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

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]

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]

Nitrous oxide (N 2 O) is an important greenhouse gas, whose production from landfill sites has not been given adequate attention yet. Municipal solid waste disposal site could be a potential contributor to N 2 O emissions. Here, we conducted a transect study to determine N 2 O flux and the abundance and activity of nitrifiers and denitrifiers across three different landfill sites (Ninghai: NH, Xiangshan: XS, and Fenghua: FH). Microbial abundance and community structure were determined using quantitative polymerase chain reaction, terminal-restriction fragment length polymorphism (T-RFLP), and clone library. The highest mean N 2 O flux (3.44 mg m −2 h −1 ) and global warming potential (1025.12 eq-CO 2 m −2 h −1 ) were detected at the XS and NH sites, respectively. Soil nutrients (dissolved organic C, dissolved organic N, and total organic C), C:N ratio, and the abundance and activity of nitrifiers and denitrifiers determined the flux of N 2 O across the three landfill cover soils. Nitrification and denitrification made comparable contribution to N 2 O production in the soils. Nitrososphaera -associated archaeal amoA gene accounted for 99% of ammonia-oxidizing archaea (AOA) sequences at the XS site, whereas soil/sediment cluster I of AOA dominated (>50%) at the NH and FH sites. The predominant ammonia-oxidizing bacteria sequences (>75%) of the FH site were affiliated with the Nitrosomonas lineage and more than half the sequences belonged to cluster 3b at the XS and NH sites. The nirK sequences affiliated with Alpha-proteobacteria ( Phyllobacteriaceae , Rhizobiaceae and Bradyrhizobiaceae ) (>78%) and nirS sequences affiliated with Beta-proteobacteria (>45%) governed the denitrifiers in the soils. Heavy metals (Cu and Cr), C:N ratio, and C sources (total C and dissolved organic C) determined the distribution of the nitrifier and denitrifier communities. In conclusion, the condition of the landfill sites contributed significantly to the N 2 O emissions, and AOA and nirK-type denitrifiers dominated the leachate-affected cover soils. [ABSTRACT FROM AUTHOR]