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Streptomyces endocoffeicus sp. nov., an endophytic actinomycete isolated from Coffea arabica (L.)

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Abstract

An aerobic, non-motile, Gram-stain positive actinomycete, designated strain CA3R110T, was isolated from the surface-sterilised root of Coffea arabica L. collected from Lampang Province, Thailand. 16S rRNA gene sequence analysis indicated that strain CA3R110T was a member of the genus Streptomyces and showed the closest similarities to Streptomyces buecherae AC541T (99.2%), followed by Streptomyces rapamycinicus NRRL B-5491T (99.1%), Streptomyces luteoverticillatus NBRC 3840T (99.1%), Streptomyces coerulescens NBRC 12758T (99.1%), and Streptomyces iranensis HM 35T (99.0%). Strain CA3R110T contained LL-diaminopimelic acid in cell peptidoglycan, MK-9(H6), and MK-9(H8) as major menaquinone, iso-C16:0, iso-C15:0, C16:0 as major fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside were detected in the cell. The chemotaxonomic characteristics possessed the typical properties of the genus Streptomyces. A low digital DNA–DNA hybridization (< 55.7%) and average nucleotide identity-blast (ANIb) (< 92.2%) values revealed that strain CA3R110T could be distinguished from any known Streptomyces species. With the differences in phenotypic and genotypic data, strain CA3R110T represents a novel species of genus Streptomyces, for which the name Streptomyces endocoffeicus sp. nov. is proposed. The type strain is CA3R110T (= TBRC 11245T = NBRC 114296T).

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Data availability

The DDBJ accession number for the 16S rRNA gene sequence of strain CA3R110T is MN116545. The whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAERRG000000000. The version described in this paper is version JAERRG010000000.

Abbreviations

ANIb:

Average nucleotide identity-BLAST

ANIm:

Average nucleotide identity-MUMmer algorithm

DAP:

Diaminopimelic acid

dDDH:

Digital DNA-DNA hybridisation

DPG:

Diphosphatidylglycerol

PE:

Phosphatidylethanolamine

OH-PE:

Hydroxy-phosphatidylethanolamine

PG:

Phosphatidylglycerol

PI:

Phosphatidylinositol

PL:

Unidentified phospholipid

NPG:

Ninhydrin-positive lipid

L:

Unidentified lipid

GGDC:

Genome to genome distance calculator

HPLC:

High performance liquid chromatography

ISP:

International Streptomyces Project

ISCC-NBS:

Inter-Society Color Council-the National Bureau of Standards

MK:

Menaquinone

ML:

Maximum-likelihood

MP:

Maximum-parsimony

NJ:

Neighbour-joining

PE:

Phosphatidylethanolamine

PI:

Phosphatidylinositol

TLC:

Thin layer chromatography

TYGS:

Type Strain Genomic Server

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Acknowledgements

This work was supported by a grant from King Mongkut’s Institute of Technology Ladkrabang Research Fund (KReF; KREF046301) to C.T. We thank the Actinobacterial Research Unit (ARU), Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, for laboratory supports.

Funding

The authors gratefully acknowledge the financial support from King Mongkut’s Institute of Technology Ladkrabang Research Fund (KReF; KREF046301) to C. T. and the Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang to A. N. (RA/TA-2562-M-021).

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Authors and Affiliations

  1. Department of Biology, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, 10520, Thailand

    Achararak Nammali & Chitti Thawai

  2. National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathum Thani, 12120, Thailand

    Chakapong Intaraudom & Pattama Pittayakhajonwut

  3. Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand

    Chanwit Suriyachadkun

  4. Department of Pharmacognosy, Faculty of Pharmacy, Srinakharinwirot University, Ongkharak, Nakhon Nayok, 26120, Thailand

    Sarin Tadtong

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

    Somboon Tanasupawat

  6. Actinobacterial Research Unit, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, 10520, Thailand

    Chitti Thawai

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  1. Achararak Nammali
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Contributions

AN and CT carried out the experiments, analysed the data, and drafted manuscript. AN and CT contributed equally to this work. CS carried out fatty acid analysis. CT supervised the project. CI, PP, ST and ST corrected and reviewed the draft.

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Correspondence to Chitti Thawai.

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Nammali, A., Intaraudom, C., Pittayakhajonwut, P. et al. Streptomyces endocoffeicus sp. nov., an endophytic actinomycete isolated from Coffea arabica (L.). Antonie van Leeuwenhoek 114, 1889–1898 (2021). https://doi.org/10.1007/s10482-021-01648-x

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