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Climate change has been intensifying soil drying and rewetting cycles, which can alter the soil microbiome structure and activity. Here we hypothesized that a soil drying-rewetting cycle enhances biodegradation and, hence, decreases the effectiveness of nitrification inhibitors (NIs). The effectiveness of DMPP (3,4-Dimethylpyrazole phosphate) and MP + TZ (3-Methylpyrazol and Triazol) was evaluated in 60-day incubation studies under a drying and rewetting cycle relative to constant low and high soil moisture conditions (40% and 80% water-holding capacity, WHC, respectively) in two different textured soils. The measurements included (i) daily and cumulative N2O-N emissions, (ii) soil NH4+-N and NO3−-N concentrations, and (iii) the composition of bacterial soil communities. Application of DMPP and MP + TZ reduced the overall N2O-N emissions under drying-rewetting (-45%), as well as under 40% WHC (-39%) and 80% WHC (-25%). DMPP retarded nitrification and decreased N2O-N release from the sandy and silt loam soils, while MP + TZ mitigated N2O-N production only from the silt loam soil. Unexpectedly, between days 30 and 60, N2O-N emissions from NI-treated soils increased by up to fivefold relative to the No-NI treatment in the silt loam soil at 80% WHC. Likewise, the relative abundance of the studied nitrifying bacteria indicated that the NIs had only short-term effectiveness in the silt loam soil. These results suggested that DMPP and MP + TZ might trigger high N2O-N release from fine-textured soil with constant high moisture after this short-term inhibitory effect. In conclusion, DMPP and MP + TZ effectively reduce N2O-N emissions under soil drying and rewetting. [ABSTRACT FROM AUTHOR]

Purpose: Summer catch crop (CC) has been introduced into the vegetable rotating system in greenhouse fields to reduce nitrogen (N) losses through crop uptake and residual N immobilization. However, the effects of planting sorghum with high N uptake and biomass, and biological nitrification inhibition (BNI) potential as a CC on soil N dynamics and subsequent crop yield remain unclear. Methods: In the two-year field experiment, the comprehensive effects of planting sorghum as CC on subsequent eggplant yield, soil mineral N dynamics, ammonia-oxidizing archaea (AOA) and bacteria (AOB) amoA gene abundances were determined, in comparison to the sweet corn and fallow treatments. Results: Compared to the fallow and sweet corn, planting sorghum as CC increased subsequent eggplant yield by 24.88% and 18.94% in the 2014–2015 and 2015–2016 over-winter growing season, respectively. CC planting reduced soil nitrate (NO3−-N) accumulation during the summer fallow season. Sorghum planting could significantly maintain higher level of ammonium (NH4+-N) concentration during the summer fallow season and the first month of succeeding over-winter season. In addition, sorghum planting reduced soil net nitrifying potential, which could be partially attributed to the decreased amoA gene abundance of AOA at the 0–30 and 30–60 cm soil layers and AOB at 0–30 cm soil layer. Conclusion: We conclude that planting sorghum in the summer fallow season is a promising strategy to retain soil NH4+-N, reduce soil NO3−-N accumulation, and enhance subsequent eggplant yield. [ABSTRACT FROM AUTHOR]

Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3−-N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. Key points: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different. [ABSTRACT FROM AUTHOR]

Straw‐decomposing microbial inoculants (MIs) have been increasingly applied to straw‐amended soils. However, the interactive effects and underlying microbial mechanisms of straw and decomposing MIs on nitrous oxide (N2O) emissions remain unclear. Here, a pot experiment with an Aquic Inceptisol was conducted to determine soil N2O emissions and the abundance and composition of microbial functional genes under six amendments: wheat straw (W), Bacillus subtilis MI (B), Streptomyces rochei MI (S), a combination of straw and B. subtilis MI (WB), a combination of straw and S. rochei MI (WS), and a control without wheat straw or MI (C). Compared with the control, the amendments of straw, decomposing MIs, and their combinations decreased soil N2O emissions by 43%, 22–30%, and 46–60%, respectively. Mechanistically, the positive relationship between ammonia‐oxidizing bacteria (AOB) and soil potential nitrification rate (PNR), along with decreased AOB abundance (−36%) following straw and decomposing MI amendments, further suggested that AOB predominated soil nitrification and was responsible for the suppressed nitrification. In addition, straw amendment increased nirK gene abundance (by 48%) and potential denitrification rate (by 11%), while the increase in nosZI gene abundance (+25%) involved in N2O consumption contributed to the decrease in N2O emissions. Overall, the additive effect of straw and decomposing MIs on soil N2O emissions was associated with two amendment‐induced changes in the abundance and composition of AOB and straw‐stimulated the abundance of the nosZI gene. Our results revealed the potential for mitigating N2O emissions following the amendments of straw and MI by influencing soil N2O‐related microbial groups. [ABSTRACT FROM AUTHOR]

To address the issue of insufficient carbon sources in urban sewage, which leads to poor nitrogen removal performance in sewage treatment systems, an anaerobic/anoxic/aerobic (AAO) pilotscale reactor was established. The reactor aimed to treat low C/N (chemical oxygen demand; COD/total nitrogen; TN) municipal wastewater (C/N<5). To enhance nitrogen removal and investigate the mechanism in the AAO process, a Pall ring modified biological suspended filler was introduced to the aerobic zone after achieving partial nitrification and denitrification (PND). The results revealed that the activated sludge-biofilm composite system can be successfully formed within 40 days, with a stable loaded biomass on the membrane at 40.06 mg/g (measured by volatile suspended solids (VSS)/filler). The aerobic zone of the activated sludge-biofilm composite system demonstrated an increase in nitrite accumulation rate (NAR) and simultaneous nitrification and denitrification efficiency (SND), from 60.46% and 19.42% in the initial stage (stage 1) to 69.62% and 46.47% in the stable forming stage (stage 3), respectively. By promoting both PND and SND pathways for nitrogen removal, the effluent from the system exhibited decreased concentrations of ammonia nitrogen (NH4+-N) at 0.11 mg/L and total nitrogen (TN) at 4.55 mg/L, indicating the significant synergistic effect of the biofilm on nitrogen removal. 16S rRNA amplification and sequencing analysis revealed that Proteobacteria was the dominant microorganism in the 60-day biofilm, accounting for 76.12% of the relative abundance. The main ammonia oxidizing bacteria (AOB) were Nitrosomanas (1.77%) and Nitrosococcus (1.69%). Meanwhile, denitrification microbial species were found to have a substantial proportion (29.11%), along with a small amount of Anammox bacteria (Anammoxoglobus, 0.35%) within the biofilm. These sequencing results were consistent with the macroscopic performance of the reactor. Overall, these findings establish a theoretical foundation for enhancing nitrogen removal in the AAO system. [ABSTRACT FROM AUTHOR]

Stable and efficient partial nitrification reaction and nitrite accumulation are essential for the operation of partial nitrification-anaerobic ammonia oxidation process. This paper investigated the changes in the performance of a partial nitrification bioreactor during the domestication process. After 40 days of domestication, the partial nitrification reaction remained stable, the nitrite accumulation rate (NAR) increased significantly to 85.7%, and the NO2--N/NH4+-N ratio stabilized at 1.25 ± 0.04. Both diversity indices (Simpson and Shannon) and richness indices (Ace and Chao1) tend to decrease with domestication. Nitrosomonas as a typical ammonia oxidizing bacterium it increased its relative abundance in the reactor from 0.02 ± 0.007% at P1 to 11.6 ± 2.2% at P2, and at P3 stage the denitrifying functional bacteria norank_f_AKYH76, Dokdonella and unclassified_f_Comamonadaceae reached 33.4 ± 12.5%, 18.8 ± 1.8%, and 10.1 ± 1.3%, respectively, and the increase in the relative abundance of these functional species was also consistent with the accumulation of nitrite nitrogen in the reactor. [ABSTRACT FROM AUTHOR]

