Beyond the Organic: A Decade Chasing Carbon in a Forgotten Lagoon

Standing on the shallow seagrass meadows of Dongsha Atoll for the first time, I was struck by how tranquil everything appeared. Crystal-clear water, lush seagrass, and brilliant white carbonate sands created the image of a perfect tropical paradise. As a chemical oceanographer, I had come to Dongsha expecting to study a textbook blue carbon ecosystem. Like many researchers, I believed these meadows captured atmospheric CO₂ through photosynthesis and locked it away by burying organic carbon. It seemed like a straightforward story‒one that had already been written.

Dongsha had other plans.

During our first field campaign in 2015, we compared two nearby seagrass meadows. One meadow was exposed to the open sea, while the other was nestled within a quiet, semi-enclosed lagoon. The results caught our attention. The lagoon consistently exhibited much lower CO₂ concentrations, higher pH, and substantially higher alkalinity than the open coast.

At first, we were delighted. Surely, we had discovered an exceptionally productive seagrass meadow.

But our excitement quickly turned into curiosity.

No matter how many times we recalculated the carbonate system, checked the sensors, or questioned our assumptions, the conclusion remained the same: photosynthesis alone could not explain the lagoon's chemistry. The ecosystem was doing something that our understanding of blue carbon simply could not explain.

Our first paper, published in 2018, proposed that the lagoon's restricted water exchange allowed alkalinity generated within the sediments to accumulate in the overlying water, thereby enhancing its capacity to buffer CO₂ (https://doi.org/10.1016/j.ecss.2018.06.006). It explained what we observed, but not why it happened.

Where was all of this alkalinity coming from?

That question stayed with us.

Science is rarely about a single dramatic breakthrough. More often, it is about returning to the same question with better ideas, new techniques, and a willingness to accept that your original explanation was incomplete.

For nearly a decade, Dongsha became our natural laboratory. Every expedition added another piece to the puzzle. We expanded our observations from seawater carbonate chemistry to continuous ecosystem metabolism (https://doi.org/10.3389/fmars.2023.1076991), sediment porewater chemistry, benthic alkalinity fluxes (https://doi.org/10.3390/jmse12112061), organic carbon content, mineral composition (https://doi.org/10.1029/2024GL112373), and seasonal variability (https://doi.org/10.3389/fmars.2021.717685). Each study revealed another clue, gradually transforming an unexpected observation into a coherent story.

Eventually, we realized that we had been focusing on only half of the carbon cycle.

For decades, seagrass meadows have been celebrated as blue carbon champions because of their extraordinary capacity to bury organic carbon. Yet beneath the seafloor, another carbon cycle was quietly at work. As microbes decomposed organic matter within the carbonate-rich sediments, the CO₂ they produced promoted the dissolution of ancient reef-derived carbonate minerals. That dissolution generated alkalinity, increasing the buffering capacity of seawater and helping maintain remarkably low CO₂ concentrations in the lagoon.

Rather than acting independently, organic and inorganic carbon cycling were tightly coupled. The seagrass was not simply storing carbon‒it was driving geochemical reactions that fundamentally altered seawater chemistry.

This realization changed the way we viewed blue carbon.

It also inspired one of the central ideas of our Communications Earth & Environment Perspective: the climate benefit of a seagrass meadow cannot be evaluated based on organic carbon burial alone. Carbonate formation releases CO₂, whereas carbonate dissolution removes it by generating alkalinity. Whether a meadow ultimately functions as a long-term atmospheric CO₂ sink depends on the balance between these opposing processes (see figure below).

To quantify that balance, we developed a new framework based on the net community production/net community calcification (NCP/NCC) compensation ratio. Our model revealed a simple threshold. Under present-day ocean conditions, organic production must exceed approximately 63% of calcification for a seagrass ecosystem to remain a net atmospheric CO₂ sink. Below that threshold, calcification-driven CO₂ release can outweigh the benefits of photosynthesis, even when substantial organic carbon is buried in the sediment.

This framework highlights the source-dependent controls on seawater carbonate chemistry. The climate-mitigation capacity of a seagrass meadow is not uniform; rather, it varies depending on the nature and origin of the underlying sediments. By distinguishing how carbon pathways operate across different geomorphic settings‒such as organic carbon-rich reef systems versus organic carbon-poor terrestrial environments‒our Perspective provides a more mechanistic framework for understanding and predicting ecosystem carbon dynamics.

Dongsha provided the perfect natural laboratory to test this idea.

Unlike many seagrass meadows, where CO₂ concentrations fluctuate dramatically between day and night, the Dongsha Inner Lagoon remains a persistent CO₂ sink throughout the year. We found that this remarkable behavior results from a unique partnership between biology and geology, driven by these source-dependent controls. Organic matter produced by the seagrass fuels the dissolution of allochthonous geogenic carbonate‒ancient carbonate sediments transported from the surrounding coral reef. In effect, the lagoon functions as a natural alkalinity factory, continuously generating alkalinity that buffers seawater and enhances atmospheric CO₂ uptake.

Looking back, our Communications Earth & Environment paper is not the story of one experiment. It is the culmination of nearly ten years spent chasing one puzzling observation that refused to fit the conventional explanation.

Perhaps the most important lesson from Dongsha is that blue carbon is more than buried organic matter. It emerges from interactions among plants, microbes, sediments, and seawater. By recognizing the coupling between organic and inorganic carbon cycling‒and the fundamental role of sediment source in regulating seawater carbonate chemistry—we can move beyond traditional blue carbon accounting toward a more complete understanding of how coastal ecosystems regulate Earth's climate.

As governments increasingly invest in seagrass restoration as a nature-based climate solution, we hope this framework encourages a nuanced approach. The question is no longer simply how much carbon is buried, but how the entire carbon cycle operates and how geology shapes that cycle. Identifying carbonate-rich "sweet spots" where organic metabolism and alkalinity generation reinforce one another, could help maximize the climate benefits of restoration while providing a more rigorous scientific foundation for future blue carbon assessments and carbon-credit schemes.

Sometimes, the biggest discoveries are not about finding something new. They come from realizing that the processes we have studied separately are connected.