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Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment

The Journal of Antibiotics volume 76, pages 93–100 (2023)Cite this article

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Abstract

A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03T, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03T is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03T was most closely related to Streptomyces tirandamycinicus HNM0039T (99.7%), Streptomyces spongiicola HNM0071T (99.4%), ‘Streptomyces marianii’ ICN19T (99.1%) and Streptomyces wuyuanensis CGMCC4.7042T (99.0%). The phylogenetic tree prepared using the 16S rRNA gene, as well as the phylogenomic tree using the genome BLAST distance phylogeny method and 81 core housekeeping genes, respectively, showed that the closest relative of strain CWH03T was S. spongiicola HNM0071T. The average nucleotide identity and digital DNA-DNA hybridization values between strains CWH03T and S. spongiicola HNM0071T were 91.46% and 44.2%, respectively, which were below the thresholds of 96% and 70% for prokaryotic conspecific assignation. The G+C content of the genomic DNA of strain CWH03T was 72.3%. Whole-cell hydrolysates of strain CWH03T contained LL-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (88.3%), and the major fatty acids were iso-C16:0 (28.4%), anteiso-C15:0 (15.0%) and iso-C15:0 (12.9%). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. Based on data obtained from phenotypic, phylogenetic, genomic, and chemotaxonomic analyses, strain CWH03T represents a novel species of the genus Streptomyces, for which the proposed name is Streptomyces pacificus sp. nov. The type strain is CWH03T ( = NBRC 114659T = TBRC 15780T).

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Acknowledgements

This work was supported by JSPS KAKENHI Grant Number 16K07229. We are grateful to Dr. Bernhard Schink for his support with nomenclature.

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan

    Miku Takahashi, Shoya Shinohara, Youji Nakagawa, Susumu Kokubo, Masayuki Hayakawa & Hideki Yamamura

  2. Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan

    Moriyuki Hamada & Tomohiko Tamura

  3. Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan

    Hideo Dohra & Shinya Kodani

  4. Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan

    Hideo Dohra & Shinya Kodani

  5. Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan

    Hideo Dohra

  6. Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan

    Shinya Kodani

  7. Yamanashi Prefectural University, Iida-5-11-1, Kofu, 400-0035, Japan

    Masayuki Hayakawa

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Correspondence to Hideki Yamamura.

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Takahashi, M., Shinohara, S., Hamada, M. et al. Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment. J Antibiot 76, 93–100 (2023). https://doi.org/10.1038/s41429-022-00589-5

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