Now, a new study published on September 22, 2025, in the open-access journal Carbon Research has cracked part of that code. By tracing the journey of dissolved organic matter (DOM) from riverbanks to estuaries, researchers have uncovered how land-based pollution and changing salinity team up to control the release of potent greenhouse gases—carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O).
The findings, led by Dr. Chuanqiao Zhou from the Department of Transdisciplinary Science and Engineering at Institute of Science Tokyo and Dr. Fei He from the Ministry of Ecology and Environment's Nanjing Institute of Environment Sciences, offer a clearer picture of one of Earth's most dynamic—and climate-critical—ecotones: the estuary.
The Estuary: A Climate Hotspot in Plain Sight
Estuaries are more than scenic transition zones. They are biogeochemical powerhouses, where freshwater rich in organic material collides with salty seawater, fueling complex microbial reactions that can either trap or release greenhouse gases.
But what drives these emissions? Is it the type of organic matter? The salt content? The microbes in between?
To answer this, the team studied three major seagoing rivers, analyzing the composition of dissolved organic matter (DOM) and measuring real-time greenhouse gas fluxes across salinity gradients.
The Land Delivers the Fuel—Lignin Takes Center Stage
One thing became immediately clear: the rivers are flooded with terrestrial-derived organic matter—stuff washed in from the land by rain and runoff. And the dominant player? Lignin, the tough, woody polymer that gives plants their structure.
In these rivers, lignin made up a staggering 68.2% to 75.3% of the total DOM. And as the water flowed from upstream to downstream, the proportion of lignin dropped—proof that land-based inputs are strongest near river sources and gradually diluted as the system moves toward the sea.
"This isn't just background noise," says Dr. Chuanqiao Zhou of Institute of Science Tokyo. "It's a massive infusion of carbon from human-altered landscapes—agriculture, deforestation, urban runoff. And it's feeding the microbial engines that drive greenhouse gas production."
Microbes in the Middle: The Invisible Workforce
That organic matter doesn't break down on its own. Enter the microbes.
The study found that the composition of DOM directly shapes the microbial community. Proteobacteria, a diverse group of bacteria known for their metabolic flexibility, dominated the scene—especially in areas rich in terrestrial DOM. These microbes feast on the incoming organic material, breaking it down and, in the process, releasing CO₂ and CH₄ as byproducts.
The result? Higher greenhouse gas emissions upstream, where terrestrial DOM is most concentrated. Average methane fluxes reached 11.5, 7.74, and 11.6 μg/m²·min across the three rivers—levels that mark these estuarine zones as active sources of climate-warming gases.
Saltwater Steps In: A Natural Brake on Emissions
But as the rivers approach the sea, something changes: salinity rises, and emissions begin to fall.
The data showed a clear negative correlation between salinity and greenhouse gas emissions, especially for nitrous oxide (N₂O)—a greenhouse gas nearly 300 times more potent than CO₂ over the short term.
Why? Salt appears to suppress microbial activity. The delicate balance of osmotic pressure makes it harder for certain bacteria to thrive, slowing down the decomposition of organic matter and reducing gas production.
"It's like nature's built-in regulator," explains Dr. Fei He from the Nanjing Institute of Environment Sciences. "As seawater mixes in, it dampens the microbial frenzy fueled by land-based inputs. This suppression effect is crucial for modeling emissions accurately—especially in coastal zones facing sea-level rise and saltwater intrusion."
Why This Matters: From Science to Climate Policy
These findings do more than satisfy scientific curiosity. They provide a framework for predicting greenhouse gas emissions in estuaries based on DOM sources and salinity dynamics—key variables that are shifting due to climate change, land use, and water management.
For policymakers, this means:
- Reducing terrestrial runoff (e.g., through better land management) could directly lower estuarine GHG emissions.
- Protecting natural salinity gradients—threatened by dams, dredging, and rising seas—is not just about biodiversity, but also about climate regulation.
A Transdisciplinary Triumph
This study is a testament to the power of collaboration across disciplines and borders.
Dr. Chuanqiao Zhou and the team at Institute of Science Tokyo brought cutting-edge transdisciplinary approaches, linking environmental engineering with climate science. Meanwhile, Dr. Fei He and colleagues at the Nanjing Institute of Environment Sciences—a key research arm of China's Ministry of Ecology and Environment—provided deep ecological insights and field expertise critical to understanding real-world estuarine systems.
Together, they've built a model for how science can address complex environmental challenges at the intersection of land, water, and climate.
The Big Picture: Estuaries in the Climate Equation
Estuaries have long been overlooked in global carbon budgets. But this study shows they are far from passive. They are active reactors, transforming land-based carbon into atmospheric gases—with consequences for the entire planet.
By pinpointing the synergy between terrestrial DOM and salinity, this research helps refine climate models and strengthens the case for integrated watershed management.
So the next time you stand at the edge of a river delta, remember: beneath the surface, a vast network of molecules and microbes is shaping the climate.
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- Title: Response of greenhouse gas emissions to synergistic effects of terrigenous organic matter input and salinity dynamics in estuary
- Keywords: Dissolved organic matter; FT-ICR-MS; Coastal river; Multi-source; Greenhouse gas emissions
- Citation: Ma, J., Wang, Z., Zhou, C. et al. Response of greenhouse gas emissions to synergistic effects of terrigenous organic matter input and salinity dynamics in estuary. Carbon Res. 4, 65 (2025). https://doi.org/10.1007/s44246-025-00235-3
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About Carbon Research
The journal Carbon Research is an international multidisciplinary platform for communicating advances in fundamental and applied research on natural and engineered carbonaceous materials that are associated with ecological and environmental functions, energy generation, and global change. It is a fully Open Access (OA) journal and the Article Publishing Charges (APC) are waived until Dec 31, 2025. It is dedicated to serving as an innovative, efficient and professional platform for researchers in the field of carbon functions around the world to deliver findings from this rapidly expanding field of science. The journal is currently indexed by Scopus and Ei Compendex, and as of June 2025, the dynamic CiteScore value is 15.4.
