Marginal seas are important areas of the ocean in biogeochemical cycling of nitrogen. Due to specific geographical locations, unique geochemical settings and diverse land-ocean interactions (including anthropogenic impacts), different marginal seas may develop and maintain microbiologically distinct environments. Does this mean that different marginal seas may support different microbial communities? Is there any commonness in the microbial communities among distinct marginal seas? In order to obtain answers to these questions, we sampled three different marginal seas of the western Pacific Ocean: the generally oligotrophic South China Sea in the subtropical and tropical latitudes, the highly eutrophic Bohai Sea in the temperate latitudes, and the methane hydrate-harboring and cold seep-rich Okhotsk Sea in the sub-polar latitudes. We compared the ecological characteristics of the nifH-harboring bacterial and archaeal communities in the marine sedimentary environments among these marginal seas. The diversities of the putative nifH gene sequences were analyzed in an ecological context that involves the prevalent environmental factors. Gene sequence data were further employed for microbial community classification, to reveal the spatial distribution characteristics of the tentative diazotrophic microorganisms in the western Pacific Ocean. Furthermore, canonical correlation analysis was used to identify the most significant environmental factors that may control the distribution and community structure of the putative N2-fixing microorganisms. These analyses help us to decode and understand the constraints (natural and anthropogenic) that influence the geographic-scale microbial distribution and their biogeochemical functions in the western Pacific Ocean.
