Breeding Rice to Recruit Diazotrophs: Plant Genetic Levers for Rhizosphere Nitrogen Fixation
Received date: 2025-12-16
Accepted date: 2026-04-03
Online published: 2026-04-21
Synthetic nitrogen (N) fertilizers sustain modern rice yields but cause substantial environmental impacts due to low nitrogen-use efficiency. Flooded paddy soils harbor diverse diazotrophs capable of biological nitrogen fixation (BNF), yet BNF is highly variable across soils, management practices, and rice genotypes. In this review, we synthesize recent evidence on how rice can be bred to more consistently recruit and stimulate N2-fixing microbiomes. We first summarize major diazotroph taxa and niches in paddy ecosystems, highlighting the emerging contribution of iron-reducing bacteria at root iron-plaque interfaces and the principal environmental ‘gates’ on BNF, including flooding regime, bioavailable iron (Fe) phases, pH, carbon (C) quality, and mineral-N inputs. We then integrate findings showing that rice genetic variation shapes diazotroph assembly and activity through four root-controlled levers: (i) root system architecture that positions rhizodeposition along redox gradients, (ii) exudate quantity and chemistry (notably flavonoids and low-molecular-weight organic acids) that fuel and signal to diazotrophs, (iii) aerenchyma-mediated radial O2 loss that creates oxic-anoxic microsites, and (iv) iron plaque formation that couples Fe-C-N cycling and provides a scaffold for N2-fixing communities. Finally, we translate these mechanisms into a breeding roadmap, proposing a BNF-supportive ideotype, candidate loci/genes from genome-wide association study (GWAS)/QTL and wild introgressions, and a validation-to-deployment pipeline combining gene editing, near-isogenic resources, marker-assisted/genomic selection, and multi-environment field testing under low-N management. We also discuss phenotyping bottlenecks, deployment constraints, and priorities for pairing BNF-supportive alleles with compatible microbiomes and agronomy practices to reduce fertilizer demand while maintaining yield.
Chu Qingnan , Li Detian , Feng Zhihang , Wang Mengcen , Sha Zhimin . Breeding Rice to Recruit Diazotrophs: Plant Genetic Levers for Rhizosphere Nitrogen Fixation[J]. Rice Science, 2026 , 33(4) : 465 -484 . DOI: 10.1016/j.rsci.2026.04.005
| [1] | Adeniji A, Fadiji A E, Ofoe S T. 2025. Redefining root exudation with proteins at the forefront of rhizosphere function. J Agric Food Chem, 73(28): 17387-17402. |
| [2] | Ahmed N, Ishfaq M, Ali G. 2023. Genetic engineering for enhanced biological nitrogen fixation in cereal crops. Trends Biotechnol, 41(4): 473-475. |
| [3] | Ajmera I, Henry A, Radanielson A M, et al. 2022. Integrated root phenotypes for improved rice performance under low nitrogen availability. Plant Cell Environ, 45(3): 805-822. |
| [4] | Ali M L, Sanchez P L, Yu S B, et al. 2010. Chromosome segment substitution lines: A powerful tool for the introgression of valuable genes from Oryza wild species into cultivated rice (O. sativa). Rice, 3(4): 218-234. |
| [5] | Armstrong W. 1964. Oxygen diffusion from the roots of some British bog plants. Nature, 204: 801-802. |
| [6] | Bao Z H, Sasaki K, Okubo T, et al. 2013. Impact of Azospirillum sp. B510 inoculation on rice-associated bacterial communities in a paddy field. Microbes Environ, 28(4): 487-490. |
| [7] | Bianco C, Andreozzi A, Romano S, et al. 2021. Endophytes from African rice (Oryza glaberrima L.) efficiently colonize Asian rice (Oryza sativa L.) stimulating the activity of its antioxidant enzymes and increasing the content of nitrogen, carbon, and chlorophyll. Microorganisms, 9(8): 1714. |
