Nitrification Processes In Soil Research Articles

15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils

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.Graphical

Neonicotinoid Effects on Soil Microorganisms: Responses and Mitigation Strategies

Pesticides play a critical role in pest management and agricultural productivity; however, their misuse or overuse can lead to adverse effects on human health and the environment, including impacts on ecosystems and contamination. Currently, neonicotinoids (NNIs) are the most widely used systemic insecticides and are questioned worldwide for their possible impacts on pollinators. After NNI application, a substantial portion is not absorbed by the plant and may accumulate in the soil, affecting the soil microbial community. In this review, we explore the main studies carried out either in the laboratory or in the field about this matter. The studies report that the application of NNIs affects soil microbial activity and can act on microbial communities differently due to their unique chemical properties, degradation in soil, soil type, effects on soil properties, and methods of application. NNIs alter the diversity, structure, and abundance of soil microbes, in some cases increasing or decreasing their representativeness in soil. Bacterial phyla like Pseudomonadota, Bacillota, Actinomycetota, and Nitrospirota increase after NNI exposure, just like the families Nitrosomonadaceae, Nitrososphaeraceae, Nitrospiraceae, Sphingomonadaceae, Streptomycetaceae, and Catenulisporaceae. At the bacterial genus level, Nitrospira was associated with a decrease in nitrification processes in soil. The bacterial genera Sphingomonas, Streptomyces, Catenulispora, Brevundimonas, Pedobacter, and Hydrogenophaga are related to NNI degradation after application. Microorganisms could minimize the impacts of NNIs in agricultural soil. Therefore, the use of bioinoculation as a bioremediation tool is explored as an alternative to contribute to agricultural sustainability.

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.

How does biochar influence soil nitrification and nitrification-induced N2O emissions?

Nitrification is a major pathway of N2O production, especially in aerobic soils. The amendment of soils with biochar has been suggested as a promising solution to regulate soil N cycle and reduce N2O emissions. However, there is a lack of comprehensive and quantitative understanding of biochar impacts on soil nitrification and nitrification-induced N2O emissions. In this study, a meta-analysis was conducted using data compiled across 95 peer-reviewed studies. Results showed that biochar in general significantly increased soil nitrification rate by 56 %, with overall no significant effect on nitrification-induced N2O emissions, suggesting that biochar likely restricted the fraction of nitrified N emitted as N2O emissions. The abundance of ammonia-oxidizing bacteria (AOB) was significantly increased by 37 % following biochar addition, but that of ammonia-oxidizing archaea (AOA) did not change significantly, indicating that the impact of biochar on AOB rather than AOA may play an important role in soil nitrification. The impacts of biochar on soil nitrification processes were heterogeneous depending on soil properties. Biochar increased soil nitrification rate and AOB abundance to a larger extent in poorly pH-buffered soils such as those with acidic pH (<5), low organic carbon (<10 g kg−1), or poor texture (rich in either sand or clay), which may be attributed to the liming and structural effects of biochar that regulate soil pH and water-air status. The overall no significant effect of biochar on nitrification-induced N2O emissions was due to a positive effect in acidic soils, a negative effect in alkaline soils, and little effect in neutral soils. This study provides a comprehensive insight into how different factors mediate the response of soil nitrification processes to biochar amendment, which contributes to a new understanding of biochar function in regulating soil N2O emissions, and can assist in designing biochar projects that would benefit soil N cycle while minimizing undesirable side effects.

Accelerated nitrification and altered community structure of ammonia-oxidizing microorganisms in the saline-alkali tolerant rice rhizosphere of coastal solonchaks

