Skip to main content
SpringerLink
Log in

Streptomyces spiramenti sp. nov., isolated from a deep-sea microbial mat

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

Strain 5675061T was isolated from a deep-sea microbial mat near hydrothermal vents within the Axial Seamount caldera on the Juan de Fuca Ridge (NE Pacific Ocean) and was taxonomically evaluated using a polyphasic approach. Morphological and chemotaxonomic properties are consistent with characteristics of the genus Streptomyces: aerobic Gram-stain-positive filaments that form spores, l,l-diaminopimelic acid in whole-cell hydrolysates, and iso-C16:0 as the major fatty acid. Phylogenetic analysis, genomic, and biochemical comparisons show close evolutionary relatedness to Streptomyces lonarensis NCL716T, S. bohaiensis 11A07T, and S. otsuchiensis OTB305T but genomic relatedness indices identify strain 5675061T as a distinct species. Based on a polyphasic characterization, identifying differences in genomic and taxonomic data, strain 5675061T represents a novel species, for which the name Streptomyces spiramenti sp. nov. is proposed. The type strain is 5675061T (=LMG 31896T = DSM 111793T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

Data availability

The 16S rRNA gene sequence for strain 5675061T was deposited in DDBJ/ENA/GenBank under the accession number OP470020. The main datasets analyzed in this work are the genomes of strain 5675061T, S. bohaiensis 11A07T, S. lonarensis NCL716T, and S. otsuchiensis OTB305T, which are deposited in DDBJ/ENA/GenBank under the accession numbers JAAVJB010000000, JAAVJC010000000, JAAVJD010000000, and BHZI01000000, respectively. The remaining genomes used in this work are listed in Table S1.

References

  • Aebischer T et al (2006) Vaccination prevents Helicobacter pylori-induced alterations of the gastric flora in mice. FEMS Immunol Med Microbiol 46:221–229

    Article  CAS  PubMed  Google Scholar 

  • Asnicar F et al (2020) Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun 11:2500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fenical W, Jensen PR (2006) Developing a new resource for drug discovery: marine actinomycete bacteria. Nat Chem Biol 2:666–673

    Article  CAS  PubMed  Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  PubMed  Google Scholar 

  • Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114

    Article  PubMed  PubMed Central  Google Scholar 

  • Kämpfer P (2015) Streptomyces. In: Trujillo ME et al (eds) Bergey’s manual of systematics of archaea and bacteria. Wiley, pp 1–414

    Google Scholar 

  • Khalifa SAM et al (2019) Marine natural products: a source of novel anticancer drugs. Mar Drugs 17:491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  CAS  PubMed  Google Scholar 

  • Kumar M, Kumar P, Das P, Solanki R, Kapur MK (2020) Potential applications of extracellular enzymes from Streptomyces spp. in various industries. Arch Microbiol 202:1597–1615

    Article  CAS  PubMed  Google Scholar 

  • Lee N, Hwang S, Kim J, Cho S, Palsson B, Cho B-K (2020) Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces. Comput Struct Biotechnol J 18:1548–1556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loughran RM et al (2020) Draft genome sequence of Streptomyces sp. strain ventii, isolated from a microbial mat near hydrothermal vents within the Axial Seamount in the Pacific Ocean, and resequencing of the type strains Streptomyces lonarensis NCL 716 and Streptomyces bohaiensis 11A07. Microbiol Resour Announc 9:e00607-00620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCauley EP, Haltli B, Kerr RG (2015) Description of Pseudobacteriovorax antillogorgiicola gen. nov., sp. nov., a bacterium isolated from the gorgonian octocoral Antillogorgia elisabethae, belonging to the family Pseudobacteriovoracaceae fam. nov., within the order Bdellovibrionales. Int J Syst Evol Microbiol 65:522–530

    Article  CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • Minh BQ et al (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530–1534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen CT, Dhakal D, Pham VTT, Nguyen HT, Sohng JK (2020) Recent advances in strategies for activation and discovery/characterization of cryptic biosynthetic gene clusters in Streptomyces. Microorganisms 8:616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’Brien J, Wright GD (2011) An ecological perspective of microbial secondary metabolism. Curr Opin Biotechnol 22:552–558

    Article  CAS  PubMed  Google Scholar 

  • Pan HQ et al (2015) Streptomyces bohaiensis sp. nov., a novel actinomycete isolated from Scomberomorus niphonius in the Bohai Sea. J Antibiot (tokyo) 68:246–252

    Article  CAS  PubMed  Google Scholar 

  • Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2015) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931

    Article  PubMed  PubMed Central  Google Scholar 

  • Sambrook J (2001) Molecular cloning : a laboratory manual/Joseph Sambrook. In: Russell DW (ed) Cold spring harbor laboratory. Cold Spring Harbor

    Google Scholar 

  • Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069

    Article  CAS  PubMed  Google Scholar 

  • Sharma TK et al (2016) Streptomyces lonarensis sp. nov., isolated from Lonar Lake, a meteorite salt water lake in India. Antonie Leeuwenhoek 109:225–235

