Molecular analysis of microbial 16s rRNA, mcrA, dsrAB and pmoA genes from deep-sea hydrothermal vent and cold seep sites

Methane and sulfide are primary sources of energy supporting the dense macrobiological communities often found in cold seep areas and both free-living and symbiotic microorganisms depend on energy provided by the sharp gradient of sulfide and the reservoir of methane in the underlying sediments. In deep-sea hydrothermal vent areas, sulfide is typically the primary source of energy for microbial primary production. To investigate microbial populations and community structure in these areas, microbial communities from both deep-sea hydrothermal vent (Rainbow and Logatchev hydrothermal vent fields, Mid-Atlantic Ridge, Atlantic Ocean; 9ºN hydrothermal vent area, East Pacific Rise, Pacific Ocean) and cold seep areas (Blake Ridge, western Atlantic Ocean; Florida Escarpment, Gulf of Mexico) were evaluated by molecular phylogenetic analysis of 16S rRNA, mcrA, dsrAB and pmoA gene sequences. Twenty-one clone libraries were obtained using DNA from friable vent chimney material (hydrothermal vent areas) and from vertically subsampled (top, middle and bottom) sediment core samples (cold seep areas), screened by RFLP and sequenced.;At the Florida Escarpment, phylogenetic analysis of bacterial 16S rDNA suggests the dominance of epsilon-Proteobacteria in the top zone, the epsilon-delta and gamma-Proteobacteria in the middle zone and the delta-Proteobacteria in the bottom zone of the core. Archaeal diversity was low throughout, but increased with depth. Cold seep mcrA sequences were distributed among the ANME-2c, -2d and -2e groups. Clone library dsrAB sequences grouped primarily within the orders Desulfobacteriales, Syntrophobacteriales and the gram-positive order Clostridales. Clone library pmoA sequences grouped among the Type I methanotrophs (gamma-proteobacteria) within the order Methylococcales. Most sequences recovered represented as-yet-uncultivated phylotypes distinct from any other cultivated or environmental clones. In addition, this investigation presents for the first time environmental mcrA sequences detected from chimney samples collected from a bare basalt, high-temperature deep-sea hydrothermal vent area that are related to ANME-2e sequences previously shown to be associated with the anaerobic oxidation of methane.