Oxidation of Nitrapyrin to 6-Chloropicolinic Acid by the Ammonia-Oxidizing Bacterium Nitrosomonas europaea

Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition

Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.

Is nitrification inhibition the bottleneck of integrating hydrothermal liquefaction in wastewater treatment plants?

Sewage sludge management poses challenges due to its environmental impact, varying composition, and stringent regulatory requirements. In this scenario, hydrothermal liquefaction (HTL) is a promising technology for producing biofuel and extracting phosphorus from sewage sludge. However, the toxic nature of the resulting process water (HTL-PW) raises concerns about integrating HTL into conventional wastewater treatment processes. This study investigated the inhibitory effects of HTL-PW on the activity of the main microbial functions in conventional activated sludge. Upon recirculation of the HTL-PW from the excess sludge into the wastewater treatment plant, the level of COD in the influent is expected to increase by 157 mgO2⋅L-1, resulting in 44% nitrification inhibition (IC50 of 197 mg⋅L-1). However, sorption of inhibitory compounds on particles can reduce nitrification inhibition to 27% (IC50 of 253 mg⋅L-1). HTL-PW is a viable carbon source for denitrification, showing nearly as high denitrification rates as acetate and only 17% inhibition at 157 mgO2⋅L-1 COD. Under aerobic conditions, heterotrophic organic nitrogen and organic matter conversion remains unaffected up to 223 mgO2⋅L-1 COD, with COD removal higher than 94%. This study is the first to explore the full integration of HTL in wastewater treatment plants for biofuel production from the excess activated sludge. Potential nitrification inhibition is concerning, and further long-term studies are needed to fully investigate the impacts.

Biological and chemical nitrification inhibitors exhibited different effects on soil gross N nitrification rate and N2O production: a 15N microcosm study

Nitrification inhibitors (NIs) are considered as an effective strategy for reducing nitrification rate and related environmental nitrogen (N) loss. However, whether plant-derived biological NIs had an advantage over chemical NIs in simultaneously inhibiting nitrification rate and N2O production remains unclear. Here, we conducted an aerobic 15N microcosmic incubation experiment to compare the effects of a biological NI (methyl 3-(4-hydroxyphenyl) propionate, MHPP) with three chemical NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), dicyandiamide (DCD), and 3,4-dimethylpyrazole phosphate (DMPP) on (i) gross N mineralization and nitrification rate and (ii) the relative importance of nitrification and denitrification in N2O emission in a calcareous soil. The results showed that DMPP significantly inhibited m_gross rate (P < 0.05), whereas DCD, nitrapyrin, and MHPP only numerically inhibited it. Gross N nitrification (n_gross) rates were inhibited by 9.48% in the DCD treatment to 51.5% in the nitrapyrin treatment. Chemical NIs primarily affected the amoA gene abundance of ammonia-oxidizing bacteria (AOB), whereas biological NIs affected the amoA gene abundance of ammonia-oxidizing archaea (AOA) and AOB. AOB's community composition was more susceptible to NIs than AOA, and NIs mainly targeted Nitrosospira clusters of AOB. Chemical NIs of DCD, DMPP, and nitrapyrin proportionally reduced N2O production from nitrification and denitrification. However, the biological NI MHPP stimulated short-term N2O emission and increased the proportion of N2O from denitrification. Our findings showed that the influence of NIs on gross N mineralization rate (m_gross) was dependent on the NI type. MHPP exhibited a moderate n_gross inhibitory capacity compared with the three chemical NIs. The mechanisms of chemical and biological NIs inhibiting n_gross can be partly attributed to changes in the abundance and community of ammonia oxidizers. A more comprehensive evaluation is needed to determine whether biological NIs have advantages over chemical NIs in inhibiting greenhouse gas emissions.

