Rapid start-up of partial nitrification reactor by exogenous AHLs and Vanillin combined with intermittent aeration.

Quorum sensing (QS) and quorum quenching (QQ) are common phenomena in microbial systems and play an important role in the nitrification process. However, rapidly start up partial nitrification regulated by N-acyl-homoserine lactones (AHLs)-mediated QS or QQ has not been reported. Hence, we chose N-butyryl homoserine lactone (C4-HSL) and N-hexanoyl homoserine lactone (C6-HSL) as the representative AHLs, and Vanillin as the representative quorum sensing inhibitor (QSI) combined intermittent aeration to investigate their effects on the start-up process of partial nitrification. The start-up speed in the group with C4-HSL or C6-HSL addition was 1.42 or 1.26 times faster than that without addition, respectively. Meanwhile, the ammonium removal efficiency with C4-HSL or C6-HSL addition was increased by 13.87 % and 17.30 % than that of the control group, respectively. And, partial nitrification could maintain for a certain period without AHLs further addition. The increase of Nitrosomonas abundance and ammonia monooxygenase (AMO) activity, and the decrease of Nitrobacter abundance and nitrite oxidoreductase (NXR) activity were the reasons for the rapid start-up of partial nitrification in the AHLs groups. Vanillin addition reduced AMO and hydroxylamine oxidoreductase (HAO) activity, and increased Nitrobacter abundance and NXR activity, thus these were not conducive to achieving partial nitrification. Denitrifying bacteria (Hydrogenophaga, Thauera and Aquimonas) abundance increased in the Vanillin group. QS-related bacteria and gene abundance were elevated in the AHLs group, and reduced in the Vanillin group. Function prediction demonstrated that AHLs promoted the nitrogen cycle while Vanillin enhanced the carbon cycle. This exploration might provide a new technical insight into the rapid start-up of partial nitrification based on QS control.

Interrogating nitritation at a molecular level: Understanding the potential influence of Nitrobacter spp.

Water resource recovery facilities (WRRFs) increasingly must maximize nitrogen and phosphorus removal, but concurrently face challenges to reduce their energy usage and environmental footprint. In particular, biological nutrient removal (BNR), which targets removal of phosphorus and nitrogen, exhibits a large energy demand. However, a BNR process achieving partial oxidation of NH3 to NO2 (nitritation) could reduce energy demands, with secondary environmental emission benefits. Research was conducted on bench-scale systems performing nitritation and nitrification to better understand how mixed microbial consortia, cultured on real wastewater, can sustain nitritation. BNR configurations achieved nitrite accumulation ratios of 64-82%, with excellent overall effluent quality. Applying phylogenetic, transcriptomic, and metabolomic methods, coupled with process monitoring, results indicate that partial nitritation may be induced through a combination of: (1) Employing ammonia-based aeration control, with an ammonia setpoint of 2, 3 mgN/L; (2) Maintaining an aerobic period DO of 1.0-2.0 mg/L; and (3) Operating BNR post-anoxically, integrated within enhanced biological phosphorus removal (EBPR). Significant nitritation was achieved despite the presence Nitrobacter spp., but nitrite oxidoreductase must be functionally impaired or structurally incomplete. Overall, this research demonstrated the value of interrogating a mixed microbial consortia at a macro and molecular level to explore unique metabolic responses such as nitritation.

The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.

Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.

Comparison of degradation kinetics of tannery wastewater treatment using a nonlinear model by salt-tolerant Nitrosomonas sp. and Nitrobacter sp.

Conventional biological treatment has been reported to be ineffective for pollutant removal in tannery wastewater due to high salinity. To overcome it, this work used salt-tolerant bacteria (STB) isolated from a membrane bioreactor to evaluate the organic and nutrient removal through a series of batch experiments. Compared with the control, the STB reactor enhanced the reduction of persistent organics by 11% based on the double exponential decay model. Besides, the removal of NH4+-N is 26% higher, satisfying the first-order decay model. The nitrification was inhibited entirely in control during 48 h, whilst the assimilation process involved 55% of total nitrogen removal. In the STB reactor, nitrification occurred after 12 h, resulting in significantly increased NO2--N and NO3--N concentrations according to the logistic function. Although nitrification was successfully activated, C/N ratios and free ammonia were identified as limiting factors for STB activity, requiring mitigation strategies in further studies.

