Extremophiles

, Volume 12, Issue 5, pp 627–640 | Cite as

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

  • James W. Voordeckers
  • My H. Do
  • Michael Hügler
  • Vivian Ko
  • Stefan M. Sievert
  • Costantino Vetriani
Original Paper

Abstract

The bacterial and archaeal communities of three deep-sea hydrothermal vent systems located on the Mid-Atlantic Ridge (MAR; Rainbow, Logatchev and Broken Spur) were investigated using an integrated culture-dependent and independent approach. Comparative molecular phylogenetic analyses, using the 16S rRNA gene and the deduced amino acid sequences of the alpha and beta subunits of the ATP citrate lyase encoding genes were carried out on natural microbial communities, on an enrichment culture obtained from the Broken Spur chimney, and on novel chemolithoautotrophic bacteria and reference strains originally isolated from several different deep-sea vents. Our data showed that the three MAR hydrothermal vent chimneys investigated in this study host very different microbial assemblages. The microbial community of the Rainbow chimney was dominated by thermophilic, autotrophic, hydrogen-oxidizing, sulfur- and nitrate-reducing Epsilonproteobacteria related to the genus Caminibacter. The detection of sequences related to sulfur-reducing bacteria and archaea (Archaeoglobus) indicated that thermophilic sulfate reduction might also be occurring at this site. The Logatchev bacterial community included several sequences related to mesophilic sulfur-oxidizing bacteria, while the archaeal component of this chimney was dominated by sequences related to the ANME-2 lineage, suggesting that anaerobic oxidation of methane may be occurring at this site. Comparative analyses of the ATP citrate lyase encoding genes from natural microbial communities suggested that Epsilonproteobacteria were the dominant primary producers using the reverse TCA cycle (rTCA) at Rainbow, while Aquificales of the genera Desulfurobacterium and Persephonella were prevalent in the Broken Spur chimney.

Keywords

Epsilonproteobacteria Aquificales ANME ATP citrate lyase Black smoker Deep-sea vent rTCA cycle 

Notes

Acknowledgments

We wish to thank the crew of R/V Atlantis, and the crew and pilots of the deep-submergence vehicle Alvin, for their skilled operations at sea. We thank Nicole LeFur for technical assistance and Ken Takai (Japan Agency for Marine-Earth Science and Technology) for kindly making genomic DNA of H. thermophila, L. acidiphila, S. autotrophica, and S. lithotrophicum available to us. This research was supported by NSF grants MCB 04–56676 (C.V.), OCE 03–27353 (C.V.), MCB 04–56689 (S.M.S.), a grant from the New Jersey Agricultural Experiment Station to C.V., and a NIH Ph.D. Training Program in Biotechnology Fellowship (NIH NIGMS 5 T32 GM08339) to J.V. M.H. was supported through a postdoctoral scholarship from the Woods Hole Oceanographic Institution.

Supplementary material

792_2008_167_MOESM1_ESM.doc (56 kb)
Table S1. Number of clones examined for each library (DOC 56 kb)

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Copyright information

© Springer 2008

Authors and Affiliations

  • James W. Voordeckers
    • 1
    • 2
  • My H. Do
    • 1
    • 2
  • Michael Hügler
    • 3
    • 4
  • Vivian Ko
    • 1
    • 2
  • Stefan M. Sievert
    • 3
  • Costantino Vetriani
    • 1
    • 2
  1. 1.Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickUSA
  2. 2.Institute of Marine and Coastal SciencesRutgers UniversityNew BrunswickUSA
  3. 3.Woods Hole Oceanographic Institution, Woods HoleMassachusettsUSA
  4. 4.Leibniz Institute of Marine Sciences, IFM-GEOMARKielGermany

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