Meta-analysis of the effect of nitrification inhibitors on the abundance and community structure of N2O-related functional genes in agricultural soils

Application of nitrification inhibitors (NIs) in agricultural systems is an important strategy to enhance fertilizer nitrogen use efficiency and mitigate soil nitrous oxide (N₂O) emissions. Here, we conducted a global meta-analysis of 88 published studies to assess the response of N₂O-related functional gene and transcript abundances, and community structure to NIs application. Application of NIs significantly reduced the abundance of ammonia-oxidizing bacteria ammonia monooxygenase (AOB amoA) genes, AOB amoA transcript and nitrite reductase (nirS and nirK) genes. The effectiveness of NIs on reducing the AOB amoA abundance was influenced by N form, soil texture, soil pH and the experimental type (field vs. laboratory). Specifically, NIs were more effective when a mixed inorganic and organic N source was applied to a medium-textured soils. The NIs effectiveness increased with increasing soil pH. The response of AOB amoA abundance to NIs application was not affected by NI type, N rate, soil moisture, soil temperature and soil organic carbon (SOC). The inhibitory effect of NIs on nirS abundance increased with increasing soil temperature. NIs decreased soil nitrifying enzyme activity (NEA) and denitrifying enzyme activity (DEA) by 34.5 % and 27.0 %, respectively, leading to an overall 63.6 % reduction of N₂O emissions. Soil NEA correlated positively with the abundance and community structure of AOB amoA but not with AOA amoA. Decrease in DEA with NIs application coincided with the decreasing nirS and nirK abundances. This global-scale assessment demonstrates that the effectiveness of NIs in reducing N₂O emissions was attributed to the inhibiting effects on AOB amoA, nirS and nirK genes. Our findings highlight that NIs' inhibition effects on bacterial ammonia-oxidizing community and the encode enzymes in transformation of nitrite to nitric oxide are the main mechanisms for mitigation of N fertilizer-induced N₂O emissions.

Management and implications of using nitrification inhibitors to reduce nitrous oxide emissions from urine patches on grazed pasture soils - A review

Livestock urine patches are the main source of nitrous oxide (N₂O) emissions in pastoral system, and nitrification inhibitors (NIs) have been widely investigated as a N₂O mitigation strategy. This study reviews the current understanding of the effect of NIs use on N₂O emissions from urine patches, including the factors that affect their efficacy, as well as the unintended consequences of NIs use. It brings together the fundamental aspects of targeted management of urine patches for reducing N₂O emissions involving inhibitors. The available literature of 196 datasets indicates that dicyandiamide (DCD), 3,4-dimethylpyrazole phosphate (DMPP), and 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin) reduced N₂O emissions from urine patches by 44 ± 2%, 28 ± 38% and 28 ± 5%, (average ± s.e.), respectively. DCD also increased pasture dry matter and nitrogen (N) uptake by 13 ± 2% and 15 ± 3%, (average ± s.e.), respectively. The effect of DMPP and nitrapyrin on pasture dry matter and N uptake, assessed in only one study, was not significant. It also suggests that harmonizing the timing of inhibitor use with urine-N transformation increase the efficacy of NIs. No negative impacts on non-targeted soil and aquatic organisms have been reported with the recommended rate of DCD applied to urine and recommended applications of DMPP and nitrapyrin for treated mineral fertilisers and manures. However, there was evidence of the presence of small amounts of DCD residues in milk products as a result of its use on livestock grazed pasture. DMPP and nitrapyrin can also enter the food chain via grazing livestock. The study concludes that for the use of NIs in livestock grazed systems, research is needed to establish acceptable maximum residue level (MRL) of NIs in soil, plant, and animal products, and develop technologies that optimise physical mixing between NIs and urine patches.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Widespread Use of the Nitrification Inhibitor Nitrapyrin: Assessing Benefits and Costs to Agriculture, Ecosystems, and Environmental Health

Agricultural production and associated applications of nitrogen (N) fertilizers have increased dramatically in the last century, and current projections to 2050 show that demands will continue to increase as the human population grows. Applied in both organic and inorganic fertilizer forms, N is an essential nutrient in crop productivity. Increased fertilizer applications, however, create the potential for more N loss before plant uptake. One strategy for minimizing N loss is the use of enhanced efficiency fertilizers, fortified with a nitrification inhibitor, such as nitrapyrin. In soils and water, nitrapyrin inhibits the activity of ammonia monooxygenase, a microbial enzyme that catalyzes the first step of nitrification from ammonium to nitrite. Potential benefits of using nitrification inhibitors range from reduced nitrate leaching and nitrous oxide emissions to increased crop yield. The extent of these benefits, however, depends on environmental conditions and management practices. Thus, such benefits are not always realized. Additionally, nitrapyrin has been shown to transport off-field, and it is unknown what effects environmental nitrapyrin could have on nontarget organisms and the ecological nitrogen cycle. Here, we review the agronomic and environmental benefits and costs of nitrapyrin use and present a series of research questions and considerations to be addressed with future nitrification inhibitor research.

Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates

Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; "Candidatus Nitrosocosmicus franklandus," "Candidatus Nitrosotalea sinensis"), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3-0.7 μM) compared to EQ (EC50 = 1-1.4 μM) and EQNL (EC50 = 26.6-129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9-248.7 μM vs EC50 = 0.6-2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8-2.1 and 1.0-6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.

The Chemistry, Biology, and Modulation of Ammonium Nitrification in Soil

Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.

Nitrification in agricultural soils: impact, actors and mitigation

Nitrogen is one of the most important nutrients for plant growth and hence heavily applied in agricultural systems via fertilization. Nitrification, that is, the conversion of ammonium via nitrite to nitrate by soil microorganisms, however, leads to nitrate leaching and gaseous nitrous oxide production and as such to an up to 50% loss of nitrogen availability for the plant. Nitrate leaching also results in eutrophication of groundwater, drinking water and recreational waters, toxic algal blooms and biodiversity loss, while nitrous oxide is a greenhouse gas with a global warming potential 300× greater than carbon dioxide. Logically, inhibition of nitrification is an important strategy used in agriculture to reduce nitrogen losses, and contributes to a more environmental-friendly practice. However, recently identified and crucial players in nitrification, that is, ammonia-oxidizing archaea and comammox bacteria, seem to be under-investigated in this respect. In this review, we give an update on the different pathways in ammonia oxidation, the relevance for agriculture and the interaction with nitrification inhibitors. As such, we hope to pinpoint possible strategies to optimize the efficiency of nitrification inhibition.

Efficiency of two nitrification inhibitors (dicyandiamide and 3, 4-dimethypyrazole phosphate) on soil nitrogen transformations and plant productivity: a meta-analysis

Dicyandiamide (DCD) and 3, 4-dimethypyrazole phosphate (DMPP) are often claimed to be efficient in regulating soil N transformations and influencing plant productivity, but the difference of their performances across field sites is less clear. Here we applied a meta-analysis approach to compare effectiveness of DCD and DMPP across field trials. Our results showed that DCD and DMPP were equally effective in altering soil inorganic N content, dissolve inorganic N (DIN) leaching and nitrous oxide (N2O) emissions. DCD was more effective than DMPP on increasing plant productivity. An increase of crop yield by DMPP was generally only observed in alkaline soil. The cost and benefit analysis (CBA) showed that applying fertilizer N with DCD produced additional revenues of $109.49 ha(-1) yr(-1) for maize farms, equivalent to 6.02% increase in grain revenues. In comparisons, DMPP application produced less monetary benefit of $15.67 ha(-1) yr(-1). Our findings showed that DCD had an advantage of bringing more net monetary benefit over DMPP. But this may be weakened by the higher toxicity of DCD than DMPP especially after continuous DCD application. Alternatively, an option related to net monetary benefit may be achieved through applying DMPP in alkaline soil and reducing the cost of purchasing DMPP products.

Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments

Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

Transformations of Aromatic Compounds by Nitrosomonas europaea

Benzene and a variety of substituted benzenes inhibited ammonia oxidation by intact cells of Nitrosomonas europaea. In most cases, the inhibition was accompanied by transformation of the aromatic compound to a more oxidized product or products. All products detected were aromatic, and substituents were often oxidized but were not separated from the benzene ring. Most transformations were enhanced by (NH(4))(2)SO(4) (12.5 mM) and were prevented by C(2)H(2), a mechanism-based inactivator of ammonia monooxygenase (AMO). AMO catalyzed alkyl substituent hydroxylations, styrene epoxidation, ethylbenzene desaturation to styrene, and aniline oxidation to nitrobenzene (and unidentified products). Alkyl substituents were preferred oxidation sites, but the ring was also oxidized to produce phenolic compounds from benzene, ethylbenzene, halobenzenes, phenol, and nitrobenzene. No carboxylic acids were identified. Ethylbenzene was oxidized via styrene to two products common also to oxidation of styrene; production of styrene is suggestive of an electron transfer mechanism for AMO. Iodobenzene and 1,2-dichlorobenzene were oxidized slowly to halophenols; 1,4-dichlorobenzene was not transformed. No 2-halophenols were detected as products. Several hydroxymethyl (-CH(2)OH)-substituted aromatics and p-cresol were oxidized by C(2)H(2)-treated cells to the corresponding aldehydes, benzaldehyde was reduced to benzyl alcohol, and o-cresol and 2,5-dimethylphenol were not depleted.