Partial nitrification is a key aspect of efficient nitrogen removal, although practically it suffers from long start-up cycles and unstable long-term operational performance. To address these drawbacks, this study investigated the effect of low intensity ultrasound treatment combined with hydroxylamine (NH 2 OH) on the performance of partial nitrification. Results show that compared with the control group, low-intensity ultrasound treatment (0.10 W/mL, 15 min) combined with NH 2 OH (5 mg/L) reduced the time required for partial nitrification initiation by 6 days, increasing the nitrite accumulation rate (NAR) and ammonia nitrogen removal rate (NRR) by 20.4% and 6.7%, respectively, achieving 96.48% NRR. Mechanistic analysis showed that NH 2 OH enhanced ammonia oxidation, inhibited nitrite-oxidizing bacteria (NOB) activity and shortened the time required for partial nitrification initiation. Furthermore, ultrasonication combined with NH 2 OH dosing stimulated EPS (extracellular polymeric substances) secretion, increased carbonyl, hydroxyl and amine functional group abundances and enhanced mass transfer. In addition, 16S rRNA gene sequencing results showed that ultrasonication-sensitive Nitrospira disappeared from the ultrasound + NH 2 OH system, while Nitrosomonas gradually became the dominant group. Collectively, the results of this study provide valuable insight into the enhancement of partial nitrification start-up during the process of wastewater nitrogen removal. [Display omitted] [ABSTRACT FROM AUTHOR]

• γ-PGA-Ca drove the highest improvements in the pH buffering capacity (pHBC) of the soil and exhibited the greatest potential in inhibiting HNO3-induced soil acidification. • The mechanism of improving pHBC by PASP-Ca or γ-PGA-Ca were protonation of carboxyl, complexing with Al3+, and cation exchange processes. • CaLS was the optimal one in inhibiting acidification and increasing exchangeable acidity during incubation via nitrification inhibition. • The sharp reduction in the population sizes of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were responsible for inhibition of nitrification by CaLS application. Soil acidification is a major threat to agricultural sustainability in tropical and subtropical regions. Biodegradable and environmentally friendly materials, such as calcium lignosulfonate (CaLS), calcium poly(aspartic acid) (PASP-Ca), and calcium poly γ-glutamic acid (γ-PGA-Ca), are known to effectively ameliorate soil acidity. However, their effectiveness in inhibiting soil acidification has not been studied. This study aimed to evaluate the effect of CaLS, PASP-Ca, and γ-PGA-Ca on the resistance of soil toward acidification as directly and indirectly (i.e., via nitrification) caused by the application of HNO 3 and urea, respectively. For comparison, Ca(OH) 2 and lignin were used as the inorganic and organic controls, respectively. Among the materials, γ-PGA-Ca drove the substantial improvements in the pH buffering capacity (pHBC) of the soil and exhibited the greatest potential in inhibiting HNO 3 -induced soil acidification via protonation of carboxyl, complexing with Al3+, and cation exchange processes. Under acidification induced by urea, CaLS was the optimal one in inhibiting acidification and increasing exchangeable acidity during incubation. Furthermore, the sharp reduction in the population sizes of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) confirmed the inhibition of nitrification via CaLS application. Therefore, compared to improving soil pHBC, CaLS may play a more important role in suppressing indirect acidification. Overall, γ-PGA-Ca was superior to PASP-Ca and CaLS in enhancing the soil pHBC and the its resistance to acidification induced by HNO 3 addition, whereas CaLS was the best at suppressing urea-driven soil acidification by inhibiting nitrification. In conclusion, these results provide a reference for inhibiting soil re-acidification in intensive agricultural systems. [Display omitted] [ABSTRACT FROM AUTHOR]

Nitrogen removal from municipal wastewater through partial nitritation-denitrification (nitritation) is challenging to accomplish in a membrane-aerated biofilm reactor (MABR) due to the reactor configuration, which potentially interferes with nitrite-oxidizing bacteria inhibition. This study investigated the impact of intermittent aeration on the development and sustenance of nitritation in a lab-scale MABR for the treatment of municipal wastewater. The study was accomplished in four phases (Phases I–IV) using a combination of continuous and intermittent aeration modes with aerated and nonaerated cycles of 10 min (5 on/5 off), 20 min (10 on/10 off), and 25 min (10 on/15 off), respectively, and a constant hydraulic retention time of 2.5 h. Biofilm development and stabilization were completed using a continuous aeration condition (Phase I). Nitrite accumulation rate, nitrate production rate, and ammonium nitrogen removal efficiency achieved in Phases II–IV were, 35%, 12%, and 99%; 76%, 3.4%, and 98%; and 94%, 1%, and 98%, respectively. Intermittent aeration significantly improved total inorganic nitrogen removal efficiency by ∼20%. Between the initiation of intermittent aeration and termination of the study, ammonia-oxidizing bacteria activities within the reactor increased by >150% from 4.53 to 12.6 mgN/h·g volatile suspended solids (VSS). In contrast, nitrite-oxidizing bacteria activities declined by >60% from 1.17 to 0.46 mgN/h·gVSS. The consistent lagging of nitrate production rate behind nitrite accumulation rate, increase in ammonia-oxidizing bacteria activities, and decline in nitrite-oxidizing bacteria activities over the operation period indicates the establishment of nitritation. This study demonstrates that using intermittent aeration, nitritation can be developed and sustained in MABR under mainstream conditions. Biological nitrogen removal from municipal wastewater is typically through the conventional activated sludge system using the traditional nitrification and denitrification pathway. However, three major issues abound with this pathway: high aeration energy, external organic carbon requirement, and the potential release of nitrous oxide. An alternative to the aforementioned process is the MABR. MABR is a low-energy technology with potential for pollutants removal through nitritation. Nitritation compares favorably to simultaneous nitrification-denitrification in terms of energy efficiency, sustainability, and operational costs. However, nitrite-oxidizing bacteria activities suppression is required for the successful establishment of nitritation. Studies have suggested that nitrite-oxidizing bacteria activity suppression can be accomplished in biological systems when operated under specific conditions, but although some of these conditions are inherent in some systems, they are absent in mainstream wastewater and MABR. Therefore, establishing nitritation in MABR for the treatment of conventionally collected sewage is challenging. This study recommends using continuous aeration to develop the biofilm and establish stable performance within the MABR, and subsequently switching the aeration mode to predetermined intermittent aeration cycles. This will reduce the dissolved oxygen concentration, suppress nitrite-oxidizing bacteria activities, and stabilize suppressed nitrite-oxidizing bacteria activities within the MABR biofilm. [ABSTRACT FROM AUTHOR]

Surface drip fertigation has demonstrated promising results regarding the mitigation of nitrous oxide (N2O) emissions. The use of subsurface irrigation may offer the possibility of reducing these emissions further due to the modification of the soil moisture profile and N allocation, both of which affect the biochemical processes leading to N2O fluxes. However, the mitigation potential of subsurface irrigation combined with different mineral nitrogen (N) fertilizers (ammonium or nitrate-based, use of nitrification inhibitors) still needs to be evaluated. To respond to this need, a 2-year field experiment was set up in central Spain to test two different drip-fertigation systems (surface and subsurface at 30 cm depth) and four N fertilization treatments (control, calcium nitrate, and ammonium sulfate with or without the nitrification inhibitor 3,4-dimethylpyrazole phosphate, DMPP) in an irrigated maize (Zea mays L.) crop. Nitrous oxide emissions, mineral N concentrations (ammonium, NH4+, and nitrate, NO3−), and abundance of key N genes involved in nitrification and denitrification processes were measured in two soil layers (0–20 and 20–40 cm). Regardless of the irrigation system, ammonium sulfate gave the highest cumulative N2O losses in both campaigns, while calcium nitrate and the use of DMPP were the most effective strategies to abate N2O fluxes in the first and second years, respectively. Differences between irrigation systems were not statistically significant for cumulative N2O emissions, despite the clear effect on topsoil mineral N (higher NH4+ and NO3− concentrations in surface and subsurface drip, respectively). Nitrous oxide emissions were positively correlated with soil NH4+ concentrations. Gene abundances were not a trustworthy predictor of N2O losses in the 1st year, although a clear inhibitory effect of fertilization on microbial communities (i.e., ammonia oxidizers, nitrite reducers, and N2O reducers) was observed during this campaign. During the second year, nitrifying and denitrifying genes were affected by irrigation (with higher abundances in the 20–40 cm layer in subsurface than in surface drip) and by the addition of DMPP (which had a detrimental effect on gene abundances in both irrigation systems that disappeared after the fertigation period). In conclusion, the use of DMPP or calcium nitrate instead of ammonium sulfate may enhance the chances for an additional mitigation in both surface and subsurface irrigation systems. [ABSTRACT FROM AUTHOR]

Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment. [ABSTRACT FROM AUTHOR]

