Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii

Abstract

The phylogenetic diversity of small-subunit rRNA genes associated with the domain Bacteria was examined (by using previously defined operational taxonomic units [C. L. Moyer, F. C. Dobbs, and D. M. Karl, Appl. Environ. Microbiol. 60:871-879, 1994]; those for Pele's Vents Bacteria are hereafter abbreviated PVB OTUs) with samples from a microbial mat at an active, deep-sea hydrothermal vent system. A cluster of phylogenetically related PVB OTUs (OTUs 2, 3, 6, and 8) was closely affiliated with Thiovulum sp. contained within the subclass of the class Proteobacteria and accounted for 60.5% of the small-subunit rRNA bacterial clone library from Pele's Vents. A second, smaller cluster of PVB OTUs (OTUs 1 and 11) was closely affiliated with Xanthomonas sp., contained within the ␥ subclass of the Proteobacteria and accounted for a total of 27.1% of the bacterial clone library. The remaining five PVB OTUs each accounted for 2.1% of the clones recovered and were affiliated with the following phylogenetic groups: PVB OTU 5 was a member of the Alteromonas group; PVB OTU 12 was a member of the Colwellia assemblage; PVB OTU 4 was loosely determined to be a member of the Thiothrix group, with the endosymbiotic bacteria from Bathymodiolus thermophilus and Calyptogena magnifica as the nearest relatives; PVB OTU 10B was a member of the Myxobacterium group; and PVB OTU 9A was a member of the Paraphyletic assemblage, with the Octopus Spring microbial mat type K clone as the closest known relative. PVB OTU 7 was determined to be a PCR-generated chimeric structure combined from two described phylotypes detected in this study, thereby decreasing the previously estimated number of major PVB OTUs from 12 to 11.

Microbial diversity and biogeochemistry of the Guaymas Basin deep‐sea hydrothermal plume

“…Notably absent from our clone libraries were sequences retrieved from GB hydrothermal deposits, chimneys and sediments (Teske et al, 2002;Dhillon et al, 2005;Pagé et al, 2008). In addition, only three sequences clustering with Epsilonproteobacteria were found; this group is typically abundant in deep-sea hydrothermal vent environments (Haddad et al, 1995;Moyer et al, 1995;Reysenbach et al, 2000;Corre et al, 2001;Longnecker and Reysenbach, 2001;Campbell et al, 2006) (Fig. 3C).…”

Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption

“…Molecular studies show the O-proteobacteria to be widespread at deep-sea hydrothermal vents associated with microbial mats [43,44,69], the vent polychete Alvinella pompejana [70,71], the vent worm Riftia pachyptila [72], and an in situ growth chamber with warm £uids [47,73]. Recently, the ¢rst representatives of this group were cultured and found to exhibit both heterotrophic and autotrophic sulfur reduction, moderate thermophily, and the ability to use hydrogen as an electron donor [74,75].…”

“…Twentyfour of these clones were most closely related (92^98%) to an uncultured bacterium, clone S17sBac16, from a hydrothermal vent microbial mat on the Southern East Paci¢c Rise [43]. Other clones in the O-proteobacteria from Marker 33 were related to uncultivated marine bacterium, including clones from a deep-sea cold seep in the Japan Trench [40], a hydrothermal microbial mat [44], deep-sea sediments [45,46], a growth chamber associated with warm hydrothermal £uids [18,47], an ectosymbiont of the hydrothermal vent shrimp Rimicaris [48], and methane seep tubeworm endosymbionts [49]. Some of the clones from Marker 33 were also related to cultured O-proteobacteria, such as Thiomicrospira denitri¢cans [50], Arcobacter spp.…”

Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea

“…Some members of these communities have previously been characterized using culturedependent and light-and electron-microscopy methods, and the presence of the filamentous sulfur-oxidizing bacteria Beggiatoa sp., Thioploca sp., Leucothrix, Thiotrix and Desmanthos has been confirmed [2,[10][11][12]. Other studies performed, using culture-independent techniques, have shown that microbial mat communities in vent or cold seep environments can be quite diverse and include prokaryotes such as Epsilonproteobacteria [13,14] or even Archaea [15], that are responsible for the filamentous structure of the mats. These organisms are thought to participate in either sulfide-or methanebased chemoautotrophy.…”