| [1] |
Horn MA, Schramm A, Drake HL. 2003. The earthworm gut: an ideal habitat for ingested N2O-producing microorganisms. |
| [2] |
Fischer K, Hahn D, Hönerlage W, Zeyer J. 1997. Effect of passage through the gut of the earthworm Lumbricus terrestris L. on Bacillus megaterium studied by whole cell hybridization. |
| [3] |
Zeibich L, Guhl J, Drake HL. 2020. Impact of water content and dietary organic carbon richness on gut bacteria in the earthworm Lumbricus terrestris. |
| [4] |
Daniel O, Anderson JM. 1992. Microbial biomass and activity in contrasting soil materials after passage through the gut of the earthworm Lumbricus rubellus Hoffmeister. |
| [5] |
Aira M, Pérez-Losada M, Crandall KA, Domínguez J. 2022. Composition, structure and diversity of soil bacterial communities before, during and after transit through the gut of the earthworm Aporrectodea caliginosa. |
| [6] |
Berg M, Stenuit B, Ho J, Wang A, Parke C, et al. 2016. Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments. |
| [7] |
Chao H, Zhong L, Schaefer I, Sun M, Junggebauer A, et al. 2025. Litter quality modulates changes in bacterial and fungal communities during the gut transit of earthworm species of different ecological groups. |
| [8] |
Ludington WB. 2024. The importance of host physical niches for the stability of gut microbiome composition. |
| [9] |
Thakur SS, Lone AR, Tiwari N, Jain SK, Yadav S. 2021. Metagenomic exploration of bacterial community structure of earthworms’ gut. |
| [10] |
Zhang Q, Zhang Z, Lu T, Yu Y, Penuelas J, et al. 2021. Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants. |
| [11] |
Liebeke M, Strittmatter N, Fearn S, Morgan AJ, Kille P, et al. 2015. Unique metabolites protect earthworms against plant polyphenols. |
| [12] |
Du S, Lin D, Zhang TL, Chu HY, Zhu D. 2026. Earthworm gut’s potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size. |
| [13] |
Sizmur T, Richardson J. 2020. Earthworms accelerate the biogeochemical cycling of potentially toxic elements: results of a meta-analysis. |
| [14] |
Sun M, Chao H, Zheng X, Deng S, Ye M, et al. 2020. Ecological role of earthworm intestinal bacteria in terrestrial environments: a review. |
| [15] |
Zhou GW, Yang XR, Sun AQ, Li H, Lassen SB, et al. 2019. Mobile incubator for iron(III) reduction in the gut of the soil-feeding earthworm Pheretima guillelmi and interaction with denitrification. |
| [16] |
Zhu G, Schmidt O, Luan L, Xue J, Fan J, et al. 2022. Bacterial keystone taxa regulate carbon metabolism in the earthworm gut. |
| [17] |
Qian F, Lu F, Yang L, Li T. 2024. Cultivation of earthworms and analysis of associated bacterial communities during earthworms’ growth using two types of agricultural wastes. |
| [18] |
Wu Z, Nguyen D, Shrestha S, Raskin L, Khanal SK, et al. 2023. Evaluation of anaerobic digestion as a mechanism to explain surplus methane production in animal rumina and engineered digesters. |
| [19] |
da Silva Freitas L, de Lima Brum R, da Silva Bonifácio A, Volcão LM, da Silva Júnior FMR, et al. 2023. Assessment of the impact of ceftriaxone on the functional profile of soil microbiota using biolog EcoPlate™. |
| [20] |
Narciso A, Barra Caracciolo A, De Carolis C. 2023. Overview of direct and indirect effects of antibiotics on terrestrial organisms. |
| [21] |
Song J, Li T, Zheng Z, Fu W, Long Z, et al. 2022. Carbendazim shapes microbiome and enhances resistome in the earthworm gut. |
| [22] |
Zhang Y, Su JQ, Liao H, Breed MF, Yao H, et al. 2023. Increasing antimicrobial resistance and potential human bacterial pathogens in an invasive land snail driven by urbanization. |
| [23] |
Liu C, Yao H, Chapman SJ, Su J, Wang C. 2020. Changes in gut bacterial communities and the incidence of antibiotic resistance genes during degradation of antibiotics by black soldier fly larvae. |
| [24] |
Yu Z, Gillings M, Ashbolt NJ, Guo J. 2025. Antimicrobial resistance in complex microbiomes: ecological evolution and public health risks. |
| [25] |
Aminov RI. 2011. Horizontal gene exchange in environmental microbiota. |
| [26] |
