Coral

Corals provide a home for over 25% of oceanic fish species and are a critical source of economic value for fisheries and tourism industries worldwide. With increasing ocean temperatures, corals are facing massive, worldwide bleaching events resulting in the deaths of entire ecosystems. These events are exacerbated by the fact that most corals are sessile and live close to the maximum temperature they can survive, meaning that slight changes can do massive damage. With ocean temperatures rising, extinction is likely for at least 30% of modern coral species if nothing is done.

One promising avenue of research is the deployment of probiotic Beneficial Microorganisms for Corals (BMCs). Via the combination of lab-based and field studies, specific probiotic consortia have been shown, in some cases, to improve coral resilience to disease. Most recently, members of our team showed that for certain species, the impact of a temperature increase of 10°C could be mitigated with a probiotic cocktail. But development of BMCs is impossible without first understanding the native microbes that live in and on corals.

The tools used for DNA sequencing on coral tissues are limited in ways that make this understanding hard to achieve. Shotgun metagenomics — which captures all of the DNA in a given environmental sample — has proven difficult for corals because they contain low microbiome biomass relative to host tissue, and because de-convolving host DNA from microbiome DNA is difficult due to a lack of high-quality genome databases and various features of coral DNA itself.

We are building a set of tools — and testing them on corals from around the world — for characterizing, isolating, and engineering the microbial communities of coral reefs. The goal is to build precision, optimized treatments to protect them from bleaching. This includes new laboratory protocols for low-biomass sequencing on coral tissue, new bioinformatics tools for host decontamination, and a growing reference database of coral-associated microbes drawn from samples across every major ocean basin.