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Identification of a virulent phage infecting species of Nitrosomonas

The ISME Journal (2023)Cite this article

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Abstract

In the first and limiting step of nitrification, ammonia (NH3) is oxidised to nitrite (NO2–) by the action of some prokaryotes, including bacteria of the Nitrosomonas genus. A potential approach to nitrification inhibition would be through the application of phages, but until now this method has been unexplored and no virulent phages that infect nitrifying bacteria have been described. In this study, we report the isolation of the first phage infecting some Nitrosomonas species. This polyvalent virulent phage (named ΦNF-1) infected Nitrosomonas europaea, Nitrosomonas communis, and Nitrosomonas nitrosa. Phage ΦNF-1 has the morphology of the Podoviridae family, a dsDNA genome of 41,596 bp and a 45.1 % GC content, with 50 predicted open reading frames. Phage ΦNF-1 was found to inhibit bacterial growth and reduce NH4+ consumption in the phage-treated cultures. The application of phages as biocontrol agents could be a useful strategy for nitrification inhibition without the restrictions associated with chemical inhibitors.

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Fig. 1: Growth of Nitrosomonas cultures in the presence of phage ΦNF-1 and the effect of the phage on the NH4+ uptake in the cultures.
Fig. 2: Morphological and genetic characterization of phage ΦNF-1.

Data availability

All data are available in the main text or the supplementary online materials. The phage genome is available at GenBank accession number OL634959.

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Acknowledgements

This work was supported by the Spanish Ministerio de Ciencia e Innovación (PID2020-113355GB-I00, the Agencia Estatal de Investigación (AEI) and the European regional fund (ERF), and the CDTI project (IDI-20190017). The study was partially supported by the Generalitat de Catalunya (2017SGR170). L. R.-R is lecturer of the Serra-Hunter program, Generalitat de Catalunya. C. G-G. has a fellowship from the University of Barcelona. L. S-C has a Maria Zambrano fellowship from the Spanish Ministerio de Universidades. M.D.R-B has a Margarita Salas fellowship from the Spanish Ministerio de Universidades.

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Authors and Affiliations

  1. Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Diagonal 643, Annex, Floor 0, E-08028, Barcelona, Spain

    Pablo Quirós, Laura Sala-Comorera, Clara Gómez-Gómez, María Dolores Ramos-Barbero, Lorena Rodríguez-Rubio, Gloria Vique & Maite Muniesa

  2. Departamento de I+D+i de Fertinagro Biotech S.L, Poligono Industrial La Paz, Teruel, Spain

    Pablo Quirós, Tula Yance-Chávez, Sergio Atarés & Ignasi Salaet

  3. Departmento de Fisiologia, Genética y Microbiología, Universidad de Alicante (UA), 03080, Alicante, Spain

    María Dolores Ramos-Barbero

  4. Departamento de Química y Tecnología de Alimentos, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain

    Sandra García-Gutierrez, Sonia García-Marco & Antonio Vallejo

  5. Centro de Estudios e Investigación para la Gestión de Riesgos Agrarios y Medioambientales (CEIGRAM), Universidad Politécnica de Madrid (UPM), Madrid, Spain

    Sandra García-Gutierrez, Sonia García-Marco & Antonio Vallejo

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  1. Pablo Quirós
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Contributions

PQ, LSC, CGG, GV, TYC, SGG, SGM performed the experiments, MDRB and LRR performed sequencing analysis, PQ, SA, AV, IS and MM conceived and funded the study, designed the experiments, and wrote the paper.

Corresponding author

Correspondence to Maite Muniesa.

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Quirós, P., Sala-Comorera, L., Gómez-Gómez, C. et al. Identification of a virulent phage infecting species of Nitrosomonas. ISME J (2023). https://doi.org/10.1038/s41396-023-01380-6

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