    Article  CAS  PubMed  Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Sivalingam P, Hong K, Pote J, Prabakar K (2019) Extreme environment Streptomyces: potential sources for new antibacterial and anticancer drug leads? Int J Microbiol 2019:5283948

    Article  PubMed  PubMed Central  Google Scholar 

  • Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Evol Microbiol 47:479–491

    Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takahashi Y, Nakashima T (2018) Actinomycetes, an inexhaustible source of naturally occurring antibiotics. Antibiotics 7:45

    Article  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Terahara T et al (2019) Streptomyces otsuchiensis sp. nov., a biosurfactant-producing actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 69:3740–3744

    Article  CAS  PubMed  Google Scholar 

  • Thornburg CC, Zabriskie TM, McPhail KL (2010) Deep-sea hydrothermal vents: potential hot spots for natural products discovery? J Nat Prod 73:489–499

    Article  CAS  PubMed  Google Scholar 

  • Waksman SA, Henrici AT (1943) The nomenclature and classification of the Actinomycetes. J Bacteriol 46:337–341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams ST, Davies FL (1967) Use of scanning electron microscope for the examination of actinomycetes. J Gen Microbiol 48:171–177

    Article  CAS  PubMed  Google Scholar 

  • Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank Nancy Shough (Southern Oregon University, SOU) for technical support and Charles Lein (Pierrepont School) for consultation on Latin use.

Funding

This work was supported by startup funds from SOU to PV. Collection and isolation of the organism was supported by the National Institutes of Health/National Institute of Allergy and Infectious Diseases (5R21AI085540-02) and an Oregon Sea Grant under award number NA10OAR4170064 (project number R/BT-52) from the National Oceanic and Atmospheric Administration’s National Sea Grant College Program, U.S. Department of Commerce, and by appropriations made by the Oregon state legislature to KLM. MOG was supported by the National Science Foundation (NSF)/EPSCoR RII Track-1: Building on the 2020 Vision: Expanding Research, Education and Innovation in South Dakota (Award OIA-1849206) and by the South Dakota Board of Regents.

Author information

Author notes

  1. Rachel M. Loughran

    Present address: Microbiology Graduate Program, University of Delaware, Newark, DE, USA

  2. Caitlin M. Diefendorf

    Present address: School of Medicine, Oregon Health and Science University, Portland, OR, USA

  3. Jassmine R. Reill-VanSise

    Present address: Cedars-Sinai Medical Center, Beverley Hills, CA, USA

  4. Oliver B. Vining

    Present address: Apeel Sciences, Goleta, CA, USA

  5. Patrick Videau

    Present address: Bayer Environmental Science, Cary, NC, USA

Authors and Affiliations

  1. Department of Biology, Southern Oregon University, Ashland, OR, USA

    Rachel M. Loughran, Caitlin M. Diefendorf, Jassmine R. Reill-VanSise, David K. Oline & Patrick Videau

  2. Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA

    Edward A. Mitchell, Oliver B. Vining, David A. Gallegos & Kerry L. McPhail

  3. Natural Sciences Department, Flagler College, St. Augustine, FL, USA

    Gregory Miller

  4. Gwynedd Mercy University, Gwynedd Valley, PA, USA

    Marc J. Koyack

  5. Institute for Imaging and Analytical Technologies, Mississippi State University, Mississippi State, MS, USA

    Orion S. Rivers

  6. Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA

    Blake Ushijima

  7. Department of Biological Sciences, The George Washington University, Washington, DC, USA

    Jimmy H. Saw

  8. Department of Chemistry, Dakota State University, Madison, SD, USA

    Michael O. Gaylor

Authors
  1. Rachel M. Loughran
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Caitlin M. Diefendorf
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jassmine R. Reill-VanSise
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Edward A. Mitchell
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Oliver B. Vining
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. David A. Gallegos
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Gregory Miller
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Marc J. Koyack
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. David K. Oline
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Orion S. Rivers
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Blake Ushijima
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Jimmy H. Saw
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Michael O. Gaylor
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Kerry L. McPhail
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Patrick Videau
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

KLMP and PV conceived of the study and all authors contributed to its design. Material preparation, experimentation, data collection, and analysis were performed by RML, Caitlin MD, JR-VS, EAM, OBV, DAG, GM, MJK, DKO, OSR, BU, JHS, and MOG. The first draft of the manuscript was written by PV and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Kerry L. McPhail or Patrick Videau.

Ethics declarations

Conflict of interest

The authors have no relevant financial or non-financial interests to disclose.

Additional information

Communicated by Erko Stackebrandt.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 591 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Loughran, R.M., Diefendorf, C.M., Reill-VanSise, J.R. et al. Streptomyces spiramenti sp. nov., isolated from a deep-sea microbial mat. Arch Microbiol 204, 717 (2022). https://doi.org/10.1007/s00203-022-03326-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00203-022-03326-6

Keywords

Search

Navigation