Coyte KZ, Stevenson C, Knight CG, Harrison E, Hall JPJ, et al. 2022. Horizontal gene transfer and ecological interactions jointly control microbiome stability. |
| [27] |
Moura de Sousa J, Lourenço M, Gordo I. 2023. Horizontal gene transfer among host-associated microbes. |
| [28] |
Brune A, Frenzel P, Cypionka H. 2000. Life at the oxic–anoxic interface: microbial activities and adaptations. |
| [29] |
Wang Y, Bai Y, Shen L, Shang B, Ji Y, et al. 2025. The rhizosphere as a hotspot for nitrite- and nitrate-dependent anaerobic oxidation of methane in paddy fields. |
| [30] |
Ali MR, Chen Y, Li M, Jafir M, Ali MR, et al. 2026. Denitrifiers make great contribution to antibiotic resistance genes dissemination in the gut of earthworms. |
| [31] |
Borodovich T, Shkoporov AN, Ross RP, Hill C. 2022. Phage-mediated horizontal gene transfer and its implications for the human gut microbiome. |
| [32] |
Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. 2024. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. |
| [33] |
Fishbein SRS, Mahmud B, Dantas G. 2023. Antibiotic perturbations to the gut microbiome. |
| [34] |
Zhao X, Wu X, White JC, Tang Z, Wu F. 2023. Micro/nanoplastics contamination of the terrestrial environment: exposure routes, dose, and co-contaminants complicate the risk calculus. |
| [35] |
Seiler C, Berendonk TU. 2012. Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture. |
| [36] |
Yu X, Tu Q, Liu J, Peng Y, Wang C, et al. 2023. Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes. |
| [37] |
Balcázar JL, Subirats J, Borrego CM. 2015. The role of biofilms as environmental reservoirs of antibiotic resistance. |
| [38] |
Hou R, Jin X, Feng J, Xue J, Chen C, et al. 2025. Deciphering the universal role of gut microbiota in pollutant transformation. |
| [39] |
Pant A, Maiti TK, Mahajan D, Das B. 2023. Human gut microbiota and drug metabolism. |
| [40] |
Quagliariello A, Ramiro RS, Couce A, Martino ME. 2022. Editorial: Integrating multi-scale approaches for predicting microbiome ecology and evolution. |
| [41] |
Zhou Z, Huang F, Chen L, Liu F, Wang B, et al. 2024. Effects of antibiotics on microbial nitrogen cycling and N2O emissions: a review. |
| [42] |
Gómez-Brandón M, Aira M, Probst M, Liu N, Zhang Z, et al. 2025. Earthworms attenuate antibiotic resistance genes and mobile genetic elements during vermicomposting of sewage sludge. |
| [43] |
Drake HL, Horn MA. 2007. As the worm turns: the earthworm gut as a transient habitat for soil microbial biomes. |
| [44] |
Krišrtu̇ek V, Ravasz K, Pižl V. 1992. Changes in densities of bacteria and microfungi during gut transit in Lumbricus rubellus and Aporrectodea caliginosa (Oligochaeta: Lumbricidae). |
| [45] |
Bahrndorff S, Alemu T, Alemneh T, Lund Nielsen J. 2016. The microbiome of animals: implications for conservation biology. |
| [46] |
Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. 2008. Worlds within worlds: evolution of the vertebrate gut microbiota. |
| [47] |
Malik AA, Martiny JBH, Brodie EL, Martiny AC, Treseder KK, et al. 2020. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. |
| [48] |
McQueen JP, Gattoni K, Gendron EMS, Schmidt SK, Sommers P, et al. 2022. Host identity is the dominant factor in the assembly of nematode and tardigrade gut microbiomes in Antarctic Dry Valley streams. |
| [49] |
Borch T, Kretzschmar R, Kappler A, Cappellen PV, Ginder-Vogel M, et al. 2010. Biogeochemical redox processes and their impact on contaminant dynamics. |
| [50] |
Wilson SJ, Megonigal JP. 2025. Nitrate reduction across soils transitioning from coastal forest to wetland are hotspots for denitrification. |
| [51] |
Zhang S, Huangfu Q, Boyle J, Wu L, Song J, et al. 2025. Hotspots and dynamics of dissolved thallium species at oxic–anoxic interfaces in flooded soils. |
| [52] |
Marschner P. 2021. Processes in submerged soils – linking redox potential, soil organic matter turnover and plants to nutrient cycling. |
| [53] |
Archer DE, Morford JL, Emerson SR. 2002. A model of suboxic sedimentary diagenesis suitable for automatic tuning and gridded global domains. |
| [54] |
