Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100, Toruń, Poland.
School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
Antonie Van Leeuwenhoek. 2022 Jun;115(6):783-800. doi: 10.1007/s10482-022-01734-8. Epub 2022 Apr 11.
A genomic-based polyphasic study was undertaken to establish the taxonomic status and biotechnological and ecological potential of a Streptomyces strain, isolate SF28, that was recovered from the litter layer in a Polish Pinus sylvestris forest. The isolate had morphological characteristics and chemotaxonomic properties consistent with its classification in the genus Streptomyces. It formed long straight chains of spores with smooth surfaces, contained LL-diaminopimelic acid, glucose and ribose in whole-organism hydrolysates, produced major proportions of straight, iso- and anteiso- fatty acids, hexa- and octa-hydrogenated menaquinones with nine isoprene units and had a polar lipid pattern composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, glycophospholipids and three uncharacterized components. Phylogenetic trees prepared using 16S rRNA gene and multilocus gene sequences of conserved housekeeping genes showed that the isolate formed a branch that was loosely associated with the type strains of several validly published Streptomyces species. A draft genome generated for the isolate was rich in natural product-biosynthetic gene clusters with the potential to produce new specialised metabolites, notably antibiotics, and stress related genes which provide an insight into how it may have become adapted to the harsh conditions that prevail in acidic forest soils. A phylogenomic tree based on the genomes of the isolate and its phylogenetic neighbours confirmed that it formed a distinct lineage well separated from its closest evolutionary relatives. The isolate shared low average nucleotide identity and digital DNA:DNA hybridization values with its phylogenomic neighbours and was also distinguished from them using a combination of cultural and micromorphological properties. Given this wealth of taxonomic data it is proposed that isolate SF28 (= DSM 113360 = PCM 3163) be classified in the genus Streptomyces as Streptomyces pinistramenti sp. nov. The isolate showed pronounced antimicrobial activity, especially against fungal plant pathogens.
采用基于基因组的多相研究方法，对从波兰云杉林凋落物层中分离到的链霉菌菌株 SF28 的分类地位、生物技术和生态学潜力进行了研究。该菌株具有与链霉菌属分类一致的形态特征和化学生物分类特征。它形成表面光滑的长直链孢子，在全细胞水解物中含有 LL-二氨基庚二酸、葡萄糖和核糖，产生大量直链、异源和前异源脂肪酸，六氢和八氢menaquinones 具有九个异戊二烯单位，极性脂类图谱由双磷脂酰甘油、磷脂酰乙醇胺、磷脂甲基乙醇胺、糖脂和三个未鉴定成分组成。使用 16S rRNA 基因和保守管家基因的多基因序列构建的系统发育树表明，该菌株与几个有效发表的链霉菌种的模式株形成了一个松散相关的分支。为该菌株生成的基因组草图富含天然产物生物合成基因簇，具有产生新的特殊代谢物的潜力，特别是抗生素和与应激相关的基因，这些基因提供了对其如何适应酸性森林土壤中普遍存在的恶劣条件的深入了解。基于该菌株及其系统发育邻居的基因组构建的系统发育基因组树证实，它与最接近的进化亲属形成了一个独特的谱系，与它们很好地区分开来。该菌株与系统发育邻居共享的平均核苷酸同一性和数字 DNA：DNA 杂交值较低，并且还可以通过组合使用培养和微观形态特征将其与它们区分开来。鉴于这些丰富的分类数据，建议将分离株 SF28（=DSM 113360=PCM 3163）归类为链霉菌属的链霉菌属新种，即链霉菌属 pinistramenti sp. nov。该菌株表现出明显的抗微生物活性，特别是对真菌植物病原体。
