Rice Rhizosphere Research Articles

Soil biological quality in rhizosphere, growth, and yield of upland rice grown on acid soil after amended biochar enriched sap of Kappaphycus alvarezii

Abstract. Rakian TC, Kilowasid LMH, Afa LO, Riskyana A, Nurazizah, Wijayanti Y, Bahrun A, Subair I, Rahni NM, Alam S, Sarawa, Karimuna L. 2023. Soil biological quality in rhizosphere, growth, and yield of upland rice grown on acid soil after amended biochar enriched sap of Kappaphycus alvarezii. Biodiversitas 24: 6780-6792. Biological soil quality is essential in evaluating soil management practices using biochar enriched for upland rice growth on acid soil. Therefore, the study aimed to (i) analyze the effect of biochar-enriched sap of Kappaphycus alvarezii (K-sap) on the abundance of Arbuscular Mycorrhizae Fungi (AMF), bacteria, and protozoa in rhizosphere soil, growth, and yield of upland rice, and (ii) the relationship between the abundance of soil biota and the growth and yield components, as well as straw N, P, and K content on acid soil. Four upland rice were grown on acid soil incubated with biochar-enriched sap for two weeks in pots. Nine treatments of the biochar-enriched sap were tested, namely control, 5% biochar-0% K-sap, 5% biochar-5% K-sap, 5% biochar -10% K-sap, 5% biochar-15% K-sap, 7.5% biochar-0% K-sap, 7.5% biochar-5% K-sap, 7.5% biochar-10% K-sap, and 7.5% biochar-15% K-sap. Each treatment was three replicates in a randomized block design. The results demonstrated that the AMF spores quantity decreased while flagellates increased in the soil rhizosphere. The P and K content increased, the N:P decreased, and P:K ratio varied in the straw of the upland rice. Plant height and total spikelets increased, while root dry weight and roots to shoots ratio (R:S) decreased with biochar enriched. The abundance of AMF spores and flagellates correlated positively and negatively with R:S. Furthermore, R:S was negatively correlated with plant height and total spikelets. Plant height and total spikelets showed a positive correlation, while root dry weight and R:S was negatively correlated with K content in shoot tissue. The P and K contents with N:P ratio and N:P with P:K were negatively correlated. In conclusion, biochar-enriched K-sap effectively regulated the activity and composition of soil biota in the rhizosphere, influencing upland rice's growth, yield, and nutrient balance uptake on acid soils.

Biological Control Ability and Antifungal Activities of Bacillus velezensis Bv S3 against Fusarium oxysporum That Causes Rice Seedling Blight

Fusarium oxysporum, a primary soil-borne fungus that affects rice seedlings globally, is responsible for rice seedling blight (RSB), which reduces seedling quality and survival rates. The synthetic fungicides used to treat this disease negatively affect human health and the environment. A biocontrol bacterial isolate, Bacillus velezensis Bv S3, isolated from the rice rhizosphere, showed a strong antagonistic effect on RSB-causing F. oxysporum. The ratio of the longest to the shortest radius of F. oxysporum following Bv S3 inoculation was 2.52 (cm/cm) in a plate standoff experiment. This was different from the other biocontrol strains. Bv S3 exhibits a wide spectrum of antifungal activity against various pathogenic fungi that cause RSB. When 10% Bv S3 liquid culture filtrate was applied, it dramatically reduced F. oxysporum spore germination and mycelial growth, with inhibition rates of 66.7%, and 45.7%, respectively, and caused hyphal malformations. Furthermore, the Bv S3 suspension (1 × 108 CFU/mL) reduced RSB by 65.5% and 76.5% in pot experiments, effectively promoted the growth of rice seedlings, and improved the activities of neutral phosphatase, urease, invertase, and catalase in rice rhizosphere soil. The active substances produced by Bv S3 were sensitive to temperature and ultraviolet irradiation, and the antifungal effect significantly increased after 90 min of exposure, with antifungal effect observed at pH 7. Bv. S3 effectively reduced the incidence of RSB and showed potential as a biocontrol agent.

