References
-
Coskun, D., Britto, D. T., Shi, W. & Kronzucker, H. J. Nitrogen transformations in modern agriculture and the role of biological nitrification inhibition. Nat. Plants 3, 17074 (2017).
-
You, L. et al. Optimized agricultural management reduces global cropland nitrogen losses to air and water. Nat. Food 5, 995–1004 (2024).
-
Robinson, N., Vogt, J., Lakshmanan, P. & Schmidt, S. Nitrogen physiology of sugarcane. Sugarcane: Physiology, Biochemistry, and Functional Biology, 169-195 https://doi.org/10.1002/9781118771280.ch8 (2013).
-
Yang, W., Li, Z., Wang, J., Wu, P. & Zhang, Y. Crop yield, nitrogen acquisition and sugarcane quality as affected by interspecific competition and nitrogen application. Field Crop Res. 146, 44–50 (2013).
-
Cardozo, N. P., de Oliveira Bordonal, R. & La, S. N. Sustainable intensification of sugarcane production under irrigation systems, considering climate interactions and agricultural efficiency. J. Clean. Prod. 204, 861–871 (2018).
-
Vandenberghe, L. P. S. et al. Beyond sugar and ethanol: the future of sugarcane biorefineries in Brazil. Renew. Sustain. Energy Rev. 167, 112721 (2022).
-
Parniske, M. Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat. Rev. Microbiol. 6, 763–775 (2008).
-
Wang, J. et al. Arbuscular mycorrhizal fungi regulate the diversity–invasion resistance relationship by influencing the role of complementarity and selection effects. N. Phytol. 246, 317–330 (2025).
-
Willing, C. E., Wan, J., Yeam, J. J., Cessna, A. M. & Peay, K. G. Arbuscular mycorrhizal fungi equalize differences in plant fitness and facilitate plant species coexistence through niche differentiation. Nat. Ecol. Evol. 8, 2058–2071 (2024).
-
Wang, G., Jin, Z., George, T. S., Feng, G. & Zhang, L. Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover. N. Phytol. 238, 2578–2593 (2023).
-
Wang, L., Zhang, L., George, T. S. & Feng, G. Hyphosphere core taxa link plant-arbuscular mycorrhizal fungi combinations to soil organic phosphorus mineralization. Soil Biol. Biochem. 201, 109647 (2025).
-
Nagy, R., Drissner, D., Amrhein, N., Jakobsen, I. & Bucher, M. Mycorrhizal phosphate uptake pathway in tomato is phosphorus-repressible and transcriptionally regulated. N. Phytol. 181, 950–959 (2009).
-
DUAN, S. et al. The interplay of direct and mycorrhizal pathways for plants to efficiently acquire phosphorus from soil. Front. Agric. Sci. Eng. 12, 47–56 (2025).
-
Martin, F. M. & van der Heijden, M. G. A. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. N. Phytol. 242, 1486–1506 (2024).
-
Sun, K. et al. Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil. ISME J. 17, 1626–1638 (2023).
-
Wang, F. et al. Exploring the secrets of hyphosphere of arbuscular mycorrhizal fungi: processes and ecological functions. Plant Soil 481, 1–22 (2022).
-
Monika, Y. N. et al. Arbuscular Mycorrhizal fungi: a potential candidate for nitrogen fixation. in (eds Vaishnav A., Arya S. S. & Choudhary D. K.) Plant Stress Mitigators: Action and Application, 217–234 (Springer Nature, 2022).
-
Tian, C. et al. Regulation of the nitrogen transfer pathway in the arbuscular mycorrhizal symbiosis: gene characterization and the coordination of expression with nitrogen flux. Plant Physiol. 153, 1175–1187 (2010).
-
Sajjad, N. et al. 12 – Nitrogen uptake, assimilation, and mobilization in plants under abiotic stress. in (eds Roychoudhury, A., Tripathi, D. K. & Deshmukh, R.) Transporters and Plant Osmotic Stress, 215–233 (Academic Press, 2021).
-
Wipf, D. et al. Trading on the arbuscular mycorrhiza market: from arbuscules to common mycorrhizal networks. N. Phytol. 223, 1127–1142 (2019).
-
Chen, Y. et al. Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions. Front. Microbiol. 15, 1323160 (2024).
-
Hetrick, B. A. D. Mycorrhizas and root architecture. Experientia 47, 355–362 (1991).
