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Identification of a virulent phage infecting species of Nitrosomonas


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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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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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.

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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).

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