Agriculture receives approximately 25 % of the annual global nitrogen input, 37 % of which subsequently runs off into adjacent low-order streams and surface water, where it may contribute to high nitrification and nitrous oxide (N2O). However, the mechanisms of nitrification and the pathways controlling N2O production in agricultural streams remain unknown. Here, we report that the third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is widespread and contributes to important ammonia oxidation with low ammonia-N2O conversion in both basin- and continental-scale agricultural streams. The contribution of comammox to ammonia oxidation (21.5 ± 2.3 %) was between that of bacterial (68.6 ± 2.7 %) and archaeal (9.9 ± 1.8 %) ammonia oxidation. Interestingly, N2O production by comammox (18.5 ± 2.1 %) was higher than archaeal (10.5 ± 1.9 %) but significantly lower than bacterial (70.2 ± 2.6 %) ammonia oxidation. The first metagenome-assembled genome (MAG) of comammox bacteria from agricultural streams further revealed their potential extensive diverse and specific metabolism. Their wide habitats might be attributed to the diverse metabolism, i.e. harboring the functional gene of nitrate reduction to ammonia, while the lower N2O would be attributed to their lacking biological function to produce N2O. Our results highlight the importance of widespread comammox in agricultural streams, both for the fate of ammonia fertilizer and for climate change. However, it has not yet been routinely included in Earth system models and IPCC global assessments. Synopsis Widespread but overlooked comammox contributes to important ammonia oxidation but low N2O production, which were proved by the first comammox MAG found in agricultural streams.

Plant growth and high yields are secured by intensive use of nitrogen (N) fertilizer, which, however, pollutes the environment, especially when N is in the form of nitrate. Ammonium is oxidized to nitrate by nitrifiers, but roots can release biological nitrification inhibitors (BNIs). Under what conditions does root-exudation of BNIs facilitate nitrogen N uptake and reduce pollution by N loss to the environment? We modeled the spatial-temporal dynamics of nitrifiers, ammonium, nitrate, and BNIs around a root and simulated root N uptake and net rhizosphere N loss over the plant\'s life cycle. We determined the sensitivity of N uptake and loss to variations in the parameter values, testing a broad range of soil-plant-microbial conditions, including concentrations, diffusion, sorption, nitrification, population growth, and uptake kinetics. An increase in BNI exudation reduces net N loss and, under most conditions, increases plant N uptake. BNIs decrease uptake in the case of (1) low ammonium concentrations, (2) high ammonium adsorption to the soil, (3) rapid nitrate- or slow ammonium uptake by the plant, and (4) a slowly growing or (5) fast-declining nitrifier population. Bactericidal inhibitors facilitate uptake more than bacteriostatic ones. Some nitrification, however, is necessary to maximize uptake by both ammonium and nitrate transporter systems. An increase in BNI exudation should be co-selected with improved ammonium uptake. BNIs can reduce N uptake, which may explain why not all species exude BNIs but have a generally positive effect on the environment by increasing rhizosphere N retention.

Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing?

The seasonal variability, pathways, and sea-to-air fluxes of nitrous oxide (N2O) and methane (CH4) in the coastal environment, where coastal upwelling and mudbanks co-exist are presented based on the monthly time-series measurements from November 2021 to December 2022. Upwelling-driven hypoxic water\'s shoreward propagation and persistence were the major factors controlling the N2O concentrations, while the freshwater influx and sedimentary fluxes modulate CH4 concentrations. The N2O concentrations were high during the southwest monsoon (up to 35 nM; 19 ± 8 nM)), followed by spring inter-monsoon (up to 19 nM; 10 ± 5 nM), and lowest during the northeast monsoon (up to 13 nM; 8 ± 2 nM), whereas the CH4 levels were high during the spring inter-monsoon (8.4 to 65 nM), followed by southwest monsoon (6.8 to 53.1 nM) and relatively lower concentrations during the northeast monsoon (3.3 to 32.6 nM). The positive correlations of excess N2O with Apparent Oxygen Utilisation (AOU) and the sum of nitrate and nitrite (NOx) indicate that nitrification is the primary source of N2O in the mudbank regime. The negative correlation of CH4 concentrations with salinity indicates considerable input of CH4 through freshwater influx. CH4 exhibited a highly significant positive correlation with Chlorophyll-a throughout the study period. Furthermore, it displayed a statistically significant positive correlation with phosphate (PO43-) during the northeast monsoon while a strong negative correlation with PO43- during the spring inter-monsoon, pointing towards the role of aerobic CH4 production pathways in the mudbank regime. N2O and CH4 exhibited a contrasting seasonal pattern of sea-to-air fluxes, characterised by the highest N2O fluxes during the southwest monsoon (hypoxia) (13 ± 10 μM m-2 d-1), followed by spring inter-monsoon (12 ± 16 μM m-2 d-1), and the lowest during the northeast monsoon (0.6 ± 3 μM m-2 d-1). Conversely, the highest sea-to-air fluxes of CH4 were noticed during the spring inter-monsoon (74 ± 56 μM m-2 d-1), followed by the southwest monsoon (45 ± 35 μM m-2 d-1), and the lowest values during the northeast monsoon (19 ± 16 μM m-2d-1). Long-term time-series measurements will be invaluable in understanding the longer-term impacts of climate-driven variability on marine biogeochemical cycles in dynamic nearshore systems.