Straw return with nitrogen (N) fertilizer can generally regulate soil N cycling by affecting the microbial community, thereby influencing crop productivity. Bacteria and fungi play a key role in nitrification, while the effects of soil microbial interactions that include protists under the condition of straw return and N fertilizer remain uncertain. Here, we evaluated the importance of the soil microbiome, particularly protists and ammonia‐oxidizing bacteria (AOB), in regulating the soil N transformation potential and wheat yields under different fertilization practices. The results showed that the activity of β‐1,4‐N‐acetylglucosaminidase (NAG) and the potential nitrification rate (PNR) increased significantly by 156.4% ~ 312.3% and 183.1% ~ 402.6% with the addition of N fertilizer and straw, respectively. The effect on PNR was greater for straw than fertilizer addition. The fertilization practices changed the microbial community structure, and there were stronger responses from the protists and AOB. The soil microbiome formed three closely co‐occurring modules (Modules 0, 1 and 2). Among them, Module 0 showed strong positive correlations with the soil total N, NAG, PNR and crop yield and may be the key ecological cluster. Moreover, the predatory protists Cercozoa, Conosa and Ochrophyta in Module 0 were significantly positively associated with the activity of NAG and the PNR, yields and AOB. The predatory protists in Module 0 may change the soil potential nitrification rate and enhance the yield of wheat by preying on the competitors of AOB. The results suggest that the incorporation of straw promotes the N transformation potential and wheat yields linked to trophic interactions between predatory protists and AOB in fluvo‐aquic soil. [ABSTRACT FROM AUTHOR]

Stream, floodplain, and wetland restorations enhance water quality and ecological function; however, soil health is prioritized infrequently in restoration planning and monitoring. Buried, historic, hydric soils—common across U.S. mid‐Atlantic valley bottoms beneath legacy sediments—are not included in most floodplain restoration designs, though they may retain favorable biogeochemical characteristics and host legacy microbial communities that could support ecosystem recovery if exhumed and preserved. To assess the efficacy of including historic hydric soils in floodplain restoration for nitrogen (N) removal, we characterized pre‐Euro‐American settlement wetland soils buried below legacy sediments and now exposed along incised streambanks across the mid‐Atlantic. We compared carbon (C) and N contents; C:N ratios; nitrate‐N and ammonium‐N concentrations; denitrification rates; functional genes for denitrification (nosZ) and nitrification (amoA for ammonia oxidizing archaea [AoA] + ammonia oxidizing bacteria [AoB]); and phospholipid fatty acid biomasses of historic wetland soils with contemporary wetland soils before and after an 1‐year incubation in a recently restored floodplain. Compared to modern wetland soils, historic hydric soils buried by legacy sediment are less nutrient‐rich, have fewer functional genes for and lower rates of denitrification, and possess significantly less microbial biomass. Following the 1‐year incubation, many of these concentrations, rates, and gene counts increased in historic soils, though not substantially. Ultimately, our results suggest that while inclusion of historic, hydric soils and their legacy microbiomes is valuable for N‐removal in floodplain restoration, the recovery of historic, hydric soils is predictably slow, and attainment of restoration goals, such as increased denitrification, may require multiple years. [ABSTRACT FROM AUTHOR]

Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia‐oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite‐oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia‐oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems. [ABSTRACT FROM AUTHOR]

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai–Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai–Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitri fication inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows. IMPORTANCE The importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitri fication increased at higher elevations. The research highlights the potential impact of elevation- induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows [ABSTRACT FROM AUTHOR]

The waterbodies have been polluted by various natural and anthropogenic activities. The aquatic waste includes ammonia as one of the most toxic pollutants. Several biological treatment systems involving anoxic and semi anoxic bacteria have been proposed for reducing nitrogen loads from wastewater and increasing the efficiency and cost effectiveness. These bacteria play a vital role in the processes involved in the nitrogen cycle in nature. However, the enrichment, sustainability and identification of bacterial communities for wastewater treatment is an important aspect. Most of the chemolithotrophs are unculturable hence their identification and measurement of abundance remains a challenging task. In this study the different bacteria involved in total nitrogen removal from the wastewater are enriched for 700 days under anoxic condition. The synthetic wastewater containing 0.382 g/L of ammonium chloride was used. Molecular identification of the bacteria involved in various steps of the nitrogen cycle was carried out based on amplification of functional genes and 16S rRNA gene Polymerase chain reaction followed by DNA sequencing. Change in the abundance of chemolithotrophs was studied using qPCR. The mutual growth of various nitrifiers along with anaerobic bacteria were identified by molecular characterisation of DNA at various time intervals with the different genes involved in the nitrogen cycle. Nitrosomonas species like Nitrosomonas europaea were identified throughout the batch scale studies possessing the genes associated with ammonia oxidizing bacteria and nitrite oxidizing bacteria which act as a complete ammonia oxidizer. The uncultured species of Nitrospira and anammox bacteria were also observed which predicts the coexistence of the anammox and comammox bacteria in a batch scale study. The coexistence of the semi anoxic and anoxic bacteria helped in the growth of these bacteria for a longer duration of time. The nitrite produced by the comammox during nitrification can be utilized by anammox as an electron carrier. The other species of denitrifiers like Pseudomonas denitrificans and Aminobacter aminovorans were also observed. It is concluded that the enrichment of semi anoxic and anoxic bacteria was faster with the increase in growth of the bacteria involved in nitrification, comammox, anammox and partial denitrification process. The bacterial growth is enhanced and the efficiency is increased which can be further used in the development of small pilot scale bioreactor for total nitrogen removal. [ABSTRACT FROM AUTHOR]

The excessive application of nitrogen fertilizer aggravated the loss of nitrogen in farmland and exerted detrimental effects on the soil and water environment. Examining the effects of N-(n-Butyl)thiophosphoric triamide (NBPT) and nitrification inhibitor dicyandiamide (DCD) on nitrification and crop yield in wheat-corn double cropping systems would provide valuable insights for improving nitrogen efficiency and ensuring a rational application of inhibitors. A field experiment lasting one and a half years was performed in the winter wheat–summer maize double agroecosystem in North China. The four treatments that were applied included (I) conventional fertilization without inhibitors (CK), (II) conventional fertilization with 0.26 g/m2 NBPT (NBPT), (III) conventional fertilization with 1.00 g/m2 DCD (DCD), and (IV) conventional fertilization with 0.26 g/m2 NBPT and 1.00 g/m2 DCD (NBPT + DCD). The results demonstrated that the combined use of NBPT and DCD exerted better effects in reducing NO3−-N leaching. Nitrification could be inhibited for up to 95 days by combining NBPT and DCD, while 21 days by DCD. Ammonia-oxidizing archaea (AOA) (R2 = 0.07159, p < 0.01) along with ammonia-oxidizing bacteria (AOB) (R2 = 0.09359, p < 0.01), rather than a complete ammonia oxidizer (comammox), were significantly and positively correlated with NO3−-N content, which indicated that the ammoxidation process was mainly regulated by AOA and AOB, instead of comammox in the winter wheat–summer maize double agroecosystem in North China. [ABSTRACT FROM AUTHOR]

The significant volatilization of NH3 during aerobic composting causes nitrogen (N) losses and environmental risks. Both iron (Fe) and biochar (BC) can influence the N conversion process in composting. Fe application can delay the maturation of materials, while biochar can enhance the quality of organic fertilizer. The combination of these two conditioners may help decrease NH3 emissions and improve organic fertilizer quality. Therefore, this study investigates the effects of different doses of FeCl3 and BC on NH3 emissions and organic fertilizer quality during composting. The results demonstrated that Fe/BC co-conditioners reduced the accumulation of NH3 emissions during composting by 11.1–48.2%, increased the total nutrient content by 0.6–15.3%, and enhanced economic and environmental benefits by 0.1–23.6 $ t−1. At the high-temperature stage of composting, Fe/BC co-conditioners decreased the pH by 0.3–1.2, but there was no significant difference compared to the control at the end of composting, and they did not affect compost maturation. The structural equation model analysis suggested that the reduction in NH3 emissions was related to ammonia-oxidizing bacteria (AOB), NH4+–N, and total nitrogen (TN). As a result, the Fe/BC co-conditioners reduced NH3 emissions by lowering the pH at the beginning of composting and increasing the content of NH4+–N. This study concludes that Fe/BC co-conditioners could complement each other to significantly reduce NH3 emissions and improve the quality of organic fertilizers. Highlights: Different doses of ferric chloride and biochar (Fe/BC) were used for aerobic composting. Fe/BC co-conditioning composting significantly reduced NH3 volatilization. Fe/BC co-conditioning composting enhanced N retention and total nutrients. NH3 emission reduction was mainly related to AOB, NH4+–N and TN during composting. Fe/BC co-conditioning composting could enhance economic and environmental benefits. [ABSTRACT FROM AUTHOR]

