Functional genome mining and taxono‐genomics reveal eco‐physiological traits and species distinctiveness of aromatic‐degrading Pseudomonas bharatica sp. nov.

Environmental Microbiology Reports - Tập 14 Số 3 - Trang 464-474 - 2022
Balaram Mohapatra1, Sonam Nain2, Rakesh Sharma2, Prashant S. Phale1
1Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, Maharashtra, India
2Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India

Tóm tắt

SummaryAssistive eco‐physiological traits are necessary for microbes to adapt and colonize at polluted niches, enabling efficient clean‐up. To demarcate species distinctiveness and eco‐physiological traits of aromatic compounds metabolizing Pseudomonas sp. CSV86T (earlier identified as Pseudomonas putida), an Indian isolate from a petrol station soil, comparative genome mining, taxono‐genomic, and physiological analyses were performed. A 6.79 Mbp genome (62.72 G + C mol%) of CSV86T encodes 6798 CDS and 238 unique genes. Naphthalene metabolism and Co‐Zn‐Cd resistance gene clusters were part of distinct genomic islands. Abundance of transporters (aromatics, organic acids, amino acids, and metals) and mobile elements (integrases, transposases, conjugative proteins) differentiated CSV86T from its closest relatives. Enhanced siderophore production for Fe‐uptake during aromatic metabolism, indole acetic acid production, and fusaric acid resistance wasvalidated by genomic attributes. Full‐length 16S‐rRNA phylogeny revealed Pseudomonas japonica WLT as a closest relative of CSV86T. However, lower genomic indices (<97% gyrB‐rpoB‐rpoD homology, <90% ANI, <50% DNA–DNA relatedness) and taxonomic differences (assimilation of organic acids, amino acids, fatty acids composition) substantially differentiated CSV86T from its closest relatives, indicating it to be a novel species as Pseudomonas bharatica. Preferential metabolism of aromatics with advantageous eco‐physiological traits renders CSV86T an ideal candidate for bioremediation and host for metabolic engineering.

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Environmental Microbiology Reports

Tập 14 Số 3

464-474

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