SCTLD (in white) encroaches on maze coral (Meandrina meandrites), one of many stony coral species susceptible to the disease. (Courtesy Ushijima Lab)

Isochoric Freezing of Coral Fragments

Dr. Mary Hagedorn, Smithsonian’s National Zoo and Conservation Biology Institute and Boris Rubinsky, UC Berkeley

Existing cryopreservation techniques are typically incompatible with field application. This is especially true in marine environments where resources and energy supplies are limited. For this project, Drs. Hagedorn and Rubinsky will adapt cutting-edge freezing technology to the preservation of coral fragments. The isochoric freezing technique involves freezing samples at constant volume rather than the traditional constant pressure techniques. This has been demonstrated to be gentler on non-coral samples, which means less cryoprotectant is required, and simpler, less artisanal protocols can be used. The technology requires no moving parts or mechanical work, making it ideal for low-resources field settings. If isochoric freezing succeeds in freezing and reviving coral fragments, this project could open the door for large-scale coral biobanks.

Photo, right: Dr. Hagedorn successfully biobanked sperm from elkhorn coral (Acropora palmata), like the one shown here. (Courtesy Smithsonian Institution)


Dr. Giacomo Bernardi, One People One Reef

Human activity has impacted coral reefs, often shifting the balance toward algal-dominated reefs, biodiversity decline, the loss of keystone species (“phase shift”), and the emergence of new ones. However, some coral species are doing surprisingly well. Thriving Montipora spongodes are taking over the coral reefs of the Ulithi atoll of Micronesia, an apparent phase shift to a monospecific scleractinian (“stony”) coral. While this means the reefs are less diverse, it also offers the opportunity to understand the genetic factors promoting resilience in the Montipora species. For this project, Dr. Bernardi will investigate the genetics of Montipora, with a focus on the genes under selection to provide insight into the coral’s resilience and adaptability. A full high-coverage genome of Montipora will be compared with other coral genomes and genetic differences between habitats will also be identified. This data may help predict coral resilience and help to better understand the dynamics of potential phase shifts in resilient corals.

Photo left: Dr. Bernardi floats above a large porites coral in the Ulithi atoll of Micronesia where the Montipora also thrive.

Creation and Cryopreservation of Coral Nanofragments

Dr. Mary Hagedorn, Smithsonian’s National Zoo & Conservation Biology Institute

The goal of this project is to develop methods to cryopreserve and thaw single-polyp nanofragments of model species of Hawaiian coral. Successfully cryopreserved and thawed nanofragments could be used for coral restoration, now or centuries from now. There is an important advantage of nanofragment cryopreservation over larvae cryopreservation (a technique that has already been developed). Nanofragment techniques will be independent of coral larvae or coral reproductive events, which occur but once a year. New methods will be used to create pinhead-sized asexual coral nanofragments that exhibit stem cell qualities and apply existing cryopreservation and ultra-rapid warming methods to freeze, store, and reanimate these fragments. New methods will also be developed to return the thawed nanofragments to seawater and demonstrate how to best utilize them to create rapidly growing coral for restoration.

Photo, right: Dr. Hagedorn successfully cryopreserved and thawed larvae from the Fungia scutaria coral in 2018.

Development of Coral Stem Cells for Recovery and Restoration

Dr. Nikki Traylor-Knowles, University of Miami Rosenstiel School of Marine and Atmospheric Science and Dr. Benyamin Rosental, Ben Gurion University, Israel

Stem cells are capable of differentiating into a wide variety of cells and have been shown in many organisms to be critical for therapeutic and regenerative applications. Improved knowledge about coral stem cells and the development of techniques for isolation and propagation will provide technology that is fundamental for the repair, recovery, and regeneration of thermotolerant corals. Using Pocillopora damicornis as a model, this project will lay the groundwork for the application of stem cell technology to the daunting challenge of coral conservation.

Photo left: A coral laboratory set-up from the Traylor-Knowles lab.

Montipora genomics—investigating success in a ‘weedy’ coral

Dr. Giacomo Bernardi, One People One Reef

The objective of this project is to use genomics and ecological data to investigate the apparent adaptive advantage that a “weedy” species of Montipora coral has exhibited in the Yap outer islands, Federated States of Micronesia. Dr. Bernardi is interested in investigating the genetics of this organism, with a particular focus on genes under selection, potentially providing a window into the resilience and adaptability of this coral.

Photo, right: A Montipora reef near Asor Island, Ulithi Atoll, Federated States of Micronesia. 

Metabolomics As a Platform for Coral Monitoring and Conservation

Dr. Debashish Bhattacharya, Rutgers University and Hawaii Institute of Marine Biology

Coral stress indicators may lead to earlier predictions of coral bleaching events. The goal of this project is to develop the knowledge needed to design and construct a portable coral stress monitoring instrument. This instrument will rely on a panel of well-characterized antibodies and redox-based sensors of stress-related enzymes and metabolites, respectively—to assess coral health prior to bleaching and to allow time to enact appropriate interventions.

Photo left: Corals at low tide outside the Hawaii Institute of Marine Biology.

Coral Stress Triggers as Targets for Genetic Intervention and Climate Change Resilience

Dr. Steve Palumbi, Stanford University

The purpose of this project was to establish a new research paradigm using pharmacological agents to explore the cellular controls that trigger coral bleaching. This project is now complete. The pharmacological agents were successful in manipulating coral gene expression, showing their utility for corals research.

A set of cellular switches may be involved in triggering coral bleaching events, the most promising of which is the unfolded protein response (UPR). This project tested the possibility that UPR is a fundamental part of the coral bleaching trigger. The typical way to test such a hypothesis is through genetic manipulation of cultured cells—yet traditional genetics techniques are not feasible in corals. Without an ability to manipulate coral genomes directly, coral geneticists cannot directly test their hypotheses. To make immediate progress, a novel strategy was borrowed from cancer research. The Palumbi laboratory used pharmacological agents, that have specific effects on highly conserved proteins, to study coral cell biochemistry.

Photo, right: A researcher from the Palumbi lab collects a coral sample.