Plantations of saline-alkali tolerant rice in coastal areas are proposed as a strategy to improve rice yield and ensure global food security. The soil nitrification process driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is an integral part of the soil nitrogen cycle and correlates with the quality of coastal solonchak. However, little is known about the effects of saline-alkali tolerant rice cultivation on the soil nitrification process in coastal solonchaks. In this study, we investigated the community structures of AOA/AOB and the nitrification rate in the rice rhizosphere along salinity gradients. The abundance and nitrification rates of AOA and AOB declined with increasing salinity. Saline-alkali-tolerant rice cultivation significantly increased the abundance of AOA and AOB amoA genes from (3.09–11.5) × 106 and (7.76–52.0) × 105 copies g−1 in soils to (16.2–50.9) × 106 and (69.2–423) × 105 copies g−1 in the rhizosphere, respectively. Compared with bulk soils, the nitrification rate of AOA and AOB in the rhizosphere increased significantly with salinity. Saline-alkali-tolerant rice cultivation enhanced the nitrification process of saline-alkali tolerant soil by increasing the nitrification contribution of AOB. Our findings offer new clues on the accelerated nitrification process in the saline-alkali tolerant rice rhizosphere in coastal solonchaks and reveal its roles in shaping AOA/AOB communities, providing suggestions for saline-alkali tolerant rice plantations in coastal solonchaks.

Combined Effects of Cadmium and Azithromycin on Soil Nitrification Process

Heavy metals and pharmaceuticals have polluted agricultural soils mainly through wastewater irrigation, fertilizers, and soil amendment with sewage sludge. This study aims to determine the synergetic toxic effect of Cd and the selected macrolide antibiotic, azithromycin (AZI), on ammonia-oxidizing bacteria (AOB) in soil, via analyzing nitrification inhibition. A short-term acute toxicity test was used to measure the formation of Nitrite (NO2-N) to indicate the nitrification potential of the aerobic nitrosomonas bacteria in the germination period. Potential nitrification rates (PNRs) of five soil samples ranged between 3.782–17.642 mg NO2-N/kg dm PNRs of soil samples positively correlated with organic matter content and neutral pH. PNRs of the tested soils were significantly affected by Cd and AZI contamination, with interactions exhibited for their simultaneous occurrence and soil pH. A significant difference (p &lt; 0.05) was found when soil samples with pH 6.5–pH 8.5 contaminated with environmentally relevant concentrations of Cd (1 mg/kg–21 mg/kg) and AZI (1 mg/kg–9 mg/kg). 50% PNR inhibition after 11 mg/kg Cd and 5 mg/kg AZI contamination was determined for the soil sample at pH 8.5, with 3.782 mg NO2-N/kg dm potential. From these outcomes, it was concluded that there was a risk of the soil nitrification process in case of simultaneous occurrence of Cd and AZI.

Soil nitrification process played a key role in alleviating continuous cropping limitation induced by fumigation

Continuous cropping causes enormous crop produce reduction, and soil fumigation is an effective approach to alleviate the limitation. Understanding the impacts of agriculture management on microbial community and its association with nutrient availability would provide strong supports for alleviating continuous cropping limitation. However, the mechanisms of fumigants in enhancing plant growth and alleviating continuous cropping barriers was not clear. In this study, fumigation treatments including chloropicrin (CP), dazomet (DZ), and untreated control (CK) were carried out at field scale, and rhizosphere bacterial community and plant phytochrome were analyzed. The results showed that fumigation had strong effects on rhizosphere bacterial community and soil properties. Fumigation treatment caused significantly reduction in rhizosphere bacterial diversity. The nitrifiers (Nitrospira and Nitrospirillum) and functional gene (ammonia oxidizing bacterial AOB amoA) were significantly inhibited by fumigation treatment, which caused significant reduction in nitrification potential (PNF). The inhibition of nitrifiers, AOB amoA gene and PNF led to significant reduction of soil NO3−-N, but increase of NH4+-N. Subsequently, plant photosynthesis was enhanced as a result of increasing leaf chlorophyll a content caused by fumigation treatment. Therefore, fumigation treatment would promote crop growth through increasing the photosynthetic pigment. The study indicated the key mechanisms fumigation promoting plant growth and alleviating cropping limitation were closely related to soil nitrifiers and nitrogen nutrients.

