Warming Seas Push Carbon Into Microbial Loop, Study of Red Sea Finds

In the warm, sunlit waters of the Gulf of Aqaba at the northern tip of the Red Sea, summer does something quietly profound to the ocean’s carbon cycle. As the surface warms and the water column settles into a stable, layered state, the microscopic algae that anchor the marine food web slow their carbon fixation, and an ever-larger share of the carbon they do capture leaks out of their cells as dissolved organic material. That dissolved carbon, rather than sinking to the deep sea as particles, is quickly consumed and respired by bacteria near the surface. A new five-month study published in the journal Ocean Science by Eyal Rahav of the Israel Oceanographic and Limnological Research and the University of California, Santa Cruz, and Adina Paytan of the University of California, Santa Cruz, documents this seasonal shift in remarkable quantitative detail, and its implications reach far beyond this small desert-fringed basin.

The ocean is one of the planet’s most important carbon reservoirs, and the efficiency with which carbon fixed by phytoplankton is transferred from the surface to the deep sea, the so-called biological carbon pump, helps determine how much carbon dioxide the ocean can lock away on climatically relevant timescales. In vast stretches of the open ocean, chronic nutrient scarcity keeps primary production low and dominated by tiny cells such as the cyanobacterium Prochlorococcus. Under these conditions, much of the newly fixed carbon never leaves the surface layer at all. Instead, it is retained and remineralized within the microbial loop, a closed circuit in which bacteria and other heterotrophic microbes rapidly recycle organic matter back into carbon dioxide. The result is a low transfer efficiency: little carbon reaches higher trophic levels or the ocean interior.

The Gulf of Aqaba offers an ideal natural laboratory for studying how this efficiency changes with the seasons. Every winter, deep convective mixing injects nutrients from below into the surface layer, fueling phytoplankton blooms. In summer, the picture reverses. Surface waters warm to between 25 and 28 degrees Celsius, and a sharp vertical temperature gradient isolates the sunlit euphotic zone from the nutrient-rich waters below. During the 2023 study period, from May to September, the researchers measured the mixed layer shoaling from about 45 meters in early summer to just 15 to 20 meters at the height of stratification in July and August. Nutrient concentrations in the upper 100 meters were correspondingly meager: nitrate plus nitrite ranged from below detection to only 0.14 micromoles per liter, orthophosphate hovered between 0.01 and 0.03 micromoles per liter, and the ratio of nitrogen to phosphorus fell well below the canonical Redfield ratio of 16 to 1, pointing to nitrogen limitation of the microbial community.

To track where the carbon actually went, the team used radiocarbon labeling. Seawater samples collected at 20-meter intervals from the surface down to 100 meters were spiked with sodium bicarbonate labeled with carbon-14 and incubated for 24 hours under ambient temperature and light. After incubation, the samples were gently filtered through glass-fiber filters with a nominal pore size of 0.7 micrometers. The carbon-14 retained on the filters measured particulate primary production, the carbon incorporated into algal biomass, while the labeled carbon passing through the filters quantified dissolved primary production, the photosynthate released extracellularly by the cells. Bacterial production was measured separately using tritiated leucine incorporation, and community respiration was estimated from the decline in dissolved oxygen in dark 24-hour incubations monitored with fiber-optic oxygen sensors. From these measurements the team calculated the percentage of extracellular release and the bacterial growth efficiency, the fraction of consumed organic carbon that bacteria convert into their own biomass rather than respire away.

The seasonal trajectory was unambiguous. Depth-integrated particulate primary production collapsed from 1.26 grams of carbon per square meter per day in May to just 0.35 grams per square meter per day as stratification intensified, a decline of more than 70 percent. Surface rates fell from roughly 25 micrograms of carbon per liter per day to about 8. Meanwhile, the fraction of total production released as dissolved organic carbon climbed steadily: the integrated percentage of extracellular release rose from 2.5 percent in May to between 5.7 and 6.4 percent during June through August, and reached 7.4 percent by September. Near the base of the euphotic zone, below 40 to 60 meters, extracellular release in individual samples climbed as high as 20 percent. The authors attribute this to nutrient stress: when carbon fixation outpaces the assimilation of nitrogen and phosphorus, cells exude excess low-molecular-weight photosynthates, effectively leaking carbon-rich, nutrient-poor dissolved organic matter into the surrounding water.

