1. Marine microbiomes All environments on Earth harbor communities of microorganisms, or “microbiomes,” that are integral to the ecosystem. Microbiomes regulate processes like nutrient cycling and animal health, and often contain thousands of different species. There are many types of microbiomes in the ocean, like those in the water column and sediments, attached to particles, or associated with higher organisms 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 there and what they are doing. Thanks to advances in sequencing technology and computational tools, we can analyze massive amounts of sequence data to extract patterns of taxonomy and function from entire communities. These analyses are collectively referred to as “-omics” methods and include genomics, metagenomics, and transcriptomics, which are the analyses of whole genomes, environmental DNA, and gene expression, respectively. In my 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. For one of my projects addressing these questions, I am part of an interdisciplinary team exploring blue hole formations. Blue holes are subsurface caverns that formed during the last ice age in calcium carbonate, or karst, bedrock. When sea level rose they became undersea structures with unique physical and chemical characteristics compared to the surrounding water column. Our first sampling expedition showed that the holes host high levels of a rare and understudied archaeal microbe. We are working on sequencing the genome of this organism using only environmental DNA to understand why it dominates the blue hole water and how it might contribute to carbon, nitrogen, or sulfur cycles.
Filtering seawater aboard a research vessel during the Blue Hole expedition in May 2019.
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.
Bugula neritina colonies being induced to spawn during a field collection trip in Morehead City, North Carolina. April 2017.
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.