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Genome Mining and Predictive Functional Profiling of Acidophilic Rhizobacterium Pseudomonas fluorescens Pt14

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Abstract

Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with P. fluorescens strain A506 and strain SS101. ANI value of strain Pt14 in relation to strain A506 was found 99.23% demonstrating a very close sub-species association at genome level. Further, orthology determination among these three phylogenetic neighbors revealed 4726 core proteins. Functional analysis elucidated significantly higher abundance of sulphur metabolism (>1×) which could be one of the reasons for the survival of strain Pt14 under acidic conditions (pH 4.65). Acidophilic bacteria have capability to oxidize sulphur into sulphuric acid which in turn can make the soil acidic and genome-wide analysis of P. fluorescens Pt14 demonstrated that this strain contributes towards making the soil acidic.

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Acknowledgements

The authors acknowledge funds from Government of India under project from Department of Biotechnology (DBT), All India Network Project on Soil Biodiversity-Biofertilizers Indian Council of Agricultural Research (ICAR) and National Bureau of Agriculturally Important Microorganisms (NBAIM). PR, NKM and AS gratefully acknowledge ICAR, DBT and NBAIM respectively for providing research fellowships.

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Authors and Affiliations

  1. Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India

    Pooja Rani, Nitish Kumar Mahato, Anukriti Sharma & Rup Lal

  2. All India Network Project on Soil Biodiversity and Biofertilizers, Indian Institute of Soil Science, Bhopal, 462038, India

    Desiraju Lakshmi Narsimha Rao

  3. Ciliate Biology Laboratory, SGTB Khalsa College, University of Delhi, Delhi, 110007, India

    Komal Kamra

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  1. Pooja Rani
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Correspondence to Rup Lal.

Additional information

Nucleotide sequence Accession Number: The complete genome sequence of Pseudomonas fluorescens strain Pt14 has been deposited at NCBI under Genbank Accession Number CP017296.1.

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Rani, P., Mahato, N.K., Sharma, A. et al. Genome Mining and Predictive Functional Profiling of Acidophilic Rhizobacterium Pseudomonas fluorescens Pt14. Indian J Microbiol 57, 155–161 (2017). https://doi.org/10.1007/s12088-017-0648-2

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