Aono Eiji, Baba Tomoya, Ara Takeshi, Nishi Tatsunari, Nakamichi Tomoko, Inamoto Eiji, Toyonaga Hiromi, Hasegawa Miki, Takai Yuki, Okumura Yoshiko, Baba Miki, Tomita Masaru, Kato Chiaki, Oshima Taku, Nakasone Kaoru, Mori Hirotada
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
Mol Biosyst. 2010 Jul;6(7):1216-26. doi: 10.1039/c000396d. Epub 2010 May 11.
Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.
深海沉积物中有机物的再矿化在海洋生物地球化学循环中很重要，细菌在这个过程中起主要作用。紫色希瓦氏菌DSS12是一种嗜冷嗜压γ-变形菌，从5110米深处的深海沉积物表层分离得到。在此，我们报告了紫色希瓦氏菌的完整基因组序列，并与从淡水湖沉积物中分离得到的奥奈达希瓦氏菌MR-1的基因组进行了比较分析。与奥奈达希瓦氏菌不同，这种深海希瓦氏菌具有很少的用于厌氧呼吸的末端还原酶，并且没有参与呼吸性铁（III）还原的c型细胞色素或外膜蛋白，而这是大多数希瓦氏菌属的特征。相反，紫色希瓦氏菌的基因组包含更多用于有氧呼吸的末端氧化酶，以及大量推测的分泌蛋白酶和多糖酶，特别是用于水解胶原蛋白、纤维素和几丁质的酶，比奥奈达希瓦氏菌编码得多。在紫色希瓦氏菌中发现了硝酸盐和亚硝酸盐的转运蛋白和同化还原酶，以及一氧化氮解毒机制（黄素血红蛋白和黄素铁氧化还原蛋白）。对紫色希瓦氏菌基因组的比较分析揭示了这种细菌对需氧环境的呼吸适应，导致表层沉积物中有机物主要进行有氧氧化，以及其有效利用多种有机物并同化无机氮作为在营养贫乏的深海海底生存策略的能力。
