[1]

Liu ZT, Ma RA, Zhu D, Konstantinidis KT, Zhu YG, et al. 2024. Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome. Nature Communications 15(1):5168

doi: 10.1038/s41467-024-49165-5
[2]

Herraiz-Carboné M, Cotillas S, Lacasa E, Sainz de Baranda C, Riquelme E, et al. 2021. Are we correctly targeting the research on disinfection of antibiotic-resistant bacteria (ARB)? Journal of Cleaner Production 320:128865

doi: 10.1016/j.jclepro.2021.128865
[3]

Hernando-Amado S, Coque TM, Baquero F, Martínez JL. 2019. Defining and combating antibiotic resistance from One Health and Global Health perspectives. Nature Microbiology 4(9):1432−1442

doi: 10.1038/s41564-019-0503-9
[4]

Song T, Zhu C, Li B, Yan M, Li H. 2023. Manure application led to higher antibiotic resistance risk in red soil compared with black soil and fluvo-aquic soil. Journal of Hazardous Materials Advances 9:100209

doi: 10.1016/j.hazadv.2022.100209
[5]

Han B, Yang F, Shen S, Mu M, Zhang K. 2023. Effects of soil habitat changes on antibiotic resistance genes and related microbiomes in paddy fields. Science of the Total Environment 895:165109

doi: 10.1016/j.scitotenv.2023.165109
[6]

Fu Y, Hu F, Wang F, Xu M, Jia Z, et al. 2025. Field-based evidence for the prevalence of soil antibiotic resistomes under long-term antibiotic-free fertilization. Environment International 195:109202

doi: 10.1016/j.envint.2024.109202
[7]

Yue Z, Zhang J, Ding C, Wang Y, Zhou Z, et al. 2023. Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years. Science of the Total Environment 869:161742

doi: 10.1016/j.scitotenv.2023.161742
[8]

Wang YZ, Zhou SYD, Zhou XY, An XL, Su JQ. 2023. Manure and biochar have limited effect on lettuce leaf endophyte resistome. Science of the Total Environment 860:160515

doi: 10.1016/j.scitotenv.2022.160515
[9]

Zou Y, Zhang Y, Zhou J, Bao C, Chen M, et al. 2022. Effects of composting pig manure at different mature stages on ARGs in different types of soil-vegetable systems. Journal of Environmental Management 321:116042

doi: 10.1016/j.jenvman.2022.116042
[10]

Gao Y, Luo W, Zhang H, Chen Y, Li Z, et al. 2023. Enrichment of antibiotic resistance genes in roots is related to specific bacterial hosts and soil properties in two soil-plant systems. Science of the Total Environment 886:163933

doi: 10.1016/j.scitotenv.2023.163933
[11]

Xiao Z, Han R, Su J, Zhu Z, Zhao Y, et al. 2023. Application of earthworm and silicon can alleviate antibiotic resistance in soil-Chinese cabbage system with ARGs contamination. Environmental Pollution 319:120900

doi: 10.1016/j.envpol.2022.120900
[12]

Shao C, Li W, Tan P, Shan A, Dou X, et al. 2019. Symmetrical modification of minimized dermaseptins to extend the spectrum of antimicrobials with endotoxin neutralization potency. International Journal of Molecular Sciences 20(6):1417

doi: 10.3390/ijms20061417
[13]

Rodríguez-Melcón C, Alonso-Calleja C, Capita R. 2024. The One Health approach in food safety: challenges and opportunities. Food Frontiers 5(5):1837−1865

doi: 10.1002/fft2.458
[14]

Wang JY, An XL, Zhang HM, Su JQ. 2024. Manure application enriches phage-associated antimicrobial resistance and reconstructs ecological network of phage-bacteria in paddy soil. Soil Biology & Biochemistry 198:109554

doi: 10.1016/j.soilbio.2024.109554
[15]

Guo YJ, Qiu TL, Gao M, Sun YM, Cheng ST, et al. 2021. Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species. Journal of Hazardous materials 415:125595

doi: 10.1016/j.jhazmat.2021.125595
[16]

Chen P, Yu KF, He YL. 2023. The dynamics and transmission of antibiotic resistance associated with plant microbiomes. Environment International 176. https://doi.org/10.1016/j.envint.2023.107986
[17]

Sun YP, Snow D, Walia H, Li X. 2021. Transmission Routes of the Microbiome and Resistome from Manure to Soil and Lettuce. Environmental Science & Technology 55(16):11102−11112

doi: 10.1021/acs.est.1c02985
[18]

Huang J, Mi J, Yan Q, Wen X, Zhou S, et al. 2021. Animal manures application increases the abundances of antibiotic resistance genes in soil-lettuce system associated with shared bacterial distributions. Science of the Total Environment 787:147667

doi: 10.1016/j.scitotenv.2021.147667
[19]

Wen X, Xu J, Worrich A, Li X, Yuan X, et al. 2024. Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach. Environment International 187:108732

doi: 10.1016/j.envint.2024.108732
[20]

Zhang Y, Zhou J, Wu J, Hua Q, Bao C. 2022. Distribution and transfer of antibiotic resistance genes in different soil-plant systems. Environmental Science and Pollution Research International 29(39):59159−59172

doi: 10.1007/s11356-021-17465-8
[21]

Yang J, Xiang J, Goh SG, Xie Y, Nam OC, et al. 2024. Food waste compost and digestate as novel fertilizers: Impacts on antibiotic resistome and potential risks in a soil-vegetable system. Science of the Total Environment 923. https://doi.org/10.1016/j.scitotenv.2024.171346
[22]

Prasain JK, Barnes S. 2024. Recent updates on diet-derived gut microbial metabolites. eFood 5(4):e181

doi: 10.1002/efd2.181
[23]

Yang C, Zhang X, Ni H, Gai X, Huang Z, et al. 2021. Soil carbon and associated bacterial community shifts driven by fine root traits along a chronosequence of Moso bamboo (Phyllostachys edulis) plantations in subtropical China. Science of the Total Environment 752:142333

doi: 10.1016/j.scitotenv.2020.142333
[24]

Spitzer CM, Lindahl B, Wardle DA, Sundqvist MK, Gundale MJ, et al. 2021. Root trait-microbial relationships across tundra plant species. New Phytologist 229(3):1508−1520

doi: 10.1111/nph.16982
[25]

Wang F, Sun R, Hu H, Duan G, Meng L, et al. 2022. The overlap of soil and vegetable microbes drives the transfer of antibiotic resistance genes from manure-amended soil to vegetables. Science of the Total Environment 828:154463

doi: 10.1016/j.scitotenv.2022.154463
[26]

Han B, Yang F, Shen S, Li Z, Zhang K. 2024. Soil metabolic processes influenced by rice roots co-regulates the environmental evolution of antibiotic resistome. Environment International 193:109116

doi: 10.1016/j.envint.2024.109116
[27]

Shen Y, Zhang B, Yao Y, Wang H, Chen Z, et al. 2024. Insights into the interactions of plant-associated bacteria and their role in the transfer of antibiotic resistance genes from soil to plant. Journal of Hazardous materials 480:135881

doi: 10.1016/j.jhazmat.2024.135881
[28]

Xiao E, Sun W, Deng J, Shao L, Ning Z, et al. 2023. The potential linkage between antibiotic resistance genes and microbial functions across soil−plant systems. Plant and Soil 493(1-2):589−602

doi: 10.1007/s11104-023-06247-5
[29]

Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, et al. 2018. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nature Microbiology 3(4):470−480

doi: 10.1038/s41564-018-0129-3
[30]

Liu W, Zhao Q, Zhang Z, Li Y, Xu N, et al. 2020. Enantioselective effects of imazethapyr on Arabidopsis thaliana root exudates and rhizosphere microbes. Science of the Total Environment 716:137121

doi: 10.1016/j.scitotenv.2020.137121
[31]

Liu Y, Cui E, Neal AL, Zhang X, Li Z, et al. 2019. Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere. Science of the Total Environment 648:12−24

doi: 10.1016/j.scitotenv.2018.08.101
[32]

Guo A, Pan C, Ma J, Bao Y. 2020. Linkage of antibiotic resistance genes, associated bacteria communities and metabolites in the wheat rhizosphere from chlorpyrifos-contaminated soil. Science of the Total Environment 741:140457

doi: 10.1016/j.scitotenv.2020.140457
[33]

Guan X, Li Y, Yang Y, Liu Z, Shi R, et al. 2025. Root exudates regulate soil antibiotic resistance genes via rhizosphere microbes under long-term fertilization. Environment International 195:109180

doi: 10.1016/j.envint.2024.109180
[34]

Zhang Z, Zhao L, Yang J, Pang J, Lambers H, et al. 2024. Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil. Environmental Science and Pollution Research International 31(15):22663−22678

doi: 10.1007/s11356-024-32578-6
[35]

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584

doi: 10.7717/peerj.2584
[36]

Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10(10):996−998

doi: 10.1038/nmeth.2604
[37]

Zhao L, Zhang H, White JC, Chen X, Li H, et al. 2019. Metabolomics reveals that engineered nanomaterial exposure in soil alters both soil rhizosphere metabolite profiles and maize metabolic pathways. Environmental Science-Nano 6(6):1716−1727

doi: 10.1039/c9en00137a
[38]

Wolthuis JC, Magnusdottir S, Pras-Raves M, Moshiri M, Jans JJM, et al. 2020. MetaboShiny: interactive analysis and metabolite annotation of mass spectrometry-based metabolomics data. Metabolomics 16:99

doi: 10.1007/s11306-020-01717-8
[39]

Lefcheck JS. 2016. ᴘɪᴇᴄᴇᴡɪsᴇSEM: piecewise structural equation modelling in R for ecology, evolution, and systematics. Methods in Ecology and Evolution 7(5):573−579

doi: 10.1111/2041-210x.12512
[40]

Zheng F, Zhou GW, Zhu D, Neilson R, Zhu YG, et al. 2022. Does plant identity affect the dispersal of resistomes above and below ground? Environmental Science & Technology 56(21):14904−14912

doi: 10.1021/acs.est.1c08733
[41]

Zhang YJ, Hu HW, Chen QL, Yan H, Wang JT, et al. 2020. Manure application did not enrich antibiotic resistance genes in root endophytic bacterial microbiota of cherry radish plants. Applied and Environmental Microbiology 86(2):e02106-19

doi: 10.1128/AEM.02106-19
[42]

Cerqueira F, Matamoros V, Bayona J, Piña B. 2019. Antibiotic resistance genes distribution in microbiomes from the soil-plant-fruit continuum in commercial Lycopersicon esculentum fields under different agricultural practices. Science of the Total Environment 652:660−670

doi: 10.1016/j.scitotenv.2018.10.268
[43]

Zhou SYD, Zhang Q, Neilson R, Giles M, Li H, et al. 2021. Vertical distribution of antibiotic resistance genes in an urban green facade. Environment International 152:106502

doi: 10.1016/j.envint.2021.106502
[44]

Frank A, Saldierna Guzmán J, Shay J. 2017. Transmission of Bacterial Endophytes. Microorganisms 5(4):70

doi: 10.3390/microorganisms5040070
[45]

Chen QL, Hu HW, Zhu D, Ding J, Yan ZZ, et al. 2020. Host identity determines plant associated resistomes. Environmental Pollution 258:113709

doi: 10.1016/j.envpol.2019.113709
[46]

Zhang R, Chen L, Niu Z, Song S, Zhao Y. 2019. Water stress affects the frequency of Firmicutes, Clostridiales and Lysobacter in rhizosphere soils of greenhouse grape. Agricultural Water Management 226:105776

doi: 10.1016/j.agwat.2019.105776
[47]

Cerqueira F, Matamoros V, Bayona J, Elsinga G, Hornstra LM, et al. 2019. Distribution of antibiotic resistance genes in soils and crops. A field study in legume plants (Vicia faba L.) grown under different watering regimes. Environmental Research 170:16−25

doi: 10.1016/j.envres.2018.12.007
[48]

Yeoh YK, Dennis PG, Paungfoo-Lonhienne C, Weber L, Brackin R, et al. 2017. Evolutionary conservation of a core root microbiome across plant Phyla along a tropical soil chronosequence. Nature Communications 8:215

doi: 10.1038/s41467-017-00262-8
[49]

Long HH, Sonntag DG, Schmidt DD, Baldwin IT. 2010. The structure of the culturable root bacterial endophyte community of Nicotiana attenuata is organized by soil composition and host plant ethylene production and perception. New Phytologist 185(2):554−567

doi: 10.1111/j.1469-8137.2009.03079.x
[50]

Wang Y, Li Y, Li H, Zhou J, Wang T. 2023. Seasonal dissemination of antibiotic resistome from livestock farms to surrounding soil and air: Bacterial hosts and risks for human exposure. Journal of Environmental Management 325:116638

doi: 10.1016/j.jenvman.2022.116638
[51]

Dai D, Brown C, Bürgmann H, Joakim Larsson DG, Nambi I, et al. 2022. Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge. Microbiome 10(1):20

doi: 10.1186/s40168-021-01216-5
[52]

Li XY, Wu WF, Wu CY, Hu Y, Xiang Q, et al. 2023. Seeds act as vectors for antibiotic resistance gene dissemination in a soil-plant continuum. Environmental Science & Technology 57(50):21358−21369

doi: 10.1021/acs.est.3c05678
[53]

Du S, Ge AH, Liang ZH, Xiang JF, Xiao JL, et al. 2022. Fumigation practice combined with organic fertilizer increase antibiotic resistance in watermelon rhizosphere soil. Science of the Total Environment 805:150426

doi: 10.1016/j.scitotenv.2021.150426
[54]

Wang L, Yu X. 2024. Research hotspots and evolution trends of food safety risk assessment techniques and methods. eFood 5(6):e70025

doi: 10.1002/efd2.70025
[55]

de Jong F, Munnik T. 2021. Attracted to membranes: lipid-binding domains in plants. Plant Physiology 185(3):707−723

doi: 10.1093/plphys/kiaa100
[56]

Mamode Cassim A, Gouguet P, Gronnier J, Laurent N, Germain V, et al. 2019. Plant lipids: Key players of plasma membrane organization and function. Progress in Lipid Research 73:1−27

doi: 10.1016/j.plipres.2018.11.002
[57]

Bahammou D, Recorbet G, Mamode Cassim A, Robert F, Balliau T, et al. 2024. A combined lipidomic and proteomic profiling of Arabidopsis thaliana plasma membrane. The Plant Journal 119(3):1570−1595

doi: 10.1111/tpj.16810
[58]

van Dam NM, Bouwmeester HJ. 2016. Metabolomics in the rhizosphere: tapping into belowground chemical communication. Trends in Plant Science 21(3):256−265

doi: 10.1016/j.tplants.2016.01.008
[59]

Mendes R, Garbeva P, Raaijmakers JM. 2013. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews 37(5):634−663

doi: 10.1111/1574-6976.12028
[60]

Macabuhay A, Arsova B, Walker R, Johnson A, Watt M, et al. 2022. Modulators or facilitators? Roles of lipids in plant root-microbe interactions. Trends in Plant Science 27(2):180−190

doi: 10.1016/j.tplants.2021.08.004
[61]

Martínez E, Cosnahan RK, Wu M, Gadila SK, Quick EB, et al. 2019. Oxylipins mediate cell-to-cell communication in Pseudomonas aeruginosa. Communications Biology 2(1):66

doi: 10.1038/s42003-019-0310-0
[62]

Chan S, Xiong P, Zhao M, Zhang S, Zheng R, et al. 2024. Anti-inflammatory effects of natural products from vitamin C-rich fruits. Food Frontiers 5(6):2383−2422

doi: 10.1002/fft2.433
[63]

Chen P, Yu K, He Y. 2023. The dynamics and transmission of antibiotic resistance associated with plant microbiomes. Environment International 176:107986

doi: 10.1016/j.envint.2023.107986
[64]

Nesru Y, Ahmed M, Mengistu A, Naimuddin M. 2025. Phytochemical screening and inhibitory effects of Catha edulis Forsk extracts on oxidation, growth, biofilm and quorum sensing of selected pathogens. Journal of Genetic Engineering and Biotechnology 23(4):100560

doi: 10.1016/j.jgeb.2025.100560