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Pangenome-driven insights into nitrogen metabolic characteristics of Citrobacter portucalensis strain AAK_AS5 associated with wastewater nitrogen removal

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Abstract

Nitrogen metabolism in the genus Citrobacter is very poorly studied despite its several implications in wastewater treatment. In the current study, Citrobacter portucalensis strain AAK_AS5 was assessed for remediation of simulated wastewater supplemented with different inorganic nitrogen sources. Combination of (NH4)2SO4 with KNO3 was the most preferred for achieving high growth density followed by (NH4)2SO4 and KNO3 alone. This was in agreement with highest ammonical nitrogen removal of 92.9% in the presence of combined nitrogen sources and the corresponding nitrate nitrogen removal of 93% in the presence of KNO3. Furthermore, these removal capacities were validated by investigating the uniqueness and the spread of metabolic features through pan-genomic approach that revealed the largest number of unique genes (2097) and accessory genes (705) in strain AAK_AS5. Of the total 44 different types of nitrogen metabolism-related genes, 39 genes were associated with the core genome, while 5 genes such as gltI, nasA, nasR, nrtA, and ntrC uniquely belonged to the accessory genome. Strain AAK_AS5 possessed three major nitrate removal pathways viz., assimilatory and dissimilatory nitrate reduction to ammonia (ANRA & DNRA), and denitrification; however, the absence of nitrification was compensated by ammonia assimilation catalyzed by gene products of the GDH and GS-GOGAT pathways. narGHIJ encoding the respiratory nitrate reductase was commonly identified in all the studied genomes, while genes such as nirK, norB, and nosZ were uniquely present in the strain AAK_AS5 only. A markedly different genetic content and metabolic diversity between the strains reflected their adaptive evolution in the environment thus highlighting the significance of C. portucalensis AAK_AS5 for potential application in nitrogen removal from wastewater.

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Data availability

This Whole Genome Shotgun project has been deposited in GenBank under the accession number SDHR00000000.

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Acknowledgements

The authors would like to acknowledge Director, CSIR-NEERI, and AcSIR-NEERI for providing essential resources for the research work. The manuscript has been checked for similarity by iThenticate software and has been assigned the manuscript number KRC No. CSIR-NEERI/KRC/2022/Jan/EBGD/1. RKG is thankful to University Grants Commission New Delhi, for the Senior Research Fellowship for carrying out this research.

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Authors and Affiliations

  1. Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India

    Rakesh Kumar Gupta, Hemant J. Purohit & Anshuman A. Khardenavis

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

    Rakesh Kumar Gupta & Anshuman A. Khardenavis

  3. NUS Environmental Research Institute, National University of Singapore, Singapore, 117411, Singapore

    Hitesh Tikariha

  4. Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore

    Hitesh Tikariha

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  1. Rakesh Kumar Gupta
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Contributions

RKG: Investigation, Formal analysis, Visualization, Data curation, Writing—Original draft. HT: Resources, Visualization, Data curation. HJP: Supervision, Methodology, Formal analysis, Writing—Review, and Editing. AAK: Writing—Review and Editing.

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Gupta, R.K., Tikariha, H., Purohit, H.J. et al. Pangenome-driven insights into nitrogen metabolic characteristics of Citrobacter portucalensis strain AAK_AS5 associated with wastewater nitrogen removal. Arch Microbiol 205, 270 (2023). https://doi.org/10.1007/s00203-023-03597-7

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