Abstract
Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01T, was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269T (98.3%). Predominant fatty acids were C16:0 iso, C16:0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01T = CCM 9049T = DSM 111582T) is proposed.
Highlights
MATERIALS AND METHODSThe genus Streptomyces was first proposed in the early 1940s (Waksman and Henrici, 1943) and has since become a popular subject of bioprospecting studies in search for new bioactive natural products
The prediction of biosynthetic gene clusters (BGCs) that could be responsible for the biosynthesis of antifungal metabolites by antiSMASH analysis (Supplementary Table 6) was further supported by the antimicrobial assays, which demonstrated that supernatants from strain P38-E01T inhibited the growth of the fungal strain C. albicans ATCC 90028 when grown in yeast extract–malt extract (YEME) broth for 7 days with an observed zone of inhibition (ZOI) of 9 mm
The phenotypic, chemotaxonomic, and genomic analyses performed in this study confirmed that strain P38E01T belongs to the genus Streptomyces and represents a novel species
Summary
The genus Streptomyces was first proposed in the early 1940s (Waksman and Henrici, 1943) and has since become a popular subject of bioprospecting studies in search for new bioactive natural products. Extraction of genomic DNA from strain P38-E01T and both Illumina short-read and PacBio longread sequencing were performed by BaseClear BV (Leiden, Netherlands). The 16S rRNA gene sequences of the type strains of closely related Streptomyces species were retrieved from NCBI GenBank database. A multilocus sequence analysis (MLSA) was performed by uploading the draft genome assemblies of strain P38-E01T and the closely related type strains to the Automated Multi-Locus Species Tree (autoMLST) web tool (Alanjary et al, 2019). For initial assessments of isolate P38-E01T ability to produce antimicrobial metabolites, supernatants from a broth culture were screened for the ability to inhibit the growth of various bacterial or fungal strains by a spot-on-lawn assay. The DMSO crude extracts of strain P38-E01T were analyzed on an Agilent 1290 HPLC system with a Zorbax bonus RP, 2.1 × 50 mm, 3.5-μm column connected to a DAD, and a QTOF was used to precisely identify antifungal metabolites
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