Bioremediation of paddy soil with amphitropic mixture markedly attenuates rice cadmium: Effect of soil cadmium removal and Fe/S-cycling bacteria in rhizosphere

Cadmium (Cd) pollution in paddy soil can easily lead to excessive Cd in rice, thereby considerably threatening human health. Microbial leaching is an effective pathway for the mobilization and removal of Cd from soil. In this study, an amphitropic mixture (AM) composed of autotrophic and heterotrophic microbial strains was used to leach Cd-contaminated paddy fields. Chemical analysis showed that the AM effectively removed 52 % of the total Cd, 39 % of the available Cd, and 60 % of the exchangeable and carbonate-bound Cd from the paddy soil. After bioleaching, the Cd in the discarded AM solution was adsorbed using a metal adsorbent. Effects of remediation on the soil nutrients or secondary pollution were not significant. Microbial analysis showed that >96 % and 67 % of the indigenous bacteria and fungi, respectively, remained in the AM-remediated soil. Double-cropped rice was cultivated to evaluate the Cd removal efficiency of grains using AM remediation. The Cd in early and late brown rice decreased by 86 % and 56 %, respectively, which was higher than that found for a series of biochemical remediation materials reported in other studies. Furthermore, the AM remediation promoted the growth of iron (Fe)- and sulfur (S)-cycling bacteria in the rice rhizosphere, such as Sulfuricurvum, Desulfurivibrio and Geobacter etc., which reduced the Cd availability in the soil and rice uptake. This study shows that AM has potential applications in the remediation of Cd-contaminated paddy fields and provides a new pathway for safe rice production.

Optimization of cellulose degrading bacteria isolated from rice rhizosphere for enhanced cellulase production and in situ residues decomposition

Optimization of cellulose degrading bacteria isolated from rice rhizosphere for enhanced cellulase production and in situ residues decomposition

Selection and Characterization of Antagonistic Bacteria as a High Potential Control Agent for Xanthomonas oryzae pv. oryzae Causing Bacterial Leaf Blight Disease in Purple Rice

Bacterial leaf blight disease is one of the most serious diseases in rice caused by Xanthomonas oryzae pv. oryzae. Purple rice is one of the rice varieties that has been infected by this pathogen. Thus, screening and selecting highly efficient antagonistic bacteria for controlling the pathogen is necessary for disease control to reduce epidemics and crop loss. Forty-eight isolates of antagonistic bacteria were isolated from rice rhizosphere soil. The highly effective antagonistic bacteria were selected by dual culture method. The results showed bacteria strains KY16 and KY17 were the most effective antagonists that were able to inhibit X. oryzae pv. oryzae. The inhibition growth zone of antagonists were approximately 12.70 mm and 11.95 mm, respectively. The morphological and some biochemical characteristics of antagonistic bacteria belong to Bacillus sp. Additionally, the antagonists KY16 and KY17 were identified as Bacillus siamensis based on 16S rRNA, gyrA, and rpoB gene sequences. Antimicrobial biosynthesis genes of the antagonistic bacteria were also examined. The results revealed that iturin A and surfactin biosynthesis genes were detectable. From this study, the selected antagonistic bacteria can be used to control the bacterial leaf blight disease of purple rice in rice paddy fields.

High-resolution chemical imaging to understand Cd activation in rice rhizosphere of karstic soils

Cadmium (Cd) activation, especially at a high spatial resolution, in paddy soils with a high geogenic Cd background is yet to be understood. To investigate the temporal and spatial patterns of Cd activation in rice rhizosphere, pot and rhizotron experiments were conducted using four paddy soils with high geogenic Cd (0.11–3.70 mg kg−1) from Guangxi, southwestern China. The pot experiment results showed that porewater Cd concentrations initially decreased and then increased over the complete rice growth period, reaching its lowest value during the late-tillering and early-filling stages. Besides, correlation analysis identified organic matter and root manganese (Mn) content as the main factors affecting rice Cd uptake, with Mn having a negative effect and organic matter having a positive effect. Sub-millimeter two-dimensional chemical imaging revealed that the distribution of labile Cd in the rhizosphere (by diffusive gradients in thin-films, or DGT) was influenced by the root system and soil properties, such as pH (by planar optode) and acid phosphatase activity (by soil zymography). Soil acid phosphatase activity increased under Cd stress. The overall pH at rice rhizosphere decreased. Moreover, a close relationship was found between the spatial distributions of soil labile Mn and Cd at the rhizosphere, with higher Mn being associated with lower Cd lability. This study highlights Mn as a key element in regulating rice Cd uptake and enlightens future Mn-based strategies for addressing Cd pollution in rice paddy soils, especially in karst areas with high geochemical background.

