An iron dioxygenase from Alcaligenes faecalis catalyzing the oxidation of pyruvic oxime to nitrite

Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification

Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, 15N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in Alcaligenes faecalis. We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that A. faecalis is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.

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

Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.

Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification

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.

Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway

Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen-rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO-1, oxidizing ammonia to hydroxylamine and ending in the production of N₂ gas. Genome analysis revealed that strain HO-1 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO-1 denitrified nitrite (not nitrate) to N₂ and N₂ O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N₂ production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO-1 and enabled E. coli accumulated hydroxylamine. Sub-cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to ¹⁵ N₂ from (¹⁵ NH₄ )₂ SO₄ . Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO-1 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N₂ .

Nitrous oxide produced directly from ammonium, nitrate and nitrite during nitrification and denitrification

A hypothermia aerobic denitrifying bacterium, Pseudomonas taiwanensis strain J488, can effectively remove multiple nitrogen sources from wastewater at 15 °C. The ammonium, nitrate and nitrite removal efficiencies were 100 %, 92.61 % and 92.49 %, respectively. Strain J488 could survive with hydroxylamine as sole nitrogen source and its removal efficiency was 97.71 %. The removal efficiency of ammonium was 100 % even in the presence of the classical inhibitors of nitrification allylthiourea and diethyldithiocarbamate. These findings fundamentally changed the picture that the ammonia monooxygenase could be inhibited by the copper chelators of allylthiourea or diethyldithiocarbamate. Similarly, the nitrite removal capacity of strain J488 was not sensitive to inhibition by Pb²⁺, and its removal efficiency was also 100 %. Additionally, by identifying the intermediates accumulation of nitrification and denitrification, using nitrification and denitrification inhibitors, measuring enzyme activities and determining N₂O concentrations, it was demonstrated that N₂O could be produced directly from ammonium, nitrate and nitrite.

Characteristics of nitrogen transformation and intracellular nitrite accumulation by the hypothermia bacterium Arthrobacter arilaitensis

A new nitrite accumulation pathway was discovered in the nitrogen conversion process of Arthrobacter arilaitensis. The extracellular nitrite reached 0.65 and 43.66 mg/L with hydroxylamine and nitrate as the sole nitrogen source, respectively. The enzyme activities of ammonia monooxygenase, hydroxylamine oxidoreductase and nitrate reductase were 0.42, 0.0014 and 0.0049 U/mg protein, respectively. The activity of nitrite reductase was completely inhibited by diethyldithiocarbamate. Intriguingly, the intracellular nitrite accumulated as high as 43.0, 42.26, 39.94 and 35.01 mg/L, when the Arthrobacter arilaitensis was incubated with Luria-Bertani medium, ammonium, nitrate and nitrite as the nitrogen source, respectively. These results confirmed that the highest concentration of intracellular nitrite was accumulated when LB was selected as the nitrogen source, followed by ammonium and nitrate, then nitrite was the least. To date, biochemical mechanism responsible for the accumulation of a high concentration of intracellular nitrite is unknown.

N2O production from hydroxylamine oxidation and corresponding hydroxylamine oxidoreductase involved in a heterotrophic nitrifier A. faecalis strain NR

N₂O production from NH₂OH oxidation involved in a heterotrophic nitrifier Alcaligenes faecalis strain NR was studied. ¹⁵N-labeling experiments showed that biological NH₂OH consumption by strain NR played a dominant role in N₂O production, although chemical reaction between NH₂OH and O₂ indeed existed. Hydroxylamine oxidoreductase (HAO) from strain NR was partially purified by (NH₄)₂SO₄ fractionation and DEAE Cartridge chromatography. The maximum activity of HAO was 9.60 mU with a specific activity of 92.04 mU/(mg protein) when K₃Fe(CN)₆ was used as an electron acceptor. The addition of Ca²⁺ promoted the HAO activity, while the presence of Mn²⁺ inhibited the enzyme activity. The optimal temperature and pH for HAO activity were 30 °C and 8. Analysis of enzyme-catalyzed products demonstrated that NH₂OH oxidation catalyzed by HAO from strain NR played significant role in the production of N₂O.

Nitrogen cycling during wastewater treatment

Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.

Pyruvic oxime dioxygenase from heterotrophic nitrifier Alcaligenes faecalis is a nonheme Fe(II)-dependent enzyme homologous to class II aldolase

Pyruvic oxime dioxygenase (POD), a key enzyme in heterotrophic nitrification, was purified from Alcaligenes faecalis, and the molecular and catalytic characteristics were reexamined. POD was purified as the homotetramer of the subunit whose molecular weight was 30,000. The deduced amino acid sequence of POD was homologous with a class II aldolase that has been regarded as the Zn^(II)-dependent enzyme catalyzing aldol reactions. The recombinant protein showed weak POD activity, and was activated by reconstitution with Fe^(II). Affinity and catalytic constants were estimated at 470 μM and 4.69 sec^-1, respectively. The POD was inactivated by EDTA to remove bound divalent metal cations. A reconstitution experiment demonstrated that Fe^(II), not Zn^(II), is essential for POD activity and that Mn^(II) could partially fulfill the function of Fe^(II). A mutant POD with replacement of His¹⁸³, corresponding to one of three Zn^(II)-binding ligands in the class II aldolase, by Asn was purified as a homotetrameric protein but showed no catalytic activities. Those results suggest that the POD is homologous to class II aldolase having non-heme Fe^(II) as a catalytic center instead of Zn^(II). A possible mechanism of the POD reaction is discussed on the basis of that of a known Fe^(II)-dependent dioxygenase.

N2O and N2 production during heterotrophic nitrification by Alcaligenes faecalis strain NR

A heterotrophic nitrifier, strain NR, was isolated from a membrane bioreactor. Strain NR was identified as Alcaligenes faecalis by Auto-Microbic system and 16S rRNA gene sequence analysis. A. faecalis strain NR shows a capability of heterotrophic nitrification and N(2)O and N(2) production as well under the aerobic condition. Further tests demonstrated that neither nitrite nor nitrate could be denitrified aerobically by strain NR. However, when hydroxylamine was used as the sole nitrogen source, nitrogenous gases were detected. With an enzyme assay, a 0.063 U activity of hydroxylamine oxidase was observed, while nitrate reductase and nitrite reductase were undetectable. Thus, nitrogenous gas was speculated to be produced via hydroxylamine. Therefore, two different metabolic pathways might exist in A. faecalis NR. One is heterotrophic nitrification by oxidizing ammonium to nitrite and nitrate. The other is oxidizing ammonium to nitrogenous gas directly via hydroxylamine.