Challenges in using allylthiourea and chlorate as specific nitrification inhibitors

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

Introduction

Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study.

Methods

The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing.

Results and Discussion

The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process

Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.

Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil

Anthropogenic nitrogen inputs lead to a high ammonium (NH4+)/nitrate (NO3-) ratio in the soil, which restricts hyphal spreading of soil fungi. Access of symbiotic fungi to roots is a prerequisite for plant-fungal interactions. Hyphosphere bacteria protect fungi from environmental stress, yet the impact of hyphosphere bacteria on adaptation of host fungi to NH4+-enriched conditions remains unclear. By developing soil microcosm assays, we report that a plant-symbiotic fungus, Phomopsis liquidambaris, harbors specific hyphosphere bacteria that facilitate hyphal spreading and assist in the root colonization in NH4+-enriched soil. Genetic manipulation, 16S rRNA gene analysis and coinoculation assays revealed that the genus Enterobacter was enriched in the hyphosphere of NH4+-sensitive wild-type compared to NH4+-preferring nitrite reductase-deficient strain. The representative Enterobacter sp. SZ2-promoted hyphal spreading is only evident in nonsterilized soil. We further identified an increased abundance and diversity of ammonia-oxidizing archaea (AOA) and a synchronously decreased NH4+:NO3- ratio following SZ2 inoculation. Microbial supplementation and inhibitor assays showed that AOA-mediated reduction in NH4+:NO3- ratio is responsible for SZ2-enhanced fungal adaptation to NH4+-enriched conditions. The Ph. liquidambaris-Enterobacter-AOA triple interaction promoted rice growth in NH4+-enriched soil. Our study reveals the essential role of hyphosphere microorganism-based hyphal spreading in plant-fungal symbiosis establishment within nitrogen-affected agroecosystems.

Differential contribution of nitrifying prokaryotes to groundwater nitrification

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

Investigation of the effect of nitrification inhibition on the performance and effluent quality of aerobic sequential batch reactors

The use of nitrification inhibition as a concentrating step for ammonium (NH₄⁺), for the purpose of increasing the potential for simultaneous recovery of phosphate (PO₄^3-) and NH₄⁺ from effluent streams of an aerobic sequencing batch reactor (SBR) system, has never been investigated in the literature. Therefore, the present study aimed to determine the effect of the inhibition of nitrification on both the reactor performance and effluent quality in a laboratory scale aerobic SBR system. In order to compare the observed results, a separate reactor, where the inhibition was not applied, was operated as a control reactor (CR) under the identical operational conditions used for the inhibitory reactor (IR). Experimental results for the reactor performance showed that effluents with low total suspended solids (< 50 mg/L) and chemical oxygen demand concentrations (> 90% of removal efficiency based on the influent concentration of 500 mg/L) were achieved for both SBRs by obtaining an activated sludge with a sludge volume index < 60 mL/g after the acclimation period. In the same period, the effluent PO₄^3-, NH₄⁺, and nitrate (NO₃^-) concentrations were found to be 17.0 ± 4.0, 1.26 ± 0.84, and 21.5 ± 39 mg/L for the CR and 10.0 ± 4.4, 3.9 ± 2.4, and 9.2 ± 1.5 mg/L for the IR, respectively. During this period, 94% of the removed NH₄⁺ (NH₄⁺_rem.) was converted to NO₃^- in the CR, indicating almost complete nitrification occurred in the reactor. However, only 47% of the NH₄⁺_rem. was converted to NO₃^- in the IR as a result of the inhibition of nitrification, meaning a partial inhibition (53%) occurred due to the inhibition treatment. These results clearly demonstrated that the inhibition of nitrification allowed the effluent NH₄⁺ concentrations to increase by suppressing the formation of NO₃^- ions. Based on the results, it can be concluded that inhibition of nitrification in an aerobic SBR system creates a potential for conserving the effluent NH₄⁺ concentration and increasing consecutive recovery of PO₄^3- together with NH₄⁺ from the effluent discharges.

