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Micromonospora veneta sp. nov., an endophytic actinobacterium with potential for nitrogen fixation and for bioremediation

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Abstract

Strain CAP181T, an endophytic actinobacterium, was isolated from a surface sterilized root sample of a native pine tree, Flinders University, Adelaide, South Australia. Chemotaxonomic data including cell wall components, major fatty acids, and major menaquinones confirmed the affiliation of strain CAP181T to the genus Micromonospora. This strain was Gram stain positive with well-developed substrate mycelia to form a single spore with hairy surface. The phylogenetic tree showed that M. coerulea NBRC 13504 T is the closest phylogenetic neighbour, sharing 99.2% 16S rRNA gene similarity and the next closest neighbor is M. chaiyaphumensis DSM 45246 T (98.7%). Genome mining of this strain revealed genes encoding to enzymes relating to nitrogen fixation and bioremediation. Based on genotypic and phenotypic studies including DNA–DNA hybridization data, strain CAP181T was different from any of the closely related species with valid names. The name proposed for the new species is Micromonospora veneta sp. nov. The type strain is CAP181T (= DSM 109713 T = NRRL B-65535 T).

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Acknowledgements

The authors thank Greg Kirby for his assistance with sampling of native plants. We are very grateful to Daniel Jardine for menaquinone analysis and Dr. Lisa O`Donovan of Adelaide Microscopy for SEM visualization.

Funding

This research project is financially supported by Mahasarakham University (Fast Track 2020) Mahasarakham University, Thailand.

Author information

Authors and Affiliations

  1. Department of Biology, Faculty of Science, Mahasarakham University, Kantaravichai, Maha Sarakham Province, 44150, Thailand

    Onuma Kaewkla

  2. Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani, 12120, Thailand

    Chanwit Suriyachadkun

  3. Department of Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford park, Adelaide, 5042, Australia

    Onuma Kaewkla & Christopher Milton Mathew Franco

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  1. Onuma Kaewkla
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  2. Chanwit Suriyachadkun
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Contributions

OK and CF planned the experiments. OK carried out the experimental work and prepared the draft manuscript. CF contributed to improve the manuscript and provided the facilities. CS prepared genomic DNA for genome sequencing purposes.

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Correspondence to Onuma Kaewkla.

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This article does not contain any studies with human participants and/or animals performed by any of the authors. The formal consent is not required in this study.

Additional information

Communicated by Erko Stackebrandt.

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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain CAP 181T is GU434267.

The GenBank/EMBL/DDBJ accession number for the draft genome of strain CAP181T is JAEMUW000000000.

Supplementary Information

Below is the link to the electronic supplementary material.

203_2021_2260_MOESM1_ESM.pptx

Supplementary Figure S1. 16S rRNA gene-based maximum parsimony tree showing the phylogenetic relationships between Micromonospora veneta CAP181T and fourteen strains with valid names belonging to the genus Micromonospora, and Actinoplanes bogorensis NBRC 110975T as the outgroup. Bootstrap values (> 50 %) based on 1000 replicates are shown at the branch nodes and asterisk (*) indicate clades that were conserved in the maximum-likelihood and maximum parsimony trees. (PPTX 844 KB)

203_2021_2260_MOESM2_ESM.pdf

Supplementary Figure S2. Two-dimensional thin-layer chromatography of polar lipids of Micromonospora veneta CAP181T. Chloroform-methanol-water (65:25:4) was used in the first direction, followed by chloroform-acetic acid-methanol-water (40:7.5:6:2) in the second direction. Abbreviations: DPG; Diphosphatidylglycerol, PE; phosphatidylethanolamine, PI; phosphatidylinositol, PIDM; phosphatidylinositol dimannosides, UnGly; unidentified glycolipid, UnA; unidentified lipid with amino group, UnPa; unidentified phospholipid with amino group, B; brown colour, X; starting point. (PDF 544 KB)s

203_2021_2260_MOESM3_ESM.tif

Supplementary Figure S3. Scanning electron microscopy showed hyphae and single spore with hairy surface of strain CAP181T grown on HPDA for 10 days at 27oC. Bar represents 2 μm.s (TIF 342 KB)

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Kaewkla, O., Suriyachadkun, C. & Franco, C.M.M. Micromonospora veneta sp. nov., an endophytic actinobacterium with potential for nitrogen fixation and for bioremediation. Arch Microbiol 203, 2853–2861 (2021). https://doi.org/10.1007/s00203-021-02260-3

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