Unlocking soil food webs for pollution remediation: A cross-trophic systems perspective

Abstract

Soil pollution is a defining feature of the Anthropocene. Industrial emissions, intensive agriculture, and waste mismanagement have loaded soils with heavy metals, legacy organics, microplastics, and other novel entities at levels that threaten biodiversity, food security, and human health. Meanwhile, climate change and land-use intensification alter soil temperature and moisture, creating complex multi-stressor conditions that conventional controlled single-variable tests rarely capture. 1) We argue that soil food webs spanning microbes, microfauna, mesofauna, and macrofauna constitute core living infrastructure for remediation and ecological risk assessment. 2) Building on recent advances, we synthesize evidence that cross-trophic interactions regulate the fate of organic pollutants, metals, and emerging contaminants, and that chemical stressors together with climate-driven shifts in temperature and moisture can reshape food-web structure, energy channels, and stability. 3) We outline how food web metrics and bioindicators can be operationalized to guide remediation design and ecological risk assessment. We propose that diverse, functionally redundant, and well-connected food webs provide resilience that buffers contaminant pulses while sustaining nutrient cycling. Realizing this potential requires trait-based multitrophic research aided by omics, synthetic biology, network analysis, and big data modeling to embed food web principles into nature-based remediation and governance.

Graphical abstract

Keywords

soil food web / bioremediation / resilience / chemical pollution / emerging contaminants / ecosystem multifunctionality

Highlight

	● Cross trophic soil food webs function as living infrastructure for remediation.
	● Ecological resilience emerges from diverse, redundant, and well-connected networks.
	● Network metrics provide early warning and design targets for field interventions.
	● Multi omics and synthetic community enable precise multitrophic nature-based remediation.

References

[1] Adams, G.O., Fufeyin, P.T., Okoro, S.E., Ehinomen, I., 2015. Bioremediation, biostimulation and bioaugmention: a review. International Journal of Environmental Bioremediation & Biodegradation3, 28–39.

[2] Aderjan, E., Wagenhoff, E., Kandeler, E., Moser, T., 2023. Natural soils in OECD 222 testing — influence of soil water and soil properties on earthworm reproduction toxicity of carbendazim. Ecotoxicology32, 403–415.

[3] Ai, S.H., Gao, X.Y., Wang, X.N., Li, J., Fan, B., Zhao, S.Q., Liu, Z.T., 2021. Exposure and tiered ecological risk assessment of phthalate esters in the surface water of Poyang Lake, China. Chemosphere262, 127864.

[4] Alidoosti, F., Giyahchi, M., Moien, S., Moghimi, H., 2024. Unlocking the potential of soil microbial communities for bioremediation of emerging organic contaminants: omics-based approaches. Microbial Cell Factories23, 210.

[5] Amacker, N., Gao, Z.L., Hu, J., Jousset, A.L.C., Kowalchuk, G.A., Geisen, S., 2022. Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities. FEMS Microbiology Ecology98, fiac057.

[6] Aparicio, J.D., Raimondo, E.E., Saez, J.M., Costa-Gutierrez, S.B., Álvarez, A., Benimeli, C.S., Polti, M.A., 2022. The current approach to soil remediation: a review of physicochemical and biological technologies, and the potential of their strategic combination. Journal of Environmental Chemical Engineering10, 107141.

[7] Bardgett, R.D., van der Putten, W.H., 2014. Belowground biodiversity and ecosystem functioning. Nature515, 505–511.

[8] Bellini, B.C., Weiner, W.M., Winck, B.R., 2023. Systematics, ecology and taxonomy of collembola: introduction to the special issue. Diversity15, 221.

[9] Borchert, E., Hammerschmidt, K., Hentschel, U., Deines, P., 2021. Enhancing microbial pollutant degradation by integrating eco-evolutionary principles with environmental biotechnology. Trends in Microbiology29, 908–918.

[10] Briones, M.J.I., 2018. The serendipitous value of soil fauna in ecosystem functioning: the unexplained explained. Frontiers in Environmental Science6, 149.

