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

Voordeckers, James W.; H., My; Hügler, Michael; Ko, Vivian; Sievert, Stefan M.; Vetriani, Costantino

doi:10.1007/s00792-008-0167-5

Cited by 44 publications

(44 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…(Figures 3 and 4) is in line with data obtained from 16S rRNA gene and ATP citrate lyase (an enzyme involved in CO 2 fixation via the reductive tricarboxylic acid cycle) libraries constructed from the same chimney sample, which revealed a prevalence of Epsilonproteobacteria of the genus Caminibacter associated with this vent (Voordeckers et al, 2008). The isolation of C. mediatlanticus, Caminibacter sp.…”

Section: Discussionsupporting

confidence: 87%

“…Genomic DNA was extracted from pooled samples of each site and from cultures of each reference strain as previously described (Vetriani et al, 2003;Voordeckers et al, 2005Voordeckers et al, , 2008.…”

Section: Dna Extractionmentioning

confidence: 99%

“…However, the isolation and characterization of a number of novel bacteria and archaea from deep-sea hydrothermal vents revealed that most of them can use nitrate in addition to sulfur as their terminal electron acceptor. During growth, these microorganisms reduce nitrate to dinitrogen (Takai et al, 2004;Nakagawa et al, 2005;Takai et al, 2006) or ammonium (Blochl et al, 1997;Vetriani et al, 2004;Voordeckers et al, 2008;Perez-Rodriguez et al, 2010, 2012. In most cases, nitrate reduction is coupled to the oxidation of molecular hydrogen (and less frequently of formate or thiosulfate), and these organisms have a shorter doubling time when nitrate, rather than sulfur, is supplemented as the terminal electron acceptor (Vetriani et al, 2004;Voordeckers et al, 2005;Perez-Rodriguez et al, 2010, 2012.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Deep-sea hydrothermal ventEpsilonproteobacteriaencode a conserved and widespread nitrate reduction pathway (Nap)

et al. 2014

Self Cite

View full text Add to dashboard Cite

Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.

show abstract

Section: Discussionsupporting

confidence: 87%

Section: Dna Extractionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Deep-sea hydrothermal ventEpsilonproteobacteriaencode a conserved and widespread nitrate reduction pathway (Nap)

et al. 2014

Self Cite

View full text Add to dashboard Cite

show abstract

“…Many hydrothermally influenced habitats have archaeal communities dominated by members of the phyla Archaeoglobus, Thermococcales, and Methanococcales (A/T/M in Fig. 8 and 13) (206,290,392,397,407,408,442,467,535,581). Basalt crust-related samples (135,163,232,354; B. N. Orcutt, K. J. Edwards, and E. Banning, unpublished data) have archaeal communities dominated by members of the MGI clade, which currently has only two cultivated representative genera, "Candidatus Nitrosopumilus" and Cenarchaeam (200,288).…”

Section: Broad Patterns In Prokaryotic Microbial Biogeographymentioning

confidence: 99%

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

Orcutt

Sylvan

Knab

et al. 2011

Microbiol Mol Biol Rev

583

499

View full text Add to dashboard Cite

SUMMARY The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

show abstract

“…The autotrophic CO 2 -fixing potential has been illustrated among phylogenetically diverse Alpha-, Gamma-and Epsilonproteobacteria in multiple hydrothermal habitats by analyzing genes encoding key enzymes of the Calvin cycle and of the reverse tricarboxylic acid cycle (Campbell et al, 2003;Campbell & Cary, 2004;Perner et al, 2007b;Voordeckers et al, 2008;Wang et al, 2009). Radioactively labeled inorganic carbon incorporation experiments with hydrothermal fluids have estimated microbial CO 2 fixation rates for these habitats (Mandernack & Tebo, 1999 and references therein).…”

Section: Introductionmentioning

confidence: 99%

Geochemical constraints on the diversity and activity of H2-oxidizing microorganisms in diffuse hydrothermal fluids from a basalt- and an ultramafic-hosted vent

Perner¹,

Petersen²,

Zielinski³

et al. 2010

FEMS Microbiology Ecology

View full text Add to dashboard Cite

Mixing processes of reduced hydrothermal fluids with oxygenated seawater and fluid-rock reactions contribute to the chemical signatures of diffuse venting and likely determine the geochemical constraints on microbial life. We examined the influence of fluid chemistry on microbial diversity and activity by sampling diffuse fluids emanating through mussel beds at two contrasting hydrothermal vents. The H 2 concentration was very low at the basalt-hosted Clueless site, and mixing models suggest O 2 availability throughout much of the habitat. In contrast, effluents from the ultramafic-hosted Quest site were considerably enriched in H 2 , while O 2 is likely limited to the mussel layer. Only two different hydrogenase genes were identified in clone libraries from the H 2 -poor Clueless fluids, but these fluids exhibited the highest H 2 uptake rates in H 2 -spiked incubations (oxic conditions, at 18 1C). In contrast, a phylogenetically diverse H 2 -oxidizing potential was associated with distinct thermal conditions in the H 2 -rich Quest fluids, but under oxic conditions, H 2 uptake rates were extremely low. Significant stimulation of CO 2 fixation rates by H 2 addition was solely illustrated in Quest incubations (P-value o 0.02), but only in conjunction with anoxic conditions (at 18 1C). We conclude that the factors contributing toward differences in the diversity and activity of H 2 oxidizers at these sites include H 2 and O 2 availability.

show abstract

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

Cited by 44 publications

References 59 publications

Deep-sea hydrothermal ventEpsilonproteobacteriaencode a conserved and widespread nitrate reduction pathway (Nap)

Deep-sea hydrothermal ventEpsilonproteobacteriaencode a conserved and widespread nitrate reduction pathway (Nap)

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

Geochemical constraints on the diversity and activity of H2-oxidizing microorganisms in diffuse hydrothermal fluids from a basalt- and an ultramafic-hosted vent

Contact Info

Product

Resources

About