This study presents a relatively low-cost method for modifying TiO2-based materials for photocatalytic bacterial inactivation. The photocatalytic inactivation of Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus epidermidis) bacteria using modified sulphated TiO2 was studied. The modification focused on the reduction of TiO2 by ammonia agents and hydrogen at 400–450 °C. The results showed a high impact of sulphate species on the inactivation of E. coli. The presence of these species generated acid sites on TiO2, which shifted the pH of the reacted titania slurry solution to lower values, around 4.6. At such a low pH, TiO2 was positively charged. The ammonia solution caused the removal of sulphate species from TiO2. On the other hand, hydrogen and ammonia molecules accelerated the removal of sulphur species from TiO2, as did heating it to 450 °C. Total inactivation of E. coli was obtained within 30 min of simulated solar light irradiation on TiO2 heat-treated at 400 °C in an atmosphere of Ar or NH3. The S. epidermidis strain was more resistant to photocatalytic oxidation. The contact of these bacteria with the active titania surface is important, but a higher oxidation force is necessary to destroy their cell membrane walls because of their thicker cell wall than E. coli. Therefore, the ability of a photocatalyst to produce ROS (reactive oxidative species) will determine its ability to inactivate S. epidermidis. An additional advantage of the studies presented is the inactivation of bacteria after a relatively short irradiation time (30 min), which does not often happen with photocatalysts not modified with noble metals. The modification methods presented represent a robust and inexpensive alternative to photocatalytic inactivation of bacteria. [ABSTRACT FROM AUTHOR]

Identifying tipping points in the relationship between aridity and gross nitrogen (N) cycling rates could show critical vulnerabilities of terrestrial ecosystems to climate change. Yet, the global pattern of gross N cycling response to aridity across terrestrial ecosystems remains unknown. Here, we collected 14,144 observations from 451 15N‐labeled studies and used segmented regression to identify the global threshold responses of soil gross N cycling rates and soil process‐related variables to aridity index (AI), which decreases as aridity increases. We found on a global scale that increasing aridity reduced soil gross nitrate consumption but increased soil nitrification capacity, mainly due to reduced soil microbial biomass carbon (MBC) and N (MBN) and increased soil pH. Threshold response of gross N production and retention to aridity was observed across terrestrial ecosystems. In croplands, gross nitrification and extractable nitrate were inhibited with increasing aridity below the threshold AI ~0.8–0.9 due to inhibited ammonia‐oxidizing archaea and bacteria, while the opposite was favored above this threshold. In grasslands, gross N mineralization and immobilization decreased with increasing aridity below the threshold AI ~0.5 due to decreased MBN, but the opposite was true above this threshold. In forests, increased aridity stimulated nitrate immobilization below the threshold AI ~1.0 due to increased soil C/N ratio, but inhibited ammonium immobilization above the threshold AI ~1.3 due to decreased soil total N and increased MBC/MBN ratio. Soil dissimilatory nitrate reduction to ammonium decreased with increasing aridity globally and in forests when the threshold AI ~1.4 was passed. Overall, we suggest that any projected increase in aridity in response to climate change is likely to reduce plant N availability in arid regions while enhancing it in humid regions, affecting the provision of ecosystem services and functions. [ABSTRACT FROM AUTHOR]

Nitrification inhibitor is essential for increasing the nitrogen utilization efficiency of agricultural plants, thus reducing environmental pollution and increasing crop yield. However, the easy volatilization and limited functional property is still the bottleneck of nitrification inhibitors. Herein, a novel water-soluble polymeric nitrification inhibitor was synthesized through the copolymerization of acrylamide and bio-based acrylic acid, which was synthesized from biomass-derived furfural, and the complexation of carboxyl groups and 3,4-dimethylpyrazole. The results showed that the nitrification inhibitor was an amorphous polymer product with a glass transition temperature of 146 °C and a thermal decomposition temperature of 176 °C, and the content of 3,4-dimethylpyrazole reached 2.81 wt%, which was 115% higher than our earlier product (1.31 wt%). The polymeric nitrification inhibitor can inhibit the activity of ammonia-oxidizing bacteria effectively, thus inhibiting the conversion of ammonium nitrogen to nitrate nitrogen and converting the insoluble phosphate into soluble and absorbable phosphate. By introducing a copolymer structure with a strong flocculation capacity, the polymeric nitrification inhibitor is further endowed with a soil-loosening function, which can increase the porosity of soil to improve the soil environment. Therefore, the nitrification inhibitor can be used in water-soluble and liquid fertilizers, as well as in high tower melting granulated compound fertilizers. [ABSTRACT FROM AUTHOR]

Replacing synthetic fertilizer by organic manure has been shown to reduce emissions of nitrous oxide (N2O), but the specific roles of ammonia oxidizing microorganisms and gross nitrogen (N) transformation in regulating N2O remain unclear. Here, we examined the effect of completely replacing chemical fertilizer with organic manure on N2O emissions, ammonia oxidizers, gross N transformation rates using a 13‐year field manipulation experiment. Our results showed that organic manure reduced cumulative N2O emissions by 16.3%–210.3% compared to chemical fertilizer. The abundance of ammonia oxidizing bacteria (AOB) was significantly lower in organic manure compared with chemical fertilizer during three growth stages of maize. Organic manure also significantly decreased AOB alpha diversity and changed their community structure. However, organic manure substitution increased the abundance of ammonia oxidizing archaea and the alpha diversity of comammox Nitrospira compared to chemical fertilizer. Interestingly, organic manure decreased organic N mineralization by 23.2%–32.9%, and autotrophic nitrification rate by 10.5%–45.4%, when compared with chemical fertilizer. This study also found a positive correlation between AOB abundance, organic N mineralization and gross autotrophic nitrification rate with N2O emission, and their contribution to N2O emission was supported by random forest analysis. Our study highlights the key roles of ammonia oxidizers and N transformation rates in predicting cropland N2O. [ABSTRACT FROM AUTHOR]

This study researched the use of biofilms to remove nitrogen compounds from municipal sewages at low temperatures, especially in winter. An aluminosilicate substrate was used to create a biofilm, which has an affinity for ammonium ions. The selection of biofilm-forming microorganisms has been shown to occur on aluminosilicate. This substrate is mainly inhabited by microorganisms that remove nitrogen compounds. As a result, microorganisms protected against external factors in the biofilm effectively remove nitrogen compounds. The TN content in sewage treated at a temperature of 10 °C was of a 4 mg/L order and was 3–5 times lower than in the reference system (classical conditions). This process involves shortened nitrification/denitrification such as Anammox. As a result of a given process, CO2 emissions were reduced and much smaller amounts of NOx were produced, positively impacting the ongoing climate changes. Microbiological DNA/RNA tests have shown that the biofilm is primarily composed of archaea and bacteria that remove nitrogen compounds, including those that oxidize ammonia. [ABSTRACT FROM AUTHOR]

Nitrosomonas europaea , an aerobic ammonia oxidizing bacterium, is responsible for the first and rate-limiting step of the nitrification process, and their ammonia oxidation activities are critical for the biogeochemical cycling and the biological nitrogen removal of wastewater treatment. In the present study, N. europaea cells were cultivated in the inorganic or organic media (the NBRC829 and the nutrient-rich, NR, media, respectively), and the cells proliferated in the form of planktonic and biofilm in those media, respectively. The N. europaea cells in the biofilm growth mode produced larger amounts of the extracellular polymeric substances (EPS), and the composition of the EPS was characterized by the chemical analyses including Fourier transform infrared spectroscopy (FT-IR) and 1H-nuclear magnetic resonance (NMR) measurements. The RNA-Seq analysis of N. europaea in the biofilm or planktonic growth mode revealed that the following gene transcripts involved in central nitrogen metabolisms were abundant in the biofilm growth mode; amo encoding ammonia monooxygenase, hao encoding hydroxylamine dehydrogenase, the gene encoding nitrosocyanine, nirK encoding copper-containing nitrite reductase. Additionally, the transcripts of the pepA and wza involved in the bacterial floc formation and the translocation of EPS, respectively, were also abundant in the biofilm-growth mode. Our study was first to characterize the EPS production and transcriptome of N. europaea in the biofilm and planktonic growth mode. [ABSTRACT FROM AUTHOR]

