Microbiome Ecology Laboratory

Over the past decade, the Microbiome Ecology Laboratory has built a research identity around understanding how microbial communities drive nutrient and carbon cycling across coastal and aquatic ecosystems. By integrating metagenomics, amplicon sequencing, functional gene quantification, and direct biogeochemical measurements, the laboratory connects microbial community structure to ecosystem-scale processes.

Nitrogen Cycling Microbiology

Nitrogen transformation processes — including anammox, denitrification, nitrification, and dissimilatory nitrate reduction to ammonium (DNRA) — are investigated across estuarine sediments, salt marshes, tidal freshwater systems, subterranean estuaries, and agricultural watersheds. A central question driving this work is how human disturbances such as agricultural runoff, dam removal, and seawater intrusion restructure the microbial guilds responsible for nitrogen removal and recycling in coastal waters.

Microplastics and Microbial Communities

The laboratory has developed a distinctive research niche demonstrating that microplastic pollution measurably alters sedimentary bacterial communities and disrupts nitrogen cycling processes. Building on this foundation, recent work has shown that microplastic biofilms serve as hotspots for both plastic-degrading microbes and nitrogen-cycling genes — linking contaminant ecology directly with functional microbial ecology.

Aquaculture and Host-Associated Microbiomes

A major and growing pillar of the laboratory involves characterizing microbiomes in the context of aquaculture health and sustainability. This includes the larval and adult microbiomes of eastern oysters, hard clams, and American lobsters, examining how hatchery conditions, harmful algal blooms, and environmental stressors shape host microbiomes and influence survival, productivity, and disease dynamics in commercially important species.

Greenhouse Gas-Cycling Microbiomes

Microbial communities mediating methane and nitrous oxide fluxes are studied in coastal salt marshes, tidal wetlands, and wastewater systems. The laboratory examines how environmental conditions — including oxygen availability, salinity gradients, and nutrient loading — interact with community composition to regulate the magnitude and variability of greenhouse gas emissions from these ecosystems.

Polar and Extreme Microbiomes

A newer frontier for the laboratory involves investigating microbiomes in polar and extreme environments. Ongoing work is decoding the gut and egg microbiomes of Antarctic pteropods (Limacina rangii), organisms sensitive to ocean acidification, while planned research targets microbial communities in Arctic river deltas and their role in regulating nutrient and carbon fluxes to the ocean — extending the laboratory's coastal biogeochemical framework to high-latitude systems under rapid climate change.