Response of substrate kinetics and biological mechanisms to various pH constrains for cultured Nitrobacter and Nitrospira in nitrifying bioreactor.

Nitrite (NO2-) oxidation is an essential step of biological nitrogen cycling in natural ecosystems, and is performed by chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Although Nitrobacter and Nitrospira are regarded as representative NOB in nitrification systems, little attention has focused on kinetic characterisation of the coexistence of Nitrobacter and Nitrospira at various pH values. Here, we evaluate the substrate kinetics, biological mechanism and microbial community dynamics of an enrichment culture including Nitrobacter (17.5 ± 0.9%) and Nitrospira (7.2 ± 0.6%) in response to various pH constrains. Evaluation of the Monod equation at pH 6.0, 6.5, 7.0, 7.5, 8.0 and 8.5 showed that the enrichment had maximum rate (rmax) and maximum substrate affinity (KS) for NO2- oxidation at pH 7.0, which was also supported by the largest absolute abundance of Nitrobacter nxrA (5.26 × 107 copies per g wet sludge) and Nitrospira nxrB (1.975 × 109 copies per g wet sludge) genes. Moreover, the predominant species for the Nitrobacter-like nxrA were N. vulgaris and N. winogradskyi, while for the Nitrospira-like nxrB, the predominant species were N. japonica, N. calida and Ca. N. bockiana. Furthermore, the rmax was strongly and positively correlated with the abundance of the Nitrobacter nxrA or Nitrospira nxrB genes, or N. winogradsk, whereas KS was positively correlated with the abundance of Nitrobacter nxrA or Nitrospira nxrB genes or Ca. N. bockiana. Overall, this study could improve basis kinetic parameters and biological mechanism of NO2- oxidation in WWTPs.

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.

Pharmaceuticals and personal care products' (PPCPs) impact on enriched nitrifying cultures.

The impact of pharmaceutical and personal care products (PPCPs) on the performance of biological wastewater treatment plants (WWTPs) has been widely studied using whole-community approaches. These contaminants affect the capacity of microbial communities to transform nutrients; however, most have neither honed their examination on the nitrifying communities directly nor considered the impact on individual populations. In this study, six PPCPs commonly found in WWTPs, including a stimulant (caffeine), an antimicrobial agent (triclosan), an insect repellent ingredient (N,N-diethyl-m-toluamide (DEET)) and antibiotics (ampicillin, colistin and ofloxacin), were selected to assess their short-term toxic effect on enriched nitrifying cultures: Nitrosomonas sp. and Nitrobacter sp. The results showed that triclosan exhibited the greatest inhibition on nitrification with EC50 of 89.1 µg L-1. From the selected antibiotics, colistin significantly affected the overall nitrification with the lowest EC50 of 1 mg L-1, and a more pronounced inhibitory effect on ammonia-oxidizing bacteria (AOB) compared to nitrite-oxidizing bacteria (NOB). The EC50 of ampicillin and ofloxacin was 23.7 and 12.7 mg L-1, respectively. Additionally, experimental data suggested that nitrifying bacteria were insensitive to the presence of caffeine. In the case of DEET, moderate inhibition of nitrification (<40%) was observed at 10 mg L-1. These findings contribute to the understanding of the response of nitrifying communities in presence of PPCPs, which play an essential role in biological nitrification in WWTPs. Knowing specific community responses helps develop mitigation measures to improve system resilience.

Community assembly mechanisms and co-occurrence patterns of nitrite-oxidizing bacteria communities in saline soils.