Activating soil nitrification by co-application of peanut straw biochar and organic fertilizer in a rare earth mining soil

The intensive mining activities to extract rare earth elements from ion-adsorption rare earth deposits have introduced massive amounts of ammonium into the tailing soils in southern China. Compared to the ubiquitous soil nitrification in cropland, forest, and grassland soils, however, there is no feasible strategy to alleviate the ammonium contamination in tailing soil. Herein, the feasibility to remove ammonium by adding ammonium adsorbents (e.g., biochar, activated carbon, and zeolite), alkaline materials, and organic fertilizer to the rare earth mining soil was explored. The amendment of rice straw biochar, activated carbon, or zeolite in combination with CaCO3 and organic fertilizer showed no significant effect on ammonium removal due to their limited capacity to elevate soil pH. However, the co-application of peanut straw biochar (PSBC), CaCO3, and organic fertilizer activated both the ammonia volatilization and soil nitrification processes. Specifically, the three components functioned as follows: organic fertilizer supplied active ammonia-oxidizing bacteria (AOB); PSBC stimulated AOB proliferation by elevating soil pH above 7.75; CaCO3 ameliorated soil acidity and reduced the lag time for activating soil nitrification. The soil ammonium removal and nitrate accumulation rates were positively correlated to the acid neutralization capacity of PSBC prepared at 400 °C–800 °C. The qPCR and microbial community analysis results indicated that Nitrosomonas europaea was the dominant AOB that was responsible for enhanced soil nitrification. Our findings pave the way for developing cost-effective strategies to remediate ammonium contamination in rare earth mining soils.

Biochar amendments and climate warming affected nitrification associated N2O and NO production in a vegetable field

Soil nitrification driven by ammonia-oxidizing microorganisms is the most important source of nitrous oxide (N2O) and nitric oxide (NO). Biochar amendment has been proposed as the most promising measure for combating climate warming; both have the potential to regulate the soil nitrification process. However, the comprehensive impacts of different aged biochars and warming combinations on soil nitrification-related N2O and NO production are not well understood. Here, 1-octyne and acetylene were used to investigate the relative contributions of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to potential nitrification-mediated N2O and NO production from the fertilized vegetable soil with different aged biochar amendments and soil temperatures in microcosm incubations. Results demonstrated that AOB dominated nitrification-related N2O and NO production across biochar additions and climate warming. Biochar amendment did not significantly influence the relative contribution of AOB and AOA to N2O and NO production. Field-aged biochar markedly reduced N2O and NO production via inhibiting AOB-amoA gene abundance and AOB-dependent N2O yield while fresh- and lab-aged biochar produced negligible effects on AOB-dependent N2O yield. Climate warming significantly increased N2O production and AOB-dependent N2O yield but less so on NO production. Notably, the relative contribution of AOB to N2O production was enhanced by climate warming, whereas AOB-derived NO showed the opposite tendency. Overall, the results revealed that field-aged biochar contributed to mitigating warming-induced increases in N2O and NO production via inhibiting AOB-amoA gene abundance and AOB-dependent N2O yield. Our findings provided guidance for mitigating nitrogen oxide emissions in intensively managed vegetable production under the context of biochar amendments and climate warming.

Factors Influencing Soil Nitrification Process and the Effect on Environment and Health

To meet the global demand for food, several factors have been deployed by agriculturists to supply plants with nitrogen. These factors have been observed to influence the soil nitrification process. Understanding the aftermath effect on the environment and health would provoke efficient management. We review literature on these factors, their aftermath effect on the environment and suggest strategies for better management. Synthetic fertilizers and chemical nitrification inhibitors are the most emphasized factors that influence the nitrification process. The process ceases when pH is &amp;lt;5.0. The range of temperature suitable for the proliferation of ammonia oxidizing archaea is within 30 to 37oC while that of ammonia oxidizing bacteria is within 16 to 23oC. Some of the influencing factors excessively speed up the rate of the nitrification process. This leads to excess production of nitrate, accumulation of nitrite as a result of decoupling between nitritation process and nitratation process. The inhibition mechanism of chemical nitrification inhibitors either causes a reduction in the nitrifying micro-organisms or impedes the amoA gene's function. The effects on the environment are soil acidification, global warming, and eutrophication. Some of the health effects attributed to the influence are methemoglobinemia, neurotoxicity, phytotoxicity and cancer. Biomagnification of the chemicals along the food chain is also a major concern. The use of well-researched and scientifically formulated organic fertilizers consisting of microbial inoculum, well-treated organic manure and good soil conditioner are eco-friendly. They are encouraged to be used to efficiently manage the process. Urban agriculture could promote food production, but environmental sustainability should be ensured.