Selenium- and chitosan-modified biochars reduce methylmercury contents in rice seeds with recruiting Bacillus to inhibit methylmercury production

Biochar could reshape microbial communities, thereby altering methylmercury (MeHg) concentrations in rice rhizosphere and seeds. However, it remains unclear whether and how biochar amendment perturbs microbe-mediated MeHg production in mercury (Hg) contaminated paddy soil. Here, we used pinecone-derived biochar and its six modified biochars to reveal the disturbance. Results showed that selenium- and chitosan-modified biochar significantly reduced MeHg concentrations in the rhizosphere by 85.83% and 63.90%, thereby decreasing MeHg contents in seeds by 86.37% and 75.50%. The two modified bicohars increased the abundance of putative Hg-resistant microorganisms Bacillus, the dominant microbe in rhizosphere. These reductions about MeHg could be facilitated by biochar sensitive microbes such as Oxalobacteraceae and Subgroup_7. Pinecone-derived biochar increased MeHg concentration in rhizosphere but unimpacted MeHg content in seeds was observed. This biochar decreased the abundance in Bacillus but enhanced in putative Hg methylator Desulfovibrio. The increasing MeHg concentration in rhizosphere could be improved by biochar sensitive microbes such as Saccharimonadales and Clostridia. Network analysis showed that Saccharimonadales and Clostridia were the most prominent keystone taxa in rhizosphere, and the three biochars manipulated abundances of the microbes related to MeHg production in rhizosphere by those biochar sensitive microbes. Therefore, selenium- and chitosan-modified biochar could reduce soil MeHg production by these microorganisms, and is helpful in controlling MeHg contamination in rice.

Multi-imaging platform for rhizosphere studies: Phosphorus and oxygen fluxes

Rhizosphere is a soil volume of high spatio-temporal heterogeneity and intensive plant-soil-microbial interactions, for which visualization and process quantification is of highest scientific and applied relevance, but still very challenging. A novel methodology for quick assessment of two-dimensional distribution of available phosphorus (P) in rhizosphere was suggested, tested, and development up to the application platform. Available P was firstly trapped by an in-situ diffusive gradients in thin-films (DGT) sampler with precipitated zirconia as the binding gel, and subsequently, the loaded gel was analyzed with an optimized colorimetric imaging densitometry (CID). The imaging platform was established linking: i) DGT, ii) planar optode, and iii) soil zymography techniques to simultaneously determine available P, oxygen, and acid phosphatase in rhizosphere at sub-millimeter spatial scales. The DGT identified available P level in rice rhizosphere were spatially overlapping to the localized redox hotspots and phosphatase activity. The spatial relationship between available P and acid phosphatase activity was dependent on root development. The root radial oxygen loss (ROL) remained active during the experimental observations (2–3 days), while a flux of available P of 10 pg cm−2 s−1 was visualized within 2–3 mm of roots, confirming the correlative response of rice roots to oxygen secretion and P uptake. Summarizing, the established imaging platform is suitable to capture spatial heterogeneity and temporal dynamics of root activities, nutrient bioavailability, ROL and enzyme activities in rhizosphere.

Contrasting response of rice rhizosphere microbiomes to in situ cadmium-contaminated soil remediation

Contrasting response of rice rhizosphere microbiomes to in situ cadmium-contaminated soil remediation

Complete Genome Sequence of Pseudomonas promysalinigenes Strain RL-WG26, a PGPR Isolated from the Rice Rhizosphere for Studying the Promotion of Plant Growth Under Salt Stress

The Pseudomonas promysalinigenes strain RL-WG26, which was previously isolated from the rhizosphere of Sea Rice 86 (SR86), could promote the plant growth and alleviate the plant salt stress of SR86 by regulating the ion concentration in plants, increasing the dry weight and chlorophyll content of plants, and reducing the proline and malondialdehyde content in roots. Here, we report the complete genome sequence of Pseudomonas promysalinigenes strain RL-WG26 to lay a foundation for deciphering the molecular mechanisms of strain RL-WG26-mediated plant salt tolerance and to further the application potential of this strain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Whole-genome sequence of Bacillus velezensis strain R22 isolated from Oryza sativa rhizosphere in Bulgaria.