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification by oxidizing nitrite to nitrate, which is a key process in the biogeochemical nitrogen cycling. However, little is known about the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. Here, we explored the effects of salinity on Nitrobacter and Nitrospira community using high-throughput sequencing and multivariate statistical analyses. Our results showed that high salinity significantly inhibited the nitrite oxidation rates and decreased the abundance of Nitrobacter and Nitrospira. Extreme salty conditions significantly altered the diversity and composition of Nitrospira community but had little effect on Nitrobacter community. Nitrobacter network in high salinity soils was more closely connected while the connectivity of Nitrospira network became weak. Nitrobacter and Nitrospira community exhibited distinct assembly processes at different salinity levels. Stochastic processes were dominant in the Nitrobacter community assembly in both low and high salinity soils. Interestingly, the assembly of Nitrospira community was governed by stochastic and deterministic processes in low and high salinity soils, respectively. To our knowledge, our study provides the first description of the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. These results can help us understand the NOB ecological roles and improve the nitrite oxidation activity in a high salinity environment.

Immobilization of nitrifying bacteria on composite based on polymers and eggshells for nitrate production.

Nitrification is a key step in biological nitrogen transformation which depends on the performance of specialized microorganisms. Generally, nitrifying bacteria present a low growth rate and performance which can be improved when immobilized as a biofilm. The development of new materials suitable for the immobilization of nitrifying microorganisms is very important in nitrification and wastewater treatment. In this study, the effect of eggshell powder on biofilm formation by Nitrosomonas europaea an ammonium-oxidizing bacteria and Nitrobacter vulgaris a nitrite-oxidizing bacteria, on new polymeric supports were analyzed. Polylactic acid, polyvinyl chloride and polystyrene were tested to produce polymer-eggshells powder composites and used as biofilm supports for nitrifying bacteria. The support material was characterized to identify the most suitable polymer-eggshells powder combination for the cell adhesion and biofilm formation. The nitrification results showed a highest nitrate production of 42 mg NO3--N/L with polylactic acid-eggshell composite, with the best surface properties for cellular adhesion. Finally, scanning electron microscopy micrographs confirmed the best biofilm formed on polylactic acid-eggshell.

Response of activity and community composition of nitrite-oxidizing bacteria to partial substitution of chemical fertilizer by organic fertilizer.

Nitrite oxidation as the second step of nitrification can become the determining step in disturbed soil systems. As a beneficial fertilization practice to maintain high crop yield and soil fertility, partial substitution of chemical fertilizer (CF) by organic fertilizer (OF) may exert a notable disturbance to soil systems. However, how nitrite oxidation responds to different proportions of CF to OF is still unclear. We sampled soils from a 4-year field experiment subject to a gradient of increasing proportions of OF to CF application. Activity, size, and structure of Nitrospira-like and Nitrobacter-like nitrite-oxidizing bacteria (NOB) community were measured. The results revealed that with increasing proportion of OF to CF application, potential nitrite oxidation activity (PNO) showed a marked decreasing trend. PNO was significantly correlated with the abundance of Nitrobacter-like but not Nitrospira-like NOB. The abundance of Nitrobacter-like was significantly influenced by soil organic matter, organic nitrogen (N), and available N. In addition, PNO was also affected by the structure of Nitrobacter-like NOB. The relative abundance of Nitrobacter hamburgensis, alkalicus, winogradskyi, and vulgaris responded differently to the proportions of OF to CF application. Organic N, organic matter, and available N were the main factor shaping their community structure. Overall, Nitrobacter-like NOB is more sensitive and plays a more important role than Nitrospira-like NOB in responding to different proportions of OF to CF application.

Robust Nitritation of Anaerobic Digester Centrate Using Dual Stressors and Timed Alkali Additions.