Selective enhancement of the fluorescent pseudomonad population after amending the recirculating nutrient solution of hydroponically grown plants with a nitrogen stabilizer

Fluorescent pseudomonads have been associated, via diverse mechanisms, with suppression of root disease caused by numerous fungal and fungal-like pathogens. However, inconsistent performance in disease abatement, after their employment, has been a problem. This has been attributed, in part, to the inability of the biocontrol bacterium to maintain a critical threshold population necessary for sustained biocontrol activity. Our results indicate that a nitrogen stabilizer (N-Serve, Dow Agrosciences) selectively and significantly enhanced, by two to three orders of magnitude, the resident population of fluorescent pseudomonads in the amended (i.e., 25 microg ml(-1) nitrapyrin, the active ingredient) and recycled nutrient solution used in the cultivation of hydroponically grown gerbera and pepper plants. Pseudomonas putida was confirmed as the predominant bacterium selectively enhanced. Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rDNA suggested that N-Serve selectively increased P. putida and reduced bacterial diversity 72 h after application. In vitro tests revealed that the observed population increases of fluorescent pseudomonads were preceded by an early growth suppression of indigenous aerobic heterotrophic bacteria (AHB) population. Interestingly, the fluorescent pseudomonad population did not undergo this decrease, as shown in competition assays. Xylene and 1,2,4-trimethylbenzene (i.e., the inert ingredients in N-Serve) were responsible for a significant percentage of the fluorescent pseudomonad population increase. Furthermore, those increases were significantly higher when the active ingredient (i.e., nitrapyrin) and the inert ingredients were combined, which suggests a synergistic response. P. putida strains were screened for the ability to produce antifungal compounds and for the antifungal activity against Pythium aphanidermatum and Phytophthora capsici. The results of this study suggest the presence of diverse mechanisms with disease-suppressing potential. This study demonstrates the possibility of using a specific substrate to selectively enhance and maintain desired populations of a natural-occurring bacterium such as P. putida, a trait considered to have great potential in biocontrol applications for plant protection.

Mono-, Bi-, and Trinuclear CuII-Cl Containing Products Based on the Tris(2-pyridylmethyl)amine Chelate Derived from Copper(I) Complex Dechlorination Reactions of Chloroform

The ligand TMPA (tris(2-pyridylmethyl)amine) and its copper complexes have played a prominent role in recent (bio)inorganic chemistry studies; the copper(I) complex [CuI(TMPA)(CH3CN)]+ possesses an extensive dioxygen reactivity, and it is also known to effect the reductive dechlorination of substrates such as dichloromethane and benzyl and allyl chlorides. In this report, we describe a set of new analogues of TMPA, ligand 6TMPAOH, binucleating Iso-DO, and trinucleating SYMM. Copper(I) complexes with these ligands and a previously described binucleating ligand DO react with chloroform, resulting in reductive dechlorination and production of [CuIIx(L)Clx]x+ (x = 1, 2, or 3). X-ray crystal structures of [CuII(6TMPAOH)Cl]PF6, [CuII2(Iso-DO)Cl2](PF6)2, [CuII2(DO)Cl2](PF6)2, and [Cu3(SYMM)Cl3](PF6)3 are presented, and the compounds are also characterized by UV-vis and EPR spectroscopies as well as cyclic voltammetry. The steric influence of a pyridyl 6-substituent (in the complexes with 6TMPAOH, Iso-DO, and SYMM) on the solid state and solution structures and redox potentials are compared and contrasted to those chlorocopper(II) complexes with a pyridyl 5'-substituent (in [CuII2(DO)Cl2](PF6)2 and in [CuII(TMPA)Cl]+). Some insights into the reductive dechlorination process have been obtained by using 2H NMR spectroscopy in following the reaction of [Cu2(Iso-DO)(CH3CN)2](PF6)2 with CDCl3, in the presence or absence of a radical trap, 2,4-di-tert-butylphenol.

