School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea.
PLoS One. 2012;7(4):e35784. doi: 10.1371/journal.pone.0035784. Epub 2012 Apr 26.
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.
海栖交替单胞菌是一种在海洋生境中广泛分布的富营养型细菌。在这些细菌中，潮间带具有独特的特点：经历季节性的温度和氧气张力变化，加上周期性地暴露于石油烃中。从受烃类污染的潮间带沉积物中分离到的海栖交替单胞菌 SN2 菌株已被证明能在那里代谢芳烃。对 SN2 菌株的基因组特征进行了生物信息学分析，并与其他两种海栖交替单胞菌的生态型 AltDE 和 ATCC 27126 进行了比较。SN2 菌株的基因组与其他两个菌株的基因组在大小、平均核苷酸同一性值、tRNA 基因、非编码 RNA、双加氧酶基因含量、信号转导基因以及全球海洋采样计划中收集的基因的代表性程度等方面存在差异。遗传特征的模式（例如，GC 含量、GC 倾斜、Karlin 特征、CRISPR 基因同源性）表明，SN2 菌株的基因组结构通过水平基因转移（HGT）发生了改变。实验证明，SN2 菌株比其他两个菌株更能耐受低温，尤其是在 5°C 时。与 HGT 假说一致，SN2 菌株中的总共 15 个基因组岛可能赋予了其适应季节性寒冷潮间带生境的生态适应性特征（特别是膜转运、芳烃代谢和脂肪酸生物合成）。
