Potential Nitrification Rates Research Articles

The cooperative interaction of AOB and comammox clade A drives nitrification and N2O emissions in a long-term organic fertilized paddy soil

The newly discovered complete ammonia oxidizer (comammox Nitrospira) is able to single-step nitrification capability, and increased our understanding of soil nitrogen cycling. However, the response of comammox and ammonia-oxidizing bacteria (AOB) and archaea (AOA) to long-term fertilization and rhizosphere effects in paddy soils and their relative contribution to the nitrification-derived N2O emissions is still unclear. Here, we collected rhizosphere and bulk soils with thirty years of different fertilization strategies, i.e., non-fertilization (CK), chemical N, P, and K application (NPK), and NPK plus pig manure application (NPKM), respectively, to test changes in nitrification potential rate (PNR), N2O emission fluxes, abundance of ammonia oxidizers and their significant drivers. The result showed that NPKM significantly increased soil C and N levels, the proportion of soil middle-size particles (40.35–148.00 μm class), and soil PNR, but decreased soil N2O emissions, especially in the drying time of paddy (P < 0.05), compared to NPK fertilization. NPKM had the highest values of AOA, AOB, and comammox clade A amoA gene copy numbers (P < 0.05), but clade B was increased by the NPK in the rhizosphere soil. Furthermore, fertilization showed greater effects on ammonia oxidizers (except for clade B) than the rhizosphere effect. Mantel test showed that SOM, TP, pH, NH4+, and NO3− were main abiotic factors causing the niche separation among ammonia oxidizers. Linear regression analysis and structural equation model (SEM) showed that both PNR and N2O emission fluxes were significantly associated with the abundance of AOB and comammox clade A (P < 0.05). Therefore, our results underline the importance of AOB together with comammox clade A in nitrification and N2O production in long-term organic fertilized paddy fields, which could provide new ideas for the mitigation of N2O emission by adopting organic fertilization scenarios in Chinese paddy fields.

Wheat straw and microbial inoculants have an additive effect on N2O emissions by changing microbial functional groups

AbstractStraw‐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.

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts.

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Vallisneria spiralis L. adaptive capacity improves pore water chemistry and increases potential nitrification in organic polluted sediments

BackgroundMacrophytes may modify benthic biodiversity and biogeochemistry via radial oxygen loss from roots. This condition contrasts sediments anoxia, allows roots respiration, and facilitates aerobic microbial communities and processes in the rhizosphere. Simultaneously, the rhizosphere can stimulate anaerobic microorganisms and processes via exudates or by favoring the build-up of electron acceptors as nitrate. As eutrophication often results in organic enrichment in sediments and large internal nutrients recycling, an interesting research question is to investigate whether plants maintain the capacity to stimulate aerobic or anaerobic microbial communities and processes also under elevated organic pollution.MethodsA manipulative experiment was carried out under laboratory-controlled conditions. Microcosms containing bare sediments and sediments transplanted with the macrophyte Vallisneria spiralis L. were created. The effect of the plant was investigated on sediments with moderate (8%) and elevated (21%) organic matter content, after an acclimatization period of 30 days. Chemical and physical parameters, microbial community composition and the potential rates of nitrification, denitrification and nitrate ammonification were measured at two different depths (0–1 and 1–5 cm) after the acclimatization period to evaluate the role of roots.ResultsVallisneria spiralis grew and assimilated pore water nutrients at the two organic matter levels and vegetated sediments had always nutrient-depleted porewaters as compared to bare sediments. Nitrifying microbes had a lower relative abundance and diversity compared to denitrifying bacteria. However, regardless of the organic content, in vegetated sediments nitrifiers were detected in deeper horizons as compared to bare sediments, where nitrification was confined near the surface. In contrast, potential denitrification rates were not affected by the presence of roots, but probably regulated by the presence of nitrate and by root-dependent nitrification. Potential nitrate ammonification rates were always much lower (< 3%) than potential denitrification rates.ConclusionsVallisneria spiralis affects N-related microbial diversity and biogeochemistry at moderate and elevated organic matter content, smoothing bottom water–pore water chemical gradients and stimulating nitrification and nitrogen loss via denitrification. These results suggest the possibility to deploy V. spiralis as a nature-based solution to counteract eutrophication in freshwater systems impacted by high loads of organic matter, for example, downstream of wastewater treatment plants.