Bacillus velezensis R22 was isolated from a rice rhizosphere in Bulgaria. Its genome (assembled into 14 scaffolds) has a size of 4.08 Mbp and a G + C content of 46.35%. Nine full biosynthetic clusters for antimicrobials were predicted, among them two new gene clusters probably encoding polyketides named macrolactin R22 and velezensin.

Research Progress of Promoting Biocontrol Bacteria in Rice Rhizosphere

The irrational application of rice chemical fertilizer and the reduction of rice quality and yield caused by rice diseases have seriously affected agricultural production and the environment. To grow rice more scientifically and greenly, plant growth-promoting rhizobacteria (PGPR) has developed rapidly as a new control method for plant diseases. The discovery of PGPR is an essential process in biological control research. PGPR has many species, excellent biological traits, diverse antagonistic mechanisms, and a wide range of parasitism, which is an essential biological control method to solve the excessive application of chemical fertilizers and pesticides in rice production and has broad development prospects. In this paper, we summarize the research progress of PGPR application to rice and other plants in recent years, expound on the direct and indirect mechanisms, and look forward to the development trend of follow-up research in order to provide a theoretical reference for the in-depth study and better application of biocontrol bacteria.

Fertilization Weakens the Ecological Succession of Dissolved Organic Matter in Paddy Rice Rhizosphere Soil at the Molecular Level.

Dissolved organic matter (DOM) is involved in numerous biogeochemical processes, and understanding the ecological succession of DOM is crucial for predicting its response to farming (e.g., fertilization) practices. Although plentiful studies have examined how fertilization practice affects the content of soil DOM, it remains unknown how long-term fertilization drives the succession of soil DOM over temporal scales. Here, we investigated the succession of DOM in paddy rice rhizosphere soils subjected to different long-term fertilization treatments (CK: no fertilization; NPK: inorganic fertilization; OM: organic fertilization) along with plant growth. Our results demonstrated that long-term fertilization significantly promoted the molecular chemodiversity of DOM, but it weakened the correlation between DOM composition and plant development. Time-decay analysis indicated that the DOM composition had a shorter halving time under CK treatment (94.7 days), compared to NPK (337.4 days) and OM (223.8 days) treatments, reflecting a lower molecular turnover rate of DOM under fertilization. Moreover, plant development significantly affected the assembly process of DOM only under CK, not under NPK and OM treatments. Taken together, our results demonstrated that long-term fertilization, especially inorganic fertilization, greatly weakens the ecological succession of DOM in the plant rhizosphere, which has a profound implication for understanding the complex plant-DOM interactions.

Contribution of Biogas Slurry-Derived Colloids to Plant P Uptake and Phosphatase Activities: Spatiotemporal Response.

The bioavailability for varied-size phosphorus (P)-binding colloids (Pcoll) especially from external P sources in soil terrestrial ecosystems remains unclear. This study evaluated the differential contribution of various-sized biogas slurry (BS)-derived colloids to plant available P uptake in the rhizosphere and the corresponding patterns of phosphatase response. Keeping the same content of total P input (15 mg kg-1), we applied different size-fractioned BS-derived colloids including nanosized colloids (NCs, 1-20 nm), fine-sized colloids (FCs, 20-220 nm), and medium-sized colloids (MCs, 220-450 nm) respectively to conduct a 45-day rice (Oryza sativa L.) rhizotron experiment. During the whole cultivation period, the dynamics of chemical characteristics and P fractions in each experimental rhizosphere soil solution were analyzed. The spatial and temporal dynamics examination of P-transforming enzymes (acid phosphatases) in the rice rhizosphere was visualized by a soil zymography technique after 5, 25, and 45 days of rice transplantation. The results indicated that the acid phosphatase activities and its hot spot areas were significantly 1) correlated with the relative bioavailability of colloidal P (RBAcoll), 2) increased with the colloid-free (truly dissolved P) and BS-derived NC addition, and 3) affected by the plant growth stage. With the nanosized BS colloid addition, the RBAcoll and plant biomass were respectively found to be the highest (64% and 1.22 g plant-1), in which the acid phosphatase-catalyzed hydrolysis of organic Pcoll played an important role. All of the above suggested that nanosized BS-derived colloids are an effective alternative to conventional phosphorus fertilizer for promoting plant P uptake and P bioavailability.

