Shen Liang, Liu Yongqin, Wang Ninglian, Adhikari Namita Paudel
Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, China.
CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100085, China.
Microorganisms. 2019 Jul 22;7(7):211. doi: 10.3390/microorganisms7070211.
Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we performed a comparative genomic analysis to uncover the genomic features of strain Y620-1 isolated from a 59 m depth of the ice core drilled from a Tibetan Plateau glacier. Strain Y620-1 had the smallest genome among the 12 cultured strains, relatively low GC content, and was placed at the root position of the phylogenomic tree. The gene family based on a nonmetric multidimensional scaling (NMDS) plot revealed a clear separation of strain Y620-1 from the reference strains. The genome of the deep ice core isolated strain contained the highest percentage of new genes. The definitive difference is that all genes required for the serine-glyoxylate cycle in one-carbon metabolism were only found in strain Y620-1, but not in any of the reference strains. The placement of strain Y620-1 in the root of the phylogenomic tree suggests that these new genes and functions are of ancient origin. All of these genomic features may contribute to the survival of Y620-1 in the glacier.
冰川已被视为以微生物生命为主导的生物群落。许多新物种已从冰川生态系统中分离出来，并且它们的生理特征已得到充分表征。然而，从深层冰芯分离出的细菌的基因组特征却了解甚少。在本研究中，我们进行了比较基因组分析，以揭示从青藏高原冰川钻取的59米深冰芯中分离出的Y620-1菌株的基因组特征。Y620-1菌株在12株培养菌株中基因组最小，GC含量相对较低，并位于系统发育树的根部位置。基于非度量多维标度（NMDS）图的基因家族显示Y620-1菌株与参考菌株明显分离。从深层冰芯分离出的菌株的基因组中新基因的比例最高。决定性的差异在于，一碳代谢中丝氨酸-乙醛酸循环所需的所有基因仅在Y620-1菌株中发现，而在任何参考菌株中均未发现。Y620-1菌株在系统发育树根部的位置表明这些新基因和功能起源古老。所有这些基因组特征可能有助于Y620-1在冰川中生存。