| [8] | Boyle J A, Simonsen A K, Frederickson M E, et al. 2021. Priority effects alter interaction outcomes in a legume-rhizobium mutualism. Proc Biol Sci, 288: 20202753. |
| [9] | Brusamarello-Santos L C C, Alberton D, Valdameri G, et al. 2019. Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae. Sci Rep, 9(1): 10573. |
| [10] | Cao W W, Cai Y F, Bao Z H, et al. 2022. Methanotrophy alleviates nitrogen constraint of carbon turnover by rice root-associated microbiomes. Front Microbiol, 13: 885087. |
| [11] | Chakraborty D, Ladha J K, Das B, et al. 2025. Global insights into nitrogen losses and efficiency in rice, wheat, and maize cultivation. Field Crops Res, 334: 110138. |
| [12] | Chan S C, Dykes E G, Hoover L R, et al. 2023. Gallionellaceae in rice root plaque: Metabolic roles in iron oxidation, nutrient cycling, and plant interactions. Appl Environ Microbiol, 89: e00570-23. |
| [13] | Chang J J, Costa O Y A, Sun Y, et al. 2025. Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions. Nat Commun, 16(1): 2038. |
| [14] | Chen K, Li N, Zhang S Y, et al. 2022. Biochar-induced changes in the soil diazotroph community abundance and structure in a peanut field trial. Biochar, 4(1): 26. |
| [15] | Chen M Y, Feng S Z, Lv H, et al. 2024. OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake. BMC Plant Biol, 24(1): 285. |
| [16] | Chen X, Marszałkowska M, Reinhold-Hurek B. 2020. Jasmonic acid, not salicyclic acid restricts endophytic root colonization of rice. Front Plant Sci, 10: 1758. |
| [17] | Chen Z, Zhu Y G, Liu W J, et al. 2005. Direct evidence showing the effect of root surface iron plaque on arsenite and arsenate uptake into rice (Oryza sativa) roots. New Phytol, 165(1): 91-97. |
| [18] | Choudhury A T M A, Kennedy I R. 2004. Prospects and potentials for systems of biological nitrogen fixation in sustainable rice production. Biol Fertil Soils, 39(4): 219-227. |
| [19] | Chu Q N, Sha Z M, Nakamura T, et al. 2016. Differential responses of soybean and sorghum growth, nitrogen uptake, and microbial metabolism in the rhizosphere to cattle manure application: A rhizobox study. J Agric Food Chem, 64(43): 8084-8094. |
| [20] | Chu Q N, Sha Z M, Maruyama H, et al. 2019. Metabolic reprogramming in nodules, roots, and leaves of symbiotic soybean in response to iron deficiency. Plant Cell Environ, 42(11): 3027-3043. |
| [21] | Chu Q N, Xue L H, Cheng Y Q, et al. 2020. Microalgae-derived hydrochar application on rice paddy soil: Higher rice yield but increased gaseous nitrogen loss. Sci Total Environ, 717: 137127. |
| [22] | Chu Q N, Sha Z M, Li D T, et al. 2023a. Oxygen nanobubble-loaded biochars mitigate copper transfer from copper-contaminated soil to rice and improve rice growth. ACS Sustain Chem Eng, 11(13): 5032-5044. |
| [23] | Chu Q N, Xing Y, He W T, et al. 2023b. Modeling ammonia emissions and abatement potential from the rice-wheat rotation fields using the calibrated DNDC model: A case study in Shanghai, China. Atmos Environ, 305: 119782. |
| [24] | Chu Q N, Liu X Y, Li D T, et al. 2025. Interfacial oxygen nanobubble for mitigating the methane emissions from aquatic ecosystems: A review. Resour Environ Sustain, 22: 100256. |
| [25] | Copeland C, Schulze-Lefert P, Ma K W. 2025. Potential and challenges for application of microbiomes in agriculture. Plant Cell, 37(8): koaf185. |