New insights into methyl bromide cooxidation by Nitrosomonas europaea obtained by experimenting with moderately low density cell suspensions

We examined the rates and sustainability of methyl bromide (MeBr) oxidation in moderately low density cell suspensions ( approximately 6 x 10(7) cells ml(-1)) of the NH(3)-oxidizing bacterium Nitrosomonas europaea. In the presence of 10 mM NH(4)(+) and 0.44, 0. 22, and 0.11 mM MeBr, the initial rates of MeBr oxidation were sustained for 12, 12, and 24 h, respectively, despite the fact that only 10% of the NH(4)(+), 18% of the NH(4)(+), and 35% of the NH(4)(+), respectively, were consumed. Although the duration of active MeBr oxidation generally decreased as the MeBr concentration increased, similar amounts of MeBr were oxidized with a large number of the NH(4)(+)-MeBr combinations examined (10 to 20 micromol mg [dry weight] of cells(-1)). Approximately 90% of the NH(3)-dependent O(2) uptake activity and the NO(2)(-)-producing activity were lost after N. europaea was exposed to 0.44 mM MeBr for 24 h. After MeBr was removed and the cells were resuspended in fresh growth medium, NO(2)(-) production increased exponentially, and 48 to 60 h was required to reach the level of activity observed initially in control cells that were not exposed to MeBr. It is not clear what percentage of the cells were capable of cell division after MeBr oxidation because NO(2)(-) accumulated more slowly in the exposed cells than in the unexposed cells despite the fact that the latter were diluted 10-fold to create inocula which exhibited equal initial activities. The decreases in NO(2)(-)-producing and MeBr-oxidizing activities could not be attributed directly to NH(4)(+) or NH(3) limitation, to a decrease in the pH, to the composition of the incubation medium, or to toxic effects caused by accumulation of the end products of oxidation (NO(2)(-) and formaldehyde) in the medium. Additional cooxidation-related studies of N. europaea are needed to identify the mechanism(s) responsible for the MeBr-induced loss of cell activity and/or viability, to determine what percentages of cells damaged by cooxidative activities are culturable, and to determine if cooxidative activity interferes with the regulation of NH(3)-oxidizing activity.

Nitrification and autotrophic nitrifying bacteria in a hydrocarbon-polluted soil

In vitro ammonia-oxidizing bacteria are capable of oxidizing hydrocarbons incompletely. This transformation is accompanied by competitive inhibition of ammonia monooxygenase, the first key enzyme in nitrification. The effect of hydrocarbon pollution on soil nitrification was examined in situ. In a microcosm study, adding diesel fuel hydrocarbon to an uncontaminated soil (agricultural unfertilized soil) treated with ammonium sulfate dramatically reduced the amount of KCl-extractable nitrate but stimulated ammonium consumption. In a soil with long history of pollution that was treated with ammonium sulfate, 90% of the ammonium was transformed into nitrate after 3 weeks of incubation. Nitrate production was twofold higher in the contaminated soil than in the agricultural soil to which hydrocarbon was not added. To assess if ammonia-oxidizing bacteria acquired resistance to inhibition by hydrocarbon, the contaminated soil was reexposed to diesel fuel. Ammonium consumption was not affected, but nitrate production was 30% lower than nitrate production in the absence of hydrocarbon. The apparent reduction in nitrification resulted from immobilization of ammonium by hydrocarbon-stimulated microbial activity. These results indicated that the hydrocarbon inhibited nitrification in the noncontaminated soil (agricultural soil) and that ammonia-oxidizing bacteria in the polluted soil acquired resistance to inhibition by the hydrocarbon, possibly by increasing the affinity of nitrifying bacteria for ammonium in the soil.