-
Nair, A., Thulasiram, H. V. & Bhargava, S. Role of jasmonate in modulation of mycorrhizae-induced resistance against fungal pathogens. in (eds Champion, A. & Laplaze, L.) Jasmonate in Plant Biology: Methods and Protocols, 109–115 (Springer, 2020).
-
Lanfranco, L., Fiorilli, V. & Gutjahr, C. Partner communication and role of nutrients in the arbuscular mycorrhizal symbiosis. N. Phytol. 220, 1031–1046 (2018).
-
Manck-Götzenberger, J. & Requena, N. Arbuscular mycorrhiza symbiosis induces a major transcriptional reprogramming of the potato sweet sugar transporter family. Front. Plant Sci. 7, 487 (2016).
-
Zhou, J. et al. SYMRK significantly affected AMF symbiosis and plant growth in maize. Plant Sci. 353, 112427 (2025).
-
Ferrol, N., Azcón-Aguilar, C. & Pérez-Tienda, J. Review: arbuscular mycorrhizas as key players in sustainable plant phosphorus acquisition: an overview on the mechanisms involved. Plant Sci. 280, 441–447 (2019).
-
Wang, S. et al. OsNLP3 and OsPHR2 orchestrate direct and mycorrhizal pathways for nitrate uptake by regulating NAR2.1-NRT2s complexes in rice. Proc. Natl. Acad. Sci. USA 122, e1878622174 (2025).
-
Cerda, A. & Alvarez, J. M. Insights into molecular links and transcription networks integrating drought stress and nitrogen signaling. N. Phytol. 241, 560–566 (2024).
-
Farhan, M. et al. Plant nitrogen metabolism: balancing resilience to nutritional stress and abiotic challenges. Phyton Int. J. Exp. Bot. 93, 581–609 (2024).
-
Shanks, C. M. et al. Nitrogen sensing and regulatory networks: it’s about time and space. Plant Cell 36, 1482–1503 (2024).
-
Forde, B. G. Nitrogen signalling pathways shaping root system architecture: an update. Curr. Opin. Plant Biol. 21, 30–36 (2014).
-
Isah, T. Stress and defense responses in plant secondary metabolites production. Biol. Res. 52, 39 (2019).
-
Johnson, N. C., Wilson, G. W. T., Bowker, M. A., Wilson, J. A. & Miller, R. M. Resource limitation is a driver of local adaptation in mycorrhizal symbioses. Proc. Natl. Acad. Sci. USA 107, 2093–2098 (2010).
-
Treseder, K. K. A. A meta-analysis of mycorrhizal responses to nitrogen, phosphorus, and atmospheric CO2 in field studies. New Phytol. 164, 347–355 (2004).
-
Govindarajulu, M. et al. Nitrogen transfer in the arbuscular mycorrhizal symbiosis. Nature 435, 819–823 (2005).
-
Hodge, A. & Fitter, A. H. Substantial nitrogen acquisition by arbuscular mycorrhizal fungi from organic material has implications for N cycling. Proc. Natl. Acad. Sci. USA 107, 13754–13759 (2010).
-
Lin, F. et al. Emerging roles of phosphoinositide-associated membrane trafficking in plant stress responses. J. Genet Genom. 49, 726–734 (2022).
-
Kumar, V., Thakur, J. K. & Prasad, M. Histone acetylation dynamics regulating plant development and stress responses. Cell Mol. Life Sci. 78, 4467–4486 (2021).
-
Wang, Q., Yung, W., Wang, Z. & Lam, H. The histone modification H3K4me3 marks functional genes in soybean nodules. Genomics 112, 5282–5294 (2020).
-
Gutjahr, C. et al. Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex. Science 350, 1521–1524 (2015).
-
Anani, O. A., Abel, I., Olomukoro, J. O. & Onyeachu, I. B. Insights to proteomics and metabolomics metal chelation in food crops. J. Proteins Proteom. 13, 159–173 (2022).
-
Wu, D., Saleem, M., He, T. & He, G. The mechanism of metal homeostasis in plants: a new view on the synergistic regulation pathway of membrane proteins, lipids and metal ions. Membranes 11, 984 (2021).
-
Donaldson, J. G. & Jackson, C. L. ARF family G proteins and their regulators: roles in membrane transport, development and disease. Nat. Rev. Mol. Cell Bio. 12, 362–375 (2011).
