Skip to main content
SpringerLink
Log in

Diversity of the culturable lichen-derived actinobacteria and the taxonomy of Streptomyces parmotrematis sp. nov.

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A total of 37 actinobacteria were isolated from eighteen lichen samples collected in Thailand. Based on the 16S rRNA gene sequences, they were identified into five genera including Actinoplanes (1 strain), Actinomadura (1 strain), Pseudosporangium (1 strain), Wangella (1 strain) and Streptomyces (33 strains). Among these isolates, strain Ptm05T, Ptm01 and Ptm12 showed low 16S rRNA gene similarity and was selected for the further taxonomic study using the polyphasic approach. These strains showed the highest 16S rRNA gene sequence similarity with Streptomyces sparsogenes ATCC 25498T (97.44–97.72%). Strain Ptm05T was selected for the type strain. The chemical cell composition of the strain was similar to the members of Streptomyces genus. LL-diaminopimelic acids were detected in the peptidoglycan. Menaquinones were MK-9(H8) and MK-9(H6). Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid, one unidentified glycolipid and one unidentified lipid were detected as the polar lipids. The predominant cellular fatty acids are anteiso-C15:0, iso-C15:0, iso-C16:0, iso-C17:0 and C16:0. The dDNA-DNA hybridization values among strain Ptm05T and its closely related Streptomyces type strains were 17.2–18.0%. In addition, the ANIb and ANIm between strain Ptm05T and related Streptomyces type strains were ranged from 75.69 to 76.13% and 85.21 to 85.35%, respectively. Based on phenotypic and genomic evidence, strain Ptm05T (= TBRC 14546T = NBRC 115203T) represents the novel species of the genus Streptomyces for which the name Streptomyces parmotrematis sp. nov. is proposed. This study showed that the lichens are the promising source of the novel actinobacterial taxa.

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.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Abbreviations

ANI:

Average nucleotide identity

dDDH:

Digital DNA-DNA hybridization

GGDC:

Genome-to-genome distance calculator

References

  • Arai T (1975) Culture media for actinomycetes. The Society for Actinomycetes Japan, Tokyo

    Google Scholar 

  • Bates ST, Cropsey GW, Caporaso JG, Knight R, Fierer N (2011) Bacterial communities associated with the lichen symbiosis. Appl Environ Microbiol 77:1309–1314

    Article  CAS  Google Scholar 

  • Bérdy J (2005) Bioactive microbial metabolites. J Antibiot 58:1–26

    Article  Google Scholar 

  • Collins M, Pirouz T, Goodfellow M, Minnikin D (1977) Distribution of menaquinones in actinomycetes and corynebacteria. Microbiology 100:221–230

    CAS  Google Scholar 

  • Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al (2020) The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 48:D606–D612

    CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Goodfellow M, Kumar Y, Labeda DP, Sembiring L (2007) The Streptomyces violaceusniger clade: a home for Streptomycetes with rugose ornamented spores. Antonie Van Leeuwenhoek 92:173–199

    Article  Google Scholar 

  • Gordon RE, Barnett DA, Handerhan JE, Pang CHN (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63

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

    Article  CAS  Google Scholar 

  • Grube M, Cardinale M, de Castro JV, Berg MHG (2009) Species-specific structural and functional diversity of bacterial communities in lichen symbioses. ISME J 3:1105–1115

    Article  Google Scholar 

  • Hayakawa M, Nonomura H (1987) Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65:501–509

    Article  CAS  Google Scholar 

  • Itoh T, Kudo T, Parenti F, Seino A (1989) Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 39:168–173

    Article  Google Scholar 

  • Kell K (1964) Color-name charts illustrated with centroid colors. Inter-Society Color Council-National Bureau of Standards, Chicago

    Google Scholar 

  • Kim M, Oh HS, Park SC, 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  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  Google Scholar 

  • Lane D (1991) 16S/23S rRNA sequencing nucleic acid techniques in bacterial systematics. Wiley, London, Chichester, pp 115–175

    Google Scholar 

  • Lechevalier HA, Lechevalier MP, Gerber NN (1971) Chemical composition as a criterion in the classification of actinomycetes. Adv Appl Microbiol 14:47–72

    Article  CAS  Google Scholar 

  • Lechevalier MP, DeBiévre C, Lechevalier HA (1977) Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260

    Article  CAS  Google Scholar 

  • Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Res Spec Publ 39:W339–W346

    CAS  Google Scholar 

  • Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10:2182

    Article  Google Scholar 

  • Minnikin D, O’donnell A, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J, (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70:5607–5612

