Climate & Frontier Biology
The open ocean has been producing methane in water that should make that impossible. Scientists have finally worked out how -- and the mechanism is missing from every major climate model on earth.
For decades, oceanographers measured something the textbooks said should not exist. Methane -- a potent greenhouse gas produced by microbes that thrive in the absence of oxygen -- was found to be supersaturated in the sunlit, oxygen-rich surface waters of the open ocean. By established biochemistry, this was impossible. The organisms responsible for methanogenesis cannot survive in oxygenated water. Yet there the methane was, year after year, in waters across the world's subtropical ocean gyres. Scientists called it the marine methane paradox. In 2025, a team of researchers from the Woods Hole Oceanographic Institution and the University of Hawaii published a study in the Proceedings of the National Academy of Sciences that finally explained what was happening -- and what they found has unsettling implications for how accurately our climate models represent the real ocean.
The paradox had been sitting in the scientific literature since the 1970s. When researchers first measured dissolved methane concentrations in surface ocean waters, they found consistent supersaturation -- levels above what would be expected from simple equilibrium with the atmosphere. The ocean surface, in other words, was not passively receiving methane from elsewhere. It was producing it, from within waters where the organisms known to make methane could not, in theory, exist.
Traditional methanogenesis requires strictly anaerobic conditions -- the complete absence of oxygen. The methanogens that perform it are killed or suppressed by oxygen. Surface ocean waters are oxygenated. The paradox was real and persistent, and proposed explanations over the decades -- microaerobic niches inside sinking particles, small oxygen-depleted zones within zooplankton guts -- were suggested but never fully confirmed or scaled to explain the pattern observed across entire ocean gyres.
The scale of the problem matters. The subtropical ocean gyres -- the vast, slow-circulating pools of warm, relatively still water that dominate the central ocean basins -- account for a substantial fraction of the global ocean surface. If methane was being produced there through a previously unknown mechanism, it represented an unaccounted-for source of a greenhouse gas roughly 80 times more potent than carbon dioxide over a 20-year period.
The PNAS study identified the mechanism with a specificity that earlier work had lacked. The key variable is not oxygen but phosphate -- the dissolved form of phosphorus that ocean microbes require for growth. In the subtropical gyres, phosphate is chronically scarce. The ocean's circulation does not bring up enough nutrient-rich deep water to meet the demands of the microbial communities in the surface layer.
When phosphate runs out, certain bacteria face a problem: they need phosphorus but cannot get it from the water. Their solution is to scavenge it from dissolved organic matter -- specifically, from a class of compounds called phosphonates, which contain carbon-phosphorus (C-P) bonds. Photosynthetic cyanobacteria in the upper ocean produce large quantities of novel polysaccharides, and bacteria break these polysaccharides down to extract the phosphorus they need. The enzyme that does this work, C-P lyase, cleaves the carbon-phosphorus bond -- and releases methane, ethylene, and propylene as gaseous byproducts.
The elegance of this explanation is that it connects the observed methane pattern directly to the nutrient geography of the ocean. The areas of highest methane supersaturation -- the subtropical gyres -- are exactly the areas of greatest phosphate scarcity. The researchers were able to show that only by linking methane production to phosphate limitation could they reproduce the global distribution of methane observed in ocean surface waters.
The marine methane paradox is not the only piece of unresolved ocean methane science. A separate line of research, published in Nature Communications in 2026, found that atmospheric deposition -- the settling of nitrogen-rich dust and aerosols from the atmosphere onto the ocean surface -- could also stimulate methane production. Dust from deserts and industrial sources fertilises ocean surface waters, feeding microbial growth and potentially triggering additional methane production pathways. These two mechanisms may be acting simultaneously in some ocean regions.
The major Earth system models -- the computational tools used to project future climate under different emissions scenarios -- do not currently incorporate this phosphate-starvation methane production pathway. This is not necessarily evidence of a large systematic error in climate projections, since the absolute methane flux from this mechanism has not yet been fully quantified. But it is a known gap: a source of a potent greenhouse gas that models are treating as zero, when observational data has been showing it is non-zero for fifty years.
Quantifying the gap and incorporating it into models is now an active area of research. The direction of the correction -- more methane than models currently estimate -- is clear. The magnitude is not yet.
What is particularly well understood about the WHOI/University of Hawaii study is the link to other confirmed phosphonate chemistry. Earlier work had established that methylphosphonate -- a specific phosphonate compound -- is produced by certain marine microbes and is associated with methane release. The new study placed this within a broader mechanistic framework, explaining not just that C-P cleavage produces methane, but why it happens where and when it does in the global ocean.
The climate implications move in a concerning direction. As the ocean warms, it becomes more stratified: the surface layer grows lighter relative to the cold deep water beneath it, reducing the vertical mixing that delivers nutrients from depth. Reduced mixing means more phosphate scarcity in the surface ocean. More phosphate scarcity means more C-P cleavage activity. More C-P cleavage means more methane. More methane in the atmosphere means more warming.
This is a positive feedback loop -- in the physics sense, where "positive" means self-amplifying rather than beneficial. Warming increases the mechanism that produces more warming. The researchers identified this as a potential hidden feedback in the climate system that is not currently represented in projections.
"A greenhouse gas source that has been sitting in plain sight since the 1970s, unaccounted for in every major climate model, now turns out to be mechanistically connected to the very warming those models are trying to project."
-- Lisa PedrosaThe appropriate caution here is that the magnitude of this feedback has not been quantified at the level needed to say how much it changes climate projections. The ocean does not produce methane on the scale of large terrestrial sources -- wetlands, permafrost, agriculture, fossil fuel infrastructure. The marine methane source is real, and it is poorly accounted for, but it is not by itself a reason to revise climate projections dramatically.
What it does represent is a reminder that the climate system contains mechanisms that are still being discovered -- and that the relationship between warming and greenhouse gas emissions is more intricate, and more self-reinforcing, than the simplified version that reaches public discourse. The ocean is not a passive reservoir. It is a dynamic system, and some of its dynamics are only now becoming legible.
© 2026 Lisa Pedrosa · lisapedrosa.com
All articles cited to primary institutional or peer-reviewed sources
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