-
Gao, Y. et al. Analysis of the molecular and biochemical mechanisms involved in the symbiotic relationship between arbuscular mycorrhiza fungi and Manihot esculenta Crantz. Front. Plant Sci. 14, 1130924 (2023).
-
Limpens, E. & Geurts, R. Transcriptional regulation of nutrient exchange in arbuscular mycorrhizal symbiosis. Mol. Plant 11, 1421–1423 (2018).
-
Kabir, A. H. et al. Arbuscular mycorrhizal fungi alleviate Fe-deficiency symptoms in sunflower by increasing iron uptake and its availability along with antioxidant defense. Plant Physiol. Biochem. 150, 254–262 (2020).
-
Moreno Jiménez, E., Ferrol, N., Corradi, N., Peñalosa, J. M. & Rillig, M. C. The potential of arbuscular mycorrhizal fungi to enhance metallic micronutrient uptake and mitigate food contamination in agriculture: prospects and challenges. N. Phytol. 242, 1441–1447 (2024).
-
Rahman, M. A. et al. Arbuscular mycorrhizal symbiosis mitigates iron (Fe)-deficiency retardation in Alfalfa (Medicago sativa L.) through the enhancement of Fe accumulation and sulfur-assisted antioxidant defense. Int. J. Mol. Sci. 21, 6 (2020).
-
Jin, X. et al. Adaptation strategies of seedling root response to nitrogen and phosphorus addition. Plants 13, 536 (2024).
-
Yang, T. et al. Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties. Front. Plant Sci. 13, 0–0 (2022).
-
Luan, M. et al. Transport and homeostasis of potassium and phosphate: limiting factors for sustainable crop production. J. Exp. Bot. 68, 3091–3105 (2017).
-
Wang, Y., Chen, Y. & Wu, W. Potassium and phosphorus transport and signaling in plants. J. Integr. Plant Biol. 63, 34–52 (2021).
-
DiTusa, S. F. et al. A member of the Phosphate transporter 1 (Pht1) family from the arsenic-hyperaccumulating fern Pteris vittata is a high-affinity arsenate transporter. N. Phytol. 209, 762–772 (2016).
-
Lu, Y. et al. Structural basis for the activity regulation of a potassium channel AKT1 from Arabidopsis. Nat. Commun. 13, 5682 (2022).
-
Yang, C. et al. Glutamine oxidation maintains the TCA cycle and cell survival during impaired mitochondrial pyruvate transport. Mol. Cell 56, 414–424 (2014).
-
Zhang, Y. & Fernie, A. R. The role of TCA cycle enzymes in plants. Adv. Biol. 7, 2200238 (2023).
-
Huang, S., Braun, H., Gawryluk, R. M. R. & Millar, A. H. Mitochondrial complex II of plants: subunit composition, assembly, and function in respiration and signaling. Plant J. 98, 405–417 (2019).
-
Luginbuehl, L. H. et al. Fatty acids in arbuscular mycorrhizal fungi are synthesized by the host plant. Science 356, 1175–1178 (2017).
-
Brinkmann-Chen, S. et al. General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH. Proc. Natl. Acad. Sci. USA 110, 10946–10951 (2013).
-
Wong, S. H., Lonhienne, T. G., Winzor, D. J., Schenk, G. & Guddat, L. W. Bacterial and plant ketol-acid reductoisomerases have different mechanisms of induced fit during the catalytic cycle. J. Mol. Biol. 424, 168–179 (2012).
-
Fraisier, V., Gojon, A., Tillard, P. & Vedele, F. D. Constitutive expression of a putative high-affinity nitrate transporter in Nicotiana plumbaginifolia: evidence for post-transcriptional regulation by a reduced nitrogen source. Plant J. 23, 489–496 (2000).
-
Hayami, N. & Yamamoto, Y. Y. Primary metabolism and transcriptional regulation in higher plants. Rev. Agric. Sci. 9, 117–127 (2021).
-
Afitlhile, M., Fukushige, H., Nishimura, M. & Hildebrand, D. F. A defect in glyoxysomal fatty acid β-oxidation reduces jasmonic acid accumulation in Arabidopsis. Plant Physiol. Biochem. 43, 603–609 (2005).
-
Wasternack, C. & Song, S. Jasmonates: biosynthesis, metabolism, and signaling by proteins activating and repressing transcription. J. Exp. Bot. 68, 1303–1321 (2017).
