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 language | English (US) |
|---|---|
| Pages (from-to) | 2932-2943 |
| Number of pages | 12 |
| Journal | Applied and Environmental Microbiology |
| Volume | 79 |
| Issue number | 9 |
| DOIs | |
| State | Published - May 2013 |
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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 journal › Article
}
TY - JOUR
T1 - Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from yellowstone national park
AU - Romano, Christine
AU - D'Imperio, Seth
AU - Woyke, Tanja
AU - Mavromatis, Konstantinos
AU - Lasken, Roger
AU - Shock, Everett
AU - McDermott, Timothy R.
PY - 2013/5
Y1 - 2013/5
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84876330604&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84876330604&partnerID=8YFLogxK
U2 - 10.1128/AEM.03591-12
DO - 10.1128/AEM.03591-12
M3 - Article
C2 - 23435891
AN - SCOPUS:84876330604
VL - 79
SP - 2932
EP - 2943
JO - Applied and Environmental Microbiology
JF - Applied and Environmental Microbiology
SN - 0099-2240
IS - 9
ER -