| [26] | Crossa J, Vitale P, et al. 2025. Expanding genomic prediction in plant breeding: Harnessing big data, machine learning, and advanced software. Trends Plant Sci, 30(7): 756-774. |
| [27] | Ding L J, Su J Q, Xu H J, et al. 2015. Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-13C-acetate probing coupled with pyrosequencing. ISME J, 9(3): 721-734. |
| [28] | Dos Santos P, Fang Z, Mason W S, et al. 2012. Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genomics, 13: 162. |
| [29] | Dwivedi S L, Vetukuri R R, Kelbessa B G, et al. 2025. Exploitation of rhizosphere microbiome biodiversity in plant breeding. Trends Plant Sci, 30(9): 1033-1045. |
| [30] | Edwards J, Johnson C, Santos-Medellín C, et al. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA, 112(8): E911-E920. |
| [31] | FAO. 2022. FAOSTAT Statistical Database. Rome, Italy: Food and Agriculture Organization of the United Nations. [2025-10-10]. http://www.fao.org/faostat/. |
| [32] | Farooq M A, Gao S, Hassan M A, et al. 2024. Artificial intelligence in plant breeding. Trends Genet, 40(10): 891-908. |
| [33] | Feng H C, Zhang N, Du W B, et al. 2018. Identification of chemotaxis compounds in root exudates and their sensing chemoreceptors in plant-growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9. Mol Plant-Microbe Interact, 31(10): 995-1005. |
| [34] | Gaby J C, Rishishwar L, Valderrama-Aguirre L C, et al. 2018. Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline. Appl Environ Microbiol, 84(4): e01512-e01517. |
| [35] | Galindo-Castañeda T, Hartmann M, Lynch J P. 2024. Location: Root architecture structures rhizosphere microbial associations. J Exp Bot, 75(2): 594-604. |
| [36] | Gao S P, Fang J, Xu F, et al. 2014. CYTOKININ OXIDASE/ DEHYDROGENASE4 integrates cytokinin and auxin signaling to control rice crown root formation. Plant Physiol, 165(3): 1035-1046. |
| [37] | Gao X P, Zhang F S, Hoffland E. 2009. Malate exudation by six aerobic rice genotypes varying in zinc uptake efficiency. J Environ Qual, 38(6): 2315-2321. |
| [38] | Gao Y H, Cabrera Serrenho A. 2023. Greenhouse gas emissions from nitrogen fertilizers could be reduced by up to one-fifth of current levels by 2050 with combined interventions. Nat Food, 4: 170-178. |
| [39] | Hasan M M, Rafii M Y, Ismail M R, et al. 2015. Marker-assisted backcrossing: A useful method for rice improvement. Biotechnol Biotechnol Equip, 29(2): 237-254. |
| [40] | Hoffland E, Wei C Z, Wissuwa M. 2006. Organic anion exudation by lowland rice (Oryza sativa L.) at zinc and phosphorus deficiency. Plant Soil, 283(1): 155-162. |
| [41] | Hori T, Müller A, Igarashi Y, et al. 2010. Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. ISME J, 4(2): 267-278. |
| [42] | Hu S W, Li T, Wang Y X, et al. 2024. Effects of free air CO2 enrichment (FACE) on grain yield and quality of hybrid rice. Field Crops Res, 306: 109237. |
| [43] | IRRI. 2023. International Rice Research Institute (IRRI): Rice Knowledge and Training Resources. [2025-10-10]. http://knowledgebank.irri.org/index.php. |
| [44] | Jia R, Yu L P, Wang M Y, et al. 2025. Unveiling the crucial role of rice root iron plaque in enhancing biological nitrogen fixation via 15N-labeling DNA-SIP and metagenomics in a model study. Biol Fertil Soils, 61(7): 1183-1196. |
| [45] | Jiang L Q, Ke D, Sun B R, et al. 2024. Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process. Microbiol Spectr, 12(4): e03330-23. |
| [46] | Jiao H W, Xu W H, Hu Y L, et al. 2022. Citric acid in rice root exudates enhanced the colonization and plant growth-promoting ability of Bacillus altitudinis LZP02. Microbiol Spectr, 10(6): e01002-e01022. |
