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新种,一种从阿塔卡马沙漠土壤中分离得到的新型放线菌。

sp. nov., a novel actinobacterium isolated from Atacama Desert soil.

机构信息

Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland.

School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.

出版信息

Int J Syst Evol Microbiol. 2020 May;70(5):3513-3527. doi: 10.1099/ijsem.0.004212.

Abstract

Three presumptive strains isolated from a high altitude Atacama Desert soil were the subject of a polyphasic study. The isolates, strains 1G4, 1G51 and 1G52, were found to have chemotaxonomic and morphological properties that were consistent with their assignment to the genus . They formed a well supported clade in 16S rRNA gene trees and were most closely related to the type strain of (99.8-99.9% similarity). They were also closely related to the type strains of (99.6 % similarity), (99.7-99.9% similarity), (98.4-99.2% similarity), (99.4-99.5% similarity) and (99.3-99.5% similarity), but were distinguished from their closest relatives by a combination of phenotypic features. Average nucleotide identity and digital DNA:DNA hybridization similarities drawn from comparisons of draft genome sequences of isolate 1G4 and its closest phylogenetic neighbours mentioned above, were well below the threshold used to assign closely related strains to the same species. The close relationship between isolate 1G4 and the type strain of was showed in a phylogenomic tree containing representative strains of family . The draft genome sequence of isolate 1G4 (size 5.18 Kb) was shown to be rich in stress related genes providing further evidence that the abundance of propagules in Atacama Desert habitats reflects their adaptation to the harsh environmental conditions prevalent in this biome. In light of all of these data it is proposed that the isolates be assigned to a novel species in the genus . The name proposed for this taxon is sp. nov., with isolate 1G4 (=DSM 107534=PCM 3003) as the type strain.

摘要

从高海拔阿塔卡马沙漠土壤中分离出的三株假定菌株是多相研究的对象。这些分离株,菌株 1G4、1G51 和 1G52,具有化学分类学和形态学特性,符合其被分配到属的特征。它们在 16S rRNA 基因树中形成了一个支持良好的分支,与 (99.8-99.9%相似度)的模式菌株最为密切相关。它们与 (99.6%相似度)、 (99.7-99.9%相似度)、 (98.4-99.2%相似度)、 (99.4-99.5%相似度)和 (99.3-99.5%相似度)的模式菌株也非常密切相关,但通过表型特征的组合与它们最接近的亲缘关系菌株区分开来。从菌株 1G4 的草图基因组序列与上述最接近的系统发育邻居的比较中得出的平均核苷酸同一性和数字 DNA:DNA 杂交相似度,都远低于用于将密切相关的菌株分配到同一物种的阈值。菌株 1G4 与 模式菌株的密切关系在包含家族代表菌株的系统基因组树中得到了体现。菌株 1G4 的草图基因组序列(大小为 5.18 Kb)富含与应激相关的基因,这进一步证明了 在阿塔卡马沙漠生境中大量存在的原因是它们适应了这种生物群落中普遍存在的恶劣环境条件。鉴于所有这些数据,建议将这些分离株分配到属中的一个新种中。提议的这个分类单元的名称为 sp. nov.,其模式菌株为 1G4 菌株(=DSM 107534=PCM 3003)。

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