Zhao Yang, Wei Hua-Mei, Yuan Jia-Li, Xu Lian, Sun Ji-Quan
Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China.
Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.
Front Microbiol. 2023 Apr 17;14:1177951. doi: 10.3389/fmicb.2023.1177951. eCollection 2023.
is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of , while 22,291 are unique genes. Although strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the -alkane-degrading genes / (97.1% of tested strains) and (96.7% of tested strains), which were responsible for medium-and long-chain -alkane terminal oxidation reaction, respectively. Most strains also have (93.3% of tested strains) and (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the strains to easily obtain carbon and energy sources from their environment for survival. The strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable strains to survive extreme stresses. The genome of each strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the and genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while , , and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.
它无处不在，具有高度的物种多样性和复杂的进化模式。为了阐明其对各种环境具有高度适应能力的机制，使用系统发育基因组学和比较基因组学方法分析了312个菌株的基因组。结果表明，该属具有开放的泛基因组和强大的基因组可塑性。泛基因组由47500个基因组成，所有基因组共有818个基因，而独特基因有22291个。尽管该菌株没有完整的糖酵解途径来直接利用葡萄糖作为碳源，但大多数菌株都含有 -烷烃降解基因 /（97.1%的测试菌株）和 （96.7%的测试菌株），它们分别负责中长链 -烷烃末端氧化反应。大多数该菌株还具有 （93.3%的测试菌株）和 （92.0%的测试菌株）基因，分别可以降解芳香族化合物儿茶酚和苯甲酸。这些能力使该菌株能够轻松地从环境中获取碳源和能源以生存。该菌株可以通过积累钾和相容性溶质（包括甜菜碱、甘露醇、海藻糖、谷氨酸和脯氨酸）来调节渗透压。它们通过合成超氧化物歧化酶、过氧化氢酶、二硫键异构酶和甲硫氨酸亚砜还原酶来应对氧化应激，这些酶可以修复活性氧造成的损伤。此外，大多数该菌株含有许多外排泵基因和抗性基因来应对抗生素应激，并且可以合成多种次生代谢产物，包括芳基多烯、β-内酯和铁载体等，以适应其环境。这些基因使该菌株能够在极端压力下生存。每个该菌株的基因组包含不同数量的原噬菌体（0 - 12个）和基因组岛（GIs）（6 - 70个），并且在基因组岛中发现了与抗生素抗性相关的基因。系统发育分析表明， 和 基因与核心基因组具有相似的进化位置，表明它们可能是通过垂直基因转移从其祖先那里获得的，而 、 、 和抗生素抗性基因可能是通过水平基因转移从其他生物体获得的。
