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Functional Genome Analysis of a Conditionally Pathogenic Rhizobacterial Strain, Pseudomonas putida AKMP7

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Abstract

This manuscript reports the whole genome sequence of a conditionally pathogenic rhizobacterial strain, Pseudomonas putida AKMP7, which has been previously reported by us to be beneficial to Arabidopsis thaliana under well-watered conditions and pathogenic to the plant under water stress. As part of a study to understand this unique behavior, the whole genome sequence of this strain was analyzed. Based on the results, it was identified that the total length of the AKMP7 genome is 5,764,016 base pairs, and the total GC content of the genome is 62.93% (typical of P. putida). Using RAST annotation pipeline, it was identified that the genome has 5605 coding sequences, 80 repeat regions, 71 tRNA genes, and 22 rRNA genes. A total of 4487 functional proteins and 1118 hypothetical proteins were identified. Phylogenetic analysis has classified it as P. putida species, with a P value of 0.03. In order to identify close relatives of this strain, comparative genomics was performed with 30 other P. putida strains, taken from publicly available genome databases, using Average Nucleotide Identity (ANI) analysis. Whole genome comparison with these strains reveals that AKMP7 possesses Type-IV Secretion System (T4SS) with conjugative transfer functionality. Interestingly, the T4SS feature is absent in all the beneficial/harmless strains of P. putida that we analyzed. All the plant pathogenic bacteria that were analyzed had the T4SS feature in their genome, indicating its role in pathogenesis. This study aims to address important gaps in understanding the molecular mechanisms involved in the conditional/opportunistic pathogenesis of plant-associated, beneficial soil bacteria, using genomics approaches.

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Acknowledgements

The authors acknowledge Department of Biotechnology, Ministry of Science and Technology, Govt. of India for funding the research (Grant No: BT/PR23697/BPA/118/315/2017). Pseudomonas putida AKMP7 strain was purchased from National Bureau of Agriculturally Important Microbes, Mau, Uttar Pradesh, India.

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Authors and Affiliations

  1. Birla Institute of Technology & Science Pilani - Hyderabad Campus, Secunderabad, India

    Raja Gopalan, Atish K. Behera & Sridev Mohapatra

  2. miBiome Therapeutics LLP, Mumbai, India

    Alka Srivastava, Vrishali Murugkar, Chandrasekhar Arigela, Nandini Dasgupta & Gautam Das

  3. Division of Microbiology, ICAR-Indian Agricultural Research Institute, Delhi, India

    Minakshi Grover

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  1. Raja Gopalan
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  2. Atish K. Behera
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  3. Alka Srivastava
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  4. Vrishali Murugkar
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  5. Chandrasekhar Arigela
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  6. Nandini Dasgupta
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  7. Gautam Das
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  8. Minakshi Grover
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  9. Sridev Mohapatra
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Contributions

This is a collaborative work between three organizations. Nenmeli Sampath Kumar R.G. and Behera, A. K.-BITS-Pilani, Hyderabad Campus performed the data analysis and prepared the manuscript. Srivatsava, A., Murugkar, V., Arigela, C., Dasgupta, N., Das, G - miBiome Therapeutics LLP helped in generation of WGS and bioinformatics analysis. Grover, M.- ICAR-IARI (principal investigator of the team that isolated and identified Pseudomonas putida AKMP7), helped in data analysis. Mohapatra, S. of BITS-Pilani, Hyderabad Campus is the principal investigator of this project.

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Correspondence to Sridev Mohapatra.

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Gopalan, R., Behera, A.K., Srivastava, A. et al. Functional Genome Analysis of a Conditionally Pathogenic Rhizobacterial Strain, Pseudomonas putida AKMP7. Curr Microbiol 81, 157 (2024). https://doi.org/10.1007/s00284-024-03677-x

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