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Genome sequence of an uncharted halophilic bacterium Robertkochia marina with deciphering its phosphate-solubilizing ability

  • Bacterial, Fungal and Virus Molecular Biology - Short Communication
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Brazilian Journal of Microbiology Aims and scope Submit manuscript

Abstract

The wide use of whole-genome sequencing approach in the modern genomic era has opened a great opportunity to reveal the prospective applications of halophilic bacteria. Robertkochia marina CC-AMO-30DT is one of the halophilic bacteria that was previously taxonomically identified without any inspection on its biotechnological potential from a genomic aspect. In this study, we present the whole-genome sequence of R. marina and demonstrated the ability of this bacterium in solubilizing phosphate by producing phosphatase. The genome of R. marina has 3.57 Mbp and contains 3107 predicted genes, from which 3044 are protein coding, 52 are non-coding RNAs, and 11 are pseudogenes. Several phosphatases such as alkaline phosphatases and pyrophosphatases were mined from the genome. Further genomic study (phylogenetics, sequence analysis, and functional mechanism) and experimental data suggested that the alkaline phosphatase produced by R. marina could potentially be utilized in promoting plant growth, particularly for plants on saline-based agricultural land.

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Fig. 1
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Data availability

The whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession QXMP00000000, with BioProject and BioSample accession PRJNA489156 and SAMN09949184, respectively. The version described in this paper is the first version (accession number QXMP01000000). The strain, Robertkochia marina CC-AMO-30DT (=JCM 18552) was obtained from the Japan Collection of Microorganisms.

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Acknowledgements

Chun Shiong Chong appreciates Fundamental Research Grant Scheme (FRGS 2019-1, project number: 5F196) from Ministry of Education Malaysia, Industry-International Incentive Grant (project number: 02M34) and Research University Grant (GUP 2018, project number: 20H43) from Universiti Teknologi Malaysia. Ming Quan Lam is grateful for a Post-Doctoral Fellowship Scheme from Universiti Teknologi Malaysia, with the project title: “Harnessing Sustainable Development Opportunities from Oil Palm Empty Fruit Bunch as Food for Black Soldier Fly Larvae”. Ming Quan Lam acknowledges Khazanah Watan Postgraduate (PhD) scholarship (scholar ID: 40852) from Yayasan Khazanah. Sye Jinn Chen is grateful to Zamalah Scholarship from Universiti Teknologi Malaysia.

Funding

This work was financially sponsored by Fundamental Research Grant Scheme (FRGS 2019-1) from Ministry of Education Malaysia, Research University Grant (GUP 2018) and Industry-International Incentive Grant from Universiti Teknologi Malaysia under project number 5F196, 20H43 and 02M34, respectively, which was granted to Chun Shiong Chong. This study was also supported by Universiti Teknologi Malaysia under the Post-Doctoral Fellowship Scheme for the Project: “Harnessing Sustainable Development Opportunities from Oil Palm Empty Fruit Bunch as Food for Black Soldier Fly Larvae”, which granted to Ming Quan Lam.

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Authors and Affiliations

  1. Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia

    Ming Quan Lam, Sye Jinn Chen, Kian Mau Goh, Fazilah Abd Manan, Adibah Yahya & Chun Shiong Chong

  2. Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Higher Education Hub, 84600, Muar, Johor, Malaysia

    Mohd Shahir Shamsir

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Contributions

Ming Quan Lam designed and performed the experiment, analyzed the data, and wrote the manuscript. Sye Jinn Chen assisted in performing the experiment and provided the expertise. Kian Mau Goh, Adibah Yahya, Fazilah Abd Manan, and Mohd Shahir Shamsir provided the expertise. Chun Shiong Chong conceived the presented idea, designed the experiment, and provided the expertise. All authors read, edited, and approved the final manuscript.

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Correspondence to Chun Shiong Chong.

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Lam, M.Q., Chen, S.J., Goh, K.M. et al. Genome sequence of an uncharted halophilic bacterium Robertkochia marina with deciphering its phosphate-solubilizing ability. Braz J Microbiol 52, 251–256 (2021). https://doi.org/10.1007/s42770-020-00401-2

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