Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions

Cold tolerance and aromatic hydrocarbon metabolism

Renukaradhya K. Math, Hyun Mi Jin, Jeong Myeong Kim, Yoonsoo Hahn, Woojun Park, Eugene L. Madsen, Che Ok Jeon

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.

Original languageEnglish
Article numbere35784
JournalPLoS One
Volume7
Issue number4
DOIs
Publication statusPublished - 2012 Apr 26

Fingerprint

Alteromonas
Aromatic Hydrocarbons
aromatic hydrocarbons
Genomics
Metabolism
cold tolerance
Oceans and Seas
Genes
genomics
metabolism
Horizontal Gene Transfer
Hydrocarbons
Gene transfer
Ecosystem
Clustered Regularly Interspaced Short Palindromic Repeats
Genome
Ecotype
Genomic Islands
Dioxygenases
Untranslated RNA

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions : Cold tolerance and aromatic hydrocarbon metabolism. / Math, Renukaradhya K.; Jin, Hyun Mi; Kim, Jeong Myeong; Hahn, Yoonsoo; Park, Woojun; Madsen, Eugene L.; Jeon, Che Ok.

In: PLoS One, Vol. 7, No. 4, e35784, 26.04.2012.

Research output: Contribution to journalArticle

Math, Renukaradhya K. ; Jin, Hyun Mi ; Kim, Jeong Myeong ; Hahn, Yoonsoo ; Park, Woojun ; Madsen, Eugene L. ; Jeon, Che Ok. / Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions : Cold tolerance and aromatic hydrocarbon metabolism. In: PLoS One. 2012 ; Vol. 7, No. 4.
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