| [47] | Kitomi Y, Hanzawa E, Kuya N, et al. 2020. Root angle modifications by the DRO1 homolog improve rice yields in saline paddy fields. Proc Natl Acad Sci USA, 117(35): 21242-21250. |
| [48] | Kumar U, Panneerselvam P, Govindasamy V, et al. 2017. Long-term aromatic rice cultivation effect on frequency and diversity of diazotrophs in its rhizosphere. Ecol Eng, 101: 227-236. |
| [49] | Kwon Y, Choi J, Kim S H, et al. 2026. Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits. ISME J, 20: wraf284. |
| [50] | Lan Y Y, Chu Q N, Liu X Y, et al. 2025a. Oxygen-nanobubble-loaded biochar increases soil carbon sequestration in rice paddies. Soil Environ Health, 3(4): 100174. |
| [51] | Lan Y Y, Xu S H, Liu X Y, et al 2025b. Mechanistic evaluation of duckwee intervention on reactive nitrogen gas fluxes from paddy soils. Nitrogen Cycl, 1: e008. |
| [52] | Li G G, Wang K X, Qin Q, et al. 2023. Integrated microbiome and metabolomic analysis reveal responses of rhizosphere bacterial communities and root exudate composition to drought and genotype in rice (Oryza sativa L.). Rice, 16(1): 19. |
| [53] | Li L N, Jia R, Qu Z, et al. 2020. Coupling between nitrogen-fixing and iron(III)-reducing bacteria as revealed by the metabolically active bacterial community in flooded paddy soils amended with glucose. Sci Total Environ, 716: 137056. |
| [54] | Li P, Pan Z, Sun J Y, et al. 2025. Anthropogenic climate change may reduce global diazotroph diversity. Nat Commun, 16: 8208. |
| [55] | Li S M, Li B Z, Shi W M. 2012. Expression patterns of nine ammonium transporters in rice in response to N status. Pedosphere, 22(6): 860-869. |
| [56] | Li T T, Li B, Wang Y Y, et al. 2025. WRKY transcription factors in rice: Key regulators orchestrating development and stress resilience. Plant Cell Environ, 48(11): 8388-8406. |
| [57] | Liang S S, Chu Q N, Ashrafi A, et al. 2025. Agricultural practices influence phosphorus transport and ecosystem health in rice-paddy systems: Insights from HYDRUS-1D simulations. Agric Ecosyst Environ, 385: 109581. |
| [58] | Liang S S, He P, Chu Q N, et al. 2026. Multi-objective optimization of rice production and environmental sustainability under climate change in the Yangtze River Delta: A DNDC-random forest framework approach. Field Crops Res, 339: 110357. |
| [59] | Lin L Y, Feng Z H, Asano H, et al. 2025. Genome-wide association study identifies key chromosomal regions in rice promoting the enrichment of diazotrophic iron-reducing bacteria in paddy soil. Plant Soil, 514(1): 269-285. |
| [60] | Liu H B, Sun H X, Du L Q, et al. 2024. Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice. ISME J, 18(1): wrae006. |
| [61] | Liu M X, Huang X, Song Y, et al. 2019. Ammonia emission control in China would mitigate haze pollution and nitrogen deposition, but worsen acid rain. Proc Natl Acad Sci USA, 116(16): 7760-7765. |
| [62] | Liu X R, Yin S, Xu S H, et al. 2024. Role of pyrochar amendment toward carbon neutrality of rice paddy field by mitigating methane emission: A global evaluation by meta-analysis. Field Crops Res, 319: 109659. |
| [63] | Lu C M, Luo J H, Sheng T L, et al. 2025. Diazotrophic communities shift with organic fertilizer substitution and growth stages in tomato field soil. Eur J Soil Biol, 126: 103746. |
| [64] | Lu Y, Zhu J K. 2017. Precise editing of a target base in the rice genome using a modified CIRSPR/Cas 9 system. Mol Plant, 10 (3): 523-525. |
