| [1] |
Zhang N, Juneau P, Huang R, He Z, Sun B, et al. 2021. Coexistence between antibiotic resistance genes and metal resistance genes in manure-fertilized soils. |
| [2] |
Huddleston JR. 2014. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. |
| [3] |
Zhou HB, Ding JT, Meng HB, Shen YJ, Wang J, et al. 2022. Survey and development analysis of resource utilization technology of livestock and poultry wastes in China. |
| [4] |
Liu B, Yu K, Ahmed I, Gin K, Xi B, et al. 2021. Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: a review. |
| [5] |
Yang Y, Chen W, Yin J, Jiang T, Zhao L, et al. 2025. Interactions between fungi and bacteria hosts carrying MGEs is dominant for ARGs fate during manure mesophilic composting. |
| [6] |
Zhang Y, Kastman EK, Guasto JS, Wolfe BE. 2018. Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. |
| [7] |
Nazir R, Du S, Shen JP, Hu HW, Wang JT, et al. 2024. Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks. |
| [8] |
Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, et al. 2018. Bacterial–fungal interactions: ecology, mechanisms and challenges. |
| [9] |
Xiao Z, Zhang Y, Li G, Carter LJ, Wang H, et al. 2021. Application of pharmaceutical waste sludge compost alters the antibiotic resistome in soil under the Chinese cabbage system. |
| [10] |
Sun Y, Liu X, Sun L, Men M, Wang B, et al. 2022. Microecological insight to fungal structure and key fungal communities regulating nitrogen transformation based on spatial heterogeneity during cow manure composting by multi-angle and multi-aspect analyses. |
| [11] |
Huang YH, Chen XH, Li QF, Lü H, Mo CH, et al. 2022. Fungal community enhanced humification and influenced by heavy metals in industrial-scale hyperthermophilic composting of municipal sludge. |
| [12] |
Kong Z, Wang M, Shi X, Wang X, Zhang X, et al. 2022. The functions of potential intermediates and fungal communities involved in the humus formation of different materials at the thermophilic phase. |
| [13] |
Lin X, Al-Dhabi NA, Li F, Wang N, Peng H, et al. 2023. Relative contribution of ammonia-oxidizing bacteria and denitrifying fungi to N2O production during rice straw composting with biochar and biogas residue amendments. |
| [14] |
Yang X, Duan P, Liu Q, Wang K, Li D. 2024. Addition of cellulose and hemicellulose degrading microorganisms intensified nitrous oxide emission during composting. |
| [15] |
Zhu P, Qin H, Zhang H, Luo Y, Ru Y, et al. 2021. Variations in antibiotic resistance genes and removal mechanisms induced by C/N ratio of substrate during composting. |
| [16] |
Ao G, Wang Z, Shi Y, Ling H, Sun S, et al. 2024. Effects of exogenously added humic acid on the fate of aminoglycoside antibiotics and humification process during aerobic compost. |
| [17] |
Schneider-Poetsch T, Ju J, Eyler DE, Dang Y, Bhat S, et al. 2010. Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin. |
| [18] |
Ananyeva ND, Castaldi S, Stolnikova EV, Kudeyarov VN, Valentini R. 2015. Fungi-to-bacteria ratio in soils of European Russia. |
| [19] |
Pan Y, Wu Y, Li X, Zeng J, Lin X. 2019. Continuing impacts of selective inhibition on bacterial and fungal communities in an agricultural soil. |
| [20] |
Jiao S, Chu H, Zhang B, Wei X, Chen W, et al. 2022. Linking soil fungi to bacterial community assembly in arid ecosystems. |
| [21] |
Yang Y, Wang J, Yin J, Cui Z, Li G, et al. 2024. Risk level and removal performance of antibiotic resistance genes and bacterial pathogens in static composting with different temperatures. |
| [22] |
Ma R, Wang J, Liu Y, Wang G, Yang Y, et al. 2023. Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting. |
| [23] |
Zhao J, Liu L, Han J, Zhang J, Li X, et al. 2026. Majorbio Cloud 2026 provides comprehensive analysis workflows for microbiome. |
| [24] |
Oksanen J, Simpson GL, Blanchet FG, Kindt R, Legendre P, et al. 2026. vegan: community ecology package. R package version 2.8-0. https://vegandevs.github.io/vegan |
| [25] |
Revelle W. 2026. psych: procedures for psychological, psychometric, and personality research. R package version 2.6.5. USA: Northwestern University. doi: 10.32614/CRAN.package.psych |
| [26] |
Ning D, Yuan M, Wu L, Zhang Y, Guo X, et al. 2020. A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. |
| [27] |
Feng K, Peng X, Zhang Z, Gu S, He Q, et al. 2022. iNAP: an integrated network analysis pipeline for microbiome studies. |
| [28] |
Bastian M, Heymann S, Jacomy M. 2009. Gephi: an open source software for exploring and manipulating networks. |
| [29] |
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. |
| [30] |
Guimarães A, Venancio A, Abrunhosa L. 2018. Antifungal effect of organic acids from lactic acid bacteria on Penicillium nordicum. |
| [31] |
Lin H, Yuan Q, Yu Q, Chen Z, Ma J. 2022. Plants mitigate nitrous oxide emissions from antibiotic-contaminated agricultural soils. |