Mitigating soil degradation in continuous cropping banana fields through long-term organic fertilization: Insights from soil acidification, ammonia oxidation, and microbial communities

Exploring the potential of organic fertilizers as a mitigating strategy against the negative consequences induced by prolonged use of inorganic fertilizers in high-intensity banana cultivation is critically essential. Ammonia-oxidizer are closely linked to soil acidification, and how they respond to the long term fertilized banana field soil still poorly understood. In this study, soil samples from long-term inorganic (CF), and inorganically plus organically fertilized banana fields (OF) (from 2010 to 2019) were used to investigate the soil acid buffer capacity (pHBC), the potential nitrification rate (PNR), and the community structure of bacteria, fungi, ammonia-oxidizing archaea (AOA), and bacteria (AOB). Compared to the natural soil (CK, unplanted, and unfertilized), the pH and pHBC in the long-term fertilized banana field (both CF and OF) were significantly reduced. However, the pHBC was 1.3 times higher in soil receiving OF treatment than that in CF treatment. Organic matter (OM) and total nitrogen (TN) were significantly increased in the OF treated soil, which were 1.88 and 1.6 times higher compared to the CF-treated ones. The PNR in banana soil was 3.71–4.85 times higher than in the natural soil. High-throughput sequencing results showed that Candidatus Nitrosospharea SCA1170-like AOA and Nitrosospira spp-like AOB were adapted to long-term fertilization in banana field soil. Potentially pathogenic bacteria, Xanthomonadaceae, were enriched in CF-treated soil compared to CK and OF soils. Opposingly, potentially beneficial Streptomyces and Arthrobacter were enriched in natural soil. Meanwhile, the OF-treated soil demonstrated a greater abundance of beneficial Bacillus and Alicyclobacillus. The study reveals that organic fertilizers ameliorate soil acidification, low organic matter content and microbial diversity compared to inorganic fertilizers for banana cultivation.

Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria.

Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40days) as compared with other organic manure. The level of PTEs (Cu2+, Fe2+, Pb2+, Cd2+, and Zn2+) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe2+, total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.

Straw addition promotes the nitrification process and the wheat yield linked to trophic interactions among microbes

AbstractStraw 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.

Sugarcane exudates as nitrification inhibitors; improvement of soybean nitrogen recovery and yield by reducing soil nitrification and N2O emission using 15N tracing techniques

BNI (biological nitrification inhibition) derived from root exudates is typically used in rotation cropping systems to increase the crop nitrogen efficiency (NUE). Recently, the root exudates secreted by three sugarcane varieties in Thailand have been found to inhibit the nitrification and accumulation. The objective of the study was to evaluate the effectiveness of the sugarcane root exudate on (i) soil nitrification rate and N dynamics (soil mineral N and nitrous oxide (N2O) emission) and (ii) growth, yield, and 15N recovery by soybean under greenhouse conditions. The experiment was laid out as a randomized complete block design (RCBD), with five treatments and four replications: (i) N fertilizer (Control); (ii) Control + Uthong 13 sugarcane root exudate (UT13); (iii) Control + Khon Kaen 3 sugarcane root exudate (KK3); (iv) Control + wild cane sugarcane root exudate (Spone) and (v) Control + dicyandiamide (DCD). 15N fertilizer was applied to a micro-plot for 15N recovery. Soybean was planted and fertilized at 75 kg ha−1 N as (NH4)2SO4. Soil samples were collected at 1, 3, 7, 14, 21 and 28 days after N fertilization (DANF) for pH, potential nitrification rate (PNR), NH4+, NO3− and MBN measurement at 0–15 and 15–30 cm soil depths. A gas sample was collected by the soil chamber technique for an N2O emissions study on the soil sampling date. The soybean growth was monitored at 30 and 60 DAP (days after planting) for height, leaf area, leaf area index (LAI), SCMR and dry weight (DW). At soybean harvest, seed yield, yield components and N uptake were recorded. Our study revealed that the sugarcane root exudates significantly decreased PNR up to 14 DANF and increased NH4+ content in soil and reduced commutative N2O–N fluxes after 14 DANF, compared to N treatment (p < 005). The root exudate treatments not only increased growth (total DW and LAI at 60 DAP), yield (number of pods and seeds per plant) and N uptake (17–19%) but also 15N recovery in the total plant. This confirms the capacity of BNIs from sugarcane root exudates. In conclusion, sugarcane root exudates can effectively mitigate N2O emissions and enhance soybean N uptake under greenhouse conditions.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate.