Nitrogen cycling in soil and its microbial community characteristics are closely related. Characteristics of soil nitrogen, community diversity of nitrogen-fixing bacteria (NFB) and ammonia oxidizers were study with a traditional farmland as control and five treatment alfalfa fields of 1-, 2-, 3-, 4- and 5-year (a) cultivation. The results showed that total nitrogen (TN) significantly increased in 3, 4 and 5 a, alkali-hydrolysable nitrogen (AHN), NH4+-N (AN), NO3−-N (NN) and SOC was the highest in 3, 5, 3, 4 a, respectively. The dominant phylum of NFB and ammonia-oxidizing bacteria (AOB) belonged to Proteobacteria with a higher diversity and abundance in 3 and 4 a. Crenarchaeota was found the dominant phylum of ammonia-oxidizing archaea (AOA) with the highest abundance in the alfalfa field planted for 2 a. The dominant genus of NFB and AOB were Azohydromonas and Nitrosospira, respectively, which showed the highest abundance in the alfalfa fields planted for 2 and 3 a, respectively. The diversity of NFB and AOB showed a significantly positive correlation with TN and AHN (p < 0.05). AOA showed a significantly negative correlation with AN (p < 0.05). Many microbial species cannot be annotated in this study, which deserves future investigation. [ABSTRACT FROM AUTHOR]

Peanuts (Arachis hypogaea L.) is an important oil and nitrogen (N) fixing crop. Urease inhibitors (UIs) and nitrification inhibitors (Nis) can mitigate the release of N and reduce the harmful effects of excessive N concentrations. However, the effect of these inhibitors on the soil nutrient-microbial activity-plant growth system is unknown in peanut. The purpose of this study was to investigate the effects and mechanism of N-(n-butyl) thiophosphoric triamide (NBPT), 3,4-dimethylpyrazole phosphate (DMPP) and sulfur-coated urea (SCU) on peanut. The results showed that comparing with urea alone, adding NBPT + DMPP inhibited the urea hydrolysis better and decreased the concentration of NH4+-N + NO3−-N by 20.8% in soil. Therefore, it increased the net photosynthetic rate, promoted the development of roots even the absorption of N by peanut, with N use efficiency (NUE) up to 20.8%. The effect of NBPT + DMPP on microorganism was better than that of NBPT alone, which considerably impacted the structure and abundances of aonia oxidizing bacteria (AOB) but not ammonia-oxidizing archaea (AOA). Specifically, g_Nitrosospira and g_Nitrosomonas decreased by 46.9% and 2.2% respectively, and g(c) Betaproteobacteria increased. Furthermore, when combined with SCU on this basis, the overall effect was clearer. [ABSTRACT FROM AUTHOR]

Nitrification is an essential biological process that converts ammonia into nitrate via nitrite. In the initial phase of nitrification, ammonia-oxidizing bacteria convert ammonia to hydroxylamine and subsequently to nitrite. The electrons generated in this process provide energy for cellular growth. In this study, we observed the inhibitory effects of plant-derived 1,4-naphthoquinones, including juglone, plumbagin, and 1,4-naphthoquinone, on nitrification in Nitrosomonas europaea, a typical nitrifying bacterium. These compounds disrupted the transfer of electrons produced during hydroxylamine oxidation to cytochrome c554, a physiological electron acceptor. In vitro electron transfer experiments confirmed the function of these three 1,4-naphthoquinones as electron acceptors in hydroxylamine oxidation. The results indicate that these compounds interfere with electron transfer to cytochrome c554 during the ammonia oxidation process leading to nitrification inhibition. Remarkably, lawsone, an isomer of juglone, exhibited no effect on the activity of hydroxylamine oxidoreductase, implying a correlation between the redox potential of each 1,4-naphthoquinone and their ability to hinder canonical electron transfer. Furthermore, X-ray crystallographic analysis revealed that juglone resides in close proximity to the catalytic heme P460 in hydroxylamine oxidoreductase. The hydrophobic environment surrounding the binding cavity appears critical for the selectivity of 1,4-naphthoquinones. [ABSTRACT FROM AUTHOR]

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3−-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil. [ABSTRACT FROM AUTHOR]

The use of biological nitrification inhibitors (BNIs) holds a great potential to effectively reduce nitrogen losses from agroecosystems and conforms with the current move toward ecological-intensified agriculture. Knowledge of the activity of BNIs to soil nitrifiers is limited and is generally based on a single Nitrosomonas europaea bioassay. We determined the in vitro activity of multiple plant-derived compounds as BNIs such as (i) root-derived compounds [sakuranetin, methyl 3-(4-hydroxyphenyl)-propionate (MHPP), and zeanone]; (ii) other phytochemicals (caffeic, quinic, chlorogenic, and shikimic acids); and (iii) analogs of statins (simvastatin), triazoles (1-butyl-4-propyltriazole, 1,4-dibutyltriazole), and zeanone (2-methoxy-1,4-naphthoquinone) on distinct soil-derived ammonia-oxidizing bacteria (AOB) (Nitrosospira multiformis and Nitrosomonas europaea), ammonia-oxidizing archaea (AOA) (Candidatus Nitrosotalea sinensis and Candidatus Nitrosocosmicus franklandianus), and a nitrite-oxidizing bacterium (NOB) (Nitrobacter sp.). Our results indicate that AOA were more sensitive than AOB to BNIs. Sensitivity within the AOA group was BNI dependent, unlike AOB, for which N. multiformis was consistently more sensitive than N. europaea. Several compounds were inhibitory to Nitrobacter sp. with MHPP and caffeic acid being more potent against NOB compared to the ammonia-oxidizing strains, an observation with potential implications for soil quality and productivity. Overall, zeanone was the most potent NI against ammonia oxidizers, while caffeic acid was the most potent BNI against Nitrobacter sp. We provide pioneering evidence for the activity range of multiple BNIs on soil nitrifiers, stress the need for revisiting the biological screening systems currently used for BNI determination, and advocate for a more thorough monitoring of the impact of BNI candidates on a range of target and non-target microorganisms. IMPORTANCE Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitri fiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings. [ABSTRACT FROM AUTHOR]

This study reports directly measured nitrification rates in the water column of western Lake Erie, which is affected by annual cyanobacterial harmful algal blooms, and across all three Lake Erie basins. Over three field seasons, 15NH4+ stable isotope tracers were employed to quantify nitrification rates, and relative abundances of ammonia-oxidizing bacteria and ammonia-oxidizing archaea were determined via qPCR. Nitrification rates ranged from undetectable to 1,270 nmol L-1 d-1 and were generally greatest in the western basin near the Maumee River mouth (a major nutrient source). Nitrification rates were highest in early summer, and often lowest during peak cyanobacterial harmful algal blooms months (August and September), before increasing again in October. In the western basin, nitrification was negatively correlated with cyanobacterial biomass. There were no consistent differences in nitrification rates between the three Lake Erie basins. Over the three years in western Lake Erie, ammonia-oxidizing bacteria and ammonia-oxidizing archaea were often present in high and similar abundances, but overall, ammonia-oxidizing bacteria exceeded ammonia-oxidizing archaea, particularly in 2017. No relationships were observed between nitrification rates and ammonia-oxidizing bacteria and ammonia-oxidizing archaea abundances. Thus, despite abundant ammonia-oxidizer DNA, lower nitrification rates during cyanobacterial harmful algal blooms suggest that nitrifiers were poor competitors for regenerated and available NH4+ during these blooms, as also observed in similar systems. Low nitrification rates during cyanobacterial harmful algal blooms could limit system nitrogen removal via denitrification, a natural pathway for its removal and a valuable ecosystem service. Lower denitrification rates allow more bioavailable nitrogen to remain in the system and support biomass and microcystin production; therefore, these results help explain how non-nitrogen-fixing cyanobacterial harmful algal blooms persist, despite low bioavailable nitrogen concentrations during these blooms, and support management efforts to reduce external nitrogen loading to eutrophic systems. [ABSTRACT FROM AUTHOR]