Rapid detection of nitrite based on nitrite-oxidizing bacteria biosensor and its application in surface water monitoring

Timely and sensitive detection of nitrite is of great significance for human health protection and water pollution treatment. However, many biosensors can only determine the comprehensive toxicity of the water, and there are few electroactive biofilm (EAB) sensors for the specific detection of pollutants. Biofilms formed by bacteria with specific functions can improve the specificity of nitrite identification by biosensors. This study developed a novel, rapidly responding, high sensitivity (958.6 μAμM^-1cm^-2), wide detection range and anti-interference electrochemical biosensor based on electroactive nitrite-oxidizing bacteria. The biosensor could accurately detect nitrite in the range of 0.3-100 mg/L within 3 min by the cyclic voltammetry (CV) method. The bioelectrode could perform stable detection of nitrite over 200 cycles. The specificity of the biosensor for detecting nitrite was demonstrated by the presence of nitrite oxidizing bacteria (NOB) and nitrite oxidase enzyme (NXR) on the electrode biofilm. The biosensor performed well in wetlands and rivers, with an RSD <14.8% in the detection of nitrite at low concentrations, and further revealed the nitrification occurrence. Our study provided a feasible way for the development of a highly sensitive, rapidly responding and stable electrochemical biosensor, which also exhibited potential applications for long-term detection of nitrite and assessment of ecological function in surface water (rivers, lakes, wetlands, marshes, etc.).

Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N₂O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.

Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems

Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.

The first comprehensive study evaluating the ecotoxicity and biodegradability of water-soluble polymers used in personal care products and cosmetics

Water-soluble polymers (WSPs) are organic materials that have been used for decades in various applications as part of paints, coatings, adhesives, washing agents, pharmaceuticals, personal care products and cosmetics. However, their ecotoxicity, biodegradability, and overall impact on the environment are still unknown. In this study four polyacrylic acid- based WSPs (three in the solid state and one in the liquid state), which are widely used in cosmetic industry, were tested in terms of their ecotoxicity and biodegradability. The ecotoxicity tests were performed using aquatic plant Lemna minor, microalga Pseudokirchneriella subcapitata, crustacean Daphnia magna, bacterium Allivibrio fischeri, and a mixed bacterial culture of activated sludge (with heterotrophic and nitrifying microorganisms tested separately). All four WSPs had low or moderate effects on the tested organisms at several endpoints. However, the liquid WSP had a specific toxic effect on the bioluminescence of Allivibrio fischeri and the oxygen consumption of nitrifying microorganisms - 100 mg/L caused 73% and 88% inhibition, respectively. Therefore, some WSPs capable of inhibiting nitrifying microorganisms could have implications for the nitrification process in wastewater treatment plants and aquatic ecosystems, despite 100 mg/L being a high tested concentration and probably difficult to reach in wastewater. All investigated WSPs were not biodegradable; therefore, their persistence in the environment could be expected.

Evaluating acute toxicity in enriched nitrifying cultures: Lessons learned

Toxicological batch assays are essential to assess a compound's acute effect on microorganisms. This methodology is frequently employed to evaluate the effect of contaminants in sensitive microbial communities from wastewater treatment plants (WWTPs), such as autotrophic nitrifying populations. However, despite nitrifying batch assays being commonly mentioned in the literature, their experimental design criteria are rarely reported or overlooked. Here, we found that slight deviations in culture preparations and conditions impacted bacterial community performance and could skew assay results. From pre-experimental trials and experience, we determined how mishandling and treatment of cultures could affect nitrification activity. While media and biomass preparations are needed to establish baseline conditions (e.g., biomass washing), we found extensive centrifugation selectively destabilised nitrification activities. Further, it is paramount that the air supply is adjusted to minimise nitrite build-up in the culture and maintain suitable aeration levels without sparging ammonia. DMSO and acetone up to 0.03% (v/v) were suitable organic solvents with minimal impact on nitrification activity. In the nitrification assays with allylthiourea (ATU), dilute cultures exhibited more significant inhibition than concentrated cultures. So there were biomass-related effects; however, these differences minimally impacted the EC₅₀ values. Using different nutrient-media compositions had a minimal effect; however, switching mineral media for the toxicity test from the original cultivation media is not recommended because it reduced the original biomass nitrification capacity. Our results demonstrated that these factors substantially impact the performance of the nitrifying inoculum used in acute bioassays, and consequently, affect the response of AOB-NOB populations during the toxicant exposure. These are not highlighted in operation standards, and unfortunately, they can have significant consequential impacts on the determinations of toxicological endpoints. Moreover, the practical procedures tested here could support other authors in developing testing methodologies, adding quality checks in the experimental framework with minimal waste of time and resources.