-
Guo, D. et al. The jasmonate pathway promotes nodule symbiosis and suppresses host plant defense in Medicago truncatula. Mol. Plant 17, 1183–1203 (2024).
-
Kaur, S., Campbell, B. J. & Suseela, V. Root metabolome of plant–arbuscular mycorrhizal symbiosis mirrors the mutualistic or parasitic mycorrhizal phenotype. N. Phytol. 234, 672–687 (2022).
-
Akram, N. A., Shafiq, F. & Ashraf, M. Ascorbic acid-A potential oxidant scavenger and its role in plant development and abiotic stress tolerance. Front. Plant Sci. 8, 613 (2017).
-
Miret, J. A. & Müller, M. AsA/DHA redox pair influencing plant growth and stress tolerance. in (eds Hossain, M. A. et al.) Ascorbic Acid in Plant Growth, Development and Stress Tolerance, 297–319 (Springer International Publishing, 2017).
-
Belmondo, S. et al. NADPH oxidases in the arbuscular mycorrhizal symbiosis. Plant Signal. Behav. 11, e1165379 (2016).
-
Fonseca-García, C. et al. Transcriptome analysis of the differential effect of the NADPH oxidase gene RbohB in Phaseolus vulgaris roots following Rhizobium tropici and Rhizophagus irregularis inoculation. BMC Genom. 20, 800 (2019).
-
Arvola, R., Abshire, E., Bohn, J. & Goldstrohm, A. C. Mechanisms of post-transcriptional gene regulation. in (eds Menon, P. K. M. J. & Goldstrohm, P. A.) Post-transcriptional Mechanisms in Endocrine Regulation, 1–36 (Springer International Publishing, 2016).
-
Ruiz-Lozano, J. M. et al. Arbuscular mycorrhizal symbiosis induces strigolactone biosynthesis under drought and improves drought tolerance in lettuce and tomato. Plant Cell Environ. 39, 441–452 (2016).
-
Wang, Y. & Wu, Q. S. Influence of sugar metabolism on the dialogue between arbuscular mycorrhizal fungi and plants. Hortic. Adv. 1, 0–0 (2023).
-
Li, H. et al. Physio-biochemical and transcriptomic features of arbuscular mycorrhizal fungi relieving cadmium stress in wheat. Antioxidants 11, 2390 (2022).
-
Mishra, A. K. et al. Potentials and prospects of AMF for soil carbon sequestration and nutrient cycling in rice-based cropping system. in (eds Parihar, M., Rakshit, A., Adholeya, A. & Chen, Y.) Arbuscular Mycorrhizal Fungi in Sustainable Agriculture: Nutrient and Crop Management, 113–129 (Springer Nature, 2024).
-
Wu, J. et al. Arbuscular mycorrhiza augments aluminum tolerance in white clover (Trifolium repens L.) by strengthening the ascorbate-glutathione cycle and phosphorus acquisition. Physiol. Mol. Biol. Plants 29, 1647–1661 (2023).
-
Scheublin, T. R., Sanders, I. R., Keel, C. & van der Meer, J. R. Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi. ISME J. 4, 752–763 (2010).
-
Marschner, P. & Baumann, K. Changes in bacterial community structure induced by mycorrhizal colonisation in split-root maize. Plant Soil. 251, 279-289 (2003).
-
Chen, E., Liao, H., Chen, B. & Shaolin, P. Arbuscular mycorrhizal fungi are a double-edged sword in plant invasion controlled by phosphorus concentration. N. Phytol. 226, 295–300 (2020).
-
He, D. et al. Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance. ISME J. 16, 2622–2632 (2022).
-
Abdel-Lateif, K., Bogusz, D. & Hocher, V. The role of flavonoids in the establishment of plant roots endosymbioses with arbuscular mycorrhiza fungi, rhizobia and Frankia bacteria. Plant Signal. Behav. 7, 636–641 (2012).
-
Besseau, S. et al. Flavonoid accumulation in arabidopsis repressed in lignin synthesis affects auxin transport and plant growth. Plant Cell 19, 148–162 (2007).
-
Brown, D. E. et al. Flavonoids act as negative regulators of auxin transport in vivo in Arabidopsis. Plant Physiol. 126, 524–535 (2001).
-
Ji, Z., Belfield, E. J., Li, S., Fu, X. D. & Harberd, N. P. Discovery of a second-site nia2 mutation in the background of multiple ArabidopsisPIF-related mutants containing the pif3-3 allele. N. Phytol. 241, 17–23 (2023).
