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. I study marine microbiomes to understand how they are shaped by resource limitation, respond to perturbations, and impact the health of their environment. For example, I am part of an interdisciplinary team exploring blue holes in the Gulf of Mexico. 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 rare and understudied microbes. The genome sequences of these taxa, which I assembled from the environmental DNA (nothing grown in the lab), provide important new insight into the ecology of low oxygen marine systems, which are projected to expand substantially with climate change. For more on blue holes check out the PBS Changing Seas episode on our expeditions, and my recent publication in The ISME Journal and accompanying blog post.
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, or in other words, 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. Understanding why and how microbes produce these small molecules has important implications for drug discovery, preventing antibiotic resistance, and understanding the fundamentals of microbial ecology and evolution. More recently, I've become interested in microbe-phytoplankton chemical interactions and how they may regulate harmful algal blooms (HABs). A small pilot study on microbial and chemical linkages associated with a bloom of the dinoflagellate Karenia brevis, which produces toxic blooms affecting much of the Gulf Coast every year, showed differences in the microbial and chemical profiles of samples with high levels of K. brevis. Learning more about these connections will help us understand how and why HABs begin and persist in coastal ecosystems.
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. I studied 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.