The drainage of peatlands followed by land use conversion significantly impacts on the fluxes of green-house gases (GHGs, i.e. CO2, CH4, and N2O) to and from the atmosphere, driven by changes in soil properties and microbial communities. In this study, we compared saturated peatlands with drained ones used for sheep grazing or cultivated, which are common in South-West Iceland. These areas exhibit different degrees of soil saturation and nitrogen (N) content, reflecting the anthropic pressure gradient. We aimed at covering knowledge gaps about lack of estimates on N2O fluxes and drainage, by assessing the emissions of GHGs, and the impact of land conversion on these emissions. Moreover, we investigated soil microbial community functional diversity, and its connection with processes contributing to GHGs emission. GHGs emissions differed between saturated and drained peatlands, with increased soil respiration rates (CO2 emissions) and N mineralization (N2O), consistent with the trend of anthropogenic pressure. Drainage drastically reduced methane (CH4) emissions but increased CO2 emissions, resulting in a higher global warming potential (GWP). Cultivation, involving occasional tillage and fertilization, further increased N2O emissions, mediated by higher N availability and conditions favorable to nitrification. Functional genes mirrored the overall trend, showing a shift from prevalent methanogenic archaea (mcrA) in saturated peatlands to nitrifiers (amoA) in drained-cultivated areas. Environmental variables and nutrient content were critical factors affecting community composition in both environments, which overall affected the GHGs emissions and the relative contribution of the three gases.

There is no doubt that hypoxia and seawater mixture are profoundly affecting the global nitrogen (N) cycle. However, their mechanisms for altering N cycling patterns in shallow coastal groundwater are largely unknown. Here, we examined shallow groundwater N transformation characteristics (dissolved inorganic N and related chemical properties) in the coastal area of east and west Shenzhen City. Results showed that common hypoxic conditions exist in this study area. Ions/Cl- ratios indicated varying levels of saltwater mixture and sulfide formation across this study area. Dissolved oxygen (DO) affects the N cycle process by controlling the conditions of nitrification and the formation of sulfides. Salinity affects nitrification and denitrification processes by physiological effects, while sulfide impacts nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) processes through its own toxicity mechanism and the provision of electron donors for DNRA organisms. Redundancy analysis (RDA) results indicate that the influence magnitude is in the following order: DO > sulfide > salinity. Seawater mixture weakened the nitrification and denitrification of groundwater by changing salinity, while hypoxia and its controlled sulfide formation not only weaken nitrification and denitrification but also stimulated the DNRA process and promotes N regeneration. In this study area, hypoxia is considered to exert greater impacts on N cycling in the coastal shallow groundwater than seawater mixture. These findings greatly improve our understanding of the consequences of hypoxia and seawater mixture on coastal groundwater N cycling.

Nitrification by aquarium biofilters transforms ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Prior to the discovery of complete ammonia-oxidizing (\"comammox\" or CMX) Nitrospira, previous research revealed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Here, we profiled aquarium biofilter microbial communities and quantified the abundance of all three known ammonia oxidizers using 16S rRNA gene sequencing and quantitative PCR (qPCR), respectively. Biofilter and water samples were each collected from representative residential and commercial freshwater and saltwater aquaria. Distinct biofilter microbial communities were associated with freshwater and saltwater biofilters. Comammox Nitrospira amoA genes were detected in all 38 freshwater biofilter samples (average CMX amoA genes: 2.2 × 103 ± 1.5 × 103 copies/ng) and dominant in 30, whereas AOA were present in 35 freshwater biofilter samples (average AOA amoA genes: 1.1 × 103 ± 2.7 × 103 copies/ng) and only dominant in 7 of them. The AOB were at relatively low abundance within biofilters (average of 3.2 × 101 ± 1.1 × 102 copies of AOB amoA genes/ng of DNA), except for the aquarium with the highest ammonia concentration. For saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. Additional sequencing of Nitrospira amoA genes revealed differential distributions, suggesting niche adaptation based on water chemistry (e.g., ammonia, carbonate hardness, and alkalinity). Network analysis of freshwater microbial communities demonstrated positive correlations between nitrifiers and heterotrophs, suggesting metabolic and ecological interactions within biofilters. These results demonstrate that comammox Nitrospira plays a previously overlooked, but important role in home aquarium biofilter nitrification.
OBJECTIVE: Nitrification is a crucial process that converts toxic ammonia waste into less harmful nitrate that occurs in aquarium biofilters. Prior research found that ammonia-oxidizing archaea (AOA) were dominant over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Our study profiled microbial communities of aquarium biofilters and quantified the abundance of all currently known groups of aerobic ammonia oxidizers. The findings reveal that complete ammonia-oxidizing (comammox) Nitrospira were present in all freshwater aquarium biofilter samples in high abundance, challenging our previous understanding of aquarium nitrification. We also highlight niche adaptation of ammonia oxidizers based on salinity. The network analysis of freshwater biofilter microbial communities revealed significant positive correlations among nitrifiers and other community members, suggesting intricate interactions within biofilter communities. Overall, this study expands our understanding of nitrification in aquarium biofilters, emphasizes the role of comammox Nitrospira, and highlights the value of aquaria as microcosms for studying nitrifier ecology.