Blackburn ND, Henry Blackburn T. 1993. A reaction diffusion model of C-N-S-O species in a stratified sediment. |
| [55] |
Liesack W, Schnell S, Revsbech NP. 2000. Microbiology of flooded rice paddies. |
| [56] |
Frindte K, Allgaier M, Grossart HP, Eckert W. 2015. Microbial response to experimentally controlled redox transitions at the sediment water interface. |
| [57] |
Corzo A, Jiménez-Arias JL, Torres E, García-Robledo E, Lara M, et al. 2018. Biogeochemical changes at the sediment–water interface during redox transitions in an acidic reservoir: exchange of protons, acidity and electron donors and acceptors. |
| [58] |
Carrera J, Saaltink MW, Soler-Sagarra J, Wang J, Valhondo C. 2022. Reactive transport: a review of basic concepts with emphasis on biochemical processes. |
| [59] |
Seaman JC, Chang H, Goldberg S, Šimůnek J. 2012. Reactive transport modeling. |
| [60] |
Jung H, Meile C. 2019. Upscaling of microbially driven first-order reactions in heterogeneous porous media. |
| [61] |
Feng R, Duan L, Shen S, Cheng Y, Wang Y, et al. 2023. Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community. |
| [62] |
Li Z, Fu J, Hu J, Li T, Xu Y. 2026. Sediment–water interface reoxygenation by NO3–LDH promotes tetracycline degradation in sediments and modulates antibiotic resistance gene dynamics. |
| [63] |
Li M, Da Y, Rafraf Ali M, Wu H, Zhou G. 2026. Insight into the role of iron(III)-reducing microflora in the arsenic biogeochemistry of earthworm (Pheretima guillemi) guts. |
| [64] |
Chapuis-Lardy L, Brossard M, Lavelle P, Schouller E. 1998. Phosphorus transformations in a ferralsol through ingestion by Pantoscolex corethrurus, a geophagous earthworm. |
| [65] |
Biswas JK, Banerjee A, Rai M, Naidu R, Biswas B, et al. 2018. Potential application of selected metal resistant phosphate solubilizing bacteria isolated from the gut of earthworm (Metaphire posthuma) in plant growth promotion. |
| [66] |
Munhoz DR, Meng K, Wang L, Lwanga EH, Geissen V, et al. 2024. Exploring the potential of earthworm gut bacteria for plastic degradation. |
| [67] |
Tian H, Zheng C, Huang X, Qi C, Li B, et al. 2024. Effects of farmland residual mulch film-derived microplastics on the structure and function of soil and earthworm Metaphire guillelmi gut microbiota. |
| [68] |
Andriuzzi WS, Ngo PT, Geisen S, Keith AM, Dumack K, et al. 2016. Organic matter composition and the protist and nematode communities around anecic earthworm burrows. |
| [69] |
Huang W, González G, Zou X. 2020. Earthworm abundance and functional group diversity regulate plant litter decay and soil organic carbon level: a global meta-analysis. |
| [70] |
Feng J, Li B, Jiang X, Yang Y, Wells GF, et al. 2018. Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. |
| [71] |
Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, et al. 2023. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. |
| [72] |
Li Z, Yang F, Yang M, Yan R, Zhang K. 2025. The mechanisms of tetracycline in shaping antibiotic resistance gene dynamics in earthworm casts during vermicomposting. |
| [73] |
Li L, Zhao J, Liu C, Deng Y, Du Y, et al. 2025. Spatial differentiation of heavy metals/metalloids, microbial risk genes and soil microbiota in a sulfur-contaminated landscape. |
| [74] |
Owagboriaye F, Mesnage R, Dedeke G, Adegboyega T, Aladesida A, et al. 2021. Impacts of a glyphosate-based herbicide on the gut microbiome of three earthworm species (Alma millsoni, Eudrilus eugeniae and Libyodrilus violaceus): a pilot study. |
| [75] |
Brantschen J, Gygax S, Mestrot A, Frossard A. 2020. Soil Hg contamination impact on earthworms’ gut microbiome. |
| [76] |
Liu L, Sun Y, Du S, Li Y, Wang J. 2024. Nanoplastics promote the dissemination of antibiotic resistance genes and diversify their bacterial hosts in soil. |
| [77] |
Shi Z, Xiong L, Li Z, Shah F, Zhou X, et al. 2025. Long-term exposure to polyethylene restructures the multi-kingdom soil microbiota in maize fields. |
| [78] |
Tang KHD. 2025. Combined toxicity of microplastics and antimicrobials on animals: a review. |
| [79] |