-
Medici, A. et al. AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat. Commun. 6, 6274 (2015).
-
Kun, Y. et al. Low phosphorus promotes NSP1–NSP2 heterodimerization to enhance strigolactone biosynthesis and regulate shoot and root architecture in rice. Mol. Plant 16, 1811–1831 (2023).
-
Singh, S., Katzer, K., Lambert, J., Cerri, M. & Parniske, M. CYCLOPS, a DNA-binding transcriptional activator, orchestrates symbiotic root nodule development. Cell Host Microbe 15, 139–152 (2014).
-
Tatebe, H. & Shiozaki, K. Chapter 91 – Protein serine/threonine-phosphatase 2C (PP2C). in (eds Bradshaw, R. A. & Dennis, E. A.) Handbook of Cell Signaling (Second Edition), 711–716 (Academic Press, 2010).
-
Wang, J., Munyampundu, J., Xu, Y. & Cai, X. Phylogeny of plant calcium and calmodulin-dependent protein kinases (CCaMKs) and functional analyses of tomato CCaMK in disease resistance. Front. Plant Sci. 6, 1075 (2015).
-
Sharma, A., Jain, K. K., Jain, A., Kidwai, M. & Kuhad, R. C. Bifunctional in vivo role of laccase exploited in multiple biotechnological applications. Appl. Microbiol Biot. 102, 10327–10343 (2018).
-
Strong, P. J. & And Claus, H. Laccase: a review of its past and its future in bioremediation. Crit. Rev. Environ. Sci. Tec. 41, 373–434 (2011).
-
Bell, C. A., Magkourilou, E., Ault, J. R., Urwin, P. E. & Field, K. J. Phytophagy impacts the quality and quantity of plant carbon resources acquired by mutualistic arbuscular mycorrhizal fungi. Nat. Commun. 15, 801 (2024).
-
Jin, H. et al. The uptake, metabolism, transport and transfer of nitrogen in an arbuscular mycorrhizal symbiosis. N. Phytol. 168, 687–696 (2005).
-
Dong, S. Study on the effects of different nitrogen, phosphorus, and potassium fertilizer ratios on sugarcane yield and quality. Sugarcane Ind. 000, 16–18 (2007).
-
Chen, Y. Study on nitrogen fertilizer requirements and optimal application periods for seed sugarcane. Guangxi Sugar Ind. 000, 47–49 (2003).
-
Wang, Y., Zhang, S. & Zhang, M. Arbuscular mycorrhizal fungal resources and germplasm resources in China (China Agriculture Press, 2012).
-
Xu, S. GRZJ method to stain arbuscular mycorrhiza fungi in the roots of Guangxi Camellia nitidissima. Chin. J. Trop. Crops 45, 215–224 (2024).
-
Trouvelot, A., Kough, J. L. & Gianinazzi-Pearson, V. Mesure du taux de mycorhization VA d’un système radiculaire. Recherche de méthodes d’estimation ayant une signification fonctionnelle. in (eds Pearson, G.- V. & Gianinazzi, S.) Physiological and Genetical Aspects of Mycorrhizae (INRA Press, 1986).
-
Bao, S. Soil agricultural chemical analysis, 3rd edn (China Agricultural Press, 2000).
-
Kakhki, M. P. & Heidary, M. TRIzol-based RNA extraction: a reliable method for gene expression studies (University of Tehran, 2014).
-
Souza, G. M. et al. Supporting data for Assembly of the 373K gene space of the polyploid sugarcane genome reveals reservoirsof functional diversity in the world’s leading biomass crop. Gigascience. 8(12), giz129 (2019).
-
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
-
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
-
Pertea et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
-
Li, J. et al. TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nat. Methods 17, 399–404 (2020).
-
Kenneth, J. L., & Thomas, D. S. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT. Methods 25, 402–408 (2001).
-
Liu, Q. et al. Bio-fertilizer affects structural dynamics, function, and network patterns of the sugarcane rhizospheric microbiota. Micro. Ecol. 84, 1195–1211 (2022).
-
Wang, J. et al. Serum metabolomics for early diagnosis of esophageal squamous cell carcinoma by UHPLC-QTOF/MS. Metabolomics 12, 116 (2016).
-
Han, C. et al. Majorbio Cloud 2024: update single-cell and multiomics workflows. iMeta 3, e217 (2024).