| [65] | Luo Y M, Zhan X D, Zhang Y X, et al. 2025. CRISPR-Cas9-mediated knockup of OsDREB1C enhances rice yield without compromising grain quality. Plant Commun, 6(10): 101433. |
| [66] | Ma J, Bei Q C, Wang X J, et al. 2019. Paddy system with a hybrid rice enhances Cyanobacteria Nostoc and increases N2 fixation. Pedosphere, 29(3): 374-387. |
| [67] | Maisch M, Lueder U, Kappler A, et al. 2019. Iron lung: How rice roots induce iron redox changes in the rhizosphere and create niches for microaerophilic Fe(II)-oxidizing bacteria. Environ Sci Technol Lett, 6(10): 600-605. |
| [68] | Martinez-Feria R, Simmonds M B, Ozaydin B, et al. 2024. Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize. Sci Rep, 14: 27754. |
| [69] | Masuda Y, Itoh H, Shiratori Y, et al. 2017. Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ, 32(2): 180-183. |
| [70] | Masuda Y, Shiratori Y, Ohba H, et al. 2021. Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application. Soil Sci Plant Nutr, 67(3): 243-247. |
| [71] | Masuda Y, Satoh S, Miyamoto R, et al. 2023. Biological nitrogen fixation in the long-term nitrogen-fertilized and unfertilized paddy fields, with special reference to diazotrophic iron-reducing bacteria. Arch Microbiol, 205(8): 291. |
| [72] | Masuda Y, Chihara M, Senoo K. 2024a. Ferrihydrite addition activated Geobacteraceae, the most abundant iron-reducing diazotrophs, and suppressed methanogenesis by heterogeneous methanogens in xylan-amended paddy soil microcosms. Microbes Environ, 39(3): ME24028. |
| [73] | Masuda Y, Mise K, Xu Z X, et al. 2024b. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. Microbiome, 12(1): 95. |
| [74] | Meng F N, Xiang D, Zhu J S, et al. 2019. Molecular mechanisms of root development in rice. Rice, 12(1): 1. |
| [75] | Mishra A, Barik S R, Lenka D, et al. 2025. Transfer of deeper rooting and phosphorus uptake QTL into the popular rice variety ‘maudamani’ via marker-assisted backcross breeding. Sci Rep, 15: 25418. |
| [76] | Mohanavel V, Muthu V, Kambale R, et al. 2024. Marker-assisted breeding accelerates the development of multiple-stress-tolerant rice genotypes adapted to wider environments. Front Plant Sci, 15: 1402368. |
| [77] | Nagata K, Nonoue Y, Matsubara K, et al. 2023. Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice. Breed Sci, 73(3): 332-342. |
| [78] | Nieland M A, Carson C M, Floyd V, et al. 2024. Product-inhibition feedbacks, not microbial population level tradeoffs or soil pH, regulate decomposition potential under nutrient eutrophication. Soil Biol Biochem, 189: 109247. |
| [79] | O’Donnell D A, Yang J, Zamora P, et al. 2025. Heritability and QTL mapping of aerial roots and other yield component traits with implications for N2 fixation in Zea Mays. BioRxiv, DOI: 10.1101/2025.09.10.675198. |
| [80] | Okamoto T, Shinjo R, Nishihara A, et al. 2021. Genotypic variation of endophytic nitrogen-fixing activity and bacterial flora in rice stem based on sugar content. Front Plant Sci, 12: 719259. |
| [81] | O’Neal L, Vo L, Alexandre G. 2020. Specific root exudate compounds sensed by dedicated chemoreceptors shape Azospirillum brasilense chemotaxis in the rhizosphere. Appl Environ Microbiol, 86(15): e01026-20. |
| [82] | Pang Z Q, Mao X Y, Zhou S Q, et al. 2023. Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage. Microbiome, 11(1): 85. |
| [83] | Paul S, Gayen D, Datta K S, et al. 2017. Analysis of high iron rice lines reveals new miRNAs that target iron transporters in roots. J Exp Bot, 67: 5811-5824. |