Organic fertilizer substitution has been promoted as a weight loss, efficient, and diversified fertilizer substitution technology in agricultural production. However, there is a lack of comprehensive assessment of the impact of organic fertilizers on N2O and NO emissions from orchards. In this study, N2O and NO emissions from peach orchards were observed annually using static dark box-gas chromatography to compare the effects of chemical fertilizer application alone and partial replacement of chemical fertilizer treatment on NO emissions from peach orchards. The results showed that the partial replacement of chemical fertilizers with organic fertilizers reduced the total N2O and NO emissions from peach orchards by 15.0 % and 9.4 %, respectively. The N2O and NO emission factors were reduced by 21.3 % and 21.1 %. The mineral N content of the soil in the organic fertilizer treatment was lower than that in the chemical fertilizer treatment alone. The organic fertilizer treatment increased the contribution of AOA to nitrification and decreased the contribution of AOB, thus reducing N2O and NO from nitrification. In addition, the results of the dual isotope mixing model[δ18O(N2O/H2O) vs. δ15NSP] indicated that the bacterial denitrification/nitrifying bacterial denitrification (bD/nD) process served as the primary pathway for N2O emissions in peach orchards. Partial substitution with organic fertilizers enhanced soil denitrification, resulting in larger reductions in the amounts of N2O and NO. Therefore, partial substitution of organic fertilizer is a viable measure to mitigate nitrogen oxide emissions from orchards and to achieve green and low-carbon development in agriculture.

Simultaneous heterotrophic nitrification and aerobic denitrification (SND) is gaining tremendous attention due to its high efficiency and low cost in water treatment. However, SND on an industrial scale is still immature since effects of coexisting pollutants, for example, heavy metals, on nitrogen removal remains largely unresolved. In this study, a HNAD bacterium (Pseudomonas sp. XF-4) was isolated. It could almost completely remove ammonium and nitrate at pH 5-9 and temperature 20 ℃-35 ℃ within 10 h, and also showed excellently simultaneous nitrification and denitrification efficiency under the coexistence of any two of inorganic nitrogen sources with no intermediate accumulation. XF-4 could rapidly grow again after ammonium vanish when nitrite or nitrate existed. There was no significant effects on nitrification and denitrification when Cd(II) was lower than 10 mg/L, and 95 % of Cd(II) was removed by XF-4. However, electron carrier and electron transport system activity was inhibited, especially at high concentration of Cd(II). Overall, this study reported a novel strain capable of simultaneous nitrification and denitrification coupled with Cd(II) removal efficiently. The results provided new insights into treatment of groundwater or wastewater contaminated by heavy metals and nitrogen.

Dissolved oxygen (DO) levels and carbon-to-nitrogen (C/N) ratio affect nitrous oxide (N2O) emissions by influencing the physiological and ecological dynamics of nitrifying and denitrifying microbial communities in activated sludge systems. For example, Nitrosomonas is a common N2O producing nitrifying bacteria in wastewater treatment plants (WWTPs), and DO conditions can affect the N2O production capacity. Previous studies have reported N2O emission characteristics under adequate DO and C/N conditions in A/O WWTPs. However, in actual operation, owing to economic and managerial factors, some WWTPs have a long-term state of low DO levels in oxic tanks and low influent C/N. Research on N2O emission characteristics in low DO-limited and low C/N ratio WWTPs is limited. This study investigated N2O emissions and the corresponding shifts in microorganisms within an anoxic-oxic (A/O) WWTP over 9-month. Quantitative PCR was used to assess the abundance of ten functional genes related to nitrification and denitrification processes, and high-throughput sequencing of the 16S rRNA gene was employed to determine the composition change of microorganisms. The findings revealed that 1) the average N2O emission factor was 1.07% in the studied WWTP; 2) the DO-limited oxic tank primarily contributed to N2O; 3) NO2-, TOC, and C/N ratios were key factors for dissolved N2O in the aerobic tank; and 4) Nitrosomonas and Terrimonas exhibited a robust correlation with N2O emissions. This research provides data references for estimating N2O emission factors and developing N2O reduction policies in WWTPs with DO-limited and low C/N ratios.