Genome-based classification of Streptomyces pinistramenti sp. nov., a novel actinomycete isolated from a pine forest soil in Poland with a focus on its biotechnological and ecological properties

Abstract

A genomic-based polyphasic study was undertaken to establish the taxonomic status and biotechnological and ecological potential of a Streptomyces strain, isolate SF28 T , that was recovered from the litter layer in a polish Pinus sylvestris forest. The isolate had morphological characteristics and chemotaxonomic properties consistent with its classi cation in the genus Streptomyces. It formed long straight chains of spores with smooth surfaces, contained LL-diaminopimelic acid and glucose and ribose in whole-organism hydrolysates, produced major proportions of straight, isoand anteisofatty acids, hexa-and octa-hydrogenated menaquinones with nine isoprenoid 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 they may have 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 con rmed that it formed a distinct lineage well separated from its closest evolutionary relatives. The isolate shared low average nucleotide index 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 T (=DSM 113360 T =PCM 3163 T ) be classi ed in the genus Streptomyces as Streptomyces pinistramenti sp. nov. The isolate showed pronounced antimicrobial activity, especially against fungal plant pathogens.

Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy

“… Inhibition zones of growth were measured in mm, the values are the mean of three replicates ± standard deviations. –, no inhibition; *isolates showing poor growth; **Antimicrobial activity of C. pinisilvae NH11 T and NF3, and S. pinistramenti SF28 T was mentioned previously ( Świecimska et al, 2021a , 2022 ). T , type strain.…”

“… Codes and names in bold indicate isolates with 16S rRNA sequence similarity at or below the 99.0% threshold for delineating actinomycete species. *Isolates recently classified as new species: 1G4 T , 1G51, and 1G52 ( Golińska et al, 2020b ); 1G6 T , 1G14, and 1G50 ( Golińska et al, 2020a ); IF11, IF17, IF19, OF1 T , OF3, and OF8 ( Świecimska et al, 2020 ); NF3 and NH11 T ( Świecimska et al, 2021a ); NF23 and NL8 T ( Świecimska et al, 2021b ); SF28 T ( Świecimska et al, 2022 ) and 5R2A7 T ( Carro et al, 2019 ). Codes for the isolates from the Atacama Desert soils: numbers 1–5 at the beginning of the code indicate the sample sites, G, HA, R2A, SCA the isolation medium and then the isolate number.…”

“…*Isolates recently classified as new species: 1G4 T , 1G51, and 1G52 ( Golińska et al, 2020b ); 1G6 T , 1G14, and 1G50 ( Golińska et al, 2020a ); IF11, IF17, IF19, OF1 T , OF3, and OF8 ( Świecimska et al, 2020 ); NF3 and NH11 T ( Świecimska et al, 2021a ); NF23 and NL8 T ( Świecimska et al, 2021b ); SF28 T ( Świecimska et al, 2022 ) and 5R2A7 T ( Carro et al, 2019 ).…”

“…The 115 isolates representing the colour-groups composed of strains from the four sampling sites were examined for their ability to inhibit the growth of Bacillus subtilis PCM 2021, Escherichia coli PCM 2057, Klebsiella pneumoniae ATCC 700603, Micrococcus luteus ATCC 10240, Proteus mirabilis CM NCU (isolate from Collegium Medicum Nicolaus Copernicus University), Pseudomonas aeruginosa ATCC 10145, Salmonella infantis SES (isolate from the Sanitary-Epidemiological Station in Toruń, Poland), Staphylococcus aureus PCM 2054 and Candida albicans ATCC 10231 using a standard agar plug method ( Fiedler, 2004 ), as described by Świecimska et al (2022) . Briefly, the isolates from the Atacama Desert and pine forest samples were grown on ISP2 and ISP3 agar ( Shirling and Gottlieb, 1966 ) at pH 7.5 and 5.5, respectively, and those from the saline soil adjacent to Lake Lonar on HA agar ( Atlas, 2010 ) supplemented with 3% NaCl and on ISP2 agar ( Shirling and Gottlieb, 1966 ), pH 8.0, following incubation for 3 weeks at 28°C.…”

“…These experiments were restricted to 71 isolates representing colour-groups composed of strains from the acidic forest samples; the isolates from the desert and saline soils were not considered as they did not grow optimally, if at all, at pH 5.5–6.0, the required range for the antifungal assays. The pine forest isolates were tested for their ability to inhibit the growth of fungal and oomycete plant pathogens using the co-culture method, as described by Świecimska et al (2021a , 2022) . To this end, the isolates were streaked on the right side of Petri plates of potato dextrose agar (PDA, Becton Dickinson, United State) and incubated for 2 weeks at 28°C.…”