Speciation and Possible Origins of Organosulfur Compounds in Rice Paddy Soils Affected by Acid Mine Drainage

Although sulfur cycling in acid mine drainage (AMD)-contaminated rice paddy soils is critical to understanding and mitigating the environmental consequences of AMD, potential sources and transformations of organosulfur compounds in such soils are poorly understood. We used sulfur K-edge X-ray absorption near edge structure (XANES) spectroscopy to quantify organosulfur compounds in paddy soils from five AMD-contaminated sites and one AMD-uncontaminated reference site near the Dabaoshan sulfide mining area in South China. We also determined the sulfur stable isotope compositions of water-soluble sulfate (δ34SWS), adsorbed sulfate (δ34SAS), fulvic acid sulfur (δ34SFAS), and humic acid sulfur (δ34SHAS) in these samples. Organosulfate was the dominant functional group in humic acid sulfur (HAS) in both AMD-contaminated (46%) and AMD-uncontaminated paddy soils (42%). Thiol/organic monosulfide contributed a significantly lower proportion of HAS in AMD-contaminated paddy soils (8%) compared to that in AMD-uncontaminated paddy soils (21%). Within contaminated soils, the concentration of thiol/organic monosulfide was positively correlated with cation exchange capacity (CEC), moisture content (MC), and total Fe (TFe). δ34SFAS ranged from -6.3 to 2.7‰, similar to δ34SWS (-6.9 to 8.9‰), indicating that fulvic acid sulfur (FAS) was mainly derived from biogenic S-bearing organic compounds produced by assimilatory sulfate reduction. δ34SHAS (-11.0 to -1.6‰) were more negative compared to δ34SWS, indicating that dissimilatory sulfate reduction and abiotic sulfurization of organic matter were the main processes in the formation of HAS.

A Bionic Walking Wheel for Enhanced Trafficability in Paddy Fields with Muddy Soil

To improve wheel trafficability in soft and muddy soils such as paddy fields, a bionic walking wheel is designed based on the structural morphology and movement mode of the feet of waders living in marshes and mudflats, similar to the muddy soil of paddy fields. The bionic walking wheel adopts the arrangement of double-row wheel legs and staggered arrays to imitate the walking posture of waders. The two legs move alternately, cooperate with each other, and improve the smoothness of movement. The cam inside the bionic walking wheel is used to control the movement mode of the feet. The flippers open before touching the ground to increase the contact area and reduce sinking, and the toes bend and grip the ground while touching the ground to increase traction. Multi-rigid-body dynamics software (Adams View 2020) is used to simulate the movement of the wheel during the wading process, and the movement coordination and interference between the wheel legs are analyzed. The simulation results show that there is no interference between the parts and that the movement smoothness is good. The interaction between the bionic walking wheel and muddy soil was analyzed via coupled EDEM-ADAMS simulation, and the simulation analysis and experiments were conducted and compared with those for a common paddy wheel. The results showed that the bionic walking wheel designed in this paper improved the drawbar pull by 113.56% compared with that of a common paddy wheel and had better anti-sinking performance. By analyzing the effect of toe grip on traction, it was found that the soil under the feet can be disturbed to provide greater traction when the toe is bent downward. This study provides a reference for improving the trafficability of walking mechanisms in soft and muddy soils, such as paddy fields.

Mobilization of Colloid- and Nanoparticle-Bound Arsenic in Contaminated Paddy Soils during Reduction and Reoxidation

The association of arsenic (As) with colloidal particles could facilitate its transport to adjacent water systems or alter its availability in soil-rice systems. However, little is known about the size distribution and composition of particle-bound As in paddy soils, particularly under changing redox conditions. Here, we incubated four As-contaminated paddy soils with distinctive geochemical properties to study the mobilization of particle-bound As during soil reduction and subsequent reoxidation. Using transmission electron microscopy-energy dispersive spectroscopy and asymmetric flow field-flow fractionation, we identified organic matter (OM)-stabilized colloidal Fe, most likely in the form of (oxy)hydroxide-clay composite, as the main arsenic carriers. Specifically, colloidal As was mainly associated with two size fractions of 0.3-40 and >130 kDa. Soil reduction facilitated the release of As from both fractions, whereas reoxidation caused their rapid sedimentation, coinciding with solution Fe variations. Further quantitative analysis demonstrated that As concentrations positively correlated with both Fe and OM concentrations at nanometric scales (0.3-40 kDa) in all studied soils during reduction and reoxidation, yet the correlations are pH-dependent. This study provides a quantitative and size-resolved understanding of particle-bound As in paddy soils, highlighting the importance of nanometric Fe-OM-As interactions in paddy As geochemical cycling.

