Ocean deoxygenation, driven by climate change and eutrophication, is expanding hypoxic zones and reshaping marine ecosystems, particularly in coastal regions such as estuaries. Microbial communities are central to organic carbon (OC) cycling in these environments, yet their adaptation to fluctuating oxygen levels remains unclear. By synthesizing global research on microbial dynamics in deoxygenated waters, alongside multi-omics and experimental insights from in situ and culture-based studies, we explore how microbes drive carbon source-sink processes under hypoxia.
On a global scale, ocean deoxygenation disrupts conventional OC cycling, shifting microbial metabolic pathways under extreme hypoxic conditions. Our multi-omics analysis of the seasonal hypoxic zone in the Yangtze Estuary shows that microbial community composition is influenced more by salinity than oxygen levels, with aerobic metabolism dominating oxygen gradients. Key taxa like Oceanospirillales and SAR11 persist under hypoxia, demonstrating community resilience. Culture experiments reveal that hypoxia significantly alters the organic matter transformation by heterotrophic bacteria, particularly Flavobacterium, slowing carbon remineralization while preserving nitrogen- and sulfur-rich compounds. A greater proportion of microbial taxa engage in networks associated with organic sulfur metabolism, which is enhanced under hypoxia. Long-term anaerobic incubation of Yangtze Estuary sediments further reveals cooperation between sulfate-reducing and sulfur-oxidizing bacteria, converting OC into less degradable organic sulfur compounds, promoting long-term carbon preservation in sediments under prolonged deoxygenation.
In conclusion, our findings highlight microbial communities’ metabolic flexibility and functional redundancy as key mechanisms to buffer against environmental changes. Even in severely hypoxic regions, microbes support carbon turnover by using alternative electron acceptors like nitrate and sulfate, switching between aerobic and anaerobic pathways. This versatility not only influences carbon source-sink dynamics but also integrates with microbial carbon pump processes, enhancing OC preservation. These results underscore microbial resilience in sustaining vital ecosystem functions, including OC cycling and burial, as global ocean deoxygenation intensifies.
 

ocean deoxygenation, organic carbon, sulfur metabolism, microbial metabolisms