Abstract
A genomic-based polyphasic study was undertaken to establish the taxonomic status and biotechnological and ecological potential of a Streptomyces strain, isolate SF28T, that was recovered from the litter layer in a Polish Pinus sylvestris forest. The isolate had morphological characteristics and chemotaxonomic properties consistent with its classification in the genus Streptomyces. It formed long straight chains of spores with smooth surfaces, contained LL-diaminopimelic acid, glucose and ribose in whole-organism hydrolysates, produced major proportions of straight, iso- and anteiso- fatty acids, hexa- and octa-hydrogenated menaquinones with nine isoprene 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 it may have become 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 confirmed that it formed a distinct lineage well separated from its closest evolutionary relatives. The isolate shared low average nucleotide identity 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 SF28T (= DSM 113360 T = PCM 3163 T) be classified in the genus Streptomyces as Streptomyces pinistramenti sp. nov. The isolate showed pronounced antimicrobial activity, especially against fungal plant pathogens.
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Data Availability
The GenBank accession numbers for the 16S rRNA and the whole-genome sequences of strain SF28T are OK576049 and JAJCXB000000000, respectively.
Abbreviations
- A2pm:
-
Diaminopimelic acid
- ANI:
-
Average nucleotide identity
- BGCs:
-
Biosynthetic gene clusters
- BLAST:
-
Basic Local Alignment Search Tool
- dDDH:
-
Digital DNA–DNA hybridization
- DSMZ:
-
German Collection of Microorganisms and Cell Cultures
- GGDC:
-
Genome to genome distance calculator
- HPLC:
-
High-performance liquid chromatography
- IBB:
-
Institute of Biochemistry and Biophysics
- ISP:
-
International Streptomyces Project
- MIDI:
-
Microbial Identification System
- ML:
-
Maximum-likelihood
- MP:
-
Maximum-parsimony
- MRE:
-
Maximal-relative-error
- PCM:
-
Polish Collection of Microorganisms
- PUAP:
-
Phylogenetic Analysis Using Parsimony
- RAST:
-
Rapid Annotation using Subsystem Technology
- TLC:
-
Thin-layer chromatography
- TNT:
-
Tree Analysis New Technology
- TYGS:
-
Type Strain Genome Server
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Acknowledgements
We are grateful to Professor Aharon Oren (Hebrew University of Jerusalem) for suggesting the species name.
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This work was supported by Grants No. 1207-B and No. 90-SIDUB.6102.40.2021.G4NCUS1 from Nicolaus Copernicus University.
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PG and MG conceived the study, PG and MŚ designed it and MŚ carried out all the experiments and was responsible for the data analyses. MŚ wrote the first draft of the manuscript which was revised by PG and MG. The final version of the manuscript was approved by all of the authors.
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Świecimska, M., Golińska, P. & Goodfellow, M. 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. Antonie van Leeuwenhoek 115, 783–800 (2022). https://doi.org/10.1007/s10482-022-01734-8
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DOI: https://doi.org/10.1007/s10482-022-01734-8