Research

Our research at the Rosenstiel School of Marine and Atmospheric Science - University of Miami (RSMAS) is focused on the study of host-associated microbes and the effect of global warming on the microbiomes of benthic and planktonic marine animals. We have a wet and dry lab, to perform experiments and bioinformatics analysis, enabling the broadest possible goals.

• The eukaryotic microbiome. Unlike the study of the bacterial fraction of the microbiome, the study of the micro-eukaryotes associated with animals has largely been restricted to visual identification or molecular targeting of particular groups. The application of high-throughput sequencing approaches, such as those used to look at bacteria, has been limited because the barcode gene we use to study microeukaryotes ecology and distribution in the environment, the 18S rRNA gene, is also present in the host animals. As a result, when host-associated microbial eukaryotes are analyzed the retrieved sequences are dominated by the host. Stemming from my work on coral-associated microeukaryotes, we successfully implemented an approach that avoids the amplification of metazoan host genes, which allows us to use high throughput methods to study the microeukaryotic communities of animals. This approach opens the door to the study of diversity and distribution of microeukaryotes in a myriad of environments, from the coral surface to the human gut.

• Effects of ocean warming on the microbiomes of benthic and planktonic marine animals. Ongoing climate change and its effects on the environment, such as rising sea temperature, has strong impacts on free-living marine microbial communities. However, the effects of global warming have not been properly studied on host-associated microbiomes. Microbiomes (both prokaryotic and eukaryotic) associated with host organisms have a strong influence on host evolution, physiology, and ecological functions. We study how environmental changes resulting from global warming affect the composition and function of the microbiomes in key members of the marine fauna and consequently how these changes affect the hosts. Currently, our study focuses on these impacts on corals, teleost fish, and zooplankton. To tackle this novel research topic, we use a combination of molecular biology, ecophysiology, and bioinformatics.

These are some of our current projects:

• A transcriptomic cell-atlas of reef coral bleaching
• Biomineralization in the Toadfish microbiome
• Koch at the reef - Understanding coral disease
• The microbiome-brain axis in the California sea hare
• PR2 database. A reference 18S rRNA sequence database

We are always open to new projects and ideas, so stayed tuned for updates and opportunities.