Zhang H, Zhang X, Sun H, Ling H, Xie R, et al. 2025. Polyvinyl chloride microplastic triggers bidirectional transmission of antibiotic resistance genes in soil-earthworm systems. |
| [80] |
Zhu D, Zheng F, Chen QL, Yang XR, Christie P, et al. 2018. Exposure of a soil collembolan to Ag nanoparticles and AgNO3 disturbs its associated microbiota and lowers the incidence of antibiotic resistance genes in the gut. |
| [81] |
Miller JH, Novak JT, Knocke WR, Young K, Hong Y, et al. 2013. Effect of silver nanoparticles and antibiotics on antibiotic resistance genes in anaerobic digestion. |
| [82] |
Yonathan K, Mann R, Mahbub KR, Gunawan C. 2022. The impact of silver nanoparticles on microbial communities and antibiotic resistance determinants in the environment. |
| [83] |
Barancheshme F, Munir M. 2017. Strategies to combat antibiotic resistance in the wastewater treatment plants. |
| [84] |
Murray LM, Hayes A, Snape J, Kasprzyk-Hordern B, Gaze WH, et al. 2024. Co-selection for antibiotic resistance by environmental contaminants. |
| [85] |
Di Cesare A, Eckert E, Corno G. 2016. Co-selection of antibiotic and heavy metal resistance in freshwater bacteria. |
| [86] |
Abilda Z, Isgandarov I, Kanat R, Daurov D, Sapakhova Z, et al. 2026. Genome-resolved metagenomics reveals co-selection of antibiotic and metal resistance in chronically polluted industrial soils. |
| [87] |
Blanco P, Hernando-Amado S, Reales-Calderon JA, Corona F, Lira F, et al. 2016. Bacterial multidrug efflux pumps: much more than antibiotic resistance determinants. |
| [88] |
Marini E, De Bernardi A, Tagliabue F, Casucci C, Tiano L, et al. 2024. Copper toxicity on Eisenia fetida in a vineyard soil: a combined study with standard tests, genotoxicity assessment and gut metagenomic analysis. |
| [89] |
Rong W, Wei Y, Chen Y, Huang L, Huang S, et al. 2024. 16S rRNA sequencing analysis uncovers dose-dependent cupric chloride effects on silkworm gut microbiome composition and diversity. |
| [90] |
Xia R, Shi Y, Wang X, Wu Y, Sun M, et al. 2022. Metagenomic sequencing reveals that the assembly of functional genes and taxa varied highly and lacked redundancy in the earthworm gut compared with soil under vanadium stress. |
| [91] |
Xia R, Sun M, Balcázar JL, Yu P, Hu F, et al. 2023. Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes. |
| [92] |
Marie JS, Mays C, Guo B, Radniecki TS, Waite-Cusic J, et al. 2024. Impact of biosolids amendment on the soil resistome and microbiome – a greenhouse study. |
| [93] |
van den Broek S, Nybom I, Conz RF, Sun Y, Bucheli TD, et al. 2025. Soil microbial and plant responses to increasing antibiotic concentration: a case study of five antibiotics. |
| [94] |
Zhang Y, Li HZ, Breed M, Tang Z, Cui L, et al. 2025. Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails. |
| [95] |
Rillig MC, Ziersch L, Hempel S. 2017. Microplastic transport in soil by earthworms. |
| [96] |
Zhu D, Delgado-Baquerizo M, Su JQ, Ding J, Li H, et al. 2021. Deciphering potential roles of earthworms in mitigation of antibiotic resistance in the soils from diverse ecosystems. |
| [97] |
Xue R, Zhang Y, Li H, Li J, Ke W, et al. 2026. Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection. |
| [98] |
Wang C, Wang L, Ok YS, Tsang DCW, Hou D. 2022. Soil plastisphere: exploration methods, influencing factors, and ecological insights. |
| [99] |
Wang K, Wang F, Yu Y, Yang S, Han Y, et al. 2025. Microplastics and soil microbiomes. |
| [100] |
Wei H, Wu L, Liu Z, Saleem M, Chen X, et al. 2022. Meta-analysis reveals differential impacts of microplastics on soil biota. |
| [101] |
Yang B, Wu L, Feng W, Lin Q. 2024. Global perspective of ecological risk of plastic pollution on soil microbial communities. |
| [102] |
Yang L, Zhang Y, Kang S, Wang Z, Wu C. 2021. Microplastics in soil: a review on methods, occurrence, sources, and potential risk. |
| [103] |
Holzinger A, Hink L, Sehl E, Rüppel N, Lehndorff E, et al. 2023. Biodegradable polymers boost reproduction in the earthworm Eisenia fetida. |
| [104] |
Huerta Lwanga E, Thapa B, Yang X, Gertsen H, Salánki T, et al. 2018. Decay of low-density polyethylene by bacteria extracted from earthworm's guts: a potential for soil restoration. |
