Research
Research
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We leverage natural and lab-based studies,
using molecular, culture, and microscopy approaches, across scales from cells to ecosystems.
Major research themes include:
(1) the roles of viruses on reefs,
(2) how microbes move around and their fates,
(3) supporting sustainable ocean solutions.
(1) How do viruses impact reef health and function?
(1) How do viruses impact reef health and function?
Dinoflagellate-infecting RNA viruses (dinoRNAVs) infect key beneficial dinoflagellate algae that live inside coral tissues. We are uncovering the genomic diversity of these viruses, discovering what they look like, and testing when dinoRNAV infections are observed, and how they impact coral health. Some recent findings include:
We tracked 54 Porites lobata corals over 3 years and found that dinoRNAV infections were common (94% of corals).
Infections were more productive close to shore (fringing reef) and in corals that experienced health issues (partial mortality).
For more details:
Howe-Kerr et al. (2023) Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape. ISME Communications 3: 27. https://doi.org/10.1038/s43705-023-00227-7
Coral diseases, such as stony coral tissue loss disease (SCTLD) and white plague (WP), are killing many Caribbean corals and have shifted the types of corals that remain on reefs. We are part of a scientific team (led by Dr. Marilyn Brandt, UVI) taking an integrative approach to understanding the causes and impacts of coral disease. Our lab is focusing on virus and Symbiodiniaceae diversity within apparently healthy and affected corals to understand their contributions to disease resistance and susceptibility. Some of our recent findings include:
We analyzed the diversity of a key coral symbiont (Symbiodiniaceae dinoflagellates) in 491 apparently healthy and SCTLD-affected coral tissues in Florida (USA) and the United States Virgin Islands, representing 9 coral species.
In 2 coral species, lesion-adjacent tissues had enriched relative abundance of a Durusdinium lineage, whereas Symbiodinium and Cladocopium lineages were relatively more abundant in apparently healthy tissues.
Our findings indicate SCTLD can act as a selective filter on coral symbiont assemblages.
For more details:
Karrick et al. (2026) Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape. ISME Communications 3: 27. https://doi.org/10.1038/s43705-023-00227-7
We integrated microscopy and multi-omics data to characterize a coral disease outbreak in the northwest Gulf of Mexico from samples of opportunity (15 diseased and healthy Pseudodiploria strigosa coral tissues).
Our findings suggest the disease outbreak was consistent with white plague, which appeared to manifest as a nutrient limitation-driven dysbiosis, potentially mediated by viruses.
Our study provides a framework for multimodal data integration to characterize coral diseases.
For more details:
Karrick & Swain et al. (in review). Integration of microscopy and multi-omics data reveals pathology of a coral disease outbreak. https://doi.org/10.21203/rs.3.rs-10349654/v1
Te Ora Fenua (Biocode 2.0) Project: We are part of a team generating foundational omics resources (host genomes, microbiomes, and viromes) and science-focused school activities for reef creatures of cultural, ecological, and economic importance in Mo'orea, French Polynesia. Creature selection and additional questions for investigation are driven by local community groups and individuals, including local French Polynesian experts leading Te Mauri Ora Project (which consolidates biocultural knowledge and generates culture-focused school activities for the same creatures). So far, Te Ora Fenua Project team is focusing on select corals, macroalgae, sea cucumbers, crabs and shrimp, with more creatures to come. Watch this space for papers and other products!
(2) How do microbes that live inside hosts get around and what happens to them as they disperse?
(2) How do microbes that live inside hosts get around and what happens to them as they disperse?
Microbial partners of corals and other animals spend most of their time physically associated with their hosts. Yet, many corals are born without microbes and have to acquire them from the environment. Corals can also pick up additional microbes from the environment after disturbances like heat waves. What processes make microbial partners widely available in the environment for uptake? We are finding that predators and grazers disperse the microbes of their prey. We hypothesize that coral microbes may experience key biological events as they travel through predator guts. Some recent findings include:
We quantified the density and diversity of viable Symbiodiniaceae cells in the feces of six Caribbean fish species in the U.S. Virgin Islands and found that they contain an average of 5 million viable Symbiodiniaceae cells ml−1.
Symbiodiniaceae diversity harbored by local corals was detected in fish feces, making them environmental hotspots of a microbe that shallow reef-building corals require to survive.
For more details:
Titus et al. (2026) Caribbean Fish Feces are an Environmental Pool of Viable Symbiodiniaceae. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2025.1715855
The reef fish feces come into contact with corals. We found that the feces of fish that eat algae (coral competitors) caused more and larger lesions on corals than feces from coral-eating fish.
Experimental controls showed that this effect resulted from microbial activity in the algae-eating fish feces, rather than physical effects (smothering) of fecal contact with corals.
Predator feces impact on coral health: it matters what you eat!
For more details:
Grupstra et al. (2023) Consumer feces impact coral health in guild-specific ways. Frontiers in Marine Science 10. https://doi.org/10.3389/fmars.2023.1110346
(3) Partnering to develop and test ocean solutions that support human communities and marine ecosystems.
(3) Partnering to develop and test ocean solutions that support human communities and marine ecosystems.
Linking Reef Restoration to Circular Bioeconomy:
Coral reefs are shifting from coral- to macroalgae-dominated states due to global change stressors. While community-led removal of excess macroalgae has demonstrated ecological benefits—including increased coral recruitment and cover—these efforts remain difficult to sustain at scale due to the lack of viable end uses for removed algal biomass.
Past and current collaborative research projects (ANR ARATA’I, Living-Lab AMWI and Moana Fenua) led by other groups have been operating in Mo’orea and Tahiti (French Polynesia) to develop integrated approaches linking reef restoration through community-led removal campaigns of proliferating Turbinaria macroalgae under a circular small-scale bioeconomy model (alginate extraction, production of farming biostimulants). Our lab (with members of UC Berkeley's International Bioeconomy & Macroalgae Center and French Polynesian collaborators) is part of a new team joining this overall effort; we are working to identify promising bioethanol generation pathways from Turbinaria. Such bioethanol can ultimately help power boats, reducing the use of fossil fuels. In parallel, we are contributing to monitoring the impacts of algae removal operations led by the Living-Lab AMWI, adding coral settlement and environmental DNA (eDNA) measurements to assess reef health outcomes. Watch this space for papers and other products!
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