| [84] | Phan P D T, Nishimura A, Yamamoto C, et al. 2023. Wild and cultivated allele effects on rice phenotypic traits in reciprocal backcross populations between Oryza rufipogon and two cultivars, O. sativa Nipponbare and IR36. Breed Sci, 73(4): 373-381. |
| [85] | Qian H Y, Zhu X C, Huang S, et al. 2023. Greenhouse gas emissions and mitigation in rice agriculture. Nat Rev Earth Environ, 4(10): 716-732. |
| [86] | Raglin S S, Kent A D. 2025. Navigating nitrogen sustainability with microbiome-associated phenotypes. Trends Plant Sci, 30(5): 471-483. |
| [87] | Saini M R, Chandran L P, Barbadikar K M, et al. 2022. Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis. Front Plant Sci, 13: 939395. |
| [88] | Schwalm H, Staudinger C, Hajirezaei M R, et al. 2024. Root exudation patterns of contrasting rice (Oryza sativa L.) lines in response to P limitation. Planta, 260(6): 123. |
| [89] | Sha Z M, Chen Z, Feng Y F, et al. 2020. Minerals loaded with oxygen nanobubbles mitigate arsenic translocation from paddy soils to rice. J Hazard Mater, 398: 122818. |
| [90] | Shang Y M, Shi H W, Liu M Z, et al. 2025. Using synthetic biology to express nitrogenase biosynthesis pathway in rice and to overcome barriers of nitrogenase instability in plant cytosol. Trends Biotechnol, 43(4): 946-968. |
| [91] | Sharma R, Yang C J, Rossi N, et al. 2025. Integrating molecular genetics with plant breeding to deliver impact. Plant Physiol, 198(3): kiaf087. |
| [92] | Singh N, Wang D, Ali L, et al. 2020. A coordinated suite of wild-introgression lines in indica and japonica elite backgrounds. Front Plant Sci, 11: 564824. |
| [93] | Su P, Kang H X, Peng Q Z, et al. 2025. Host metabolites explain microbiome variation between different rice genotypes. Microbiome, 13(1): 185. |
| [94] | Thomas J, Kim H R, Rahmatallah Y, et al. 2019. RNA-seq reveals differentially expressed genes in rice (Oryza sativa) roots during interactions with plant-growth promoting bacteria, Azospirillum brasilense. PLoS One, 14(5): e0217309. |
| [95] | Valette M, Rey M, Doré J, et al. 2020. Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria. Physiol Mol Biol Plants, 26(12): 2537-2551. |
| [96] | Verma P K, Verma S, Pandey N. 2022. Root system architecture in rice: Impacts of genes, phytohormones and root microbiota. 3 Biotech, 12(9): 239. |
| [97] | Wan Y, Ma Z, Lang J P, et al. 2025. Host genotype-driven assembly of bacterial communities in the rice root microdomains. Soil Ecol Lett, 7(3): 250330. |
| [98] | Wang C, Shen Y, Fang X T, et al. 2024. Reducing soil nitrogen losses from fertilizer use in global maize and wheat production. Nat Geosci, 17(10): 1008-1015. |
| [99] | Wang L X, Chen M X, Lam P Y, et al. 2022. Multifaceted roles of flavonoids mediating plant-microbe interactions. Microbiome, 10(1): 233. |
| [100] | Wang X J, Bei Q C, Yang W, et al. 2020. Unveiling of active diazotrophs in a flooded rice soil by combination of NanoSIMS and 15N2-DNA-stable isotope probing. Biol Fertil Soils, 56(8): 1189-1199. |
| [101] | Wang X M, Wu M, Wei Z J, et al. 2024. Investigating drivers of free-living diazotroph activity in paddy soils across China. Soil Biol Biochem, 199: 109601. |
| [102] | Wiggins G, Thomas J, Rahmatallah Y, et al. 2022. Common gene expression patterns are observed in rice roots during associations with plant growth-promoting bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. Sci Rep, 12(1): 8827. |