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 nitrification 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.IMPORTANCEThe 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 nitrification 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.

Changes in soil microbe-mediated carbon, nitrogen and phosphorus cycling during spontaneous succession in abandoned Pb[sbnd]Zn mining areas

The mechanism through which soil microorganisms mediate carbon and nutrient cycling during mine wasteland restoration remained unknown. Using soil metagenome sequencing, we investigated the dynamic changes in soil microbial potential metabolic functions during the transition from biological soil crusts (BSC) to mixed broad-conifer forest (MBF) in a typical PbZn mine. The results showed soil microorganisms favored carbon sequestration through anaerobic and microaerobic pathways, predominantly using efficient, low-energy pathways during succession. Genes governing carbon degradation and aerobic respiration increased by 19.56 % and 24.79 %, respectively, reflecting change toward more efficient and intensive soil carbon utilization in late succession. Nitrogen-cycling genes mediated by soil microorganisms met their maximum influence during early succession (sparse grassland, SGL), leading to a respective increase of 75.29 % and 76.81 % in the net potential nitrification rate and total nitrogen content. Mantel and correlation analyses indicated that TOC, TN, Zn and Cd contents were the main factors affecting the soil carbon and phosphorus cycles. Soil AP content emerged as the primary influencer of genes associated with the nitrogen cycle. These results shed light on the dynamic shifts in microbial metabolic activities during succession, providing a genetic insight into biogeochemical cycling mechanisms and underscoring crucial factors influencing soil biogeochemical processes in mining regions.

The addition of discrimination inhibitors stimulations discrimination potential and N2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems.

Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level. In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation. The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N2O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N2O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N2O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA. The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N2O emission, which has important implications for soil nitrogen cycle.

Controls on in-stream nitrogen loss in western Lake Erie tributaries

Management efforts to reduce cyanobacterial harmful algal blooms (cHABs) in the Great Lakes have focused on decreasing tributary inputs of phosphorus (P). Recent research has indicated that reduction of both P and nitrogen (N) can lessen cHABs severity. Microbially mediated N cycling in streambed sediment may reduce N riverine loads, yet little is known about in-stream N processing rates in the Maumee River Basin, a major source of nutrients to Lake Erie. During summer of 2019 and 2021, we sampled streambed sediment to measure potential nitrification and denitrification rates using the acetylene block method at 78 sites throughout the Maumee River network. We used structural equation models to identify indirect and direct drivers of denitrification. Precipitation was greater in 2019, resulting in a 67 % increase in mean discharge, 41 % of farm fields to be fallow, and a 50 % reduction in fertilizer use. During summer field surveys, median stream-water nitrate concentrations were not different between 2019 and 2021. Median denitrification rates were 13.3 mg N/m2/h and 31.2 mg N/m2/h, respectively, indicating high potential to remove N. Nitrate concentrations and nitrification rates were strong direct drivers of denitrification, especially in 2019 when coupled nitrification–denitrification sustained denitrification. Nitrate concentrations varied with land use. Notably, nitrate concentrations increased with the area of fallow land, which may indicate the presence of a legacy N source. These findings indicate that promoting streambed denitrification could reduce N loads to Lake Erie, but legacy N currently stored in the system may mask N reduction efforts.

Nitrogen Enriched Organic fertilizer (NEO) elevates nitrification rates shortly after application but has no lasting effect on nitrification in agricultural soils

Amidst population growth, escalating food costs, limited arable land, and farmland degradation, the adoption of innovative technologies—like organic waste recycling and nutrient recovery—is crucial for enhancing the resilience of global agri-food systems. Nitrogen-Enriched Organic fertilizer (NEO) is produced using a new method, where dinitrogen (N2) is captured from the air through a plasma process and mixed with slurries or digestates as nitrate (NO3-) and nitrite (NO2-). This process leads to solid slurry acidification and a high NO2- content, potentially yielding toxic inorganic or organic N compounds. This study investigated the impact of NEO derived from cattle slurry and biogas digestate on soil nitrification—conversion of NH4+ to NO2- and NO3- by aerobic autotrophic bacteria and archaea. We investigated and compared the potential nitrification rates in soil samples from two agricultural trials (cereal and grass) treated with NEO and other fertilizers after two consecutive fertilization years. Additionally, we examined the immediate nitrification response to NEO through 73-hour soil incubations. Our results revealed that NEO significantly stimulated nitrification rates in agitated soil slurries, regardless of the feedstock used, surpassing rates observed in ammonium controls. Similarly, this pattern was also observed in loosely placed soil samples, with high nitrification rates occurring with NEO and ammonium chloride. Interestingly, the differences in nitrification rates between field-fertilized soil samples were minimal and inconsequential, suggesting that while NEO exhibits a rapid boost in nitrification rates shortly after application, this effect is not sustained ≈ six months after fertilization under field conditions. Consequently, NEO indicates its potential as an environmentally benign fertilizer without adversely affecting soil nitrification.