Nitrogen is commonly removed from wastewater by nitrification to nitrate followed by nitrate reduction to N2. Shortcut N removal saves energy by limiting ammonia oxidation to nitrite, but nitrite accumulation can be unstable. We hypothesized that repeated short-term exposures of ammonia-oxidizing communities to free ammonia (FA) and free nitrous acid (FNA) would stabilize nitritation by selecting against nitrite-oxidizing bacteria (NOB). Accordingly, we evaluated ammonium oxidation of anaerobic digester centrate in two bench-scale sequencing batch reactors (SBRs), seeded with the same inoculum and operated identically but with differing pH-control strategies. A single stressor SBR (SS/SBR) using pH set-point control produced HNO3, while a dual stressor SBR (DS/SBR) using timed alkalinity addition (TAA) produced HNO2 (ammonium removal efficiency of 97 ± 2%; nitrite accumulation ratio of 98 ± 1%). The TAA protocol was developed during an adaptation period with continuous pH monitoring. After adaptation, automated TAA enabled stable nitritation without set-point control. In the SS/SBR, repeatedly exposing the community to FA (8-10 h/exposure, one exposure/cycle) selected for FA-tolerant ammonia-oxidizing bacteria (Nitrosomonas sp. NM107) and NOB (Nitrobacter sp.). In the DS/SBR, repeatedly exposing the community to FA (2-4 h/exposure, three exposures/cycle) and FNA (4-6 h/exposure, two exposures/cycle) selected for FA- and FNA-resistant AOB (Nitrosomonas IWT514) and against NOB, stabilizing nitritation.

Nitratation in pilot-scale bioreactors fed with effluent from a submerged biological aerated filter used in the treatment of dog wastewater.

Nitrification is a biochemical process that allows oxidation of ammonium ion to nitrite, and nitrite to nitrate in a system. Aerobic processes, such as use of submerged biological aerated filter (SBAF), enable nitrification. However, some variables that are entirely unavailable or not available at the required concentration range may hamper the process. In this study, nitratation under high dissolved oxygen (DO) concentrations was evaluated in laboratory-scale bioreactors containing 10% inoculum (0.5 kg kg-1) fed with affluent from a SBAF that receive the sewage generated from washing the bays of a dog kennel. The following variables were monitored over time: ammoniacal nitrogen (12.44-29.62 mg L-1), nitrite (0.28-0.54 mg L-1), nitrate (1.75-3.55 mg L-1), pH (8.11 ± 0.62), temperature (21.61 ± 1.24°C) and DO (9.69 ± 0.36 mg L-1). Quantification of nitrifying bacteria by the multiple tube technique showed the value of 1.4 × 1012 MPN mL-1for ammonia-oxidizing bacteria (AOB) and 9.2 × 1014 MPN mL-1 for nitrite-oxidizing bacteria. These values were higher than those found in a synthetic medium, which can be explained by the greater availability of ammonium and nitrite in the effluent. By the extraction of genomic DNA, and PCR, with specific primers, the presence of the AmoA (Ammonia monooxygenase) gene for AOB and of the Nitrobacter was detected in the bioreactor samples. By PCR-DGGE, the sequenced bands showed high similarity with denitrifying bacteria, such as Pseudomonas, Limnobacter, Thauera, Rhodococcus, and Thiobacillus. Thus, the saturation of dissolved oxygen in the system resulted in improvement in the nitratation step and allowed detection of bacterial genera involved in the process.

Beneficiary of nitrifying bacteria for enhancing lettuce (Lactuca sativa) and vetiver grass (Chrysopogon zizanioides L.) growths align with carp (Cyprinus carpio) cultivation in an aquaponic system.

