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Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment

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Abstract

Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413T, was 98.5%. However, the DNA–DNA hybridization values (8–58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ω7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ω7c). Their G+C contents ranged from 68.0  to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The type strain of the species is USMAA1020T (= DSM 19416T = KCTC 32390T).

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Change history

  • 28 December 2017

    In the original publication of the article, it was noted that Fig. 1 present an image of Cupriavidus malaysiensis strain USMAHM13 and not of strain USMAA1020, as indicated in the figure legend. The image in the original version is thus noted to serve as a record of strain USMAHM13 and the corrected version of Fig. 1 is reprinted below.

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Acknowledgements

The authors acknowledge the technical expertise of the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures for providing bacterial systematic analysis based on a polyphasic approach. This work was supported by the MOSTI, Malaysia and Universiti Sains Malaysia, Penang, Malaysia.

Funding

This study was funded by the Ministry of Science, Technology and Innovation, Malaysia, (09-05-IFN-BPH-002, 02-05-23-SF0003 and 02-05-23-SF0023), Universiti Sains Malaysia (1001/PBIOLOGI/811304, 1001/PCCB/870009) and also USM Science Fellowship (RU: 1001/441/29301/CIPS/AUPE001) awarded to Hema Ramachandran.

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Authors and Affiliations

  1. School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia

    Hema Ramachandran, Kumar Sudesh & Al-Ashraf Abdullah Amirul

  2. Quest International University Perak, 30250, Ipoh, Perak, Malaysia

    Hema Ramachandran

  3. Centre for Chemical Biology, Universiti Sains Malaysia, Sains@USM, 11900, Bayan Lepas, Penang, Malaysia

    Nur Asilla Hani Shafie & Al-Ashraf Abdullah Amirul

  4. Universiti Kuala Lumpur (UniKL-MICET) Taboh Naning, 78000, Alor Gajah, Melaka, Malaysia

    Mohamad Noor Azizan

  5. National Poison Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia

    Mohamad Isa Abdul Majid

  6. Malaysian Institute of Pharmaceuticals and Nutraceuticals (IPharm), National Institutes of Biotechnology Malaysia (NIBM), MOSTI, 11700, Penang, Malaysia

    Al-Ashraf Abdullah Amirul

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  1. Hema Ramachandran
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  2. Nur Asilla Hani Shafie
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A correction to this article is available online at https://doi.org/10.1007/s10482-017-0998-0.

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Ramachandran, H., Shafie, N.A.H., Sudesh, K. et al. Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment. Antonie van Leeuwenhoek 111, 361–372 (2018). https://doi.org/10.1007/s10482-017-0958-8

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