Effect of Streptomyces JD211 application on soil physicochemical properties and N2O emission characteristics of rice rhizosphere

Biocontrol agent, as a pollution-free and sustainable plant disease control method, can inhibit the spread of soil-borne diseases and promote the growth of crops. However, there are few studies on the effect of biocontrol agent on N2O emission in rice soil. In this study, after the application of the biocontrol agent Streptomyces JD211, N2O emission from rice soil were measured, and the relationship between the agent and soil N2O emissions were studied in soil chemistry and molecular biology. The results showed that the application of Streptomyces JD211 can significantly reduce the rate of N2O emission from rice soil. The NH4+-N and NO3−-N contents in rice soil decreased in a short period of time after the application of Streptomyces JD211, while the mineral N content in the soil remained stable with rice growth. 16S rRNA gene sequencing and metagenomic sequencing revealed Streptomyces JD211 application mainly increased the relative abundance of Burkholderia and Streptomyces in the soil microbial community, reduced the relative abundance of hao, norB, norC genes, and increased the relative abundance of nosZ and hcp genes. Streptomyces JD211 application promoted N2O transformation and weakened N2O production pathways, which ultimately reduced N2O emissions from rice soils. This study provided new insight of biocontrol agents to regulate soil N2O emissions, which is of great significance for the development and application of biocontrol bacteria and farmland environmental protection.

Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils.

Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to crops. Here we found that a synthetic community composed of highly Al-resistant bacterial strains isolated from the rice rhizosphere increased rice yield by 26.36% in acidic fields. The synthetic community harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation. The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil. These findings highlight the potential of microbial tools for advancing sustainable agriculture in acidic soils.

Investigation of iron-reducing and iron-oxidizing bacterial communities in the rice rhizosphere of iron-toxic paddy field: a case study in Burkina Faso, West Africa

ABSTRACT Iron (Fe) toxicity in rice is one of the serious problems in some paddy fields in West African areas. Microbial community structures involved in the redox cycle of Fe have not been revealed in the Fe-toxic paddy fields. The present study investigated the bacterial community structure and the abundance of Gallionellaceae, Geobacteraceae, and Anaeromyxobacteraceae, as the representative indicator bacteria of Fe oxidizers and reducers, in the bulk and rhizosphere soils and rice roots of a Fe-toxic paddy field in Burkina Faso (BF)in 2017–2019. Thosein a paddy field in Anjo, Japan (AN) were also analyzed for comparison. The amplicon sequencing analysis revealed that the BF rhizosphere soil was characterized by typical anaerobic bacterial groups like Firmicutes and Deltaproteobacteria, including several potential Fe reducers. The relative abundance of Gallionellaceae, lithotrophic Fe oxidizers, in the BF rice roots was significantly lower than that in the AN rice roots. Quantitative PCR analysis showed that the ratios of Gallionellaceae to Geobacteraceae and to Anaeromyxobacteraceae were higher in the rice roots than in the soils irrespective of the fields. However, the ratios of Gallionellaceae to Geobacteraceae were lower in the BF soils and roots than in the AN soils and roots. The ratios of Gallionellaceae to Anaeromyxobacteraceae in the BF soils were also lower than those in the AN soils. These findings indicated the relative predominance of Geobacter- and Anaeromyxobacter-related Fe reducers over Gallionellaceae-related Fe oxidizers in the rice rhizosphere of the BF field, corresponding well to the circumstances of Fe-toxic soil: higher Fe(II) amounts in the soil. Since Fe(II)-oxidizing activity at rice roots is an important factor as a primary defense system against Fe(II) in the soil solution, the ratios of Gallionellaceae to Geobacteraceae and to Anaeromyxobacteraceae may serve as an indicator of potential Fe(II)-oxidizing activity of rice rhizosphere. Further studies focusing on the activity of Fe oxidizers and Fe reducers at rice roots under effective cultivation practices and in various types of Fe-toxic paddy fields will help to promote a better understanding of the Fe-toxic soil circumstances and to establish sustainable rice cultivation in the Fe-toxic soils.