That leaked carbon did not linger. Dissolved primary production, though modest at 0.02 to 0.03 grams of carbon per square meter per day, correlated positively with bacterial production, which ranged from 0.08 to 0.16 grams of carbon per square meter per day and was highest in mid- to late summer. This coupling suggests that freshly released dissolved substrates directly fuel heterotrophic bacteria, forming a tight conduit between algal photosynthesis and microbial consumption. A statistical analysis of all depth-resolved measurements across the five cruises reinforced the picture: dissolved production correlated significantly with bacterial production, while particulate production showed a negative correlation with chlorophyll, indicating that carbon fixation and release track physiological activity rather than standing biomass. Chlorophyll itself was concentrated in a deep chlorophyll maximum between 60 and 100 meters, which the authors interpret as a photo-acclimation maximum, cells packing more chlorophyll per unit biomass under low light, rather than a true biomass maximum.

Perhaps the most consequential finding concerns bacterial growth efficiency. Despite the decline in primary production, bacterial respiration remained substantial throughout the summer, between 0.23 and 0.52 grams of carbon per square meter per day across the upper 100 meters. As a result, bacterial growth efficiency stayed low to moderate, ranging from 13 percent in May and June to 28 to 30 percent later in the season. In other words, for every unit of organic carbon the bacteria processed, the majority was respired back into dissolved inorganic carbon rather than converted into biomass that could enter the food web or sink. The authors argue that in the hyper-oligotrophic, warm, and physically isolated summer water column, nutrient limitation forces bacteria to respire surplus carbon through overflow metabolism to satisfy their nutritional demands while covering high basal metabolic costs. This contrasts with systems such as the Taiwan Strait, where recent work has reported elevated growth efficiencies, suggesting that oligotrophy alone does not dictate bacterial metabolism; substrate quality, stoichiometry, and physical setting all matter.

The authors also addressed a potential methodological concern: because Prochlorococcus cells are smaller than the nominal 0.7-micrometer pore size of glass-fiber filters, some cells might pass through and inflate the dissolved fraction. Prior work, they note, shows that under low-vacuum filtration comparable to their protocol, roughly 95 percent of Prochlorococcus cells are retained, and chlorophyll recovery on glass-fiber filters matches that of finer 0.2-micrometer membranes in oligotrophic waters. Moreover, the seasonal rise in extracellular release tracked changes in nutrient availability and microbial physiology rather than chlorophyll biomass, supporting the interpretation that the increase reflects a genuine physiological response of nutrient-stressed algae rather than a filtration artifact.

The broader significance lies in what this seasonal snapshot implies for a warming ocean. Climate change is intensifying density stratification across low- and mid-latitude seas, and the Gulf of Aqaba’s summer regime may foreshadow conditions becoming more widespread. If stronger stratification generally shifts carbon allocation from particulate biomass toward dissolved pathways, then more of the ocean’s primary production will be recycled within the surface microbial loop rather than exported to depth, weakening the biological carbon pump and shortening the residence time of carbon in the ocean’s upper layers. The authors call for long-term observations and targeted experiments that manipulate stratification, nutrient supply, and temperature, integrated with trait-based ecosystem models, to predict how microbial communities will adjust their carbon processing as oligotrophication progresses. For now, the message from this small corner of the Red Sea is clear: as the sea warms and stratifies, the microbes that dominate its surface waters become increasingly efficient recyclers and increasingly poor couriers of carbon to the deep.

Subject of Research: Seasonal water-column stratification and microbial carbon cycling in the oligotrophic Gulf of Aqaba, northern Red Sea

Article Title: Seasonal stratification regulates carbon allocation between particulate and dissolved pathways in the Gulf of Aqaba

Article References: Rahav, E., & Paytan, A. (2026). Seasonal stratification regulates carbon allocation between particulate and dissolved pathways in the Gulf of Aqaba. Ocean Science, 22(5), 2711-2723. https://doi.org/10.5194/os-22-2711-2026

Image Credits: AI Generated

DOI: 10.5194/os-22-2711-2026

Keywords: ocean carbon cycle, biological carbon pump, Gulf of Aqaba, Red Sea, water-column stratification, primary production, dissolved organic carbon, bacterial respiration, bacterial growth efficiency, microbial loop, oligotrophic ocean, ocean warming