Denitrification contributes to N2O emission in paddy soils

Denitrification is vital to nitrogen removal and N₂O release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of N₂O emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential N₂O emission rate, enzymatic activity for N₂O production and reduction, gene abundance, and community composition during denitrification were investigated using the ¹⁵N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential N₂O emission rates were 0.51 ± 0.20 μmol⋅N⋅kg^-1⋅h^-1, which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for N₂O production was 2.77-8.94 times than that for N₂O reduction, indicating an imbalance between N₂O production and reduction. The gene abundance ratio of nir to nosZ from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the norB gene without nosZ genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to N₂O emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g N₂O⋅m^-2⋅yr^-1 in surface paddy soils.

[Mechanism and Environmental Effect on Nitrogen Addition to Microbial Process of Arsenic Immobilization in Flooding Paddy Soils]

China is one of the largest rice producers in the world, and rice production plays an important role in food security. Currently, arsenic pollution in paddy soils is one of most serious soil pollutions in China. Since paddy soils are maintained in a flooding anoxic condition for long periods, the rate and extent of arsenic transformation processes governed by microbial activities are stronger than that of chemical processes. Thus, understanding the key processes and relating mechanisms of microbial arsenic fixation in paddy soils will provide a theoretical basis for controlling arsenic pollution in paddy soils. In this study, based on a comprehensive analysis of arsenic migration in paddy soils and relating influencing factors, two important pathways relating to As(Ⅲ) fixation through microbial activities were illustrated:microbial ČFe(Ⅱ) oxidation coupled with As(Ⅲ) fixation (indirect process) and direct fixation through microbial As(Ⅲ) oxidation (direct process). Additionally, the influences of speciation and the distribution of nitrogen in paddy soils to the processes of microbial arsenic fixations were discussed and by extension, the expressions of key genes and metabolic mechanisms relating to microbial arsenic fixation and nitrogen transformation. Finally, the recent advances in microbial remediation used to control arsenic pollution in paddy soils were summarized, and relating future perspectives targeting microbial remediation were proposed.

[Responses of Cd Accumulation in Rice and Spectral Characteristics of Soil Dissolved Organic Matter Regulated by Soil Amendments]

Studying the chemical composition and characteristic differences of soil dissolved organic matter (DOM) is significant for understanding the mechanism of Cd immobilization by soil amendments. Soil amendments have been widely applied to contaminated farmlands to reduce the accumulation of heavy metals in crops, but the spectral characteristics of DOM in soils under amendment regulation have rarely been studied. Typical Cd-contaminated paddy soil from South China was collected, three categories of amendments (organic-based, inorganic-based, and lime-based, a total of 11 types) were applied, rice planting pot trials were done, and the effects of different amendments on soil DOM were investigated. The spectral characteristics of rhizosphere soil DOM under the regulation of different amendments were comparatively analyzed using UV-Vis spectroscopy, 3D fluorescence spectroscopy, and parallel factor analysis (PARAFAC). The results showed that the lime-based amendments increased the soil pH and promoted the dissolution of organic matter from the soil solid phase, resulting in a significant increase in soil DOM content. Compared with that of the control, organic-based amendments increased the relative molecular weight and recent autochthonous origin contribution of soil DOM, inorganic-based amendments increased the aromatic content and hydrophobic components of soil DOM, and lime-based amendments increased the chromogenic components and the degree of humification of soil DOM. Four fluorescence components, C1 (255/465), C2 (325/400), C3 (275/390), and C4 (240/460), were identified using PARAFAC and verified with the OpenFluor database, all of which were humic-like. Two types of spectra corroborated with each other, indicating that soil DOM dominated by humus-like matter originated from terrestrial source input. The correlation analysis showed that the fluorescent component C4 of soil DOM could be used to predict Cd accumulation in brown rice in the red limestone soil-rice system. These results will provide a reference for the selection of the appropriate soil amendments.

