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Streptomyces alkaliterrae sp. nov., isolated from an alkaline soil, and emended descriptions of Streptomyces alkaliphilus, Streptomyces calidiresistens and Streptomyces durbertensis
Systematic and Applied Microbiology ( IF 3.4 ) Pub Date : 2020-10-27 , DOI: 10.1016/j.syapm.2020.126153
Magdalena Świecimska , Patrycja Golińska , Imen Nouioui , Magdalena Wypij , Mahendra Rai , Vartul Sangal , Michael Goodfellow

A polyphasic study was undertaken to establish the taxonomic position of six representative streptomycetes isolated from an alkaline soil adjacent to a meteoric alkaline soda lake in India. Chemotaxonomic, cultural and morphological properties of the isolates were consistent with their classification in the genus Streptomyces. The isolates formed extensively branched substrate mycelia and aerial hyphae that differentiated in straight chains of spores with smooth surfaces. They contained LL-diaminopimelic acid in the wall peptidoglycan, produced either hexa- or octa-hydrogenated menaquinones with nine isoprene units, major amounts of saturated, iso- and anteiso- fatty acids and phosphatidylethanolamine as the characteristic polar lipid. The isolates grew well at 30 °C, pH 9 and in the presence of 3 to 5% (w/v) sodium chloride. Isolates OF1T, OF3 and OF8 formed a distinct clade within the Streptomyces 16S rRNA gene tree sharing relatively high sequence similarities with the type strains of Streptomyces durbertensis (99.3%), Streptomyces palmae (98.1%) and Streptomyces xinghaiensis (98.3%), but can be distinguished from them using combinations of phenotypic properties. A phylogenomic tree based on draft genome sequences of the isolates and S. durbertensis DSM 104538T confirmed the phylogenetic relationships. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values calculated from the whole genome sequences of isolate OF1T and S. durbertensis DSM 104538T were low at 92.0% and 45.2%, respectively, indicating that they belong to different genomic species. Consequently, on the basis of the genomic, phylogenetic and associated phenotypic data it is proposed that isolates OF1T, OF3 and OF8 be assigned to the genus Streptomyces as Streptomyces alkaliterrae sp. nov. with strain OF1T (NCIMB 15195T =PCM 3001T) as the type strain. Isolates IF11, IF17 and IF19, and S. alkaliphilus DSM 42118T were shown to belong to the same taxospecies and together with S. calidiresistens DSM 42108T comprised a well supported clade in the Streptomyces 16S rRNA gene tree. Isolate IF17 and S. alkaliphilus DSM 42118T formed a well-supported clade in the phylogenomic tree, had almost identical digital G + C similarity values, produced long straight chains of smooth-surfaced spores and shared ANI and dDDH values (98.0 and 79.6%, respectively) consistent with their assignment to the same genomic species. In light of all of the data isolates IF11, IF17 and IF19 should be seen as authentic stains of S. alkalihilus. Data acquired in the present study have also been used to emend the descriptions of S. alkaliphilus, S. calidiresistens and S. durbertensis. The genomes of isolates IF17, and OF1T, OF3 and OF8 contain relatively high numbers of biosynthetic gene clusters some of which were discontinously distributed indicating ones predicted to express for novel specialised metabolites.



中文翻译:

链alkaliterrae SP。十一月,从碱性土壤中分离,并仔细的校勘的描述链霉菌alkaliphilus链霉菌calidiresistens链霉菌durbertensis

进行了一项多相研究,以确定从与印度的一块碱性苏打湖相邻的碱性土壤中分离出的六种代表性链霉菌的生物分类位置。分离株的化学分类,文化和形态特性与其在链霉菌属中的分类一致。分离物形成广泛分支的底物菌丝体和气生菌丝,它们在具有光滑表面的孢子的直链中分化。它们在壁肽聚糖中含有LL-二氨基庚二酸,生成具有九个异戊二烯单元的六氢或八氢氢化萘醌,大量的饱和,和对映体-脂肪酸和磷脂酰乙醇胺为特征性极性脂质。分离株在30°C,pH 9和3至5%(w / v)氯化钠存在下生长良好。分离物OF1,T3,OF3和OF8在链霉菌16S rRNA基因树中形成了独特的进化枝,与杜氏链霉菌(99.3%),棕榈链霉菌(98.1%)和星海链霉菌(98.3%)的菌株具有较高的序列相似性,但是可以使用表型属性的组合来区别它们。基于分离株和S. durbertensis DSM 104538 T的基因组序列草案的系统树证实了系统发育关系。从分离物OF1 T杜氏链球菌DSM 104538 T的全基因组序列计算得出的平均核苷酸同一性(ANI)和数字DNA-DNA杂交(dDDH)值分别较低,分别为92.0%和45.2%,表明它们属于不同的基因组物种。因此,基因组,系统发育和相关联的表型数据的基础上提出,分离OF1 Ť,OF3和OF8被分配给属链霉菌链霉菌alkaliterrae藻。十一月 应变为OF1 T(NCIMB 15195 T = PCM 3001 T)作为类型应变。分离物IF11,IF17和IF19,和S. alkaliphilus DSM 42118 Ť显示出属于同一taxospecies和连同S. calidiresistens DSM 42108 Ť包括在一个很好的支持进化枝链霉菌16S rRNA基因树。分离IF17和嗜碱链球菌DSM 42118 T在系统发育树中形成了一个支撑良好的进化枝,具有几乎相同的数字G + C相似度值,产生了光滑表面孢子的长直链,并且共享了ANI和dDDH值(分别为98.0和79.6%),与它们分配给相同的基因组物种。在光的所有数据的分离物IF11,IF17和IF19应该被看作是地道的污渍S. alkalihilus。数据在本研究中获得的也被用来订正的说明S. alkaliphilusS. calidiresistensS. durbertensis。分离株IF17和OF1 T的基因组,OF3和OF8包含相对大量的生物合成基因簇,其中一些不连续地分布,表明预计将表达新的专门代谢产物。

更新日期:2020-11-06
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