Intensification of nitrification processes in soil by ultraviolet (UV) irradiation

This study highlights the application of UV radiation for soil treatment with regard to agricultural plant growth intensification. The influence of the parameters of ultraviolet radiation (intensity and wavelength) on the value of the redox potential in the soil was quantified. The experimental tests carried out in soils, plants, seeds with ultraviolet radiation lamps for changing the accumulation of the most mobile nitrate forms of nitrogen were defined.

Influence of polyethylene terephthalate microplastic and biochar co-existence on paddy soil bacterial community structure and greenhouse gas emission

Microplastic (MP) contamination is ubiquitous in agricultural soils. As a cost-effective soil amendment, biochar (BC) often coincides with MP exposure. However, little research has been conducted regarding the independent and combined effects of MPs and BC on the soil microbiome and N2O/CH4 emissions. Therefore, in this study, polyethylene terephthalate (PET) and wheat straw-derived BC were used, respectively, as representative MP and BC during an entire rice growth period. The high-throughput sequencing results showed that PET alone lowered bacterial diversity by 26.7%, while PET and BC co-existence did not induce apparent change. The relative abundances of some microbes (e.g., Cyanobacteria, Verrucomicrobia, and Bacteroidetes) that are associated with C and N cycling were changed at the phylum and class levels by all the treatments. In comparison with the control, the treatment of BC, PET, and their co-existence reduced the cumulative CH4 emissions by 50%, 53%, and 61%, respectively. The higher mitigation by BC + PET may be the result of higher soil Eh and a consequently lower methanogenesis functional gene mcrA abundance in the treated soils. In addition, BC and PET alone, as well as their combined treatment, increased the abundance of nitrification genes, enhancing the soil nitrification process. However, the relative contribution of the nitrification process to N2O emission was possibly lower than that of denitrification, in which the N2O reductase gene nosZ was found to be the primary gene regulating N2O emissions. BC alone increased nosZ abundance by 42.3%, thereby showing the potential in suppressing N2O emission. In contrast, when BC was co-added with PET, the nosZ abundance lowered possibly because of increased soil aeration, and thus its cumulative N2O emission was 38% higher than the BC treatment. Overall, these results demonstrated that BC and PET function differently in soil ecosystems when they coexisted.

Dominance of archaeal ammonia-oxidizers in soil nitrification across different soil types and fertilities in North China plain

Microbially mediated soil nitrification process was largely limited by ammonia-oxidizing archaea (AOA) and bacteria (AOB), which further affect nitrogen (N) loss and retention with concomitant impacts on both crop productivity and environment. However, the spatial distribution of ammonia-oxidizers and their varying contributions to soil nitrification activity at provincial scale are poorly explored. 135 agricultural soils across different soil types and fertility conditions were collected from Henan province in North China Plain to draw the map of soil AOA and AOB abundance with quantitative PCR analysis. Soil nitrification potential (NP) and the relative contribution of AOA and AOB to NP that recovers after acetylene inactivation were essentially determined among the five major soil types. The abundance of ammonia-oxidizers, which was positively and significantly related with pH, was obviously predominated by AOA with AOA/AOB ranging 1.96–9.79 at provincial scale. AOA contributed more (at 60%–79%) to soil nitrification in acidic and neutral soils (Lime concretion black soil, Yellow-cinnamon soil, Paddy soil and Cinnamon soil) with significant relationships with its higher abundance, pH, soil organic carbon and ammonium nitrogen. On the contrary, the even contribution of AOB compared with AOA in alkaline Fulvo-aquic soil showed poor relationship with its abundance but was strongly affected by soil N availability. In summary, AOA even with lower abundance showed stronger function in acidic and ammonia-limited soil environments, but AOB with higher abundance tends to be the leader of soil nitrification in alkaline and substrate-rich soils of Henan province.