| [103] | Wu C, Ye Z H, Li H, et al. 2012. Do radial oxygen loss and external aeration affect iron plaque formation and arsenic accumulation and speciation in rice? J Exp Bot, 63(8): 2961-2970. |
| [104] | Wu J D, Liu S J, Zhang H Y, et al. 2025. Flavones enrich rhizosphere Pseudomonas to enhance nitrogen utilization and secondary root growth in Populus. Nat Commun, 16: 1461. |
| [105] | Xiao W D, Ye X Z, Zhu Z Q, et al. 2021. Continuous flooding stimulates root iron plaque formation and reduces chromium accumulation in rice (Oryza sativa L.). Sci Total Environ, 788: 147786. |
| [106] | Xiong C, Singh B K, Zhu Y G, et al. 2024. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development. mSystems, 9(4): e01055-23. |
| [107] | Xiong J B, Lu J Q, Li X H, et al. 2021. Effect of rice (Oryza sativa L.) genotype on yield: Evidence from recruiting spatially consistent rhizosphere microbiome. Soil Biol Biochem, 161: 108395. |
| [108] | Yan D W, Tajima H, Cline L C, et al. 2022. Genetic modification of flavone biosynthesis in rice enhances biofilm formation of soil diazotrophic bacteria and biological nitrogen fixation. Plant Biotechnol J, 20(11): 2135-2148. |
| [109] | Yang Z K, Zhao T J, Cheng H, et al. 2024. Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize. G3 Genes Genomes Genet, 14(3): jkad286. |
| [110] | Yu L P, Jia R, Liu S Q, et al. 2025. Rice root iron plaque as a mediator to stimulate methanotrophic nitrogen fixation. Environ Sci Technol, 59(38): 20411-20420. |
| [111] | Yu L P, Jia R, Liu S Q, et al. 2024. Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia. ISME Commun, 4: ycae030. |
| [112] | Yu S, Feng Y F, Xue L H, et al. 2019. Biowaste to treasure: Application of microbial-aged hydrochar in rice paddy could improve nitrogen use efficiency and rice grain free amino acids. J Clean Prod, 240: 118180. |
| [113] | Yu Y J, Zhang J W, Petropoulos E, et al. 2018. Divergent responses of the diazotrophic microbiome to elevated CO2 in two rice cultivars. Front Microbiol, 9: 1139. |
| [114] | Yuan Z F, Gustave W, Ata-Ul-Karim S T, et al. 2022. Distinct and dynamic distributions of multiple elements and their species in the rice rhizosphere. Plant Soil, 471(1/2): 47-60. |
| [115] | Zhang C M, Chu Q N, Sha Z M, et al. 2026. Trade-off of phosphate mediated iron plaque formation and cell chemical remodeling on cadmium uptake and translocation in rice. Plant Physiol Biochem, 230: 110702. |
| [116] | Zhang J Y, Liu Y X, Zhang N, et al. 2019. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol, 37(6): 676-684. |
| [117] | Zhang Z C, Masuda Y, Xu Z X, et al. 2023. Active nitrogen fixation by iron-reducing bacteria in rice paddy soil and its further enhancement by iron application. Appl Sci, 13(14): 8156. |
| [118] | Zhao J W, Chen Y T, Tao Q, et al. 2026. Enhanced CO2 coordinates the spatial recruitment of diazotrophs in rice via root development. Plant Cell Environ, 49(7): 3678-3693. |
| [119] | Zhao Y, Hu Y F, Dai M Q, et al. 2009. The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice. Plant Cell, 21(3): 736-748. |
| [120] | Zhou Q, Yuan R, Zhang W Y, et al. 2023. Grain yield, nitrogen use efficiency and physiological performance of indica/Japonica hybrid rice in response to various nitrogen rates. J Integr Agric, 22(1): 63-79. |
| [121] | Zhou Y H, Liu L Z, Guo B Q, et al. 2025. Transformative impact of three decades of nitrogen-based fertilization on diazotrophic communities and co-occurrence patterns in soils of Northeast China. Microbiol Spectr, 13(9): e01443-24. |
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