Mitigating the adverse effect of warming on rice canopy and rhizosphere microbial community by nitrogen application: An approach to counteract future climate change for rice

The adverse impact of climate change on crop production continues to increase, necessitating the development of suitable strategies to mitigate these effects and improve food security. Several studies have revealed how global warming negatively impacts the grain-filling stage of rice and that this effect could be mitigated by nitrogen; however, the impact of nitrogen application on rice canopy and rhizosphere microbial communities remains unclear. We conducted a study using an open-field warming system. Results showed that warming influenced rice canopy by decreasing aboveground biomass and harvest index, whereas nitrogen application had positive effect on rice production under warming conditions by increasing the plant nitrogen content, biomass, harvest index and soil fertilities. Moreover, soil ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3−-N) contents were significantly decreased under warming, which were higher after nitrogen application. Notably, warming and nitrogen fertilizer caused 19 % (P < 0.01) and 7 % (P < 0.05) variations, respectively, in the β diversity of the microbial community, respectively. The impact of warming was significant on NH4+-N-related microorganisms; however, this impact was weakened by nitrogen application for microbes in the rhizosphere. This study demonstrated that enhanced nitrogen fertilizer can alleviate the adverse impact of warming by weakening its effects on rhizosphere microbes, improving soil fertility, promoting rice nitrogen uptake, and increasing the aboveground biomass and harvest index. These findings provide an important theoretical basis for developing practical, responsive cultivation strategies.

Organic rice rhizosphere fungi produce cellulase and chitinase as a biological control agent

Food crop security and security is a challenge in the agricultural sector to produce quality and healthy food products for consumption by the community. The use of synthetic fungicides to induce plant resistance negatively affects the abundance and diversity of biological agents.Cellulose enzymes and chitinase enzymes are capable lytic enzymes that degrade the cell walls of pathogenic fungi in plants. This study aims to isolate organic rice rhizosphere fungi and test their ability to produce cellulase and chitinase enzymes. Isolate the rice rhizosphere fungi using the spread-plate method, while testing the isolates producing cellulose enzymes using CMC mediaand testing isolates producing chitinase enzymes usingCDYA mediaadded with colloidal chitin.Penicillium sp. had the highest enzyme Hydrolysis Capacity (HC) value of 1.70 mm for cellulase and 1.19 mm for chitinase, followed byPaecilomycessp. with an HC of 1.52 mm for cellulaseand 1.12 mm for chitinase.Aspergillus sp. the HC of the cellulase and chitinase was 1.10 mm and 1.04 mm, while Trichoderma sp. the cellulose and the chitinase HC were 1.03 mm and 1.02 mm.

Italian ryegrass (Lolium multiflorum L.)-rice (Oryza sativa L.) rotation promotes the nitrogen cycle in the rice rhizosphere through dominant ammonia-oxidizing bacteria

The dominant ammonium bacteria established in different crop rotations are directly related to the conversion and utilization of nitrogen (N) in paddy soil. This study investigated the ammonia oxidation process in the rice rhizosphere of Italian ryegrass (Lolium multiflorum L.)-rice (IRR), celery (Apium graveolens)-rice (CLR) and winter fallow-rice (WFR) rotations in South China through the amoA functional gene analysis based on Miseq high-throughput sequencing platform and qPCR methods. The abundance of amoA gene in IRR was increased by 116.67 % (P < 0.05) and 42.76 % (P > 0.05) compared with CLR and WFR, respectively. Nitrosomonas became the dominant genus in the rhizosphere of IRR, with the highest relative abundance (59.30 %). The contents of soil organic matter, total N and nitrate nitrogen (NO3−-N) in the rice rhizosphere soil in IRR were significantly higher than other two treatments (P < 0.05) by 12.47–14.31 %, 16.88–25.00 %, and 97.48–159.60 %, respectively. Although lower microbial diversity was observed in IRR, the soil fluorescein diacetate hydrolysis enzyme activities and ammonia monooxygenase activities in the rice rhizosphere were higher in IRR than those in CLR and WFR (P < 0.05). Also, the soluble sugar and crude protein of milled rice were highest in IRR among the three rotation treatments (P < 0.05). The ammonia oxidation efficiency of ammonium-oxidizing bacteria was largely dependent on key taxa, such as Nitrosomonas (dominant genus in IRR), rather than the dynamics of AOB community structure. The key amoA-nitrifier taxa of the AOB community developed in IRR are capable of promoting rice production by improving soil N cycle efficiency and reducing the loss of N. Our findings illustrate the regulatory mechanism of IRR on the rice rhizosphere AOB community and reveal the important role of winter ryegrass in promoting soil nitrogen cycling during nutrient transformation of agricultural ecosystems in paddy fields.