Analysis of Nitrogen Transformation Characteristics and Influencing Factors of Forestland Soil in the Qinghai-Tibet Plateau: A Case Study of the Qilian Mountains and Southeast Tibet

Mineralization and nitrification, two important processes of the N cycle in forest ecosystems, play an important role in the maintenance of ecosystem function and soil environmental quality. The net mineralization rate and net nitrification rate are two common indexes for evaluation of the N supply and N loss risk in soil. In order to study the soil N transformation characteristics and their influencing factors in woodlands of the Qinghai-Tibet Plateau, the inorganic N concentrations, net N mineralization rates, and net nitrification rates of 327 soils sampled from the Qilian Mountains and Southeast Tibet were analyzed using indoor incubation experiments. The results showed that the inorganic N concentration, net N mineralization rate, and net nitrification rate of the woodland soil in Southeast Tibet ［109.70 mg·kg-1, 3.08 mg·(kg·d)-1, and 2.19 mg·(kg·d)-1］ were significantly higher than those in the Qilian Mountains ［49.47 mg·kg-1, 0.70 mg·(kg·d)-1, and 0.69 mg·(kg·d)-1］. The net mineralization rate of soil was positively correlated with the mean annual temperature (MAT), mean annual precipitation (MAP), moisture index, and soil organic matter concentrations (P<0.001). There were no significant positive relationships between the net nitrification rate and the MAT and MAP, but the net nitrification rate was positively correlated with the net N mineralization rate (P<0.001). These results indicated that the N supply ability of woodland soil in Southeast Tibet is significantly higher than that in the Qilian Mountains, and the hydrothermal conditions (MAT and MAP) are likely responsible for the difference in the net mineralization rate between the two studied regions. The net mineralization rate is the limiting factor for the net nitrification rate, which has an important influence on the spatial distribution of the forest soil nitrification process in the Qinghai-Tibet Plateau. These results emphasize the important roles of climatic and environmental factors, such as hydrothermal conditions, on the net N mineralization and nitrification rates of woodland soil in the Qinghai-Tibet Plateau, and will further deepen the understanding of the law of soil N transformation in woodlands in the Qinghai-Tibet Plateau.

Canonical ammonia oxidizers, rather than comammox Nitrospira, dominated autotrophic nitrification during the mineralization of organic substances in two paddy soils

Chemoautotrophic canonical ammonia-oxidizers and complete ammonia oxidizers (comammox) are responsible for ammonia oxidation, which is the rate-limiting step of nitrification in terrestrial ecosystems. However, the relative importance of autotrophic nitrification and the related active nitrifiers during mineralization of organic substances with different C/N ratios have not been fully elucidated to date. In this study, 15N tracing and 13CO2-DNA-based stable isotope probing (DNA-SIP) techniques were employed to investigate the responses of soil nitrification processes and the active nitrifying phylotypes in acidic and neutral paddy soils with amendment of glutamine (Gln) or rice straw with low C/N (LS) or high C/N (HS). Acetylene (C2H2) was utilized to differentiate autotrophic and heterotrophic nitrification. The results indicated that C2H2 completely blocked the production of 15NO3− in Gln and LS treatments, implying the predominance of autotrophic nitrification with the N derived from the mineralization of Gln and LS. Neither 15NH4+ nor 15NO3− was detected in the HS-amended soils, suggesting that NH4+ derived from organic N mineralization was immobilized immediately by microorganisms. In the DNA-SIP microcosms, the abundance of ammonia-oxidizing bacteria (AOB) in the unamended control (CK), Gln and LS treatments of acidic paddy soil increased by 22.1-, 71.9- and 27.6-fold, respectively. A significantly larger proportion of Nitrosospira-like AOB, rather than ammonia-oxidizing archaea (AOA) and comammox Nitrospira, was labelled by 13CO2, indicating that AOB made a stronger contribution to autotrophic nitrification in acidic paddy soil. The active nitrification of neutral paddy soil was predominated by AOA affiliated with the Nitrososphaera viennensis lineage in the CK and LS microcosms but by Nitrosospira-like AOB in the Gln microcosm. These results suggest the significance of autotrophic nitrification catalysed by canonical ammonia oxidizers, rather than comammox, during the mineralization of organic substances with low C/N in paddy soils.

