Baker N R, Zhalnina K, Yuan M, Hermana D, Ceja-Navarro J A, Sasse J, Singh A, Gonçalves C, Ma J, Dunlap C, Northen T R, Brodie E L, Firestone M K. 2024. Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes. Proceedings of the National Academy of Sciences of the United States of America, 121, e2303439121.

Balazadeh S, Schildhauer J, Araújo W L, Munné-Bosch S, Fernie A R, Proost S, Humbeck K, Mueller-Roeber B. 2014. Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: Transcriptomic and metabolomic consequences. Journal of Experimental Botany, 65, 3975–3992. 

Bardgett R D, van der Putten W H. 2014. Belowground biodiversity and ecosystem functioning. Nature, 515, 505–511.

Bender S F, Wagg C, van der Heijden M G A. 2016. An underground revolution: Biodiversity and soil ecological engineering for agricultural sustainability. Trends in Ecology & Evolution, 31, 440–452.

Bhadwal S S, Verma S, Hassan S, Kaur S. 2024. Unraveling the potential of hydrogen sulfide as a signaling molecule for plant development and environmental stress responses: A state-of-the-art review. Plant Physiology and Biochemistry, 212, 108730.

Bi Q F, Li K J, Zheng B X, Liu X P, Li H Z, Jin B J, Ding K, Yang X R, Lin X Y, Zhu Y G. 2020. Partial replacement of inorganic phosphorus (P) by organic manure reshapes phosphate mobilizing bacterial community and promotes P bioavailability in a paddy soil. Science of the Total Environment, 703, 134977. 

Brakhage A A. 2013. Regulation of fungal secondary metabolism. Nature Reviews Microbiology, 11, 21–32.

Branco S, Schauster A, Liao H L, Ruytinx J. 2022. Mechanisms of stress tolerance and their effects on the ecology and evolution of mycorrhizal fungi. New Phytologist, 235, 2158–2175.

Burghardt L T, Epstein B, Hoge M, Trujillo D I, Tiffin P. 2022. Host-associated rhizobial fitness: Dependence on nitrogen, density, community complexity, and legume genotype. Applied and Environmental Microbiology, 88, e0052622.

Cao T, Zang X, Ren J, Liu J, Yang D. 2024. Cover crop alters rhizosphere sediments to recruit plant growth-promoting microorganisms, enhancing peanut production. Applied Soil Ecology, 203, 105620. 

Chen S, Waghmode T R, Sun R, Kuramae E E, Hu C, Liu B. 2019a. Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization. Microbiome, 7, 1–13.

Chen S, Zhu Y, Shao T, Long X, Gao X, Zhou Z. 2019b. Relationship between rhizosphere soil properties and disease severity in highbush blueberry (Vaccinium corymbosum). Applied Soil Ecology, 137, 187‒194. 

Cheng N, Peng Y, Kong Y, Li J, Sun C. 2018. Combined effects of biochar addition and nitrogen fertilizer reduction on the rhizosphere metabolomics of maize (Zea mays L.) seedlings. Plant and Soil, 433, 19–35.

Cheng Z, Zhou Y, Zhang H, Wu Z, Yang J, Chen Q, Wei X. 2022. Influence of fertilization on soil microbial communities and soil quality in the rhizosphere. Soil Biology and Biochemistry, 164, 108466.

Das P P, Singh K R, Nagpure G, Mansoori A, Singh R P, Ghazi I A, Kumar A, Singh J. 2022. Plant-soil-microbes: A tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices. Environmental Research, 214, 113821.

Dunn M F. 2015. Key roles of microsymbiont amino acid metabolism in rhizobia-legume interactions. Critical Reviews in Microbiology, 41, 411–451.

Evans S, Martiny J B, Allison S D. 2017. Effects of dispersal and selection on stochastic assembly in microbial communities. ISME Journal, 11, 176–185. 

Farrar K, Bryant D, Cope-Selby N. 2014. Understanding and engineering beneficial plant–microbe interactions: Plant growth promotion in energy crops. Plant Biotechnology Journal, 12, 1193–1206.

Frantzeskakis L, Di Pietro A, Rep M, Schirawski J, Wu C, Panstruga R. 2020. Rapid evolution in plant–microbe interactions: A molecular genomics perspective. New Phytologist, 225, 1134–1142.

