1. Marine microbiomes All environments on Earth have distinct communities of microorganisms, or “microbiomes,” that are integral to ecosystem function. Microbiomes regulate processes like nutrient cycling and animal health, and often contain thousands of different species. The ocean is home to many different microbiomes, including those in the water column and sediments, attached to particles, or associated with animals like plankton. However, most microbes have yet to be cultured in a laboratory. Instead, we rely on DNA and RNA sequencing to answer basic questions about who is present and what their functional roles are. Thanks to recent advances in sequencing technology and computational tools, we can analyze large-scale sequence data to extract patterns of taxonomy and function from entire communities. These analyses are sometimes referred to as “-omics” methods in reference to terms like genomics, metagenomics, and transcriptomics, which are the analysis of whole genomes, environmental DNA, and gene expression, respectively. As a postdoc at Georgia Tech, I am studying marine and aquarium systems to understand how microbiomes are shaped by competition, respond to perturbations, and impact the health of their environment.
Field work in the Bahamas, 2013.
2. Microbial chemical ecology Bacteria produce small chemical compounds with a wide range of bioactivities, including antibiotic and anticancer properties. These compounds, also known as “secondary metabolites” or “natural products,” have been studied for decades as an avenue for drug discovery. I am interested in their ecological roles - why bacteria produce them in nature. My Ph.D. work focused on the chemical ecology of marine sediment-inhabiting bacteria called Actinomycetes, which are particularly "talented" with their chemistry. Actinomycetes make a huge range of antibiotics, many of which, such as streptomycin and erythromycin, are used in the clinic. I studied three species that are differentiated in part by their "secondary metabolome," or chemical repertoire. Understanding why and how microbes produce these small molecules has important implications for drug discovery, preventing antibiotic resistance, and understanding the fundamentals fundamentals of microbial ecology and evolution.
The tropical crab Caphyra rotundifrons spends most of its life in a tuft of the alga Chlorodesmis fastigiata, which contains toxic chemicals that deter most herbivores. It is thought that the C. rotundifrons diet consists almost exclusively of C. fastigiata, suggesting that the crab gut is specially adapted to detoxify or process the deterrent compounds. I am currently studying the microbiome of both partners in this mutualism to better understand the role of microbes in facilitating the crab's tolerance to the alga. The field component of this research was conducted in Mo'orea, French Polynesia.
Bugula neritina colonies being induced to spawn during a field collection trip in Morehead City, North Carolina.
3. Host-associated symbionts All animals, from ants to humans, have internal and external microbiomes that play important roles in regulating host health. Insects are among the most well-studied host-microbiome systems, and the human microbiome is an active area of research because of linkages between the gut microbiome and diseases. Marine invertebrate microbiomes, in contrast, are poorly understood. At Georgia Tech, I am studying the microbiome of the bryozoan Bugula neritina to better understand the role of an uncultured symbiont in the context of a complex microbiome. This symbiont holds high pharmaceutical and biotechnological interest because it produces anti-cancer molecules called bryostatins, but it has so far resisted efforts to grow apart from B. neritina. I hypothesize that this microbe interacts with other members of the B. neritina microbiome and the first part of this study was recently published in Aquatic Microbial Ecology. The role of symbiotic bacteria in producing, processing, or degrading bioactive compounds is an exciting field in microbial chemical ecology and marine invertebrates are ideal systems for discovery in these areas.