Microbial Responses to Biochar Soil Amendment and Influential Factors: A Three-Level Meta-Analysis.

Biochar is a multifunctional soil conditioner capable of enhancing soil health and crop production while reducing greenhouse gas emissions. Understanding how soil microbes respond to biochar amendment is a vital step toward precision biochar application. Here, we quantitatively synthesized 3899 observations of 24 microbial responses from 61 primary studies worldwide. Biochar significantly boosts microbial abundance [microbial biomass carbon (MBC) > colony-forming unit (CFU)] and C- and N-cycling functions (dehydrogenase > cellulase > urease > invertase > nirS) and increases the potential nitrification rate by 40.8% while reducing cumulative N2O by 12.7%. Biochar derived at lower pyrolysis temperatures can better improve dehydrogenase and acid phosphatase and thus nutrient retention, but it also leads to more cumulative CO2. Biochar derived from lignocellulose or agricultural biomass can better inhibit N2O through modulating denitrification genes nirS and nosZ; repeated biochar amendment may be needed as inhibition is stronger in shorter durations. This study contributes to our understanding of microbial responses to soil biochar amendment and highlights the promise of purpose-driven biochar production and application in sustainable agriculture such that biochar preparation can be tuned to elicit the desired soil microbial responses, and an amendment plan can be optimized to invoke multiple benefits. We also discussed current knowledge gaps and future research needs.

Patterns and determinants of nitrification and denitrification potentials across 24 rice paddy soils in subtropical China

Nitrification and denitrification processes are major pathways for nitrogen (N) losses in agricultural soils, and highly depend on soil properties. Improved understanding of soil nitrification and denitrification processes is essential for better N management in agroecosystems. However, the effects of geochemical properties on nitrification and denitrification potentials remain largely uncertain, especially in paddy soils. Here, we investigated the patterns and controlling factors of nitrification and denitrification potentials across 24 paddy soil sampling sites (varied in soil texture, pH, and contents of soil organic carbon (SOC), nutrients, and exchangeable metals) in major rice-producing areas of Hubei Province, China. The results showed substantial variations in the potential rates of nitrification (0.46–17.65 mg N kg−1 soil d−1) and denitrification (6.31–18.12 mg N kg−1 soil d−1) across the paddy soil sampling sites. Soil pH and SOC were the predominant factors regulating nitrification and denitrification potentials, respectively. Nitrification potential strongly increased with soil pH at value above 6.2, while showed an insignificant correlation with pH at value below 6.2. Increased soil pH stimulated nitrification potential via enhanced NH4+ availability, likely due to increased soil active iron (Fe) and manganese (Mn) oxides facilitating chemisorption. Denitrification potential strongly positively correlated with SOC at value below 15 g kg−1, dissolved organic carbon and nitrate contents, but had little relationship with active Fe and Mn properties and clay contents. The potentials of nitrification uncoupled with denitrification, possibly resulting from their distinct controlling factors across the paddy soils. Overall, these findings could help improve the understanding of the key factors controlling potential nitrification and denitrification across paddy soils, and provide a theoretical basis for optimizing agricultural management to mitigate N losses.

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.

