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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 15 N-urea incubation has not been totally clarified. The 15 N-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 C 2 H 2 almost completely inhibited NO 3 - -N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15 N-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 15 N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15 N-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., (© 2024. The Author(s).)

Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

To meet the growing population's demand for food, humans have introduced large amounts of nitrogen fertilizers into agricultural systems, resulting in highly nitrified environments in most farmland soils. In highly nitrified environments, the application of nitrogen fertilizer easily leads to the formation of nitrate (NO3−) and subsequent leaching, resulting in very low utilization rates. Moreover, nitrogen loss can cause harm to both the environment and human health, making it necessary to inhibit the nitrification process. Nitrification inhibitors can suppress nitrification, and inhibitors derived biologically from plant roots are gaining attention due to their low cost and environmental friendliness. Sorghum, as a crop capable of growing in arid environments, holds economic value and also possesses the ability to secrete biological nitrification inhibitors. This article utilizes sorghum as a case study to review different types of BNIs (MHPP, sorgoleone, and sakuranetin), their mechanisms of inhibition, and influencing factors. This article summarizes the contributions of these inhibitors in reducing N2O emissions and increasing food production, while also providing insight into future research directions for sorghum's biological nitrification inhibitors in terms of agricultural production efficiency. BNIs are expected to play an important role in improving agricultural production and reducing environmental pollution. [ABSTRACT FROM AUTHOR]

Purpose: Microbial nitrification plays an important role in nitrogen cycling in ecosystems. Nitrification is performed by ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) including complete ammonia oxidizers. However, the relative importance of nitrifiers in autotrophic nitrification in relation to soil pH is still unclear.Materials and methods: Combining DNA-based stable isotope probing (SIP) and molecular biological techniques, we investigated the abundance, structure, and activity of AOA, AOB, and NOB along a pH-gradient (3.97-7.04) in a vegetable cropped soil.Results and discussion: We found that AOA abundance outnumbered AOB abundance and had a significantly negative relationship with soil pH. The abundances of NOB Nitrospira 16S rRNA, nxrB gene, and Nitrobacter nxrA gene were affected by soil pH. Incubation of soil with 13CO2 and DNA-SIP analysis demonstrated that significant 13CO2 assimilation by AOA rather than by AOB occurred in the acidic soils, whereas the labeled 13C level of AOA was much less in the neutral soil than in the acidic soils. There was no evidence of 13CO2 assimilation by NOB except for Nitrobacter with NxrB gene at pH 3.97. Phylogenetic analysis of AOA amoA gene in the 13C- and 12C-labeled treatments showed that the active AOA mainly belonged to Nitrososphaera in the acidic soils.Conclusions: These results suggested that the main performer of nitrification was AOA in the acidic soils, but both AOA and AOB participated in nitrification in the neutral soil with low nitrification activity. NOB Nitrospira and Nitrobacter did not grow in the soils with pH 4.82-7.04 and other populations of NOB were probably involved in nitrite oxidation in the vegetable cropped soil. [ABSTRACT FROM AUTHOR]

Nitrification, as a crucial step in nitrogen cycling and plant nutrition, is a biologically mediated process responsible for enormous losses of nitrogen fertilizer and a contributor to environmental pollution. The recent progress in our understanding of nitrification and nitrifiers, specifically in acidic soils, is discussed and reviewed. At one time it was assumed that rates of nitrification are relatively low in acidic soils. However, more recent studies have demonstrated nitrification down to pH 3.0 and that the rate of nitrification can equal, or even exceed, that found in neutral soils. Studies on acidic forest soils in Europe noted that they have a high potential for nitrate production. Furthermore, using the 15 N isotope-dilution technique it was shown that net nitrification measurements can markedly underestimate gross nitrification in these natural and highly organic systems. Using selective inhibitors it has been demonstrated that heterotrophic nitrifiers can contribute to nitrification. While heterotrophic nitrification can be performed by a wide range of bacteria and fungi, inhibitor studies point to fungi to be mainly responsible. Autotrophic ammonia-oxidizing bacteria (AOB), such as Nitrosomonas and Nitrosospira , have been known for some considerable time but have generally found to be inactive in acidic conditions. The discovery of ammonia monooxygenase in uncultured archaea that were functionally active at low pH pointed to an autotrophic microbial group (ammonia oxidizing archaea, AOA) that might be adapted to low substrate (ammonia) concentrations and responsible for nitrification in the wider range of acidic grassland and cultivated soils. Obligately acidophilic AOA have more recently been cultivated while stable isotope probing has been used to confirm the dominance of AOA over AOB in acidic soils. Detailed molecular studies using both 16S rRNA and amo A (ammonia monooxygenase sub-unit A) gene sequencing are continuing to expand our appreciation of the diversity of both AOB and AOA and how this varies over different pH ranges and in different ecosystems. Similar work is being directed towards nitrite oxidizing bacteria (NOB) but to date we do not fully know the role of pH in controlling NOB activity. Such understanding of nitrification and nitrifiers will help develop new effective nitrification inhibitors and aid the management of nitrogen cycling in acidic soils. [ABSTRACT FROM AUTHOR]