Nitrapyrin reduced ammonia oxidation with different impacts on the abundance of bacterial and archaeal ammonia oxidisers in four agricultural soils

The compound nitrapyrin can act as a potential nitrification inhibitor (NI) when applied with ammonium (NH4+)-based N fertiliser. The efficacy of nitrapyrin applications may be soil dependent however, being influenced by soil texture, organic carbon (C), and moisture. The objective of this study was to assess the effects of nitrapyrin on the nitrification process in soils of different physicochemical characteristics and resident microbial communities. Four agricultural soils were incubated in microcosms for five weeks, after which nitrapyrin effects were assessed for soil NH4+, nitrate (NO3−), the microbial functional genes ammonia-monooxygenase (amoA) and nitrite oxidoreductase (nxr), and bacterial and archaeal nitrifier genera using 16S rRNA sequencing. Nitrapyrin co-applied with urea ammonium nitrate (UAN) fertiliser inhibited nitrification, shown by increased retention of NH4+ in all four soils and a lower accumulation of NO3− in three of the four soils compared to UAN treated soil. These results are most likely due to the inhibition of growth of ammonia oxidising bacteria (AOB) as nitrapyrin plus UAN reduced bacterial amoA abundance in three of the four soils compared to the UAN treatment. This study is the first to report increased archaeal amoA abundance in response to the co-application of nitrapyrin and UAN in four soils, possibly due to reduced competition from AOB. The bacterial nitrifier genera Nitrosospira and Nitrospira and archaeal nitrifier genus Nitrososphaera were detected in all four soils using 16S rRNA sequencing. The effects of nitrapyrin on downstream N transformations were assessed based on nxr and Nitrospira abundance though no conclusive treatment effects could be discerned for the four soils. Our results provide evidence of the interplay of AOB, ammonia oxidising archaea (AOA) and nitrite-oxidising bacteria (NOB) in nitrapyrin and fertiliser treated soils and will be useful in developing strategies to improve the efficacy of nitrification inhibitors in future studies.

Land use pattern effects after 30 years of shifting cropland to fallow land on soil ammonia-oxidizer community

Sympatric differentiation of ammonia-oxidizing archaea and bacteria may occur due to differences in ammonia availability during agricultural activities such as fertilization, which shift key biological drivers of soil nitrification processes. Restoring native habitat from intensive agricultural activities (e.g. converting cropland into fallow land) reduces fertilizer inputs, which has the potential to change active ammonia-oxidizers and thus nitrification rates. We incubated soils from fields under 30 years fallow and under continuous cropping to understand shifts in ammonia-oxidizers and nitrification processes. Thirty years of land fallow practices sharply decreased the abundance and activity of soil ammonia-oxidizing bacteria compared to continuous cropping. Nitrification in cropland was driven mainly by ammonia-oxidizing bacteria while ammonia-oxidizing archaea were the main drivers of nitrification in fallow soil. Conversion of cropland into fallow land shifted the dominant active ammonia-oxidizers from ammonia-oxidizing bacteria to archaea, and the low nitrification rates in fallow soil were caused by the lack of active ammonia-oxidizing bacteria rather than N substrate availability.

Macroscopic Observation of Soil Nitrification Kinetics Impacted by Copper Nanoparticles: Implications for Micronutrient Nanofertilizer.

The potential agricultural use of metal nanoparticles (NPs) for slow-release micronutrient fertilizers is beginning to be investigated by both industry and regulatory agencies. However, the impact of such NPs on soil biogeochemical cycles is not clearly understood. In this study, the impact of commercially-available copper NPs on soil nitrification kinetics was investigated via batch experiments. The X-ray absorption near edge structure spectroscopy analysis showed that the NPs readily oxidized to Cu(II) and were strongly retained in soils with minimum dissolution (<1% of total mass). The Cu2+ (aq) at 1 mg/L showed a beneficial effect on the nitrification similar to the control: an approximately 9% increase in the average rate of nitrification kinetics (Vmax). However Vmax was negatively impacted by ionic Cu at 10 to 100 mg/L and CuNP at 1 to 100 mg/L. The copper toxicity of soil nitrifiers seems to be critical in the soil nitrification processes. In the CuNP treatment, the suppressed nitrification kinetics was observed at 1 to 100 mg/kg and the effect was concentration dependent at ≥10 mg/L. The reaction products as the results of surface oxidation such as the release of ionic Cu seem to play an important role in suppressing the nitrification process. Considering the potential use of copper NPs as a slow-release micronutrient fertilizer, further studies are needed in heterogeneous soil systems.

