Scientists at NOAA’s Atlantic Oceanographic & Meteorological Lab and the Northern Gulf Institute applied omics techniques to provide the first basin-scale assessment of the microbial communities at the base of marine ecosystems across the Gulf region. The new study from Dr. Luke Thompson’s group, conducted by Dr. Sean Anderson and co-authors, is the largest environmental DNA (eDNA) or microbiome survey of the Gulf of America ever performed.
Scientists collected environmental DNA (eDNA) – genetic material from whole microbes or shed by marine life into the environment – during the 2021 Gulf and Ocean Monitoring Ecosystems and Carbon Cruise (GOMECC). These samples unlock crucial new insights into the microscopic life across an entire basin – from nearshore coastal ecosystems out to the open Gulf. By analyzing the microbial communities throughout the water column, we can better understand how they are being impacted by changing environmental conditions.
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Changes in the composition of these microbial communities in any given region has cascading effects, influencing the biodiversity and feasibility of commercially viable species to survive and flourish in a specific region. Understanding how microbial diversity throughout the water column varies with changing conditions – changes in salinity, temperature, nutrient levels – could unlock key insights and provide early indicators of how entire ecosystems will be impacted by exacerbated environmental stressors, including ocean acidification.
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By sampling eDNA on the GOMECC-4 research cruise in the Summer of 2021 and applying omics techniques, scientists at AOML have successfully assessed variations in microbial communities on a basin scale that begins to close that gap.
They tied changes in microbial communities into three clusters representing surface waters and the photic zone, the deep chlorophyll maximum (DCM) – i.e. the greatest depth at which phytoplankton growth is optimized – and waters near the seafloor. With the greatest diversity of species found in the photic zone, the team was also able to tie the abundance of cyanobacteria Prochlorococcus and Synechococcus with related changes in salinity, temperature, and pH.
Using an advanced modeling technique, scientists at AOML integrated environmental DNA analysis with chemical and biological parameters also measured at each station within the photic zone to expand and extrapolate beyond the cruise path. This enabled the team to examine changes in microbial communities in the uppermost region of the water column beyond the sampling points and examine how the abundance of specific species may be an indication of environmental stressors.
An estimated 180 eDNA sequences from prokaryotes were identified as significant indicators of areas with acidified waters while 224 sequences were indicators of less acidic areas. In the photic zone, Ostreococcus sp. and Gephyrocapsa huxleyi were indicators of more acidified waters while Euduboscquella was associated with relatively less acidic waters. This finding indicates that exacerbated ocean acidification may lead to slower-growing bacteria becoming more abundant in the long-term.
As ocean acidification continues to increase across the Gulf region, marine heatwaves have also impacted and persisted across the Gulf region. Eutrophication (i.e. excessive levels of nutrients) in coastal regions have led to harmful algal blooms and dead zones greater in size than Delaware that have deleterious impacts on biodiversity. Yet our understanding of microbial communities across the region – and how they vary with depth, changes in salinity, nutrients and oxygen levels and changing ocean chemistry – remains in its early stages.
This study captured the complex microbial compositions and how they are impacted by changing environmental stressors at an unprecedented scale. However, as crucial ecosystems throughout the Gulf region continue to face changes, the need for sustained monitoring of microbial community dynamics across the basin – and their cascading impacts on marine food webs – becomes even more critical.
“This study describes microbial biogeography and diversity patterns that had not been examined previously at such spatial scales in the Gulf,” said lead author Dr. Sean Anderson, who collected and analyzed these samples while at AOML and NGI. “This serves as an important resource for future microbial investigations and ecosystem inferences.”
Therefore, this study’s findings provide a crucial baseline for future research to monitor the fundamental life forms that fuel the marine ecosystems we depend on.
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This research was supported in funding by NOAA’s Ocean Acidification Program (OAP).
Chris Malanuk, NOAA Atlantic Oceanographic & Meteorological Laboratory, 25 February 2026. Article.