Combined liquid phase microextraction and fiber-optics-based cuvetteless micro-spectrophotometry for sensitive determination of ammonia in water and food samples by the indophenol reaction

The Berthelot reaction for ammonia is revisited with the aim of miniaturization and addressing interferences as encountered with food and water samples. Headspace single drop microextraction of ammonia in phosphoric acid served to attain selectivity in complex matrices, and liquid-liquid microextraction of red or blue indophenol species into 1-octanol-isooctane (60:40, v/v) resulted into high sensitivity. Fiber-optics-based cuvetteless micro-spectrophotometry has been used for colorimetric determination on microliter volumes of extract. The linear dynamic range, limit of detection and enrichment factor have been found to be 0.2-3 mg kg^-1, 0.14 mg kg^-1 and 38, respectively, measuring red species for milk, cheese and beer (4.9-5.5% error; 4.8-6.3% RSD; n = 5); and 5-400 µg L^-1, 0.4 µg L^-1 and 137, respectively, measuring blue species for water samples (3.3-5.7% error; 3.6-6.8% RSD; n = 5). A plausible reaction scheme has been proposed for nitroprusside catalysis in indophenol reaction.

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.

DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH₄ ⁺ or NO₂ ^- in the presence of ¹³C-HCO₃ ^- (labeled) or ¹²C-HCO₃ ^- (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO₃ ^- uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H₁₃CO₃ ^- uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.

Determination of optimal dose of allylthiourea (ATU) for the batch respirometric test of activated sludge

Allylthiourea is a known specific inhibitor for ammonium oxidiser to suppress its oxygen uptake, and is commonly used for various kinds of batch respirometric tests to detect heterotrophic respiration in activated sludge. However, when high heterotrophs were present in the sample, it appeared the inhibitor was noticeably degraded and reached below the inhibition threshold after a couple of days, which resulted in overestimation of the heterotrophic respiration. The biological decomposition of the inhibitor was expressed with a Monod-type rate expression having a half-saturation coefficient of 980 mg-COD/L and maximum specific growth rate of 1.0 d^-1. The developed kinetic model, including the growth and decay of the heterotrophs and nitrifiers, indicated that the ATU with about 90 mg-ATU/L which was initially dosed to the system would reach below the inhibition threshold of 1.0 mg-ATU/L after 10 days when 750 mg-COD/L of heterotrophs were present. From the kinetic model, an empirical formula to calculate a safe minimum ATU dose for the batch respirometric test was elaborated. The model also provided a modified experimental procedure to accurately estimate the initial heterotrophic biomass concentration in the sample and its specific decay rate based on IWA Activated Sludge Models.

Characterization and Local Emission Sources for Ammonia in an Urban Environment

Ammonia levels were evaluated in the urban environment of Madrid City, Spain. A total of 110 samplers were distributed throughout the city. Vehicle traffic density, garbage containers and sewers were identified as local emission sources of ammonia. The average ammonia concentrations were 4.66 ± 2.14 µg/m³ (0.39-11.23 µg/m³ range) in the winter and 5.30 ± 1.81 µg/m³ (2.33-11.08 µg/m³ range) in the summer. Spatial and seasonal variations of ammonia levels were evaluated. Hotspots were located in the south and center of Madrid City in both winter and summer seasons, with lower ammonia concentrations located in the north (winter) and in the west and east (summer). The number of representative points that were needed to establish a reliable air quality monitoring network for ammonia was determined using a combined clustering and kriging approach. The results indicated that 40 samplers were sufficient to provide a reliable estimate for Madrid City.