Effects of nitrogen fertilizer application on carbon dioxide emissions from soils with different inorganic carbon contents.

The application of nitrogen (N) fertilizer results in decreases of soil pH, but its effects on CO2 emission from soils with different inorganic carbon contents remain unclear. An closed-jar incubation experiment was conducted to examine the effects of N fertilizer and nitrification inhibitor (DCD) on soil pH and CO2 emissions from three soil types with different contents of soil inorganic carbon (SIC), including paddy soil (PS), lime concretion black soil (CS), and eum-orthic anthrosols (AS). There were three treatments for each soil type, including control (N0), 0.2 g·kg-1 N fertilizer (N0.2), and its combination with DCD (N0.2+DCD). Soil pH, contents of mineral N (NH4+, NO3-), and CO2 emissions were measured. The results showed that N fertilizer addition significantly reduced soil pH and increased soil CO2 cumulative emissions in each type of soil. Compared to control, the CO2 cumulative emissions after 49 days incubation from the three soil types were enhanced by 39.4%, 23.4%, and 71.8% for PS, CS, AS soils, respectively. The soil pH of N0.2+DCD for three soil types were significantly higher than N0.2 after 49 days incubation, indicating that DCD application inhibited soil nitrification process. There were no significant differences in the mean CO2 cumulative emissions of PS and CS soils between N0.2 and N0.2+DCD treatments; however, N0.2+DCD treatment significantly reduced cumulative CO2 emissions from AS soil by 12.5%. Soil inorganic carbon can effectively buffer soil acidification caused by N fertilizer addition. The CO2 emission in calcareous soil following N addition is not only derived from the mineralization of soil organic carbon, but also from the dissolution of inorganic carbon. Given the large differences in soil inorganic carbon content in different regions of China, the problem of soil acidification and soil inorganic carbon pool consumption caused by long-term large amount of N fertilizer inputs deserve more attention.

Acute response of soil denitrification and N2O emissions to chlorothalonil: A comprehensive molecular mechanism

The fungicide chlorothalonil (CHT) has been widely used in the tea orchard due to its high-efficiency and sterilization. It has been reported that repeated application of CHT inhibits soil nitrification process. However, the acute impact of CHT on soil denitrification and associated N2O emissions is unclear. This study evaluated nitrate (NO3−) removal, denitrifying gene abundance and denitrifying enzyme activity of tea orchard soil after a 72-h-exposure to CHT. It was found that increasing CHT from 5 to 25 mg kg−1 suppressed the NO3− removal efficiency from 74.6% to 54.1%, but increased N2O emissions from 23.1% to 94.8%. Following treatment with 25 mg kg−1 of CHT, the abundances of the nirK, nirS and nosZ genes were reduced by 31.6%, 22.1%, and 50.7%, respectively. Alternatively, the declines of the electron transport system activity (ETSA) value and adenosine triphosphate (ATP) content suggested that CHT had an inhibitory effect on microbial metabolism. Enzyme activity studies further revealed that the decrease of nitrate reductase (NAR), nitrite reductase (NIR) and nitric oxide reductase (NOR) activities was the main reason for the suppression of denitrification by CHT. Furthermore, positive correlations were observed between denitrifying reductase activity and the intracellular metabolism, indicating that the decrease in microbial metabolism should also be responsible for the inhibitory effect of CHT on the denitrifying process. Overall, it was found that the acute exposure of soil to CHT could inhibit the denitrification process and significantly increase N2O emissions, which might result in destruction of the soil nitrogen cycle and exacerbation of global warming.