| [32] |
Bergelson J, Mittelstrass J, Horton MW. 2019. Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. |
| [33] |
Chen W, Feng Z, Chang Y, Xu S, Zhou K, et al. 2023. Comparing the bacterial composition, succession and assembly patterns in plastisphere and kitchen waste composting with PLA/PBAT blends. |
| [34] |
Gao C, Xu L, Montoya L, Madera M, Hollingsworth J, et al. 2022. Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities. |
| [35] |
Tan L, Zeng WA, Xiao Y, Li P, Gu S, et al. 2021. Fungi-bacteria associations in wilt diseased rhizosphere and endosphere by interdomain ecological network analysis. |
| [36] |
Zhao B, Xing P, Wu QL. 2021. Interactions between bacteria and fungi in macrophyte leaf litter decomposition. |
| [37] |
Li M, Yao J, Sunahara G, Duran R, Liu B, et al. 2023. Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil. |
| [38] |
Chen C, Li P, Yin M, Wang J, Sun Y, et al. 2023. Deciphering characterization of seasonal variations in microbial communities of marine ranching: diversity, co-occurrence network patterns, and assembly processes. |
| [39] |
Chen J, Wang P, Wang C, Wang X, Miao L, et al. 2020. Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river. |
| [40] |
Zhang M, He LY, Liu YS, Zhao JL, Zhang JN, et al. 2020. Variation of antibiotic resistome during commercial livestock manure composting. |
| [41] |
Li S, Zhu Y, Zhong G, Huang Y, Jones KC. 2024. Comprehensive assessment of environmental emissions, fate, and risks of veterinary antibiotics in China: an environmental fate modeling approach. |
| [42] |
Chopra I, Roberts M. 2001. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. |
| [43] |
Sköld O. 2001. Resistance to trimethoprim and sulfonamides. |
| [44] |
Wang L, Wang J, Wang J, Zhu L, Yang L, et al. 2019. Distribution characteristics of antibiotic resistant bacteria and genes in fresh and composted manures of livestock farms. |
| [45] |
Dong Z, Wang J, Wang L, Zhu L, Wang J, et al. 2022. Distribution of quinolone and macrolide resistance genes and their co-occurrence with heavy metal resistance genes in vegetable soils with long-term application of manure. |
| [46] |
Wang F, Fu YH, Sheng HJ, Topp E, Jiang X, et al. 2021. Antibiotic resistance in the soil ecosystem: a One Health perspective. |
| [47] |
Zhang AN, Gaston JM, Dai CL, Zhao S, Poyet M, et al. 2021. An omics-based framework for assessing the health risk of antimicrobial resistance genes. |
| [48] |
Pajarillo EAB, Lee E, Kang DK. 2021. Trace metals and animal health: interplay of the gut microbiota with iron, manganese, zinc, and copper. |
| [49] |
Sun W, Qian X, Gu J, Wang XJ, Zhang L, et al. 2017. Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion. |
| [50] |
Wang C, Jia Y, Li J, Li P, Wang Y, et al. 2023. Influence of microbial augmentation on contaminated manure composting: metal immobilization, matter transformation, and bacterial response. |
| [51] |
Ge ZB, Chen MM, Xie WY, Huang K, Zhao FJ, et al. 2023. Natural microbial reactor-based sensing platform for highly sensitive detection of inorganic arsenic in rice grains. |
| [52] |
Qiu T, Huo L, Guo Y, Gao M, Wang G, et al. 2022. Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost. |
| [53] |
Wang Q, Gu J, Wang X, Ma J, Hu T, et al. 2020. Effects of nano-zerovalent iron on antibiotic resistance genes and mobile genetic elements during swine manure composting. |
| [54] |
Zhou Z, Song Z, Gu J, Wang X, Hu T, et al. 2022. Dynamics and key drivers of antibiotic resistance genes during aerobic composting amended with plant-derived and animal manure-derived biochars. |
| [55] |
Qiu X, Feng M, Zhou G, Wang H. 2022. Effects of mineral additives on antibiotic resistance genes and related mechanisms during chicken manure composting. |
| [56] |
Li N, Islam MT, Kang S. 2019. Secreted metabolite-mediated interactions between rhizosphere bacteria and Trichoderma biocontrol agents. |
| [57] |
Wu J, Zhou M, Zheng J, Feng S, Han Z, et al. 2026. Bacterial-fungal interactions shape the distribution of antibiotic resistance genes in soil-vegetable systems under organic fertilization. |
| [58] |
Ismaila AA, Ahmad K, Siddique Y, Wahab MAA, Kutawa AB, et al. 2023. Fusarium wilt of banana: current update and sustainable disease control using classical and essential oils approaches. |
| [59] |
Wang J, Ou Y, Li R, Tao C, Liu H, et al. 2024. The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil. |
| [60] |
Wang YF, Qiao M, Duan GL, Li G, Zhu D. 2021. Insights into the role of the fungal community in variations of the antibiotic resistome in the soil collembolan gut microbiome. |
| [61] |
Nazir R, Shen JP, Wang JT, Hu HW, He JZ. 2017. Fungal networks serve as novel ecological routes for enrichment and dissemination of antibiotic resistance genes as exhibited by microcosm experiments. |