Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep‐sea hydrothermal environments

Abstract

To contribute to the identification of methanogens, methanotrophs and sulfate-reducing bacteria (SRB) in microbial communities from the 13 degrees N (East Pacific Rise) and Rainbow (Mid-Atlantic Ridge) hydrothermal vent fields, we investigated the diversity of mcrA, pmoA and dsrAB genes sequences. Clone libraries were obtained using DNA isolated from fragments of diffuse vents, sediment and in situ samplers. The clones were categorized by restriction fragment length polymorphism, and representatives of each group were sequenced. Sequences were related to that of hyperthermophilic (order Methanopyrales and family Methanocaldococcaceae), thermophilic and mesophilic (family Methanococcaceae) methanogens, thermophilic (proposed genus 'Methylothermus') and mesophilic type I methanotrophs, and hyperthermophilic (order Archaeoglobales), thermophilic (order Thermodesulfobacteriales) and mesophilic (family Desulfobulbaceae) SRB. Several of the obtained sequences were distantly related to the genes of cultivated organisms, providing evidence of the existence of novel lineages in the three functional groups. This study provides for the first time an insight into the diversity of several functional genes of deep-sea hydrothermal system microorganisms.

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

“…Subgroup PM-1 fell within the MCG-2, PM-2 fell within the MCG-4, PM-3 through PM-5 fell within the MCG-1, PM-6 fell within the MCG-3, PM-7 fell within the MCG-8 in some treeing methods and PM-8 fell within the MCG-17 (Webster et al, 2006). pMARA-5 (Nercessian et al, 2005) fell within MCG-17. MBGC (Vetriani et al, 1999) fell within the MCG-8.…”

“…A total of 17 subgroups of MCGs (MCG-1-MCG-17) were supported in both distance and maximum likelihood inferences. These included the previously named MCG-1 through MCG-4 (Sørensen and Teske, 2006), C3 (Inagaki et al, 2006) that we renamed MCG-15, and pMARA-4 (Nercessian et al, 2005) that we renamed MCG-16 for consistency ( Figure 1). However, these previously named subgroups covered only 21% of the MCG database.…”

Culture dependent and independent analyses of 16S rRNA and ATP citrate lyase genes: a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge

“…and revealed the presence of sulfate reducing bacteria and archaea and of methanotrophic 75 bacteria (Nakagawa et al 2004, Nercessian et al 2005a). Furthermore, 16S rRNA-based 76 studies of vent microbial communities indicated that Epsilonproteobacteria were 77 associated with sulfide structures (Hoek et al 2003, Longnecker et al 2001, and showed 78 that between 66 and 98% of the microorganisms associated with various types of 79 colonization substrates that were deployed in the vicinity of chimney orifices belonged to 80 this class of the Proteobacteria (Alain et al 2004, Lopez-Garcia et al 2003.…”

GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

“…The unique mineralogical and chemical compositions of a chimney in the early stages of its formation may support a distinct pioneering microbial community (8,9). By analyzing the conserved specific functional genes (such as nifH and mcrA), the metabolic diversity of some specific organisms in the mature chimneys was partially investigated (10,11). However, because of a lack of appropriate detection technologies, the metabolic diversity and dynamics of wholemicrobial communities in primitive and mature chimneys have not been examined.…”