Migration and Removal of Labile Cadmium Contaminants in Paddy Soils by Electrokinetic Remediation without Changing Soil pH

Electrokinetic remediation (EKR) is a viable, advanced cleaning strategy that can permanently reduce the toxicity of soil contaminants. However, EKR is prone to causing changes in soil pH. The negative impacts must be minimized if field-scale application is to be realized. In this study, EKR with polarity reversal was used to avoid soil pH polarization and to clean up cadmium (Cd)-contaminated paddy soils. Results showed that Cd desorbed from oxidizable and residual fractions to labile and easily available parts. Soil moisture content above 0.35 g g⁻¹ was conductive to achieving the desirable Cd-migration rate. The exchangeable Cd phase eventually migrated from both ends of that soil compartment towards the intermediate. Moreover, the addition of citric acid at the concentration of 0.1 mol L⁻¹ was an effective enhancement strategy. The methodology enriched Cd contaminants to specific sites. The technology can be used for electrokinetic-assisted phytoremediation during the rice growing period. Hyperaccumulator is planted in the intermediate area to remove the Cd contaminants. On the other hand, Cd removal is achieved in the region close to the electrodes. The present study provides a theoretical basis for in situ remediation. It has a wider significance for field-scale application.

The Aging Process of Cadmium in Paddy Soils under Intermittent Irrigation with Acid Water: A Short-Term Simulation Experiment

Cadmium (Cd)-contaminated paddy soils are a big concern. However, the effect of irrigation with acid water on the migration and transformation of Cd and the effect of alternating redox conditions caused by intermittent irrigation on Cd aging processes in different depths of paddy soils are unclear. This study revealed Cd fractionation and aging in a Cd-contaminated paddy soil under four irrigation periods with acid water and four drainage periods, by applying a soil columns experiment and a sequential extraction procedure. The results showed that the dynamic changes of soil pH, oxidation reduction potential (ORP), iron (Fe) oxides and dissolved organic carbon (DOC) throughout the intermittent irrigation affected the transformation of Cd fractions. After 32 days, the proportion of exchangeable Cd (F1) to the total Cd decreased with a reduction of 24.4% and 20.1% at the topsoil and the subsoil, respectively. The labile fractions of Cd decreased, and the more immobilizable fractions of Cd increased in the different depths of soils due to the aging process. Additionally, the redistribution of the Fe and Mn oxide-bound Cd (F3) and organic matter and secondary-sulfide-bound Cd (F4) occurred at different depths of soils during the incubation time. Overall, the bioaccessibility of Cd in the subsoil was higher than that in the topsoil, which was likely due to the leaching and accumulation of soluble Cd in the deep soil. In addition, the aging processes in different depths of soils were divided into three stages, which can be mainly described as the transformation of F1 into F3 and F4.

Effect of Soil Solution Properties and Cu2+ Co-Existence on the Adsorption of Sulfadiazine onto Paddy Soil

Paddy soils are globally distributed and saturated with water long term, which is different from most terrestrial ecosystems. To better understand the environmental risks of antibiotics in paddy soils, this study chose sulfadiazine (SDZ) as a typical antibiotic. We investigated its adsorption behavior and the influence of soil solution properties, such as pH conditions, dissolved organic carbon (DOC), ionic concentrations (IC), and the co-existence of Cu²⁺. The results indicated that (1) changes in soil solution pH and IC lower the adsorption of SDZ in paddy soils. (2) Increase of DOC facilitated the adsorption of SDZ in paddy soils. (3) Cu²⁺ co-existence increased the adsorption of SDZ on organic components, but decreased the adsorption capacity of clay soil for SDZ. (4) Further FTIR and SEM analyses indicated that complexation may not be the only form of Cu²⁺ and SDZ co-adsorption in paddy soils. Based on the above results, it can be concluded that soil solution properties and co-existent cations determine the sorption behavior of SDZ in paddy soils.

