Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord

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.

The Potential Use of Actinomycetes as Microbial Inoculants and Biopesticides in Agriculture

“…The microbial concentration in the product is directly related to proper colonization and efficacy since the number of viable cells disposed of in the crop needs to be enough to promote the nutrition and protection of the plant (227). One of the main challenges faced in developing actinomycete-based products is to achieve high culture concentrations at large-scale production, once they show a slower reproduction rate than other bacteria (228,229). In addition, liquid cultures of actinomycetes tend to form aggregates and mycelial pellets, making homogenization difficult (230).…”

Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments

“…The fatty acid profile of the strains is in agreement with reported Streptomyces species; for instance S. colonosanans MUSC 93J T , S. tardus P38-E01 T , S. spinosus SBTS01 T and S. shenzhenensis subsp. oryzicola W18L9 T , which contain anteiso-C 15:0 (21.3–26.6%) and iso-C 16:0 (15.1–30.0%) as major fatty acids ( Law et al, 2017 ; Králová et al, 2021 ; Kaewkla et al, 2022 ). The whole-cell sugars of G1–G3 were glucose and ribose ( Supplementary Figures S2A–C ).…”

“…The fatty acids profiles of G1-G3 are presented in Table 2. The major cellular fatty acids (percentage greater than 10%) in G1 and G2 were anteiso-C 15:0 (25.83 and 25.12%, respectively), iso-C 16:0 (18.28 and 15.90%) and C 16:0 (14.14 and 14.34%); ) and iso-C 16:0 (15.1-30.0%) as major fatty acids (Law et al, 2017;Králová et al, 2021;Kaewkla et al, 2022). The whole-cell sugars of G1-G3 were glucose and ribose (Supplementary Figures S2A-C).…”

Function of CAZymes encoded by highly abundant genes in rhizosphere microbiome of Moringa oleifera

“…However, when we consider the factor of plant exudates, we might explain this contradicting results by the differential response of the genus due to the exposure to different exudates of two different plants, e.g., Brassica napus in prior research ( Jiménez-Gómez et al, 2019 ), while Moringa oleifera in the present study . Another recent report indicated that a member of genus Streptomyces harbors 186 CAZyme domain sequences, where families of the CAZy class GH are the most abundant followed by those of GT ( Králová et al, 2021 ). This makes the rhizosphere microbiome of Moringa oleifera a good source of these economically-important enzymes.…”