Cold-seep sediment harbors phylogenetically diverse uncultured bacteria

Abstract

A culture-independent molecular phylogenetic survey was carried out on the bacterial community in cold-seep sediment at Edison Seamount, south of Lihir Island, Papua New Guinea. Small-subunit rRNA genes were amplified directly from the sediment DNA by PCR and cloned. The majority of the cloned 16S rRNA gene sequences were most closely related to as-yet-uncultivated microorganisms found in deep-sea sediments, and were primarily affiliated with one of four groups: the gamma-, delta-, and epsilon-subdivisions of Proteobacteria, and Cytophaga-Flavobacterium-Bacteroides. We did not recover any sequences related to cyanobacteria, prochlorophytes, and alpha-Proteobacteria, which are known to occur in great abundance within the surface mixed layer of the Atlantic and Pacific Oceans. The majority of the cloned gamma- and epsilon-Proteobacterial sequences were closely related to chemoautotrophic sulfuroxidizing symbionts of marine benthic fauna, and the delta-Proteobacterial sequences to sulfate- and sulfur-reducing bacteria, indicating that they might play an important role in chemoautotrophic primary production and the sulfur cycle in the cold-seep area. These results demonstrate the high diversity of the bacterial community in the cold-seep sediment, and substantially expand knowledge of the extent of bacterial diversity in this formidable and unique habitat.