The aquaponic system is an alternative strategy to treat aquaculture waste and achieve food independence. Bacteria play vital roles in the aquaponic system as they can transform ammonia or ammonium into nitrite and then into nitrate, which is more favorable for bacteria, fish, and plants. The objective of this study was to determine the effect of nitrifying bacteria (Nitrosomonas europaea Winogradsky and Nitrobacter winogradskyi Winslow) on the aquaponic system in terms of water quality, nutrient availability, and productivity of carp (Cyprinus carpio), lettuce (Lactuca sativa var. crispa), and vetiver grass (Chrysopogon zizanioides L.). The experiment consisted of four treatments: aquaculture of carp as a control for fish (A), hydroponic of lettuce and vetiver grass without nutrient addition as a control for plants (B), aquaponic (carp, lettuce, vetiver grass) (C), and aquaponic with nitrifying bacteria addition (D). The results showed nitrifying bacteria addition had a significant effect on daily growth rate (DGR) and relative growth rate (RGR) of lettuce within a treatment; on the other hand, the nitrifying bacteria did not give a significant effect to RGR of vetiver grass. The growth rate, specific growth rate, and survival rate of the carp in aquaculture treatment (A) were lower than in both aquaponic treatments (C and D). Nitrifying bacteria addition in the aquaponics system had a significant effect of increasing the orthophosphate concentration. Water quality was also indicated to be better in the aquaponic system than in the aquaculture system. The integration of aquaculture and hydroponics with the addition of nitrifying bacteria enables the formation of microorganism communities, nitrate, and orthophosphate, which lead to the improvement of water quality, nutrient availability, and plant growth.

Insight into functionally active bacteria in nitrification following Na+ and Mg2+ exposure based on 16S rDNA and 16S rRNA sequencing.

Despite increasing interests in osmotic membrane bioreactors, the information regarding the bacterial toxicity effects of reversely transported draw solute (RTDS) is limited. In this study, two representative draw solutes (NaCl and MgCl2) were used at different concentrations (0, 2.5, 5.0, 7.5 and 10.0 g/L) to evaluate their toxicity in a continuous nitrifying bioreactor. Notably, Mg2+ selectively inhibited the activity of ammonia-oxidizing bacteria (AOB), which decreased to 11.3% at 7.5 g-Mg2+/L. The rRNA-based analysis was more effective than the rDNA-based analysis to elucidate the relationship between active communities of nitrifying bacteria and the actual nitrifying performance. Nitrosomonas europaea, a representative AOB, was vulnerable to Mg2+ in comparison to Na+. In contrast, the dominant nitrite-oxidizing bacteria (NOB), Nitrobacter winogradskyi and Nitrolancea hollandica, maintained a relevant level of relative abundance for achieving nitrite oxidation after exposure to 10 g/L Na+ and Mg2+. This fundamental inhibition information of the draw solute can be applied to set the operational regime preventing the critical solute concentration in mixed liquor of nitrifying OMBRs.

Vitamin B12-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification.

Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth's climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B12) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche-for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene-Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene-Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.

[Effect of Free Hydroxylamine on the Activity of Two Typical Nitrite-oxidizing Bacteria].

The sludge from enrichment of Nitrobacter and Nitrospira was used as a research object and batch tests were performed. The inhibitory effects of hydroxylamine on Nitrobacter and Nitrospira under the same pH and different hydroxylamine concentration gradients, the same hydroxylamine concentration, and different pH gradients were investigated. The results showed that under the same pH condition, the activity of Nitrobacter decreased with increasing hydroxylamine concentration. Under the same hydroxylamine concentration (HA=5 mg·L-1) at a higher pH environment (pH ≥ 7.5), hydroxylamine produced more free hydroxylamine (FHA) and the inhibitory effect on Nitrobacter was improved. At a low pH environment (pH≤7), ionic hydroxylamine promoted the activity of Nitrobacter. The inhibitory effect of hydroxylamine on Nitrospira was limited. When pH=7.5 and hydroxylamine concentration was 45 mg·L-1, the relative activity of Nitrospira was 82%. The NOB growth rate kinetics model and the non-substrate inhibition linear equation were used to describe the effect of FHA on Nitrobacter and Nitrospira activity. The coefficient of determination R2 was 0.90 and 0.94, respectively. FHA may be the main reason for inhibiting the activity of Nitrobacter and Nitrospira.

The limited effects of carbonaceous material amendments on nitrite-oxidizing bacteria in an Alfisol.