[Simulation Cadmium (Cd) Accumulation in Typical Paddy Soils in South China]

The simulation analysis of the migration path and soil accumulation trend of Cd in paddy soil systems could contribute to improved scientific and reasonable risk decision-making. In this study, based on a regional survey of environmental media in Youxian County, Hunan Province, a pollutant accumulation model (PAM) was built to predict the cumulative trend of Cd in paddy soils. Combined with Monte Carlo simulation, the PAM model was used to evaluate the effectiveness and sustainability of various remediation measures. Results showed that the probability of Cd accumulation in paddy soils in Youxian County exceeded that of the national soil environmental quality standard by 2-fold and was up to 82.1%, and the average accumulation rate reached 4.28 μg·(kg·a)^-1 after 50 years of cultivation under current input pattern. Sensitivity analysis results showed that atmospheric deposition and rice uptake were the key processes affecting Cd accumulation in paddy soils. Results of a multi-scenario simulation showed that the comprehensive measures, such as reducing the straw returning, optimizing the layout of industrial and mining enterprises that reduce the atmospheric deposition of Cd, and cleaning irrigation water, could reduce the Cd accumulation in paddy soils by 43.7% and reduce the probability of light Cd pollution by 80.6% after 50 years, which would be an effective long-term measure to prevent and control Cd pollution risk in paddy soils.

Microbiomes inhabiting rice roots and rhizosphere

Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.

Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, "everything is everywhere, but the environment selects," although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths.IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.

[Effects of Biochar Amendment on Soil Microbial Biomass Carbon, Nitrogen and Dissolved Organic Carbon, Nitrogen in Paddy Soils]

Biochar can influence soil microbial biomass. It is not clear how biochar amendment affects soil microbial biomass carbon and nitrogen (MBC and MBN) and dissolved organic carbon and nitrogen (DOC and DON) in double-cropping rice soils. To address this problem, two subtropical double-cropping rice soils (S1 and S2) were selected for an incubation experiment. S1 is developed from granite-weathered red soil and S2 is developed from Quaternary red clay. The following three wheat straw-derived biochar application rates were used, without N fertilizer, in each paddy soil:0%, 1%, and 2% of soil weight, represented by CK, LB, and HB, respectively. After a 70 d incubation, soil mean MBC was 877.03 mg·kg^-1, 832.11 mg·kg^-1, and 849.30 mg·kg^-1 in S1 for the three application rates, and 902.94 mg·kg^-1, 874.19 mg·kg^-1, and 883.22 mg·kg^-1, respectively, in S2. S1+LB, S1+HB, and S2+LB treatments reduced soil mean MBC compared to the CK treatment (P<0.05). This may be attributed to biochar inhibiting microbial growth by adsorbing soil organic carbon and other low-molecular-weight organic matter. Low biochar application rates decreased mean soil MBN by 9.45% compared to the CK treatment in S1 (P<0.05). No significant differences in mean MBC/MBN were observed among the S1 treatments, but LB reduced MBC/MBN in S2 (P<0.05). Due to the soluble organic carbon content and strong alkalinity of biochar, biochar amendment increased mean soil DOC by 4.42%-22.20% and 10.57%-35.47% in S1 and S2, respectively (P<0.05). However, biochar amendment (except for the S2+HB treatment) decreased mean soil DON in both paddy soils. This may have resulted from the adsorption of soil organic nitrogen by biochar and N consumption during the decomposition of the organic carbon within biochar. Biochar amendment increased mean soil DOC/DON in both paddy soils (P<0.05) and mean DOC/DON increased with an increase in the biochar application rate. Based on these results, biochar amendment increased soil dissolved organic carbon, decreased soil microbial biomass, and enhanced the nitrogen deficit in double-cropping paddy soils. Therefore, biochar should be combined with the application with fertilizer in double-cropping rice systems in subtropical central China.

