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Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil

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Abstract

Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated the highest methanol removal (73.28%) in terms of soluble chemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.

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Data availability

The whole-genome sequence of P. aeruginosa. AAK/M5 was deposited into the NCBI GenBank under the BioProject and the accession numbers PRJNA649053 and GCA_014076625.1, respectively.

Code availability

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Acknowledgements

Authors would like to acknowledge Director, CSIR-NEERI and AcSIR- NEERI for providing essential resources for the research work The manuscript has been internally checked for plagiarism through iThenticate software and assigned the KRC No. CSIR-NEERI/KRC/2021/OCT/EBGD/4. Ashish Kumar Singh is thankful to CSIR, New Delhi for Senior Research Fellowship while Rakesh Kumar Gupta is thankful to UGC, New Delhi for Senior Research Fellowship for carrying out this research.

Funding

This work was supported by funds from the Science and Engineering Research Board (SERB), New Delhi [Grant Number EMR/2016/006589].

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  1. Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India

    Ashish Kumar Singh, Rakesh Kumar Gupta, Hemant J. Purohit & Anshuman Arun Khardenavis

  2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Ashish Kumar Singh, Rakesh Kumar Gupta & Anshuman Arun Khardenavis

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  1. Ashish Kumar Singh
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AKS: investigation, formal analysis, visualization, data curation, writing-original draft. RKG: resources, visualization, data curation. AAK: acquisition of financial support, conceptualization, methodology, formal analysis, writing-review and editing, project administration. HJP: supervision, writing-review and editing.

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Singh, A.K., Gupta, R.K., Purohit, H.J. et al. Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil. World J Microbiol Biotechnol 38, 140 (2022). https://doi.org/10.1007/s11274-022-03311-7

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