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Draft genome sequence and functional analysis of Lysinibacillus xylanilyticus t26, a plant growth-promoting bacterium isolated from Capsicum chinense rhizosphere

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Abstract

Capsicum chinense is the chilli species containing the highest amount of capsaicin, and is an important traditional spice crop of Northeast India. Capsaicinoids derived from C. chinense are used in anticancer and anti-obesity treatments, as temperature regulators, in pain therapy, and as antioxidants. The current production and yield are very low due to the lack of organized cultivation and scientific inputs, and various plant diseases. Synthetic pesticides are frequently applied to boost yields, which creates potential risks to the environment, crops, and humans. The use of plant growth-promoting rhizobacteria is an alternative strategy in crop disease management to reduce the dependency on agrochemicals, which have detrimental effects on the environment. Lysinibacillus xylanilyticus t26 isolated from the C. chinense rhizosphere has shown good prospects in plant growth promotion and biocontrol. It showed strong antagonistic activity against Pythium ultimum ITCC 1650, Rhizoctonia solani ITCC 6491, and Fusarium oxysporum ITCC 6246. The draft genome sequencing of L. xylanilyticus t26 yielded a total of 5.69 Mbp with a G+C content of 36.80%. Genome analysis revealed that L. xylanilyticus t26 is very similar to L. xylanilyticus MH683160.1, and is phylogenetically related to L. xylanilyticus IBBPo7. Bioinformatics analysis predicted that it harbored type III polyketides, non-ribosomal peptides, terpenes, and lantibiotics including cerecidin, bacteriocins, siderophores, and thiopeptides, which are important traits of rhizobacteria for the utilization of minerals and to compete with other microbes for food. The strain t26 is a potential biocontrol agent for soil-borne fungal diseases. In this study, we derived the possible siderophore production pathways through the analysis of L. xylanilyticus t26 draft genome and plant growth response bioassays. The availability of genome data provides information that this draft genome harbored a siderophore BGC, which is 33% similar to petrobactin.

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Funding

This work was supported by the Department of Biotechnology, Government of India.

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Authors and Affiliations

  1. Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat, Imphal, 795 001, India

    T A Phazna, Ng Ngashangva, Randhir Babu Singh Yentrembam, Pulok Mukherjee, Chandradev Sharma & Indira Sarangthem

  2. Plant Immunity Laboratory, National Institute of Plant Genome research (NIPGR), New Delhi, 110 067, India

    Ranjeet Maurya & Praveen K Verma

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  1. T A Phazna
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  2. Ng Ngashangva
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Contributions

SID, DS, and PKV conceived and designed the experiments. NN, PTA, and RMP wrote the paper. PTA, MP, CA, and CS isolated the genomic DNA from selected PGPR strains. Agri-genome Kerala performed the sequencing. NN, SID, and MP performed the analysis. SID, DS, and PKV provided technical advice, analysis support, and oversight.

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Correspondence to Indira Sarangthem.

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Corresponding editor: Ashis Kumar Nandi

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Phazna, T.A., Ngashangva, N., Yentrembam, R.B.S. et al. Draft genome sequence and functional analysis of Lysinibacillus xylanilyticus t26, a plant growth-promoting bacterium isolated from Capsicum chinense rhizosphere. J Biosci 47, 36 (2022). https://doi.org/10.1007/s12038-022-00264-9

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