Geisseler D, Scow K M. 2014. Long-term effects of mineral fertilizers on soil microorganisms – a review. Soil Biology and Biochemistry, 75, 54–63.

Han Q, Ma Q, Chen Y, Tian B, Xu L, Bai Y, Chen W, Li X. 2020. Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. The ISME journal, 14, 1915–1928. 

He J, Zhang L, Van Dingenen J, Desmet S, Goormachtig S, Calonne-Salmon M, Quinet M, Kyndt T, Nguyen H T, Venieraki A. 2024. Arbuscular mycorrhizal hyphae facilitate rhizobia dispersal and nodulation in legumes. ISME Journal, 18, 185.

van der Heijden M G A, Bardgett R D, van Straalen N M. 2008. The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters, 11, 296–310.

Hernández G, Valdés-López O, Ramírez M, Goffard N, Weiller G, Aparicio-Fabre R. 2009. Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants. Plant Physiology, 151, 1221–1238.

Hu M, Le Y, Sardans J, Yan R, Zhong Y, Sun D, Tong C, Peñuelas J. 2023. Moderate salinity improves the availability of soil P by regulating P-cycling microbial communities in coastal wetlands. Global Change Biology, 29, 276–288.

Huang Z, Xu W, Su S, Li X, Wang P, Liu Y, Zhou Q, Ma X. 2020. Influence of potassium on lipid metabolism and associated metabolites in plant rhizospheres. Journal of Experimental Botany, 71, 2043–2055.

Hungria M, Nogueira M A, Araujo R S. 2013. Co-inoculation of soybeans and common beans with rhizobia and azospirilla: Strategies to improve sustainability. Biology and Fertility of Soils, 49, 791–801.

Jiao S, Chen W, Wang J, Du N, Li Q, Wei G. 2018. Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. Microbiome, 6, 1–13. 

Jin Z, Jiang F, Wang L, Declerck S, Feng G, Zhang L. 2024. Arbuscular mycorrhizal fungi and Streptomyces: Brothers in arms to shape the structure and function of the hyphosphere microbiome in the early stage of interaction. Microbiome, 12, 83.

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. 2016. KEGG for integrating and interpreting large-scale molecular datasets. Nucleic Acids Research, 44, D457–D462.

Kuhlisch C, Pohnert G. 2015. Metabolomics in chemical ecology. Natural Product Reports, 32, 937–955.

Lange E, Tautenhahn R, Neumann S, Gröpl C. 2008. Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC bioinformatics, 9, 1–19. 

Lekberg Y, Arnillas C A, Borer E T, Bullington L S, Fierer N, Kennedy P G, Leff J W, Luis A D, Seabloom E W, Henning J A. 2021. Nitrogen and phosphorus fertilization consistently favor pathogenic over mutualistic fungi in grassland soils. Nature Communications, 12, 3484.

Levy-Booth D J, Prescott C E, Grayston S J. 2014. Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil Biology and Biochemistry, 75, 11–25. 

Liu C, Gu W, Liu C, Shi X, Li B, Chen B, Zhao T, Wang G. 2024. Tryptophan regulates sorghum root growth and enhances low nitrogen tolerance. Plant Physiology and Biochemistry, 212, 108737.

Liu E, Yan C, Mei X, He W, Bing S, Liu Q, Chen Y, Luo J, Fan F. 2010. Long-term effect of chemical fertilizer, straw, and manure on soil chemical and biological properties in northwest China. Geoderma, 158, 173–180.

Love M I, Huber W, Anders S. 2014. DESeq2: Moderated estimation of fold change and dispersion for RNA-seq data. Genome Biology, 15, 550.

Mus F, Crook M B, Garcia K, Garcia C A, Geddes B A, Kouri E D, Paramasivan P, Ryu M H, Oldroyd G E D, Poole P S, Udvardi M K, Voigt C A, Ané J M, Peters J W. 2016. Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Applied and Environmental Microbiology, 82, 3698–3710.

Nehlig A. 2018. Interindividual differences in caffeine metabolism and factors driving caffeine consumption. Pharmacological Reviews, 70, 384–411.

Pang G, Li X, Ding M, Jiang S, Chen P, Zhao Z, Gao R, Song B, Xu X, Shen Q, Cai F M, Druzhinina I S. 2023. The distinct plastisphere microbiome in the terrestrial-marine ecotone is a reservoir for putative degraders of petroleum-based polymers. Journal of Hazardous Materials, 453, 131399.

Philippot L, Raaijmakers J M, Lemanceau P, van der Putten W H. 2013. Going back to the roots: The microbial ecology of the rhizosphere. Nature Reviews Microbiology, 11, 789–799.

Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C. 2015. Microbial interactions in the rhizosphere: Beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition processes. A review. Biology and Fertility of Soils, 51, 403–415.

Qian F, Huang X, Su X, Bao Y. 2022. Responses of microbial communities and metabolic profiles to the rhizosphere of Tamarix ramosissima in soils contaminated by multiple heavy metals. Journal of Hazardous Materials, 438, 129469.

Qiao M, Sun R, Wang Z, Dumack K, Xie X, Dai C, Jiang Y, Zhang Z, Dong X, Bai Y. 2024. Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification. Nature Communications, 15, 2924.

Savarese C, Cozzolino V, Verrillo M, Vinci G, Martino A D, Scopa A, Piccolo A. 2022. Combination of humic biostimulants with a microbial inoculum improves lettuce productivity, nutrient uptake, and primary and secondary metabolism. Plant and Soil, 481, 285–314.

Siciliano S D, Palmer A S, Winsley T, Lamb E, Bissett A, Brown M V, Dorst J V, Ji M, Ferrari B C, Grogan P, Chu H, Snape I. 2014. Soil fertility is associated with fungal and bacterial richness, whereas pH is associated with community composition in polar soil microbial communities. Soil Biology and Biochemistry, 78, 10–20. 

Sokol N W, Slessarev E, Marschmann G L, Nicolas A, Blazewicz S J, Brodie E L, Firestone M K, Foley M M, Hestrin R, Hungate B A, Koch B J, Stone B W, Sullivan M B, Zablocki O, LLNL Soil Microbiome Consortium, Pett-Ridge J. 2022. Life and death in the soil microbiome: How ecological processes influence biogeochemistry. Nature Reviews Microbiology, 20, 415–430.

Thomas H. 2013. Senescence, ageing and death of the whole plant. New Phytologist, 197, 696–711.

Trivedi P, Delgado-Baquerizo M, Anderson I C, Singh B K. 2016. Response of soil properties and microbial communities to agriculture: Implications for primary productivity and soil health indicators. Frontiers in Plant Science, 7, 990. 

Wang C, Kuzyakov Y. 2024. Mechanisms and implications of bacterial–fungal competition for soil resources. The ISME Journal, 18, wrae073.

Wang D, Xie L, Liu Y, Chen T, Yang F, Zhou Z, Zhang X, Huang M. 2021. Influence of nitrogen on microbial communities and metabolite profiles in the plant rhizosphere. Journal of Experimental Botany, 72, 2058–2071.

Wang J, Cao X, Wang C, Chen F, Feng Y, Yue L, Wang Z, Xing B. 2022. Fe-based nanomaterial-induced root nodulation is modulated by flavonoids to improve soybean (Glycine max) growth and quality. ACS Nano, 16, 21047–21062. 

Wang J, Wu C, Li J, Zhang H. 2021. Effects of long-term fertilization on soil microbial community and metabolic profiles in a wheat-maize cropping system. Applied Soil Ecology, 158, 103799.

Wei W, Guan D, Ma M, Jiang X, Fan F, Meng F, Li L, Zhao B, Zhao Y, Cao F, Chen H, Li J. 2023. Long-term fertilization coupled with rhizobium inoculation promotes soybean yield and alters soil bacterial community composition. Frontiers in Microbiology, 14, 1161983. 

Wei W, Ma M, Jiang X, Fan F, Meng F, Cao F, Chen H, Guan D, Li L, Li J. 2025. Long-term effects of nitrogen fertilization and Bradyrhizobium inoculation on diazotrophic community structure and diversity in soybean cultivation. Applied Soil Ecology, 206, 105806.

Wei W, Ma M, Jiang X, Meng F, Cao F, Chen H, Guan D, Li L, Li J. 2024. Soil P-stimulating bacterial communities: Response and effect assessment of long-term fertilizer and rhizobium inoculant application. Environmental Microbiome, 19, 86.

Withers E, Hill P W, Chadwick D R, Jones D L. 2020. Use of untargeted metabolomics for assessing soil quality and microbial function. Soil Biology and Biochemistry, 143, 107758.

Withers E, Hill P W, Chadwick D R, Jones C D, McCartney A. 2020. Use of untargeted metabolomics for assessing soil quality and microbial function. Soil Biology and Biochemistry, 143, 107758.

Wolde-Meskel E, van Heerwaarden J, Abdulkadir B, Kassa S, Aliyi I, Degefu T, Erkuah G, Giller K E. 2018. Additive yield response of chickpea (Cicer arietinum L.) to rhizobium inoculation and phosphorus fertilizer across smallholder farms in Ethiopia. Agriculture Ecosystems and Environment, 261, 144–152.

Wu Y, Sun P, Liu H, Li J, Yang X, Jiang Y, Zhao Y. 2020. The roles of rhizobial inoculation in the modulation of soybean root exudates and associated microbial communities. Soil Biology and Biochemistry, 143, 107756.

Xiao J F, Zhou B, Ressom H W. 2012. Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trac-trends in Analytical Chemistry, 32, 1–14.

Xie Z, Yu Z, Li Y, Wang G, Liu X, Tang C, Lian T, Adams J, Liu J, Liu J, Herbert S J, Jin J. 2022. Soil microbial metabolism on carbon and nitrogen transformation links the crop-residue contribution to soil organic carbon. npj Biofilms and Microbiomes, 8, 14.

Xu H, Yang Y, Tian Y, Xu R, Zhong Y, Liao H. 2020. Rhizobium inoculation drives the shifting of rhizosphere fungal community in a host genotype dependent manner. Frontiers in Microbiology, 10, 3135.

Xun W, Huang T, Zhao J, Ran W, Wang B, Shen Q, Zhang R. 2015. Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities. Soil Biology and Biochemistry, 90, 10–18.

Yang L, Kang Y, Li N, Wang Y, Mou H, Sun H, Zhang R, Wang T. 2024. Unlocking hormesis and toxic effects induced by cadmium in Polygonatum cyrtonema Hua based on morphology, physiology, and metabolomics. Journal of Hazardous Materials, 465, 133447.

Yue H, Yue W, Jiao S, Kim H, Lee Y, Wei G, Zhou Z, Liu Q. 2023. Plant domestication shapes rhizosphere microbiome assembly and metabolic functions. Microbiome, 11, 70.

Zhang W, Hou H, Zhang D, Zhu B, Yuan H, Gao T. 2022. Transcriptomic and metabolomic analysis of soybean nodule number improvements with the use of water-soluble humic materials. Journal of Agricultural and Food Chemistry, 71, 197–210.

Zheng Q, Hu Y, Zhang S, Noll L, Böckle T, Dietrich M, Herbold C W, Eichorst S A, Woebken D, Richter A, Wanek W. 2019. Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity. Soil Biology and Biochemistry, 136, 107521. 

Zhou J, Ning D. 2017. Stochastic community assembly: Does it matter in microbial ecology? Microbiology and Molecular Biology Reviews, 81, 10–1128??.

Zhou Y, Wei Y, Zhao Z, Li J, Li H, Yang P, Tian S, Ryder M, Toh R, Yang H, Denton D D. 2022. Microbial communities along the soil-root continuum are determined by root anatomical boundaries, soil properties, and root exudation. Soil Biology and Biochemistry, 171, 108721.

Zhu S, Vivanco J M, Manter D K. 2016. Nitrogen fertilizer rate affects root exudation, the rhizosphere microbiome, and nitrogen-use efficiency of maize. Applied Soil Ecology, 107, 324–333.

Zia R, Nawaz M S, Siddique M J, Hakim S, Imran A, Bhat R. 2021. Plant survival under drought stress: Implications, adaptive responses, and integrated rhizosphere management strategy for stress mitigation. Microbiology Research, 242, 126626.