Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification

Abstract

Alcaligenes faecalis is a heterotrophic nitrifying bacterium that oxidizes ammonia and generates nitrite and nitrate. When A. faecalis was cultivated in a medium containing pyruvate and ammonia as the sole carbon and nitrogen sources, respectively, high concentrations of nitrite accumulated in the medium whose carbon/nitrogen (C/N) ratio was lower than 10 during the exponential growth phase, while the accumulation was not observed in the medium whose C/N ratio was higher than 15. Comparative transcriptome analysis was performed using nitrifying and non-nitrifying cells of A. faecalis cultivated in media whose C/N ratios were 5 and 20, respectively, to evaluate the fluctuations of gene expression during induction of heterotrophic nitrification. Expression levels of genes involved in primary metabolism did not change significantly in the cells at the exponential growth phase under both conditions. We observed a significant increase in the expression levels of four gene clusters: pod cluster containing the gene encoding pyruvic oxime dioxygenase (POD), podh cluster containing the gene encoding a POD homolog (PODh), suf cluster involved in an iron-sulfur cluster biogenesis, and dnf cluster involved in a novel hydroxylamine oxidation pathway in the nitrifying cells. Our results provide valuable insight into the biochemical mechanism of heterotrophic nitrification.

Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification

“…Xu and coworkers ( 29 ) recently reported that knockout mutants of A. faecalis POD were still able to produce NO 2 − , which likely can be explained by the presence of several homologs of POD. Consistently, Tsujino and coworkers ( 59 ) showed that one of these homologs (designated PODh2 in our study) was also capable of pyruvic oxime oxidation, albeit at 5.5% of the rate of POD. This homolog was also significantly up-regulated during NH 2 OH production in our study.…”

Alcaligenes ammonioxydans HO-1 antagonizes Bacillus velezensis via hydroxylamine-triggered population response

“…It is of note that HO-1 did not have an antagonistic effect on closely related Alcaligenes species. Alcaligenes strains typically produce HA during nitrogen metabolism; consequently, they may have developed strategies for converting HA to other non-toxic substances (Tsujino et al, 2021;Wu et al, 2021).…”

“…Mutations could have interesting consequences between the two coexisting bacteria. Since Alcaligenes produce HA during nitrogen metabolism, they must have strategies for converting HA to non-toxic substances to detoxify it (Tsujino et al, 2021;Wu et al, 2021). Could HA-induced mutations render V4 more resistant to this compound after a period of time in combined colonies?…”

Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification

“…Recently, we performed a comparative transcriptome analysis using A. faecalis and con rmed that the pod gene is activated under nitri cation-inducing conditions (Tsujino et al 2021). The result of the transcriptome analysis also suggested that the pod gene and the four adjacent genes were transcribed as a single polycistronic mRNA.…”

“…To date, the A. faecalis enzyme is the only POD whose catalytic function has been characterised and whose involvement in nitri cation has been clearly demonstrated (Tsujino et al 2017(Tsujino et al , 2021. BLAST analysis revealed that the putative pod genes were present in many species of microorganisms, including bacteria in the phyla Proteobacteria and Actinobacteria, and fungi classi ed in the phylum Ascomycota (Tsujino et al 2017).…”