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Environmental Adaptations of an Extremely Plant Beneficial Bacillus subtilis Dcl1 Identified Through the Genomic and Metabolomic Analysis

  • Plant Microbe Interactions
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Abstract

Bacterial endophytes ubiquitously colonize the internal tissues of plants and promote the plant growth through diverse mechanisms. The current study describes the mechanistic basis of plant-specific adaptations present in an extremely beneficial endophytic bacterium. Here, the endophytic Bacillus subtilis Dcl1 isolated from the dried rhizome of Curcuma longa was found to have the drought tolerance, IAA and ACC deaminase production and phosphate solubilization properties. The whole genome sequencing and annotation further showed the genome of B. subtilis Dcl1 to have the size of 4,321,654 bp. This also showed the presence of genes for IAA, H2S, acetoin, butanediol, flagella and siderophore production along with phosphate solubilization and biofilm formation for the B. subtilis Dcl1. In addition, the genes responsible for the synthesis of surfactin, iturin, fengycin, bacillibactin, bacillaene, bacilysin, chitinase, chitosanase, protease and glycoside hydrolase could also be annotated from the genome of B. subtilis Dcl1. Identification of genes for the glycine betaine, glutamate and trehalose further indicated the drought stress tolerance features of B. subtilis Dcl1. The presence of the genetic basis to produce the catalase, superoxide dismutase, peroxidases, gamma-glutamyltranspeptidase, glutathione and glycolate oxidase also indicated the plant oxidative stress protective effect of B. subtilis Dcl1. Identification of these properties and the demonstration of its plant probiotic effect in Vigna unguiculata confirmed the applicability of B. subtilis Dcl1 as a biofertilizer, biocontrol and bioremediator agent to enhance the agricultural productivity.

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Acknowledgements

The authors acknowledge the Director, the Inter-University Instrumentation Centre and Sophisticated Analytical Instrument Facility (SAIF), Mahatma Gandhi University, Kottayam for providing LC–MS/MS analysis facility and also the Coordinator DST-PURSE II Programme support for the facility provided. The authors also acknowledge the Director School of Environmental Sciences for the ICP-MS facility provided.

Funding

This study was financially supported by the Kerala State Plan Fund project and also Kerala State Council for Science, Technology and Environment (KSCSTE) Kerala Biotechnology Commission for KSCSTE-KBC-YIPB Programme.

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Authors and Affiliations

  1. School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, Kerala, 686 560, India

    Aswathy Jayakumar & E. K. Radhakrishnan

  2. Department of Biotechnology, SAS SNDP Yogam College, Pathanamthitta, Kerala, India

    Indu C. Nair

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  1. Aswathy Jayakumar
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  2. Indu C. Nair
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Correspondence to E. K. Radhakrishnan.

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Highlights

• Experimental confirmation of highly plant beneficial adaptations of endophytic Bacillus subtilis Dcl1

• Whole genome sequencing–based annotation of plant beneficial adaptations of endophytic Bacillus subtilis Dcl1

• Elucidation of plant probiotic potential of endophytic Bacillus subtilis Dcl1

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Jayakumar, A., Nair, I.C. & Radhakrishnan, E.K. Environmental Adaptations of an Extremely Plant Beneficial Bacillus subtilis Dcl1 Identified Through the Genomic and Metabolomic Analysis. Microb Ecol 81, 687–702 (2021). https://doi.org/10.1007/s00248-020-01605-7

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