Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from yellowstone national park

Christine Romano, Seth D'Imperio, Tanja Woyke, Konstantinos Mavromatis, Roger Lasken, Everett Shock, Timothy R. McDermott

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

We describe the complete genome sequences of four closely related Hydrogenobaculum sp. isolates (>99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different from Hydrogenobaculum sp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite {left open bracket}As(III){right open bracket} oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRI PR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum of Hydrogenobaculum genotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.

Original languageEnglish (US)
Pages (from-to)2932-2943
Number of pages12
JournalApplied and Environmental Microbiology
Volume79
Issue number9
DOIs
StatePublished - May 2013

Fingerprint

national parks
genomics
national park
genome
Genome
gene
NADH dehydrogenase (ubiquinone)
Genes
Clustered Regularly Interspaced Short Palindromic Repeats
Deoxyribodipyrimidine Photo-Lyase
Plastoquinone
Metagenome
geyser
genes
Ecotype
Electron Transport Complex I
analysis
Recreational Parks
DNA
Thiosulfates

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology
  • Medicine(all)

Cite this

Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from yellowstone national park. / Romano, Christine; D'Imperio, Seth; Woyke, Tanja; Mavromatis, Konstantinos; Lasken, Roger; Shock, Everett; McDermott, Timothy R.

In: Applied and Environmental Microbiology, Vol. 79, No. 9, 05.2013, p. 2932-2943.

Research output: Contribution to journalArticle

Romano, Christine ; D'Imperio, Seth ; Woyke, Tanja ; Mavromatis, Konstantinos ; Lasken, Roger ; Shock, Everett ; McDermott, Timothy R. / Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from yellowstone national park. In: Applied and Environmental Microbiology. 2013 ; Vol. 79, No. 9. pp. 2932-2943.
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