Kinetic characterization of the inactivation of ammonia monooxygenase in Nitrosomonas europaea by alkyne, aniline and cyclopropane derivatives

The kinetic mechanisms of seven inactivators of ammonia oxidation activity in cells of the nitrifying bacterium, Nitrosomonas europaea were investigated. The effects of the inactivators were specific for ammonia monooxygenase (AMO) which oxidizes ammonia to hydroxylamine. The aniline derivatives, 1,3-phenylenediamine and p-anisidine, were potent inactivators of AMO while other derivatives were ineffective as inactivators. Two cyclopropane derivatives, 1, 2-dimethylcyclopropane and cyclopropyl bromide, were inactivators while cyclopropane was not an inactivator. The mechanisms of three alkynes, 1-hexyne, 3-hexyne, and acetylene, were also examined. For all seven compounds, the inactivation of AMO was irreversible, time-dependent, first-order, and dependent on catalytic turnover. Saturation of the rate of inactivation was indicated for p-anisidine (kinact=2.85 min-1; KI=1.0 mM) and cyclopropyl bromide (kinact=4.4 min-1; KI=97 microM), but not for any of the remaining five inactivators, including acetylene. Ammonia slowed the rate of inactivation for acetylene and cyclopropyl bromide, but enhanced the rate of inactivation for the remaining inactivators. All seven compounds appear to be mechanism-based inactivators of AMO.

A bioluminescence assay using Nitrosomonas europaea for rapid and sensitive detection of nitrification inhibitors

An expression vector for the luxAB genes, derived from Vibrio harveyi, was introduced into Nitrosomonas europaea. Although the recombinant strain produced bioluminescence due to the expression of the luxAB genes under normal growing conditions, the intensity of the light emission decreased immediately, in a time-and dose-dependent manner, with the addition of ammonia monooxygenase inhibitors, such as allylthiourea, phenol, and nitrapyrin. When whole cells were challenged with several nitrification inhibitors and toxic compounds, a close relationship was found between the change in the intensity of the light emission and the level of ammonia-oxidizing activity. The response of bioluminescence to the addition of allylthiourea was considerably faster than the change in the ammonia-oxidizing rate, measured as both the O2 uptake and NO2- production rates. The bioluminescence of cells inactivated by ammonia monooxygenase inhibitor was recovered rapidly by the addition of certain substrates for hydroxylamine oxidoreductase. These results suggested that the inhibition of bioluminescence was caused by the immediate decrease of reducing power in the cell due to the inactivation of ammonia monooxygenase, as well as by the destruction of other cellular metabolic pathways. We conclude that the assay system using luminous Nitrosomonas can be applied as a rapid and sensitive detection test for nitrification inhibitors, and it will be used to monitor the nitrification process in wastewater treatment plants.

Cloning, nucleotide sequence, and regulatory analysis of the Nitrosomonas europaea dnaK gene

The dnaK gene of an ammonia-oxidizing bacterium, Nitrosomonas europaea, was cloned and sequenced. It was found that the dnaK gene product was highly homologous to previously analyzed dnaK gene products from other organisms at the amino acid level. Two partial open reading frames located upstream and downstream of the dnaK gene were also found and identified as grpE and dnaJ genes, respectively, by the predicted amino acid homology of their gene products to other bacterial GrpE and DnaJ proteins. Transcription of the dnaK gene was strongly induced by a heat shock from 30 to 37 degrees C. An analysis of the expression of the dnaK gene fused to the lacZ translational reporter gene also showed eightfold increase in beta-galactosidase activity after the heat shock induction. Heat-inducible transcription start sites of the dnaK gene, revealed by primer extension analysis, were located 16 and 17 nucleotides upstream from the translational start codon of the dnaK gene, and the predicted promoter sequence showed a homology to the consensus sequence of sigma 32-dependent heat shock promoters of gram-negative bacteria. The upstream region of the dnaK gene did not contain the inverted repeat structure that was involved in the regulation of the heat shock gene of several gram-negative and gram-positive bacteria. Therefore, we conclude that the heat shock regulatory mechanism of the N. europaea dnaK gene may be similar to the sigma 32-dependent mechanism observed in other gram-negative bacteria.

