Abstract:Microbial ammonia oxidation is a key and rate-limiting step of the nitrogen cycle. Three previously known ammonia oxidation pathways (i.e., nitrification, anaerobic ammonia oxidation [Anammox], and complete ammonia oxidation [Comammox]) are mediated by autotrophic microbes.
“…These results indicated that DnfA alone was enough, in the presence of molecular O 2 , FAD, and NADH, for in vitro hydroxylamine oxidation, and that DnfB and DnfC were not necessary for the in vitro assay. Although a recent study showed that DnfB and DnfC were essential for Dirammox with strain JQ135 ( 23 ), how they are involved in the oxidation of ammonia remains unclear. Figure 2 DnfA bound and converted hydroxylamine to nitrogen.…”
“…These results indicated that DnfA alone was enough, in the presence of molecular O 2 , FAD, and NADH, for in vitro hydroxylamine oxidation, and that DnfB and DnfC were not necessary for the in vitro assay. Although a recent study showed that DnfB and DnfC were essential for Dirammox with strain JQ135 ( 23 ), how they are involved in the oxidation of ammonia remains unclear. Figure 2 DnfA bound and converted hydroxylamine to nitrogen.…”
“…It was also demonstrated that the production of N 2 from ammonia in HO-1 was the activity of Dirammox, but not that of nitrite denitrification (Wu et al, 2021). This result was further confirmed in strain JQ135 (Xu et al, 2022), another Alcaligenes strain with the same ability of Dirammox as HO-1. The knockout of denitrification pathway in strain JQ135 did not change its N 2 yield under aerobic conditions (Xu et al, 2022).…”
Section: Introductionmentioning
confidence: 53%
“…This result was further confirmed in strain JQ135 (Xu et al, 2022), another Alcaligenes strain with the same ability of Dirammox as HO-1. The knockout of denitrification pathway in strain JQ135 did not change its N 2 yield under aerobic conditions (Xu et al, 2022). This novel pathway is conducted by enzymes encoded by the gene cluster dnfT1RT2ABCD defined in the genome of HO-1; and just dnfABC could enable recombinant Escherichia coli strain to generate hydroxylamine and N 2 from ammonia (Wu et al, 2021).…”
Section: Introductionmentioning
confidence: 53%
“…Recently, dnfABC was further proved to be the genetic basis for Dirammox and regulated by dnfR in another Alcaligenes strain, JQ135 (Xu et al, 2022). Here, it was found that high homogeneity of Dirammox was among the members of the genus Alcaligenes.…”
Section: Discussionmentioning
confidence: 89%
“…These seven genes were annotated as 3-phosphoserine/phosphohydroxythreonine transaminase, PLP-dependent aminotransferase family protein, serine hydroxymethyltransferase, diiron N-oxygenase, 2Fe-2S ironsulfur cluster binding domain-containing protein, glutamine amidotransferase, and pyridoxine/pyridoxal/pyridoxamine kinase, respectively (Wu et al, 2021). Among the seven genes, only dnfA encoded an N-oxygenase catalyzing the oxidation of hydroxylamine to N 2 , and its deletion resulted in the total loss of Dirammox activity in strain JQ135 (Xu et al, 2022). Therefore, dnfA was selected as a marker gene of Dirammox pathway for the following investigations.…”
Nitrogen cycle is an essential process for environmental health. Dirammox (direct ammonia oxidation), encoded by the dnfT1RT2ABCD cluster, was a novel pathway for microbial N2 production defined in Alcaligenes ammonioxydans HO-1. Here, a copy of the cluster dnfT1RT2ABCD as a whole was proved to have existed and very conserved in all Alcaligenes genomes. Phylogenetic analyses based on 16S rRNA gene sequences and amino acid sequences of DnfAs, together with G + C content data, revealed that dnf cluster was evolved associated with the members of the genus Alcaligenes. Under 20% O2 conditions, 14 of 16 Alcaligenes strains showed Dirammox activity, which seemed likely taxon-related. However, the in vitro activities of DnfAs catalyzing the direct oxidation of hydroxylamine to N2 were not taxon-related but depended on the contents of Fe and Mn ions. The results indicated that DnfA is necessary but not sufficient for Dirammox activity. The fact that members of the genus Alcaligenes are widely distributed in various environments, including soil, water bodies (both freshwater and seawater), sediments, activated sludge, and animal–plant-associated environments, strongly suggests that Dirammox is important to the nitrogen cycle. In addition, Alcaligenes species are also commonly found in wastewater treatment plants, suggesting that they might be valuable resources for wastewater treatment.
Bacteria capable of direct ammonia oxidation (Dirammox) play important roles in global nitrogen cycling and nutrient removal from wastewater. Dirammox process, NH3 → NH2OH → N2, first defined in Alcaligenes ammonioxydans HO‐1 and encoded by dnf gene cluster, has been found to widely exist in aquatic environments. However, because of multidrug resistance in Alcaligenes species, the key genes involved in the Dirammox pathway and the interaction between Dirammox process and the physiological state of Alcaligenes species remain unclear. In this work, ammonia removal via the redistribution of nitrogen between Dirammox and microbial growth in A. ammonioxydans HO‐1, a model organism of Alcaligenes species, was investigated. The dnfA, dnfB, dnfC, and dnfR genes were found to play important roles in the Dirammox process in A. ammonioxydans HO‐1, while dnfH, dnfG, and dnfD were not essential genes. Furthermore, an unexpected redistribution phenomenon for nitrogen between Dirammox and cell growth for ammonia removal in HO‐1 was revealed. After the disruption of the Dirammox in HO‐1, more consumed NH4+ was recovered as biomass‐N via rapid metabolic response and upregulated expression of genes associated with ammonia transport and assimilation, tricarboxylic acid cycle, sulfur metabolism, ribosome synthesis, and other molecular functions. These findings deepen our understanding of the molecular mechanisms for Dirammox process in the genus Alcaligenes and provide useful information about the application of Alcaligenes species for ammonia‐rich wastewater treatment.
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