Increasing evidence indicates that nitrification is a vital factor in crop growth and nitrous oxide emission. Nitrification and urease inhibitors have been demonstrated to be effective in inhibiting the nitrification process and are widely used as fertilizer additives in agricultural soils. However, the effects of these inhibitors on rice N uptake and N 2 O production through denitrification in paddy soils remain unclear. In the present work, we compared the influences of nitrification inhibitors dicyandiamide (DCD), nitrapyrin (2-chloro-6-(trichloromethyl) pyridine; NP) and N-(n-butyl) thiophosphoric triamide (NBPT) on rice growth, the fate of urea nitrogen (N), and the abundances and activities of ammonia oxidizers and denitrifiers. The fate of urea N was determined by the 15N isotope labeling technique, and the abundances of ammonia oxidizers and denitrifiers were determined using qPCR. All three inhibitors improved rice growth mainly due to the increase in urea N use efficiency. Urea N uptake was negatively correlated with nitrification. The growth of ammonia-oxidizing bacteria (AOB), important in nitrification, was directly blocked by DCD. Additionally, NP and NBPT impeded the growth of ammonia-oxidizing archaea (AOA). In addition, NP significantly increased the microbial biomass to promote more residual urea N in soil and increased soil N transformation. NBPT significantly inhibited urea hydrolysis indirectly affecting nitrification. All three inhibitors decreased the potential denitrification rate (PDR) at the rice heading stage but had little effect on the denitrifier gene abundance except for nitrapyrin, which decreased the nirK gene abundance. DCD and NBPT may reduce the denitrification activity by decreasing the denitrification substrate (NO 3 −) concentration. These results suggest that DCD, NP and NBPT have a beneficial effect on improving rice N uptake and have the potential to reduce N 2 O generation through denitrification. A conceptual model for the effect of inhibitors on rice growth and N2O generation through denitrification. Red arrows mean positive effect, blue arrows mean negative effect and gray arrows mean no effect. Unlabelled Image • Inhibitors improved rice growth by increasing urea N use efficiency. • DCD blocked AOB growth while NP and NBPT blocked AOA growth. • NP increased soil N transformation by increasing microbial biomass. • NP decreased nirK gene abundance to prevent denitrification. • DCD and NBPT decreased denitrification potential by reducing substrate concentration. [ABSTRACT FROM AUTHOR]

[Display omitted] • The effect of biodegradable microplastics (MPs) on abiotic CO 2 varied among soils. • The CO 2 partial pressure controlled the carbonate-derived CO 2 in the short period. • Ammonia-oxidizing bacteria likely drove abiotic CO 2 in the long term. The presence of biodegradable microplastics (MPs) has the potential to affect soil pH, and possibly accelerate or inhibit the loss of soil inorganic carbon (SIC) in calcareous soils. However, most researchers have focused on the release of biotic carbon dioxide (CO 2) from soils following MP amendments, and few studies have investigated SIC-derived CO 2. In this experiment, three typical biodegradable MPs were applied to three calcareous soils amended with 1 % 13C-labeled (99 % atom) carbonate, and the release of CO 2 originating from SIC was quantified. The total CO 2 emissions, soil pH, and microbial functional genes involved in soil nitrification and denitrification were also detected. Throughout the experiment, the contribution of 13C-labeled carbonate to total CO 2 emissions ranged from 0.42 % to 3.31 %. The impact of biodegradable MPs on SIC-derived CO 2 varied with incubation period. At the early stage (≤20 days), the amendment of three biodegradable MPs increased the abiotic CO 2 in some cases, and the CO 2 emissions from 13C-labeled SIC were positively correlated with the total CO 2 originating from the decomposition of SOC and MPs. At the late stage (20–70 days), the presence of biodegradable MPs inhibited the release of CO 2 from 13C-labeled carbonate in most treatments. Moreover, there were negative relationships of SIC-derived CO 2 with soil pH and the amoA gene of ammonia-oxidizing archaea (AOA), but positive correlations of SIC-derived CO 2 with amoA of ammonia oxidizing bacteria (AOB) and nirK and nirS genes encoding nitrate reductase in denitrification. Our results indicate that long-term exposure to biodegradable MPs probably regulates the release of H+ in the nitrification process by controlling AOB, and then controlling the dynamics of SIC in calcareous soils. [ABSTRACT FROM AUTHOR]