Earthworms can significantly accelerate soil nitrification and N2O emissions by stimulating microbial communities in the soil and their gut. However, the response of earthworm-mediated N transformation to nitrification inhibitors (e.g., 3,4-dimethylpyrazole phosphate, DMPP) is mostly unknown. In this study, soils with or without earthworms were treated with four different concentrations of DMPP (0%, 1%, 2%, and 3%), and samples were collected at six different time points (days 3, 5, 7, 14, 21, and 30 of incubation). The presence of earthworms resulted in the highest soil NH4+ content and lowest NO3– content in DMPP-treated soil, which could be attributed to the highest ureC gene abundance and lowest soil ammonia-oxidizing bacteria (AOB) abundance. Approximately 75% of the earthworm-induced N2O emission could be suppressed by DMPP application, and earthworms also resulted in weak correlations between soil N-related gene abundance (bacterial amoA and nirK) and N2O emission, while such correlations could be strengthened when both DMPP and earthworms were applied. Besides, DMPP application could also significantly suppresses the nitrification and denitrification functions of earthworm gut microbiota, suggesting that the earthworm-induced N2O emission might be mainly produced by the denitrifier communities within their gut. In addition, the earthworm-induced fluctuations in soil NO3− and NH4+ content further resulted in significant losses of earthworm gut microbial diversity, while such losses could be alleviated by DMPP application, which enhanced the C-, P-, and S-cycling capacities of gut microbiota. Altogether, we suggest that DMPP can effectively inhibit nitrification in earthworm-treated soil, subsequently enhancing the earthworm gut microbiota's metabolic capacities. [ABSTRACT FROM AUTHOR]

The recently discovered complete ammonia oxidizers (comammox Nitrospira) have fundamentally changed the perceptions of two-step nitrification. Previous studies suggest that comammox Nitrospira may outcompete canonical ammonia oxidizers under ammonia-limited conditions (e.g., acidic soils). However, there is no convincing evidence that links comammox Nitrospira activity to nitrification in acidic soils. Here, we report the relative contributions of ammonia-oxidizing bacteria (AOB), archaea (AOA), and comammox Nitrospira to nitrification in four orchard soils with different ages (5Y, 10Y, 20Y, and 30Y) and one adjacent natural forest soil (NF) in China. DNA-based stable-isotope probing demonstrated that both AOA and AOB assimilated 13CO2 in the nonacidic NF, 5Y, and 10Y soils, although a small shift from the light fractions to heavy fractions was observed for comammox Nitrospira clade A in the 10Y soil. Comammox Nitrospira clade A rather than AOA and AOB was labeled by 13CO2 in strongly acidic 30Y soil. In strongly acidic 20Y soil, comammox Nitrospira clade A was much more heavily labeled than AOB. These results suggest the different contributions of ammonia oxidizers to nitrification in orchard soils with different ages and a greater functional importance of comammox Nitrospira than canonical ammonia oxidizers in ammonia oxidation in the tested strongly acidic orchard soils. [ABSTRACT FROM AUTHOR]

In order to reveal the biological diversity and the evolution of microbial community structure in the process of sludge cultivation and acclimation at the start-up stage of simultaneous partial nitrification and denitrification (SNAD) process, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the microbial community structure in different operating periods. And molecular cloning was used for species identification and phylogenetic analysis. The 16S rDNA sequence analysis of the characteristic bands of the DGGE profile of total bacteria showed that the bacterial populations in the sludge were rich in diversity, and β- proteobacteria were slightly more abundant and maintained a relatively stable dominant position. With the operation of the reactor, the secondary populations were strengthened and became new dominant communities, such as Firmicutes, γ- proteobacteria, Bacteroides and so on. The 16S rDNA sequence analysis of the characteristic bands of the DGGE profile of ammonia-oxidizing bacteria showed that the strains obtained by sequencing basically belonged to Nitrosomonas of β-proteobacteria. The fast growth rate of this genus made it the dominant ammonia-oxidizing bacteria (AOB) in the activated sludge systems. [ABSTRACT FROM AUTHOR]

Nutrient addition has a significant impact on plant growth and nutrient cycling. Yet, the understanding of how the addition of nitrogen (N) or phosphorus (P) significantly affects soil gross N transformations and N availability in temperate desert steppes is still limited. Therefore, a 15N tracing experiment was conducted to study these processes and their underlying mechanism in a desert steppe soil that had been supplemented with N and P for 4 years in northwestern China. Soil N mineralization was increased significantly by P addition, and N and P additions significantly promoted soil autotrophic nitrification, rather than NH4+‐N immobilization. The addition of N promoted dissimilatory NO3− reduction to NH4+, while that of P inhibited it. Soil NO3−‐N production was greatly increased by N added alone and by that of N and P combined, while net NH4+‐N production was decreased by these treatments. Soil N mineralization was primarily mediated by pH, P content or organic carbon, while soil NH4+‐N content regulated autotrophic nitrification mainly, and this process was mainly controlled by ammonia‐oxidizing bacteria rather than archaea and comammox. NH4+‐N immobilization was mainly affected by functional microorganisms, the abundance of narG gene and comammox Ntsp‐amoA. In conclusion, gross N transformations in the temperate desert steppe largely depended on soil inorganic N, P contents and related functional microorganisms. Soil acidification plays a more key role in N mineralization than other environmental factors or functional microorganisms. [ABSTRACT FROM AUTHOR]

Background and aims: Biological nitrification inhibition (BNI) is a trait that could improve nitrogen-use efficiency of a crop. We studied varietal differences in BNI potential of rice at the vegetative phase when plants were subjected to water stress. Methods: We obtained water-soluble root exudates (RE) and water-extracts of crushed root tissues (RT) from two-week-old seedlings of five rice cultivars grown continuously under adequate water or under water stress and assessed their ability to suppress the activity of Nitrosomonas europaea and the growth of lettuce seedlings. We also investigated how growing rice under continuously saturated (TC) and unsaturated (TU) soil moisture conditions affected potential nitrification rate (PNR) and community structure of ammonia-oxidizing bacteria (AOB) in the rhizosphere compared with bulk soil. Results: We observed that only RT at ≥ 0.50 mg ml−1 suppressed the activity of N. europaea with significant (p < 0.05) differences among rice cultivars. Subjecting rice cultivars PI312777 and PI338046 to water stress significantly (p < 0.05) increased BNI of RT. Inhibition of lettuce root growth by RT was strongly correlated with its BNI (r = 0.83, p < 0.05). In T-RFLP profiles of AOB, the relative abundance of T-RF R205 was lower in TU than in TC in all cultivars except Rexmont. Conclusions: The rice cultivars studied produced compounds that could inhibit ammonia oxidizers, but the degree of BNI differed based on the moisture stress experienced by the crop. Lineages of rice cultivars with known allelopathic potential would be promising candidates to consider for BNI potential. [ABSTRACT FROM AUTHOR]

With excessive nitrogen (N) input, high nitrous oxide (N2O) emissions are frequently observed in greenhouse vegetable fields. We hypothesized that the underlying production mechanisms can be derived across a wide selection of vegetable fields in the middle and lower reaches of the Yangtze River. Thus, we investigated the emission characteristics and relative contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and other microbial processes to the N2O production from five long-term greenhouse vegetable fields through an incubation experiment with combined inhibition methods. The results showed that the ammonia oxidation process is the dominant contributor to N2O production at all five sites, accounting for 88–97% of the total N2O emissions. Regardless of acidic, neutral, or alkaline soil, AOA-driven N2O emission rates were consistently higher than AOB-driven N2O emission rates. Both AOA-driven and AOB-driven N2O emissions exhibited positive correlations with soil pH, with significant increases in soil N2O production associated with high pH levels. Therefore, general production mechanisms were derived, such that more attention should be paid to AOA-driven N2O emissions and to vegetable soils with a relatively high pH in the middle and lower reaches of the Yangtze River. [ABSTRACT FROM AUTHOR]

Reservoirs are important sites for nitrogen processing, especially those located in agricultural and urban watersheds. Nitrogen inputs promote N2O production and emission, but the microbial pathways controlling N2O have been seldom studied in reservoir water columns. We determined N2O concentration in the water column of 12 reservoirs during the summer stratification and winter mixing. We explored the potential microbial sources and sinks of N2O by quantifying key genes involved in ammonia oxidation (bacterial and archaeal amoA) and denitrification (nirS and nosZ). Dissolved N2O varied up to three orders of magnitude (4.7–2441.2 nmol L−1) across systems, from undersaturated to supersaturated values (37%–24,174%) depending on reservoirs and depths. N2O concentration depended on nitrogen and oxygen availabilities, with the lowest and highest N2O values at suboxic conditions. Ammonia‐oxidizing archaea dominated over ammonia‐oxidizing bacteria but were not related to the dissolved N2O. In contrast, the abundance of the nirS gene was significantly related to N2O concentration, and three orders of magnitude higher than amoA abundance. Denitrifying bacteria appeared consistently in the water column of all reservoirs. The nirS and nosZ genes appeared in oxic and suboxic waters, but they were more abundant in suboxic waters. The nitrate concentration, and nirS and nosZ relative abundances explained the dissolved N2O. Besides, nirS abundance was related positively with total phosphorus and cumulative chlorophyll a, a proxy for fresh organic matter. Therefore, P inputs, not just N inputs, promoted N2O production by denitrification in the water column of reservoirs. [ABSTRACT FROM AUTHOR]

