A novel endophytic species, Streptomyces colwelliae sp. nov., isolated from root nodule of Alnus glutinosa.

Abstract

Background: Streptomyces strains remain one of the most promising bacteria for novel drug discovery and are of general interest for pharmaceutical, biotechnological, and agricultural applications. They have been successfully used in agriculture to protect a number of crops, including wheat and rice, against fungal infections.

Method and results: Streptomyces sp. Agncl-13^T was isolated from the surface sterilised root nodule of Alnus glutinosa, Newcastle upon Tyne, UK, and subjected to polyphasic taxonomic analysis and genome mining for plant growth promoting genes. Phenotypic, genetic and genomic data distinguished strain Agncl-13^T from Streptomyces species with validly published names. Whole cell hydrolysates of the strain were rich in LL-DAP. Strain Agncl-13^T had diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, aminolipids, a glycolipid, a glycophospholipid, phospholipids and unidentified lipids, as polar lipids; as well as iso-C_15:0, anteiso-C_15:0, iso-C_16:0, C_16:0, iso-C_17:0, and anteiso-C_17:0 as major fatty acids (> 5%), and MK-9(H₆) and MK-9(H₄) as predominant menaquinones (> 10%). Digital DNA-DNA hybridization values between the genomic sequence of strain Agncl-13^T and its phylogenomic relatives were below the threshold of 70%. The average nucleotide identity scores were below the thresholds 95-96% (bacteria) and 96.7% (Streptomyces) for bacteria species demarcation, respectively. The strain had several gene clusters whose products are involved in plant growth promotion. It was able to fix nitrogen, solubilise phosphate, and produce siderophore and ACC deaminase. In addition, strain Agncl-13^T contained several secondary metabolite biosynthetic gene clusters which had a low similarity confidence to known BCGs. The strain displayed antimicrobial activity against Escherichia coli ΔtolC, Proteus vulgaris, multidrug resistant Staphylococcus aureus, and Candida albicans.

Conclusions: Based on polyphasic taxonomic data, the strain Agncl-13^T = DSM 118684^T = CECT 31215^T is considered as a novel species for which the name Streptomyces colwelliae sp. nov. is proposed. This study highlights the ecological features of strain Agncl-13^T, which might be used as biocontrol agent and biofertilizer for sustainable agriculture. Further research investigations are needed to confirm the potential application of the proposed novel type strain.