The presence of microplastics (MPs) under flooded conditions is beneficial for nitrifiers and denitrifiers to produce nitrous oxide (N 2 O), but their dose effect remains unclear. This study evaluated the impact of different doses of polyethylene (PE) MPs on the release of N 2 O from paddy soils cultivated for different years. Compared with unpolluted soils, low doses of MPs (≤ 0.1%) had a negligible influence on N 2 O emissions, and high amounts of MPs (≥ 0.5%) significantly (p < 0.05) increased N 2 O emissions from the paddy soils cultivated for 3, 15 and 40 years by 2.5–4.3, 3.9–8.5 and 8.9–27.7 times, respectively. Moreover, an exponential model indicated that a 0.2% concentration of PE MPs appeared to be the dose threshold that accelerated the release of N 2 O from the all soils. Increased MP concentrations accelerated N 2 O emissions by affecting microbial functional genes involved in N 2 O production and reduction, but microbial taxonomic attributes involved in nitrogen cycling played an insignificant role in controlling N 2 O emissions. Overall, our results indicated that high doses (≥ 0.5%) of PE MPs essentially accelerated the emission of N 2 O from rice soils, and a longer cultivation period (40 years) enhanced the positive effect of MPs on N 2 O emissions. [Display omitted] • Low doses (≤ 0.1%) of microplastic (MP) had a negligible influence on N 2 O emissions. • High concentrations of MP (≥ 0.5%) significantly increased N 2 O emissions. • The 0.2% MP dose appeared to be the threshold that accelerated the release of N 2 O. • Paddy soil cultivated for 40 years enhanced the positive effect of MP on N 2 O emissions. [ABSTRACT FROM AUTHOR]

Increasing evidence shows that fertilization plays a key role in improving nitrogen (N) storage and increasing N supply capacity in paddy soils. How fertilizer regimes (N application rate, substitution rate, and fertilizer type) and environmental variables (soil pH and SOM) affect N pools, nitrification processes (abundance of nitrifying microorganisms, nitrification rate), and N losses (NH 3 volatilization and N 2 O emission) in paddy soils is still unclear. Here, we conducted a meta-analysis by compiling a total of 1307 individual experimental observations from 64 peer-reviewed publications to evaluate the impacts of N fertilization with other amendments (manure, biochar, or nitrification inhibitors) on the abovementioned paddy soil N sequestration and turnover. Overall, fertilization increased N pools (total N, NH 4 +-N, and NO 3 −-N content) and the abundance of main nitrifying microorganisms (AOA and AOB) by 7.3 % to 51.4 % and 70.3 % to 146.9 % in paddy soil, respectively, while stimulating NH 3 volatilization and N 2 O emissions by 277.3 % and 149.7 %, respectively. The increased N losses following fertilization were positively correlated with the expansion of paddy soil N pools. In particular, the substitution of organic fertilizer for chemical fertilizer at 30 % to 70 % had a better effect on elevating soil N sequestration, while a substitution rate of >70 % reduced N losses. Moreover, the application of biochar and nitrification inhibitors was conducive to increasing total N, NH 4 +-N, and NH 3 volatilization and reducing N 2 O emissions in fertilized paddy soils. Our findings indicated that fertilization regimes substantially stimulated N pools and N losses in paddy ecosystems. Thus, to avoid environmental and economic consequences, the optimization of N management and adjusting soil properties should be considered to increase N use efficiency and suppress N losses. • Fertilization regimes increased N pools but stimulated N losses (NH 3 and N 2 O) in paddy soil. • Organic fertilizers alone had a better effect on elevating soil N pools and reducing N losses. • Amendments of biochar and inhibitors increased soil N pools but reduced NH 3 volatilizations. • N management should site-specifically be considered to increase N pools and suppress N losses. [ABSTRACT FROM AUTHOR]