Soil biota associated with soil N cycling under multiple anthropogenic stressors in grasslands

Soil nitrogen (N) processes and statuses are two essential components for soil N cycling in terrestrial ecosystems. Although studies have estimated the effects of multiple anthropogenic stressors (e.g., nutrient enrichment and soil acidification) on soil N cycling, how multiple trophic levels of soil biota regulate the responses of soil N processes and statuses under multiple anthropogenic stressors has not yet been studied. We established an N and phosphorus (P) enrichment and acid addition experiment in a semi-arid grassland on the Mongolian Plateau. After five years, our results showed that soil acidification strongly inhibited soil N processes (via decreasing N mineralization rate, potential nitrification rate, and potential denitrification rate) and soil N statuses (via decreasing dissolved organic N, NO3−-N, and microbial biomass N). Acid addition-induced declines in soil N processes or N statuses were mainly associated with the inhibition of the abundance/richness of soil N-related bacteria and nematodes. Compared with soil acidification, N or P enrichment had relatively minor effects on soil N processes or N statuses, except for the N enrichment-induced decline in the potential nitrification rate and increase in soil NH4+-N and P enrichment-induced decline in soil NO3−-N. Furthermore, we found that the responses of soil N processes or statuses to nutrient enrichment were different between non-acidified soils and acidified soils. Overall, our results evidenced that soil biota strongly mediated the responses of soil N processes and statuses to nutrient enrichment and acid addition in semi-arid grasslands, and soil acidification weakened the associations between soil biota and soil N cycling. These findings indicate that we should concentrate more on the importance of soil biota in maintaining ecosystem N functions and services against a background of global change.

Influence of seaweed extracts on the degradation and effectiveness of 3,4-dimethylpyrazole phosphate

3,4-Dimethylpyrazole phosphate (DMPP) is acknowledged as one of the most efficient nitrification inhibitors (NIs); however, researchers have suggested that its effectiveness needs to be further improved. The authors combined the biostimulant seaweed extract (SE) with DMPP and conducted an indoor incubation experiment to initially investigate the impact of the influence of SE on the degradation and effectiveness of DMPP. Meanwhile, a method for the extraction and determination of DMPP was developed. DMPP performed better, with a longer effective time in loess than black soil, and SE showed a delayed effect on DMPP degradation of DMPP at the beginning of the incubation and then accelerated the degradation process. This was attributed to the adsorption effect of SE on DMPP, consequently reducing its effectiveness. The SE delayed the hydrolysis of urea in various soils; however, no significant impact on urease activity was observed (P &lt; 0.05) (P &lt; 0.05). Furthermore, it also increased potential nitrification rate (PNR) from 10 to 21 days and promoting the rapid transformation of NH4+-N in black soil. The SE reduced PNR within 21 days and inhibited nitrification in loess. In addition, the SE appeared to mitigate the adverse effects of excessive nitrogen on microorganisms The combination of DMPP and SE was not conducive to the inhibition of soil nitrification, and this formulation in field applications requires further investigation.

Sediment depth-related variations of comammox Nitrospira: Evidence in the Three Gorges Reservoir, China

The recent discovery of comammox Nitrospira as complete ammonia-oxidizing microorganism has fundamentally revolutionized our understanding of nitrogen cycling in sediment environments. However, knowledge regarding their abundance, biodiversity, community structure, and interactions is predominantly limited to the upper layers (0–20 cm). To address this gap, we collected sediment samples along profiles ranging from 0 to 300 cm in depth at three locations within the middle segment of the Three Gorges Reservoir (TGR), China. Quantitative real-time PCR (qPCR) analyses suggested that comammox bacteria were not only ubiquitous in deep sediments but also more abundant than ammonia-oxidizing bacteria (AOB). Ammonia monooxygenases subunit A (amoA) gene amplicon sequencing illuminated that comammox bacteria were more sensitive to sedimental depth compared to AOB and ammonia-oxidizing archaea (AOA), as evidenced by a more significant decline in community diversity and similarity over distance along sediment vertical profiles. Notably, we discovered that the amoA gene abundance, alpha- and beta-diversity of comammox bacteria exerted an essential contribution to potential nitrification rates according to random forest model. Phylogenetic analysis indicted that most comammox bacteria within sediment samples belonged to clade A.2. Intriguingly, the average relative abundance of comammox clade A.2 displayed a noteworthy rise with sediment depth, whereas clade A.1 demonstrated a converse pattern, unveiling distinct ecological niche adaptations of these two clades along the sediment profile. Ecological network analysis further revealed closer interactions between comammox bacteria and canonical ammonia oxidizers in the superficial layer (0–40 cm), with the network structure gradually simplifying from superficial to deep sediment (200–300 cm). Overall, these findings broaden the current recognition of the geographic distribution and niche segregation of comammox bacteria at the fine scale of the sediments ecosystems and provide insights into sediment depth-related variations of their coexistence network patterns in large freshwater reservoirs.