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

Extremophiles (2011) 15:105116 DOI 10.1007/s00792-010-0340-5

ORIGINAL PAPER

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

Thomas A. Auchtung Galina Shyndriayeva

Colleen M. Cavanaugh

Received: 4 November 2010 / Accepted: 15 November 2010 / Published online: 12 December 2010 Springer 2010

Abstract The candidate archaeal division Korarchaeota is known primarily from deeply branching sequences of 16S rRNA genes PCR-amplied from hydrothermal springs. Parallels between the phylogeny of these genes and the geographic locations where they were identied suggested that Korarchaeota exhibit a high level of endemism. In this study, the inuence of geographic isolation and select environmental factors on the diversication of the Korarchaeota was investigated. Fourteen hot springs from three different regions of Kamchatka, Russia were screened by PCR using Korarchaeota-specic and general Archaea 16S rRNA gene-targeting primers, cloning, and sequencing. Phylogenetic analyses of these sequences with Korarchaeota 16S rRNA sequences previously identied 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-specic 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 identication sites united sequence clusters at different phylogenetic levels, suggesting varied roles of these factors in the diversication of Korarchaeota.

Keywords 16S rRNA gene Abundance Hydrothermal

Kamchatka Korarchaeota Phylogeny

Introduction

Korarchaeota is a proposed archaeal division that has been characterized primarily by analysis of small subunit ribosomal RNA (16S rRNA) gene sequences detected exclusively in high temperature hydrothermal environments on continents, in shallow water, and in the deep ocean (Barns et al. 1996; Auchtung et al. 2006). Korarchaeota are of particular interest because of their deeply rooted position in phylogenetic analyses (Barns et al. 1996). 16S rRNA gene sequence analyses strongly suggest that they are a monophyletic group; however, their position relative to other Archaea is weakly supported. The only reported genome sequence of a Korarchaeota is from Korarchaeum cryptolum, a putative peptide-fermentor that was enriched in...