{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T04:02:26Z","timestamp":1776052946703,"version":"3.50.1"},"reference-count":60,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T00:00:00Z","timestamp":1730073600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"crossref","award":["# RGPIN-2016-06061"],"award-info":[{"award-number":["# RGPIN-2016-06061"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n               <jats:title>Background<\/jats:title>\n               <jats:p>Strain JAM1<jats:sup>T<\/jats:sup> and strain GP59 of the methylotrophic, bacterial species <jats:italic>Methylophaga nitratireducenticrescens<\/jats:italic> were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate (${\\mathrm{NO}}_{3}^{-}$) reduction. Strain JAM1<jats:sup>T<\/jats:sup> can reduce ${\\mathrm{NO}}_{3}^{-}$ to nitrite (${\\mathrm{NO}}_{2}^{-}$) but not ${\\mathrm{NO}}_{2}^{-}$ to nitric oxide (NO) as it lacks a NO-forming ${\\mathrm{NO}}_{2}^{-}$ reductase. Strain GP59 on the other hand can carry the complete reduction of ${\\mathrm{NO}}_{3}^{-}$ to N<jats:sub>2<\/jats:sub>. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before ${\\mathrm{NO}}_{3}^{-}$ reduction occurs. In strain JAM1<jats:sup>T<\/jats:sup> cultures, ${\\mathrm{NO}}_{3}^{-}$ reduction begins immediately with accumulation of ${\\mathrm{NO}}_{2}^{-}$. Furthermore, ${\\mathrm{NO}}_{3}^{-}$ is reduced under oxic conditions in strain JAM1<jats:sup>T<\/jats:sup> cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Methods<\/jats:title>\n               <jats:p>Both strains were cultured under oxic conditions either with or without ${\\mathrm{NO}}_{3}^{-}$, or under anoxic conditions with ${\\mathrm{NO}}_{3}^{-}$. Transcript levels of selected denitrification genes (<jats:italic>nar1<\/jats:italic> and <jats:italic>nar2<\/jats:italic> encoding ${\\mathrm{NO}}_{3}^{-}$ reductases, <jats:italic>nirK<\/jats:italic> encoding ${\\mathrm{NO}}_{2}^{-}$ reductase, <jats:italic>narK12f<\/jats:italic> encoding ${\\mathrm{NO}}_{3}^{-}$\/${\\mathrm{NO}}_{2}^{-}$transporter) and regulatory genes (<jats:italic>narXL<\/jats:italic> and <jats:italic>fnr<\/jats:italic>) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Results<\/jats:title>\n               <jats:p>The transcript levels of <jats:italic>nar1<\/jats:italic> were very low in strain GP59 cultured under oxic conditions without ${\\mathrm{NO}}_{3}^{-}$. These levels were 37 times higher in strain JAM1<jats:sup>T<\/jats:sup> cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1<jats:sup>T<\/jats:sup> before the inoculation of the oxic and anoxic cultures to carry ${\\mathrm{NO}}_{3}^{-}$ reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the <jats:italic>nnrS3<\/jats:italic> gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions with ${\\mathrm{NO}}_{3}^{-}$ than those in both strains cultured under oxic conditions without ${\\mathrm{NO}}_{3}^{-}$. Since NnrS senses NO, these results suggest that strain GP59 reduced ${\\mathrm{NO}}_{3}^{-}$ to NO under oxic conditions, but because of the oxic environment, NO is oxidized back to ${\\mathrm{NO}}_{3}^{-}$ by flavohemoproteins (NO dioxygenase; Hmp), explaining why ${\\mathrm{NO}}_{3}^{-}$ reduction is not observed in strain GP59 cultured under oxic conditions.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Conclusions<\/jats:title>\n               <jats:p>Understanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities.<\/jats:p>\n            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