Microevolution and Adaptive Strategy of Psychrophilic Species Flavobacterium bomense sp. nov. Isolated From Glaciers
Microevolution and Adaptive Strategy of Psychrophilic Species Flavobacterium bomense sp. nov. Isolated From Glaciers
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嗜冷物种波门黄杆菌的微进化和适应策略。
DOI：
10.3389/fmicb.2019.01069
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发表时间：
2019-05-22
影响因子：
5.2
通讯作者：
Xin, Yu-Hua
中科院分区：
文献类型：
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作者：
Liu, Qing;Liu, Hong-Can;Xin, Yu-Hua
青藏高原众多的山地冰川栖息着丰富的微生物。冰川表面的微生物暴露在寒冷、贫瘠、高紫外线辐射的环境中。尽管高通量测序揭示了冰川上的微生物群落组成，但人们对某些细菌种群的微进化和适应策略知之甚少。在这项研究中，我们采用多相方法确定了从青藏高原冰川中分离出的 11 株嗜冷黄杆菌菌株的分类地位，并进行了比较基因组分析。基于串联单拷贝基因序列的系统发育树显示，11 个菌株聚集在一起，形成黄杆菌属中一个独特且新颖的分支。这些菌株之间的平均核苷酸同一性（ANI）值高于96%。然而，它们与相关物种之间的值远低于 90%，表明它们代表了一个新物种，并且被命名为 Flavobacter bomense sp。十一月被提议。这种新黄杆菌属菌株的核心和辅助基因组显示出多种不同的基因内容和代谢途径模式。为了推断核心基因组的进化驱动力，我们发现同源重组对核苷酸取代的贡献是突变的两倍。在它们的基因组中发现了一系列编码在冷适应中具有已知或预测作用的蛋白质的基因，例如冷休克蛋白、蛋白视紫红质、渗透保护和膜相关蛋白。对32个黄杆菌型菌株和11个新菌株的最适生长温度（OGT）≤20°C组和OGT>20°C组进行比较分析，发现多种氨基酸取代，包括OGT≤20°C组中脯氨酸和谷氨酰胺含量降低以及蛋氨酸和异亮氨酸含量增加，这可能有助于增加蛋白质在低温下的灵活性。 温度。因此，这项研究在冰川中发现了一种新的黄杆菌属物种，它具有高度的种内多样性和多种适应机制，使它们能够应对极端的栖息地并繁衍生息。
Numerous mountain glaciers located on the Tibetan Plateau are inhabited by abundant microorganisms. The microorganisms on the glacier surface are exposed to the cold, barren, and high-ultraviolet radiation environments. Although the microbial community composition on glaciers has been revealed by high-throughput sequencing, little is known about the microevolution and adaptive strategy of certain bacterial populations. In this study, we used a polyphasic approach to determine the taxonomic status of 11 psychrophilic Flavobacterium strains isolated from glaciers on the Tibetan Plateau and performed a comparative genomic analysis. The phylogenetic tree based on the concatenated single-copy gene sequences showed the 11 strains clustered together, forming a distinct and novel clade in the genus Flavobacterium. The average nucleotide identity (ANI) values among these strains were higher than 96%. However, the values much lower than 90% between them and related species indicated that they represent a novel species and the name Flavobacterium bomense sp. nov. is proposed. The core and accessory genomes of strains in this new Flavobacterium species showed diverse distinct patterns of gene content and metabolism pathway. In order to infer the driving evolutionary forces of the core genomes, homologous recombination was found to contribute twice as much to nucleotide substitutions as mutations. A series of genes encoding proteins with known or predicted roles in cold adaptation were found in their genomes, for example, cold-shock protein, proteorhodopsin, osmoprotection, and membrane-related proteins. A comparative analysis of the group with optimal growth temperature (OGT) ≤ 20°C and the group with OGT > 20°C of the 32 Flavobacterium type strains and 11 new strains revealed multiple amino acid substitutions, including the decrease of the proline and glutamine content and the increase of the methionine and isoleucine content in the group with OGT ≤ 20°C, which may contribute to increased protein flexibility at low temperatures. Thus, this study discovered a novel Flavobacterium species in glaciers, which has high intraspecific diversity and multiple adaptation mechanisms that enable them to cope and thrive in extreme habitats.