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Extremophiles

, Volume 15, Issue 1, pp 105–116 | Cite as

16S rRNA phylogenetic analysis and quantification of Korarchaeota indigenous to the hot springs of Kamchatka, Russia

  • Thomas A. Auchtung
  • Galina Shyndriayeva
  • Colleen M. Cavanaugh
Original Paper

Abstract

The candidate archaeal division Korarchaeota is known primarily from deeply branching sequences of 16S rRNA genes PCR-amplified from hydrothermal springs. Parallels between the phylogeny of these genes and the geographic locations where they were identified suggested that Korarchaeota exhibit a high level of endemism. In this study, the influence of geographic isolation and select environmental factors on the diversification of the Korarchaeota was investigated. Fourteen hot springs from three different regions of Kamchatka, Russia were screened by PCR using Korarchaeota-specific and general Archaea 16S rRNA gene-targeting primers, cloning, and sequencing. Phylogenetic analyses of these sequences with Korarchaeota 16S rRNA sequences previously identified from around the world suggested that all Kamchatka sequences cluster together in a unique clade that subdivides by region within the peninsula. Consistent with endemism, 16S rRNA gene group-specific quantitative PCR of all Kamchatka samples detected only the single clade of Korarchaeota that was found by the non-quantitative PCR screening. In addition, their genes were measured in only low numbers; small Korarchaeota populations would present fewer chances for dispersal to and colonization of other sites. Across the entire division of Korarchaeota, common geographic locations, temperatures, or salinities of identification sites united sequence clusters at different phylogenetic levels, suggesting varied roles of these factors in the diversification of Korarchaeota.

Keywords

16S rRNA gene Abundance Hydrothermal Kamchatka Korarchaeota Phylogeny 

Notes

Acknowledgments

We are grateful to the participants of the workshop ‘Kamchatka 2005: Biodiversity, Molecular Biology, and Biogeochemistry of Thermophiles’, and in particular Mark Young and Frank Robb, for field measurements, encouragement, and logistical support, Kalsang Namgyal for sequencing assistance, the Tiedje lab for PAUP access, Kevin Griffith and Hajime Kobayashi for electroporation guidance, and Chris Marx, Peter Girguis, Frank Stewart, Irene Newton, and anonymous reviewers for helpful comments on the manuscript. Funding was provided in part by an NSF Young Researchers travel award and Harvard Graduate Student Council travel grant to T.A.A., and a Harvard College Research Program grant to G.S.

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Copyright information

© Springer 2010

Authors and Affiliations

  • Thomas A. Auchtung
    • 1
    • 2
  • Galina Shyndriayeva
    • 1
    • 3
  • Colleen M. Cavanaugh
    • 1
  1. 1.Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUSA
  2. 2.Working Bugs LLCEast LansingUSA
  3. 3.Centre for the History of Science, Technology and MedicineImperial CollegeLondonUK

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