River to Remedy: DOE Program Supports Texas A&M Research on Gulf Coast Microbes

Texas A&M University oceanography assistant professor Dr. Sarah Hu received a Community Science Program New Investigator Award from the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI), supporting research that explores how communities of microbes break down organic matter as freshwater from the Mississippi River enters the Gulf of Mexico. 

The award provides access to large-scale sequencing through metabolomics and data analysis through the JGI, a facility supported by the DOE that promotes research related to complex biological and environmental systems. The program is designed for investigators new to the institute and provides funding for pilot studies that can eventually help develop future large-scale projects. 

Hu’s project, River to Remedy: Capturing Microbial Transformations of Organic Matter at the Terrestrial–Aquatic Interface, examines microbial transformations at the river-to-ocean boundary. “This proposal is to get a massive amount of sequence data back,” Hu said. “We have sampling off the coast of Louisiana, where the Mississippi River flows into the Gulf.” 

Instead of treating the river like a single point of origin, Hu’s team takes samples along transects from coastal waters offshore, tracking how freshwater and land material influence marine ecosystems. “We’re trying to understand what happens at the terrestrial–aquatic interface, where freshwater from the Mississippi enters the Gulf, and how that signal gets diluted as we move away from the river plume,” Hu said.

Hu’s research focuses on microorganisms that support marine ecosystems and regulate how energy and nutrients move through food webs. “The foundation of all ocean food webs is microorganisms,” Hu said. “They act like tiny engines that run everything: carbon cycling, energy flow, all of it.” 

Her work focuses on identifying which microbes are present in the ocean, what they are doing and which biological and chemical processes they influence. To answer those questions, Hu uses metagenomic and metatranscriptomic approaches that allow researchers to extract and analyze genetic material from environmental samples. “When we study environmental samples, we extract DNA — the A’s, T’s, C’s, and G’s,” Hu said. “That gives us a map of who’s there.” 

In the Mississippi River–Gulf system, that genetic map helps Hu’s team examine how nutrients and land-plant material introduced by the river reshape microbial communities and the broader food web.

Hu said the DOE award serves as an entry point for expanding this line of research. “It’s an exciting launch point. This area has been studied for a long time, but now we can get a massive amount of new data that will fuel many projects.” 

She collaborates with Yina Liu, an assistant professor in Texas A&M’s Department of Oceanography, and Arianna Krinos of Brown University. Hu focuses on identifying microbial community members and their genetic potential, while Liu studies the metabolites produced as those pathways operate. “Using genetic sequences, I can build a map of what microbes are present and what pathways they can use,” Hu said. “Dr. Liu measures the metabolites produced as those pathways operate. Together, we get a more complete picture.” 

Beyond the technical analysis, Hu said the broader goal of the project is to understand how microbial processes shape the health of a system that affects much of the country. “The ‘remedy’ part of the project is exciting,” Hu said. “The Mississippi River drains much of the U.S. into the Gulf, influencing the entire region. If we understand which microbes help maintain balance, we can better predict disruptions and potentially mediate them in the future.”