Changes in Structural and Functional Responses of Bacterial Communities under Different Levels of Long-Term Compost Application in Paddy Soils

Soils amended for long-term with high levels of compost demonstrated greater abundance of bacterial members of the phylum Bacteroidetes whereas a decreasing trend in the relative abundance of phylum Acidobacteria was noted with increasing levels of compost. Metabolic profiles predicted by PICRUSt demonstrated differences in functional responses of the bacterial community according to the treatments. Soils amended with lower compost levels were characterized by abundance of genes encoding enzymes contributing to membrane transport and cell growth whereas genes encoding enzymes related to protein folding and transcription were enriched in soils amended with high levels of compost. Thus, the results of the current study provide extensive evidence of the influence of different compost levels on bacterial diversity and community structure in paddy soils.

[Effects of Varying Long-term Fertilization on Organic Carbon Mineralization and Priming Effect of Paddy Soil]

A laboratory incubation experiment was conducted using the ¹⁴C isotope labeling technique to study the characteristics of organic carbon mineralization and their response to glucose addition when treated with a combination of straw and chemical fertilizer (ST), inorganic fertilizer (NPK), and non-fertilization (CK). The cumulative mineralization rate (ratio of accumulated mineralization amount to total organic carbon content) in CK reaches 1.64% at the end of incubation (56 days). The cumulative mineralization rate during NPK and ST treatments is significantly lower than that in CK (by 0.34% and 0.39%, respectively). This indicates that long-term fertilization affects the soil carbon sequestration. Varying long-term fertilization influences the response of paddy soil to glucose addition and leads to different levels of the priming effect. The priming effect on soil organic carbon mineralization of the three treatments gradually changes from negative to positive with increasing incubation time. The significantly negative cumulative priming effect in ST and NPK after 56 d is 22.07 and 9.05 times higher than that in CK, respectively. The results of the structural equation model indicate that the NH₄⁺-N and DOC contents indirectly influence the cumulative priming effect on soil organic carbon by affecting the MBC and MBN contents. The NH₄⁺-N concentration has a direct and significant negative effect on the cumulative priming effect. In conclusion, long-term fertilization treatments reduce the cumulative organic carbon mineralization rate of paddy soil. Fertilizer, especially the combination of straw and chemical fertilizer, enhances the soil carbon sequestration and accumulation.

[Effects of Microbial Activities on Mercury Methylation in Farmland near Mercury Mining Area]

In order to study the main effect of microbial activities on mercury(Hg) methylation in farmland, mercury contaminated upland soils and paddy soils near Hg mining area were sampled as experimental soils. Four treatments were designed including only sterilization as the control, accelerating the activities of sulfate reducing bacteria(SRB), inhibiting the SRB's activities, and accelerating the activities of iron-reducing bacteria(FeRB), to know the effects of microbial and non-microbial factors on mercury methylation in soils. The results were as follows:the highest concentration of methylmercury(MeHg) was observed in soils with SRB accelerated treatment, and the increments of MeHg concentrations in upland soils and paddy soils ranged from 0.15 μg·kg^-1 to 0.38 μg·kg^-1 and 1 μg·kg^-1 to 2 μg·kg^-1, respectively. Comparatively, little increments of MeHg concentration were seen in soils with SRB inhibited treatment and FeRB accelerated treatment, which were lower than 0.025 μg·kg^-1. Compared with upland soils, more MeHg was formed in Paddy soils and the concentrations of MeHg in paddy soils were 4-9 times of that in upland soils. Variation in the number of SRB in soils was similar to that in the concentration of MeHg in soils, and the number of SRB was positively correlated with the concentration of MeHg concentrations in soils(R²=0.57,P<0.01). The above results indicated that activities of reducing bacteria, especially SRB, played key role in the methylation in soils. In addition, more attention should be paid to paddy soils due to the high potential of methylation when conducting any assessment and taking any measure to manage the health risk caused by the exposure to mercury.

Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics

Waterlogged paddy soils possess anoxic zones in which microbes actively induce reductive nitrogen transformation (RNT). In the present study, a shotgun RNA sequencing analysis (metatranscriptomics) of paddy soil samples revealed that most RNT gene transcripts in paddy soils were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter. Despite the frequent detection of the rRNA of these microbes in paddy soils, their RNT-associated genes have rarely been identified in previous PCR-based studies. This metatranscriptomic analysis provides novel insights into the diversity of RNT microbes present in paddy soils and the ecological function of Deltaproteobacteria predominating in these soils.

The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors

Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75–1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray–Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors.