Streptomyces harenosi sp. nov., a home for a gifted strain isolated from Indonesian sand dune soil

Abstract

A polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65T, recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34T, although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus , Streptomyces griseomycini , Streptomyces griseostramineus , Streptomyces labedae , Streptomyces lomondensis and Streptomyces spinoverrucosus . A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34T. These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA–DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65T (=NCIMB 15211T=CCMM B1302T=ICEBB-03T) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.

Genome-based classification of the Streptomyces violaceusniger clade and description of Streptomyces sabulosicollis sp. nov. from an Indonesian sand dune

“…Isolate PRKS01-29 T was isolated from an arid, non-saline soil sample (pH 5.8., organic matter content 0.06%) collected just below the surface of a sand dune in the Parangkusumo Region (8° 1′7 513″ S/ 110° 19′ 11.04″ E) of Yogyakarta Province, Java, Indonesia following incubation on Actinomycete Isolation Agar (HiMedia, Einhausen, Germany), pH 7.3, supplemented with cycloheximide (50 µg/mL), nalidixic acid (25 µg/mL) and nystatin (25 µg/mL) and incubated for 7 days at 45 °C, as described previously (Kusuma et al 2020 ). The isolate and S. albiflaviniger DSM 41598 T , S. iranensis DSM 41954 T , S. javensis DSM 41764 T , S. malaysiensis NBRC 13472 T , S. rapamycinicus NRRL 5491 T and S. rhizosphaericus NRRL B-24304 T and S. violaceusniger DSM 40583 T were maintained on yeast extract-malt extract agar (International Streptomyces Project medium 2 [ISP 2]., Shirling and Gottlieb 1966 ) and as mixtures of hyphal fragments and spores in 20%, v/v glycerol at −20 °C and −80 °C.…”

“…Growth from the ISP 2 preparation was examined for spore-chain arrangement and spore-surface ornamentation using a scanning electron microscope (Tescan Vega 3, LMU instrument) and the procedure described by O’Donnell et al ( 1993 ). The ability of the test and associated marker strains to grow at different temperatures, pH regimes and in the presence of various concentrations of sodium chloride was carried out in triplicate, as mentioned by Kusuma et al ( 2020 ). Standard chromatographic methods were used to detect the isomers of diaminopimelic acid (A 2 pm) (Staneck and Roberts 1974 ), whole-organism sugars (Lechevalier and Lechevalier 1970 ) and for menaquinones and polar lipids by applying the integrated procedure of Minnikin et al ( 1984 ), using appropriate controls.…”

“…Genomic DNA was extracted from wet biomass of single colonies of the isolate, S. albiflaviniger DSM 41598 T and S. javensis DSM 41764 T , grown on ISP 2 agar for 7 days at 28 °C, following the protocol provided by MicrobesNG (Birmingham, UK) ( http://www.microbesng.uk ) and sequenced on an Miseq instrument (Illumina, San Diego, USA). The quality of the extracted DNA preparations and the sequencing of genomic DNA libraries was achieved, as described by Kusuma et al ( 2020 ). The libraries were sequenced following the 2 × 250-bp paired-end protocol (MicrobesNG, Birmingham, UK).…”

“…The classification of Streptomyces species is especially challenging given the high number of validly published species ( https://www.bacterio.net.streptomyces.html ), the limited resolution of 16S rRNA gene sequences in their delineation (Labeda et al 2012 , 2017 ) and evidence that the genus is underspeciated (Yamac et al 2011 ; Hamm et al 2017 ). However, multi-locus sequence analyses (MLSA) of concatenated protein-coding house-keeping genes (Ayed et al 2018 ; Kusuma et al 2020 ; Li et al 2020 ; Martinet et al 2020 ) and comparative surveys of whole-genome sequences (Nouioui et al 2018 ) provide invaluable data for the circumscription of novel Streptomyces species. MLSA analyses have revealed a correlation between the delineation of phylogenetic clades and associated phenotypic properties (Rong and Huang 2014 ; Labeda et al 2014 ), as exemplified by the assignment of streptomycetes with spiral chains of rugose ornamented spores to a well supported taxon (Labeda et al 2017 ), known as the Streptomyces violaceusniger clade (Sembiring et al 2000 ; Kumar and Goodfellow 2008 , 2010 ).…”

Chemical and genomic analyses of a marine-derived Streptomyces sp. V17-9 producing amino acid derivatives and siderophores

“…A sequence identity cutoff value of 97%-98% for 16S rRNA gene sequences has been accepted for species identification (Stackebrandt and Goebel, 1994;Yarza et al, 2008). Despite the high 16S rDNA sequence similarity, bacterial strains were often classified as different species according to additional analyses (Antony-Babu et al, 2017;Kusuma et al, 2020;Saygin et al, 2020;Maiti and Mandal, 2021). Thus, genome-based analyses, including dDDH and OrthoANI calculations, were performed on the 2,061 Streptomyces genomes.…”