Porewater composition, microbial diversity and lipid biomarkers in shallow sediments of the Haima cold seeps in the South China sea

Surface sediment biogeochemical processes were investigated in Haima, a representative deep-sea methane seep system in the South China Sea. Centimeter-scale high-resolution analyses of porewater geochemistry, microbial diversity, and lipid biomarkers were conducted to characterize variations in sediment environments and microbial assemblages. The depleted porewater concentrations indicated the occurrence of coupled anaerobic methane oxidation, microbial sulfate reduction, and authigenic mineral formation, whereas organic matter input and degradation remained stable across sampling sites, exerting minimal disturbance to seepage-associated biogeochemical cycles. Community sequencing analyses identified Proteobacteria and Crenarchaeota as the dominant bacterial and archaeal taxa in shallow sediments, respectively. The spatial distribution of microbial communities showed weak correlations with sampling depth and sedimentary conditions, suggesting that variable methane seepage activities may serve as an important driver of community structural differentiation rather than vertical stratification, although this interpretation remains constrained by the limited number of sediment cores (one core per seepage condition). Archaeal communities exhibited more distinct biogeographic differentiation and lower spatial similarity than bacterial communities, potentially indicating higher environmental sensitivity of archaea to heterogeneous seepage habitats. ROV02 possessed significantly lower microbial diversity than ROV11 supportting the hypothesis that intense methane seepage may modulates sediment microbial assemblages through physical flushing and environmental filtering effects. However, given the limited sample size, this association warrants further verification through expanded sampling. By integrating multidimensional evidence from porewater geochemistry, microbial community assembly, and lipid biomarker signatures, this study clarifies the differential responses of geochemical cycling and benthic microbial communities to variable methane seepage intensities at the Haima cold seep. The findings provide robust observational data and mechanistic insights for understanding microbially mediated biogeochemical processes in deep-sea cold seep ecosystems of the South China Sea.