Carbonaceous materials are soil conditioners that affect nitrogen cycles. However, how carbonaceous materials influence nitrite-oxidizing bacteria (NOB) is yet unclear. In this study, we investigated the NOB community and its potential activities under different treatments (control, biochar, straw, limestone, biochar + limestone, and straw + limestone) in an Alfisol, a type of arable soil depleted in calcium carbonate but enriched in aluminum- and iron-bearing minerals. Treatments with limestone increased soil pH, and straw inputs caused an increment of available potassium (AK). Ammonia (NH4+) was inversely changed under the straw and biochar + limestone amendments. None of the treatments significantly impacted the abundance of Nitrobacter (nxrA) or the potential nitrite oxidation activity (PNO). The abundance of Nitrospira (nxrB) increased in the biochar + limestone-treated samples and was significantly correlated with PNO, pH, and AK. High-throughput sequencing results showed that the α-diversity of NOB did not change in response to the treatments. The dominant Nitrobacter OTUs were affiliated within the Clusters 3, 4, 8, and 9 (a new cluster named in this study), while those of Nitrospira were in the lineage II and Namibian soil cluster 2. The limited compositional variation for Nitrobacter was explained by pH, and that for Nitrospira by pH, TN, and NH4+. Among all available data in this study, the richness of Nitrospira was the most important predictor (73%) for PNO. Therefore, we assumed that the community of nitrite oxidizers (Nitrospira) could be relatively redundant in function, supported by the observation that the carbonaceous inputs did not impact either the potential activity or the α-diversity but did affect the abundance and community composition.

Adaptation of nitrifying community in activated sludge to free ammonia inhibition and inactivation.

Sludge treatment using free ammonia (FA) is an innovative approach that was recently reported effective achieving stable mainstream nitrogen removal via the nitrite pathway. This study aims to investigate the adaptation of nitrifying community and the response of nitrification performance to high-level of FA exposure under real wastewater conditions. Two parallel lab-scale sequencing batch reactors were operated and fed with real municipal wastewater, with one receiving sludge treatment by FA and another as a control. While the FA approach rapidly achieved partial nitrification with a nitrite accumulation ratio (NAR) of approximately 60%, the partial nitrification eventually failed due to nitrite-oxidizing bacteria (NOB) adaptation to FA inactivation. NOB activity in the inoculum was suppressed by 82% after exposure to FA at ~220 mg NH3-N/L. However, towards the end of the experiments, significantly higher NOB activities were observed after exposure to the same level of FA. Distinct behaviours of NOB observed in batch tests during the study supported the reactor operational data and strongly suggested the adaptation of NOB under the FA stress. Furthermore, microbial community analysis revealed the underlying mechanism of the observed adaptation: the dominant NOB changed from Nitrospira to Candidatus Nitrotoga. It is for the first time shown that Ca. Nitrotoga are highly resistant to FA inhibition and inactivation in comparison to Nitrospira and Nitrobacter. In addition, while the Nitrosomonas genus was always the dominant ammonia-oxidizing bacteria (AOB) throughout the study, different shift in a species level was observed.

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.

Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations.

Some temperate tree species are associated with very low soil nitrification rates, with important implications for forest N dynamics, presumably due to their potential for biological nitrification inhibition (BNI). However, evidence for BNI in forest ecosystems is scarce so far and the nitrifier groups controlled by BNI-tree species have not been identified. Here, we evaluated how some tree species can control soil nitrification by providing direct evidence of BNI and identifying the nitrifier group(s) affected. First, by comparing 28 year-old monocultures of several tree species, we showed that nitrification rates correlated strongly with the abundance of the nitrite oxidizers Nitrobacter (50- to 1000-fold changes between tree monocultures) and only weakly with the abundance of ammonia oxidizing archaea (AOA). Second, using reciprocal transplantation of soil cores between low and high nitrification stands, we demonstrated that nitrification changed 16 months after transplantation and was correlated with changes in the abundance of Nitrobacter, not AOA. Third, extracts of litter or soil collected from the low nitrification stands of Picea abies and Abies nordmanniana inhibited the growth of Nitrobacter hamburgensis X14. Our results provide for the first time direct evidence of BNI by tree species directly affecting the abundance of Nitrobacter.