    Article  Google Scholar 

  • Phongsopitanun W, Matsumoto A, Inahashi Y, Kudo T, Mori M, Shiomi K, Takahashi Y, Tanasupawat S (2016) Actinoplanes lichenis sp. nov., isolated from lichen. Int J Syst Evol Microbiol 66:468–473

    Article  CAS  Google Scholar 

  • Ping X, Takahashi Y, Seino A, Iwai Y, Ōmura S (2004) Streptomyces scabrisporus sp. nov. Int J Syst Evol Microbiol 54:577–581

    Article  Google Scholar 

  • Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931

    Article  CAS  Google Scholar 

  • Saeng-In P, Phongsopitanun W, Savarajara A, Tanasupawat S (2018) Streptomyces lichenis sp. nov., isolated from lichen. Int J Syst Evol Microbiol 68:3641–3646

    Article  CAS  Google Scholar 

  • Saeng-In P, Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat S (2021) Actinoplanes lichenicola sp. nov. and Actinoplanes ovalisporus sp. Nov., isolated from lichen in Thailand. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.004921

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. Newark, DE: MIDI inc.

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

  • Sierra MA, Danko DC, Sandoval TA, Pishchany G, Moncada B, Kolter R, Mason CE, Zambrano MM (2020) The microbiomes of seven lichen genera reveal host specificity, a reduced core community and potential as source of antimicrobials. Front Microbiol 11:398. https://doi.org/10.1099/ijsem.0.004921

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sripreechasak P, Athipornchai A (2019) Potential antimicrobial properties of Streptomyces isolated from Sammuk Mountain soil, Chonburi Province, Thailand. J Adv Pharm Technol 10:195–199

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

    Article  CAS  Google Scholar 

  • Suriyachadkun C, Chunhametha S, Thawai C, Tamura T, Potacharoen W, Kirtikara K, Sanglier JJ (2009) Planotetraspora thailandica sp. nov., isolated from soil in Thailand. Int J Syst Evol Microbiol 59:992–997

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kadler O et al (1987) International committee on systematic bacteriology. report of the ad hoc committee on the reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterialgenome assemblies from short and long sequencing reads. PLOS Comput Biol 13:e1005595

    Article  Google Scholar 

  • Williams S, Cross T (1971) Chapter XI actinomycetes. Method Microbiol, Academic Press 4:295–334

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank the Pharmaceutical Research Instrument Center, Faculty of Pharmaceutical Sciences, Chulalongkorn University, for providing research facilities. We thank Professor Aharon Oren for the etymology of the strain.

Funding

This project was funded by the National Research Council of Thailand.

Author information

Authors and Affiliations

  1. Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand

    Achiraya Somphong, Somboon Tanasupawat & Wongsakorn Phongsopitanun

  2. Lichen Research Unit, Department of Biology, Faculty of Science, Ramkhamhaeng University, Bangkok, 10240, Thailand

    Vasun Poengsungnoen & Kawinnat Buaruang

  3. National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120, Thailand

    Chanwit Suriyachadkun

  4. Department of Biotechnology, Faculty of Science, Burapha University, Chonburi, 20131, Thailand

    Paranee Sripreechasak

  5. Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok, 10330, Thailand

    Wongsakorn Phongsopitanun

Authors
  1. Achiraya Somphong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vasun Poengsungnoen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kawinnat Buaruang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chanwit Suriyachadkun
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Paranee Sripreechasak
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Somboon Tanasupawat
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wongsakorn Phongsopitanun
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

AS carried out the experiment including isolation of the actinobacteria, sequencing the 16S rRNA gene sequences and the polyphasic taxonomy of the novel strain. VP and KB collected, preserved and identified the lichen samples. CS and PS analysed the chemotaxonomic study. ST provide the conceptual advice. WP decided the study, proofread the manuscript and provided the conceptual advice.

Corresponding author

Correspondence to Wongsakorn Phongsopitanun.

Ethics declarations

Conflicts of interest

The authors declare that there are no conflicts of interest.

Additional information

Publisher's Note

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

The DDBJ accession number for the 16S rRNA gene sequence of strain Ptm05T, Ptm01 and Ptm12 are, MZ922479, OL770019 and OL774519, respectively.

The DDBJ/ENA/GenBank accession number for the draft genome and SRA of strain Ptm05T is JAINVZ000000000.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 435 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Somphong, A., Poengsungnoen, V., Buaruang, K. et al. Diversity of the culturable lichen-derived actinobacteria and the taxonomy of Streptomyces parmotrematis sp. nov.. Antonie van Leeuwenhoek 115, 911–920 (2022). https://doi.org/10.1007/s10482-022-01744-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-022-01744-6

Keywords

Search

Navigation