Evidence for an iron center in the ammonia monooxygenase from Nitrosomonas europaea

Binding of the ligand, nitric oxide, in the presence of reductant was used to identify a ferrous S = 3/2 signal, characteristic of a ferrous nitrosyl complex, and a g= 2.03 copper or iron signal in membranes of the ammonia-oxidizing bacterium, Nitrosomonas europaea. The same ferrous S = 3/2 signal is thought to be a component of the membrane-associated methane monooxygenase (pMMO) of Methylococcus capsulatus Bath, since it is seen in the membrane fraction of cells expressing pMMO and in the purified enzyme, but not in the membrane fraction of cells expressing the soluble MMO [Zahn, J.A. and DiSpirito, A.A. (1996) J. Bacteriol. 178, 1018-1029]. Treatment of resting membranes or cells of N. europaea with nitrapyrin, 2-chloro,6-trichloromethylpyridine, resulted in the increase in magnitude of a g = 6, high-spin ferric iron signal. In the presence of NO and reductant, nitrapyrin prevented the formation of the S = 3/2 nitrosyl-iron complex while increasing the intensity of the g = 6 signal. Nitrapyrin is a specific inhibitor of, and is reduced by, the ammonia monoxygenase (AMO) [Bédard, C. and Knowles, R. (1989) Microbiol. Rev. 53, 68-83]. Taken together the data suggest that iron capable of forming the S = 3/2 complex is a catalytic component of AMO of N. europaea, possibly a part of the oxygen-activating center. Inactivation of the membrane-associated AMO with acetylene did not diminish the S = 3/2 nitrosyl-iron signal, the g = 6 signal, or the g = 6 signal.

Reductive dehalogenation of the trichloromethyl group of nitrapyrin by the ammonia-oxidizing bacterium Nitrosomonas europaea

Suspensions of Nitrosomonas europaea catalyzed the reductive dehalogenation of the commercial nitrification inhibitor nitrapyrin (2-chloro-6-trichloromethylpyridine). The product of the reaction was identified as 2-chloro-6-dichloromethylpyridine by its mass fragmentation and nuclear magnetic resonance spectra. A small amount of 2-chloro-6-dichloromethylpyridine accumulated during the conversion of nitrapyrin to 6-chloropicolinic acid in an aerated solution in the presence of ammonia (T. Vannelli and A.B. Hooper, Appl. Environ. Microbiol. 58:2321-2325, 1992). Nearly stoichiometric conversion of nitrapyrin to 2-chloro-6-dichloromethylpyridine occurred at very low oxygen concentrations and in the presence of hydrazine as a source of electrons. Under these conditions the turnover rate was 0.37 nmol of nitrapyrin per min per mg of protein. Two specific inhibitors of ammonia oxidation, acetylene and allylthiourea, inhibited the rate of the dehalogenation reaction by 80 and 84%, respectively. In the presence of D2O, all 2-chloro-6-dichloromethylpyridine produced in the reaction was deuterated at the methyl position. In an oxygenated solution and in the presence of ammonia or hydrazine, cells did not catalyze the oxidation of exogenously added 2-chloro-6-dichloromethylpyridine to 6-chloropicolinic acid. Thus, 2-chloro-6-dichloromethylpyridine is apparently not an intermediate in the aerobic production of 6-chloropicolinic acid from nitrapyrin.

Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea

Nitrosomonas europaea, a chemolithotrophic bacterium, was found to contain two copies of the gene coding for the presumed active site polypeptide of ammonia monooxygenase, the 32-kDa acetylene-binding polypeptide. One copy of this gene was cloned, and its complete nucleotide sequence is presented. Immediately downstream of this gene, in the same operon, is the gene for a 40-kDa polypeptide that copurifies with the ammonia monooxygenase acetylene-binding polypeptide. The sequence of the first 692 nucleotides of this structural gene, coding for about two-thirds of the protein, is presented. These sequences are the first sequences of protein-encoding genes from an ammonia-oxidizing autotrophic nitrifying bacterium. The two protein sequences are not homologous with the sequences of any other monooxygenase. From radioactive labelling of ammonia monooxygenase with [14C]acetylene it was determined that there are 23 nmol of ammonia monooxygenase per g of cells. The kcat of ammonia monooxygenase for NH3 in vivo was calculated to be 20 s-1.