The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is an insect commonly used for the bioconversion of various organic wastes. Not only can the BSF convert organic waste into macromolecular organic substances, such as insect proteins, but it can also lessen the pollution associated with these waste products by reducing ammonia emissions, for example. In this study, we measured the effects of adding fruit fermentation broth (Fer) and commercial lactic acid bacteria fermentation broth (Em) to kitchen waste (KW), as deodorizing auxiliary substances, on the growth performance of black soldier fly larvae (BSFL), the intestinal flora structure of BSFL, the ammonia emission from the KW substrate, and the microbial community structure of the KW substrate. We found that the addition of Fer or Em increased the body weight of BSFL after 6 d of culture, increasing the growth rate by 9.96% and 7.96%, respectively. The addition of Fer not only reduced the pH of the KW substrate but also increased the relative abundance of probiotics, such as Lactobacillus, Lysinibacillus, and Vagococcus, which inhibited the growth of ammonifiers such as Bacillus, Oligella, Paenalcaligenes, Paenibacillus, Pseudogracilibacillus, and Pseudomonas, resulting in the reduction of ammonia emission in the KW substrate. Moreover, the addition of Fer or Em significantly increased the relative abundances of Bacteroides, Campylobacter, Dysgonomonas, Enterococcus, and Ignatzschineria in the gut of BSFL and increased the species diversity and richness in the KW substrate. Our findings provide a novel way to improve the conversion rate of organic waste and reduce the environmental pollution caused by BSF. [ABSTRACT FROM AUTHOR]

Background and aims: Biological nitrification inhibition (BNI) is a chemical ecological phenomenon whereby plants specifically suppress nitrification by releasing inhibiting compounds from roots, an effective strategy for improving nitrogen uptake by limiting nitrogen losses from agricultural fields. During this study, we have aimed at characterizing hydrophilic BNI activity released from maize roots to understand the chemical basis for BNI function in maize. Methods: Maize plants were grown hydroponically and root exudates were collected using water-based solutions and hydrophilic BNI activity was extracted. We isolated the target BNI compounds by a combination of chromatographic techniques and bioassays using a recombinant luminescent ammonia-oxidizing bacterium Nitrosomonas europaea (pHLUX20). Results: We identified 6-methoxy-2(3H)-benzoxazolone (MBOA) as the responsible BNI compound with a median effective dose (ED50) = 0.76 μM. MBOA inhibited the conversion of NH3 to NH2OH as well as NH2OH to NO2− in N. europaea, suggesting that MBOA blocks both ammonia monooxygenase and hydroxylamine oxidoreductase enzymatic pathways. Treatment with MBOA significantly suppressed NO2− and NO3− production during soil incubation, but this activity was reduced subsequently due to biodegradation of MBOA by soil microbes. A quantification experiment revealed that MBOA accounted for nearly 50% of the total BNI activity in hydrophilic and hydrophobic exudates from maize roots. A soil incubation test showed that two previously identified benzoxazinoids, HDMBOA and HDMBOA-β-glucoside, can be eventually transformed into MBOA. Conclusion: We elucidated MBOA as the key component of BNI in maize. Collectively, the present findings will serve as the groundwork for construction of an advanced environment-friendly agricultural system. [ABSTRACT FROM AUTHOR]

An important role of nitric oxide (NO) as either a free intermediate in the NH3 oxidation pathway or a potential oxidant for NH3 or NH2OH has been proposed for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively. However, tracing NO metabolism at low concentrations remains notoriously difficult. Here, we use electrochemical sensors and the mild NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1- oxyl 3-oxide (PTIO) to trace apparent NO concentration and determine production rates at low micromolar concentrations in the model AOB strain Nitrosomonas europaea. In agreement with previous studies, we found that PTIO does not affect NH3 oxidation instantaneously in both Nitrosospira briensis and Nitrosomonas europaea, unlike inhibitors for ammonia oxidation such as allylthiourea and acetylene, although it effectively scavenged NO from the cell suspensions. Quantitative analysis showed that NO production by N. europaea amounted to 3.15% to 6.23% of NO2 – production, whereas N. europaea grown under O2 limitation produced NO equivalent to up to 40% of NO2 – production at high substrate concentrations. In addition, we found that PTIO addition to N. europaea grown under O2 limitation abolished N2O production. These results indicate different turnover rates of NO during NH3 oxidation under O2-replete and O2-limited growth conditions in AOB. The results suggest that NO may not be a free intermediate or remain tightly bound to iron centers of enzymes during hydroxylamine oxidation and that only NH3 saturation and adaptation to O2 limitation may lead to significant dissociation of NO from hydroxylamine dehydrogenase. IMPORTANCE Ammonia oxidation by chemolithoautotrophic ammonia-oxidizing bacteria (AOB) is thought to contribute significantly to global nitrous oxide (N2O) emissions and leaching of oxidized nitrogen, particularly through their activity in nitrogen (N)-fertilized agricultural production systems. Although substantial efforts have been made to characterize the N metabolism in AOB, recent findings suggest that nitric oxide (NO) may play an important mechanistic role as a free intermediate of hydroxylamine oxidation in AOB, further implying that besides hydroxylamine dehydrogenase (HAO), additional enzymes may be required to complete the ammonia oxidation pathway. However, the NO spin trap PTIO was found to not inhibit ammonia oxidation in AOB. This study provides a combination of physiological and spectroscopic evidence that PTIO indeed scavenges only free NO in AOB and that significant amounts of free NO are produced only during incomplete hydroxylamine oxidation or nitrifier denitrification under O2-limited growth conditions. [ABSTRACT FROM AUTHOR]

The responses of soil nitrogen (N) transformations to climate change are crucial for biome productivity prediction under global change. However, little is known about the responses of soil gross N transformation rates to drought gradient. Along an aridity gradient across the 2700 km transect of drylands on the Qinghai‐Tibetan Plateau, this study measured three main soil gross N transformation rates in both topsoil (0–10 cm) and subsoil (20–30 cm) using the laboratorial 15N labeling. The relevant soil abiotic and biotic variables were also determined. The results showed that gross N mineralization and nitrification rates steeply decreased with increasing aridity when aridity was less than 0.5 but just slightly decreased with increasing aridity when aridity was larger than 0.5 at both soil layers. In topsoil, the decreases of the two gross rates were accompanied by the similar decreased patterns of soil total N content and microbial biomass carbon with increasing aridity (p <.05). In subsoil, although the decreased pattern of soil total N with increasing aridity was still similar to the decreases of the two gross rates (p <.05), microbial biomass carbon did not change (p >.05). Instead, bacteria and ammonia oxidizing archaea abundances decreased with increasing aridity when aridity was larger than 0.5 (p <.05). With an aridity threshold of 0.6, gross N immobilization rate increased with increasing aridity in wetter region (aridity < 0.6) accompanied with an increased bacteria/fungi ratio, but decreased with increasing aridity in drier region (aridity > 0.6) where mineral N and microbial biomass N also decreased at both soil layers (p <.05). This study provided new insight to understand the differential responses of soil N transformation to drought gradient. The threshold responses of the gross N transformation rates to aridity gradient should be noted in biogeochemical models to better predict N cycling and manage land in the context of global change. [ABSTRACT FROM AUTHOR]

To clarify the effect of enhanced UV-B radiation on soil nitrogen transformation and its biological processes in paddy fields, the effects of enhanced ultraviolet-B radiation (0, 2.5, 5.0 and 7.5 kJ m−2) on soil nitrogen transformation and N2O emission, functional microbial quantity, enzyme activity, and gene expression during the growth period (tillering, jointing, booting and maturity stage) of rice were investigated in situ in a rice paddy field in the Yuanyang terraces, Yunnan Province, southwest China. The results show that UV-B radiation decreased the NH4+-N content, increased the NO3–N content in the rhizosphere, decreased N2O emissions from paddy fields, and significantly affected the properties of soil nitrogen transforming microorganisms. The 5.0 kJ m−2 UV-B radiation increased the quantity of ammonifying bacteria and ammonia oxidizing bacteria by 18–160% and 34–151%, respectively, decreased the urease activity in the rice rhizosphere by 11.9–27%; and significantly increased the expression of AOB-amoA and nosZ genes. Thus, the enhanced UV-B radiation increased the ammonia-oxidizing bacteria and AOB-amoA and nosZ gene expression, promoted the transformation of NH4+-N to NO3–N in the rice rhizosphere, and reduced N2O emissions in the paddy field. [ABSTRACT FROM AUTHOR]