| [105] |
Peng BY, Su Y, Chen Z, Chen J, Zhou X, et al. 2019. Biodegradation of polystyrene by dark (Tenebrio obscurus) and yellow (Tenebrio molitor) mealworms (Coleoptera: Tenebrionidae). |
| [106] |
Sanchez-Hernandez JC, Capowiez Y, Ro KS. 2020. Potential use of earthworms to enhance decaying of biodegradable plastics. |
| [107] |
Yang Y, Wang J, Xia M. 2020. Biodegradation and mineralization of polystyrene by plastic-eating superworms Zophobas atratus. |
| [108] |
Zrimec J, Kokina M, Jonasson S, Zorrilla F, Zelezniak A. 2021. Plastic-degrading potential across the global microbiome correlates with recent pollution trends. |
| [109] |
Gao T, Jiang Y, Han Y, Wāng Y. 2026. Intestinal microplastic debris, flora dysbiosis, and insidious combined hazards across diverse aquatic and terrestrial organisms. |
| [110] |
Lin D, Yang G, Dou P, Qian S, Zhao L, et al. 2020. Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment. |
| [111] |
Papazlatani C, Garbeva P, Huerta Lwanga E. 2024. Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms. |
| [112] |
Qiu X, Qi Z, Ouyang Z, Liu P, Guo X. 2022. Interactions between microplastics and microorganisms in the environment: modes of action and influencing factors. |
| [113] |
Wu L, Zhou X, Lai C, Ma M, Qin L, et al. 2026. Microplastics–pollutant interactions in environmental systems: mechanisms, ecological effects, and implications for sustainable management. |
| [114] |
Wang F, Fu YH, Sheng HJ, Topp E, Jiang X, et al. 2021. Antibiotic resistance in the soil ecosystem: a One Health perspective. |
| [115] |
Gao C, Bezemer TM, de Vries FT, van Bodegom PM. 2024. Trade-offs in soil microbial functions and soil health in agroecosystems. |
| [116] |
Taylor AR, Taylor AFS. 2014. Assessing daily egestion rates in earthworms: using fungal spores as a natural soil marker to estimate gut transit time. |
| [117] |
Prieto R, Zou A, Sampedro L, Whyte LG, Driscoll BT, et al. 2026. Earthworm gut possesses unique nosZ sequences for complete denitrification. |
| [118] |
Cui HX, Bi QF, Ye J, Li YC, Liao H, et al. 2026. Horizontal gene transfer between bacteriophages and their hosts is a key factor in the bloom of antibiotic resistance genes in Metaphire californica. |
| [119] |
Adomako MO, Wu J, Yu FH. 2025. Ecological and evolutionary responses of earthworm holobionts to environmental changes. |
| [120] |
Berg G, Antonietti M, Egamberdieva D, Korsten L, Wicaksono WA. 2026. Microbiome-inspired solutions to save human and planetary health. |
| [121] |
Berg G, Dorador C, Egamberdieva D, Kostka JE, Ryu CM, et al. 2024. Shared governance in the plant holobiont and implications for one health. |
| [122] |
Dang F, Wang Q, Huang Y, Wang Y, Xing B. 2022. Key knowledge gaps for One Health approach to mitigate nanoplastic risks. |
| [123] |
Diner RE, Allard SM, Gilbert JA. 2024. Host-associated microbes mitigate the negative impacts of aquatic pollution. |
| [124] |
García G, Carlin M, Cano RJ. 2025. Holobiome harmony: linking environmental sustainability, agriculture, and human health for a thriving planet and One Health. |
| [125] |
Gigl F, Abdullahi M, Benkwitz-Bedford S, Eastwood N, Zhou J, et al. 2026. Challenging evolutionary paradigms: Daphnia populations resurrected from unpolluted environments show enhanced detoxification ability to aromatic pollutants. |
| [126] |
Perković S, Paul C, Vasić F, Helming K. 2022. Human health and soil health risks from heavy metals, micro(nano)plastics, and antibiotic resistant bacteria in agricultural soils. |
| [127] |
Suthar S. 2010. Pilot-scale vermireactors for sewage sludge stabilization and metal remediation process: comparison with small-scale vermireactors. |
| [128] |
Gajalakshmi S, Ramasamy EV, Abbasi SA. 2001. Assessment of sustainable vermiconversion of water hyacinth at different reactor efficiencies employing Eudrilus eugeniae Kinberg. |
| [129] |
Enebe MC, Erasmus M. 2023. Vermicomposting technology - a perspective on vermicompost production technologies, limitations and prospects. |