Geographic divergence of “Sulfolobus islandicus” strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars

Abstract

Ten well-annotated genomes of “Sulfolobus islandicus” strains from different geographic locations have been released at the NCBI database. Whole genome based composition vector trees indicate that these strains show the same branching patterns as originally reported by multi-locus sequence analysis. To determine whether the ten strains meet the criteria for separate species, DNA–DNA hybridization (DDH) was performed in silico. DDH values of strains from the same geographic location, i.e., Iceland, Kamchatka and North America, ranged from 82.4 to 95.4 %, clearly qualifying them as members of the same species. The lowest DDH values found between locations ranged from 75.5 to 76.6 %, which exceed the 70 % DDH threshold for a species thereby indicating they are all members of the same species based on the currently accepted definition. The clear divergences of strains from the different geographic locations are sufficiently great to consider them as separate geovars. “S. islandicus” has not yet been validly named and a type strain has not been deposited in culture collections. We urgently recommend that those who study the organism fulfill the criteria of the International Code of Nomenclature of Bacteria in order to designate a type strain and to identify and deposit related strains of this species to make them available to the broader scientific community.

CVTree3 Web Server for Whole-Genome-Based and Alignment-Free Prokaryotic Phylogeny and Taxonomy

“…However, effectively inferring phylogenetic trees from the genome sequences and comparing the branching orders with taxonomy at all ranks present challenges. To this end, the composition vector (CV) approach to prokaryotic phylogeny developed by our group in the last decade [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] , [23] , [24] has the potential to meet this challenge. In this paper, we describe the latest version (Version 3) of the CVTree web server and demonstrate its applications.…”

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis

“…Although the CVTree method adds more agreement than discrepancy to the 16S rRNA results, the difference between the two approaches certainly deserves in-depth scrutiny. In addition, since high resolution power at the species level and below is a prominent advantage of CVTree as compared to 16S rRNA sequence analysis [ 12 , 60 ], we will elaborate on this aspect in the future when the amount of sequenced archaeal genomes will have increased substantially.…”

Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals

“…This, combined with difficulties obtaining pure cultures, led to the use of mixed and misidentified strains during the early stages of Sulfolobus research (Grogan, 1989 ). S. islandicus was isolated more recently (Zillig et al, 1993 ), but has suffered from similar confusion: fresh isolates are reported so frequently that no single strain has been dominant enough to be thoroughly characterized; in fact, the species name islandicus is not yet officially recognized (Zuo et al, 2014 ).…”

“…Genome sequences are available for the type strain of S. acidocaldarius (DSM 639) (Chen et al, 2005 ) and S. solfataricus strain P2 (DSM 1616) (She et al, 2001 ), while nearly 20 different strains of S. islandicus have been sequenced. None of the islandicus strains are available from culture collections and no type strain has been designated (Zuo et al, 2014 ). Sulfolobus species, particularly S. islandicus , have been isolated in conjunction with viruses (Guo et al, 2011 ), and have played an important role in understanding the diversity and host interactions of archaeal viruses (Zillig et al, 1993 ; Greve et al, 2004 ; Bize et al, 2009 ; Prangishvili, 2013 ).…”