In this study, we sought to investigate the impact of urbanization, the presence of concrete river bottoms, and nutrient pollution on microbial communities along the L.A. River. Six molecular markers were evaluated for the identification of bacteria, plants, fungi, fish, and invertebrates in 90 samples. PCA (principal components analysis) was used along with PAM (partitioning around medoids) clustering to reveal community structure, and an NB (negative binomial) model in DESeq2 was used for differential abundance analysis. PCA and factor analysis exposed the main axes of variation but were sensitive to outliers. The differential abundance of Proteobacteria was associated with soft-bottom sites, and there was an apparent balance in the abundance of bacteria responsible for nitrogen cycling. Nitrogen cycling was explained via ammonia-oxidizing archaea; the complete ammonia oxidizers, Nitrospira sp.; nitrate-reducing bacteria, Marmoricola sp.; and nitrogen-fixing bacteria Devosia sp., which were differentially abundant at soft-bottom sites (p adj < 0.002). In contrast, the differential abundance of several cyanobacteria and other anoxygenic phototrophs was associated with the impervious sites, which suggested the accumulation of excess nitrogen. The soft-bottom sites tended to be represented by a differential abundance of aerobes, whereas the concrete-associated species tended to be alkaliphilic, saliniphilic, calciphilic, sulfate dependent, and anaerobic. In the Glendale Narrows, downstream from multiple water reclamation plants, there was a differential abundance of cyanobacteria and algae; however, indicator species for low nutrient environments and ammonia-abundance were also present. There was a differential abundance of ascomycetes associated with Arroyo Seco and a differential abundance of Scenedesmaceae green algae and cyanobacteria in Maywood, as seen in the analysis that compared suburban with urban river communities. The proportion of Ascomycota to Basidiomycota within the L.A. River differed from the expected proportion based on published worldwide freshwater and river 18S data; the shift in community structure was most likely associated with the extremes of urbanization. This study indicates that extreme urbanization can result in the overrepresentation of cyanobacterial species that could cause reductions in water quality and safety. [ABSTRACT FROM AUTHOR]

The assembly mechanisms shaping the elevational patterns of diversity and community structure in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are not well understood. We investigated the diversities, co-occurrence network patterns, key drivers, and potential activities of AOA and AOB communities along a large altitudinal gradient. The α-diversity of the AOA communities exhibited a monotonically decreasing pattern with increasing elevation, whereas a sinusoidal pattern was observed for the AOB communities. The mean annual temperature was the single factor that most strongly influenced the α-diversity of the AOA communities; however, the interactions of plant richness, soil conductivity, and total nitrogen made comparable contributions to the α-diversity of the AOB communities. Moreover, the β-diversities of the AOA and AOB communities were divided into two distinct clusters by elevation, i.e., low- (1800–2600 m) and high-altitude (2800–4100 m) sections. These patterns were attributed mainly to the soil pH, followed by variations in plant richness along the altitudinal gradient. In addition, the AOB communities were more important to the soil nitrification potential in the low-altitude section, whereas the AOA communities contributed more to the soil nitrification potential in the high-altitude section. Overall, this study revealed the key factors shaping the elevational patterns of ammonia-oxidizing communities and might predict the consequences of changes in ammonia-oxidizing communities. [ABSTRACT FROM AUTHOR]

Background and aims: Sorghum (Sorghum bicolor) is able to exude allelochemicals with biological nitrification inhibition (BNI) capacity. Therefore, sorghum might be an option as cover crop since its BNI ability may reduce N pollution in the following crop due to a decreased nitrification. However, BNI exudation is related to the physiological state and development of the plant, so abiotic stresses such as drought might modify the rate of BNI exudation. Hence, the objective was to determine the effect of drought stress on sorghum plants' BNI release. Methods: The residual effects of sorghum crops over ammonia-oxidizing bacteria (AOB) were monitored in a 3-year field experiment. In a controlled-conditions experiment, sorghum plants were grown under Watered (60% WFPS) or Moderate drought (30% WFPS) conditions, and fertilized with ammonium sulphate (A), ammonium sulphate + DMPP (A+D), or potassium nitrate (KNO3−). Soil mineral N was determined, and AOB populations were quantified. Additionally, plant biomass, isotopic discrimination of N and C, and photosynthetic parameters were measured in sorghum plants. Results: In the driest year, sorghum was able to reduce the AOB relative abundance by 50% at field conditions. In the plant-soil microcosm, drought stress reduced leaf photosynthetic parameters, which had an impact on plant biomass. Under these conditions, sorghum plants exposed to Moderate drought reduced the AOB abundance of A treatment by 25% compared to Watered treatment. Conclusion: The release of BNI by sorghum under limited water conditions might ensure high soil NH4+-N pool for crop uptake due to a reduction of nitrifying microorganisms. [ABSTRACT FROM AUTHOR]

Background: Recently, it has been found that nitrogen (N) deposition strongly affects the coverage of biocrusts. However, we know little about the response of exopolysaccharides (EPSs), the key cementing material in the formation and stability of biocrusts, to N deposition. Method: Three N-sources including nitrate, ammonia and urea were added to biocrusts at three rates (2 mg/g, 4 mg/g, 8 mg/g) to evaluate the effect of N additions on the growth of biocrusts and the abundance of EPS. Results: Our results showed 2 mg/g of nitrate–N had no obvious effect on the cyanobacterial biomass, while 4 and 8 mg/g of nitrate–N inhibited the growth of Microcoleus vaginatus, the dominant cyanobacterium in biocrusts, but promoted other cyanobacteria growth. Ammonia-N and urea-N strongly decreased the cyanobacterial biomass, indicated by chlorophyll-a and 16 s rRNA gene copy-numbers. On the whole, N additions had a positive impact on the α-biodiversity of biocrusts. However, Ammonia-N and urea-N shifted the bacterial communities from more Cyanobacteria to more Proteobacteria and Actinobacteria. Notably, lesser-N (2 mg/g) promoted the excretion of EPSs, while greater-N (8 mg/g) had the opposite effect, and the total proportion of rhamnose and fucose in EPSs decreased in all treatment groups. Conclusion: N additions (except 2 mg/g of nitrate–N) reduced cyanobacterial biomass and affected the bacterial communities in biocrusts, which would obstruct the development and succession of biocrusts. Meanwhile, the simultaneous reductions of the EPSs contents and proportion of rhamnose and fucose in EPSs may further reduce stability and persistence of cyanobacterial biocrusts, after N additions. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) are important intermediate links in the nitrogen cycle. Apart from the AOA and AOB communities in soil, we further investigated co-occurrence patterns and microbial assembly processes subjected to inorganic and organic fertilizer treatments for over 35 years. The amoA copy numbers and AOA and AOB communities were found to be similar for the CK and organic fertilizer treatments. Inorganic fertilizers decreased the AOA gene copy numbers by 0.75–0.93-fold and increased the AOB gene copy numbers by 1.89–3.32-fold compared to those of the CK treatment. The inorganic fertilizer increased Nitrososphaera and Nitrosospira. The predominant bacteria in organic fertilizer was Nitrosomonadales. Furthermore, the inorganic fertilizer increased the complexity of the co-occurrence pattern of AOA and decreased the complexity pattern of AOB comparing with organic fertilizer. Different fertilizer had an insignificant effect on the microbial assembly process of AOA. However, great difference exists in the AOB community assembly process: deterministic process dominated in organic fertilizer treatment and stochastic processes dominated in inorganic fertilizer treatment, respectively. Redundancy analysis indicated that the soil pH, NO3−N, and available phosphorus contents were the main factors affecting the changes in the AOA and AOB communities. Overall, this findings expanded our knowledge concerning AOA and AOB, and ammonia‐oxidizing microorganisms were more disturbed by inorganic fertilizers than organic fertilizers. [ABSTRACT FROM AUTHOR]

Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha−1 was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha−1 (52.7–56.5%) and when manure was added (72.7–99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha−1 (58.4–84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management. [ABSTRACT FROM AUTHOR]

The ammonia monooxygenase (AMO) is a key enzyme in ammonia‐oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper‐containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co‐oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well‐established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia‐oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (Ki) for methane and methanol were 2.2 and 20 μM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia‐oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in 'Ca. Nitrosocosmicus franklandus C13' in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one‐carbon (C1) compounds in ammonia‐oxidizing archaea. [ABSTRACT FROM AUTHOR]

The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils. [ABSTRACT FROM AUTHOR]