Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico

Methanotrophs are ubiquitous in soil, fresh water and the open ocean, but have not been well characterized in deep-sea hydrocarbon seeps and gas hydrates, where methane is unusually abundant. Here we report the presence of new functional genes for the aerobic oxidation of methane by methanotrophs in marine sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. Samples were collected from two hydrate locations (GC185 and GC234): one hydrocarbon-seep location at a brine pool (GC233) and one background-marine location about 1.2 miles north of the brine pool (NBP). Community DNA was extracted from each location to establish clone libraries for the pmoA functional gene using a PCR-based cloning approach. Three hundred and ninety clones were screened by sequencing and 46 operational taxonomic units were obtained. Eight operational taxonomic units were present in every sample; one of them was predominant and accounted for 22.8–25.3% of each clone library. Principal-component analysis indicated that samples GC185 and GC234 were closely related and, along with GC233, were significantly different from NBP. These results indicate that methanotrophic communities may be similarly impacted by hydrocarbons at the gas-hydrate and seep sites, and can be distinguished from methanotrophic communities in the normal marine sediment. Furthermore, cluster analysis showed that 84.8% of operational taxonomic units from all samples formed distinct clusters, which could not be grouped with any published pmoA sequences, indicating that a considerable number of novel methanotrophic species may exist in the Gulf of Mexico.