[11] Broerse, M., Oorsprong, H., van Gestel, C.A.M., 2012. Cadmium affects toxicokinetics of pyrene in the collembolan Folsomia candida. Ecotoxicology21, 795–802.

[12] Burian, A., Pinn, D., Peralta-Maraver, I., Sweet, M., Mauvisseau, Q., Eyice, O., Bulling, M., Röthig, T., Kratina, P., 2022. Predation increases multiple components of microbial diversity in activated sludge communities. The ISME Journal16, 1086–1094.

[13] Cachada, A., Rocha-Santos, T., Duarte, A.C., 2018. Soil and pollution: an introduction to the main issues. In: Duarte, A.C., Cachada, A. Rocha-Santos, T., eds. Soil Pollution. London: Academic Press, 1–28.

[14] Charan, K., Bhattacharyya, P., Bhattacharya, S.S., 2024. Vermitechnology transforms hazardous red mud into benign organic input for agriculture: insights on earthworm-microbe interaction, metal removal, and soil-crop improvement. Journal of Environmental Management354, 120320.

[15] Chen, J., Xia, X.H., Zhang, Z.R., Wen, W., Xi, N.N., Zhang, Q.R., 2020. The combination of warming and copper decreased the uptake of polycyclic aromatic hydrocarbons by spinach and their associated cancer risk. Science of the Total Environment727, 138732.

[16] Correa-Garcia, S., Corelli, V., Tremblay, J., Dozois, J.A., Mukula, E., Séguin, A., Yergeau, E., 2023. Soil fauna-microbial interactions shifts fungal and bacterial communities under a contamination disturbance. PLoS One18, e0292227.

[17] Correa-García, S., Pande, P., Séguin, A., St-Arnaud, M., Yergeau, E., 2018. Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation. Microbial Biotechnology11, 819–832.

[18] da Silva, I.G.S., de Almeida, F.C.G., da Rocha e Silva, N.M.P., Casazza, A.A., Converti, A., Sarubbo, L.A., 2020. Soil bioremediation: overview of technologies and trends. Energies13, 4664.

[19] Dai, W., Liu, M.Q., Wang, N., Ye, X.F., Liu, Y., Yao, D.D., Wang, L., Cui, Z.L., Yan, P.R., Cheng, C.X., Huang, Z.L., Wang, H., 2023. Positive contribution of predatory bacterial community to multiple nutrient cycling and microbial network complexity in arsenic-contaminated soils. Applied Soil Ecology185, 104792.

[20] Das, D., Baruah, R., Sarma Roy, A., Singh, A.K., Deka Boruah, H.P.D., Kalita, J., Bora, T.C., 2015. Complete genome sequence analysis of Pseudomonas aeruginosa N002 reveals its genetic adaptation for crude oil degradation. Genomics105, 182–190.

[21] de Bello, F., Lavorel, S., Hallett, L.M., Valencia, E., Garnier, E., Roscher, C., Conti, L., Galland, T., Goberna, M., Májeková, M., Montesinos-Navarro, A., Pausas, J.G., Verdú, M., E-Vojtkó, A., Götzenberger, L., Lepš, J., 2021. Functional trait effects on ecosystem stability: assembling the jigsaw puzzle. Trends in Ecology & Evolution36, 822–836.

[22] De la Vega-Camarillo, E., Arreola-Vargas, J., Antony-Babu, S., Mathur, S.K., Santos, J.A., Shim, W.B., 2025. Machine learning-guided synthetic microbial communities enable functional and sustainable degradation of persistent environmental pollutants. bioRxiv, 2025–092025–09.

[23] de Ruijter, V.N., Redondo-Hasselerharm, P.E., Gouin, T., Koelmans, A.A., 2020. Quality criteria for microplastic effect studies in the context of risk assessment: a critical review. Environmental Science & Technology54, 11692–11705.

[24] De Silva, S., Carson, P., Indrapala, D.V., Warwick, B., Reichman, S.M., 2023. Land application of industrial wastes: impacts on soil quality, biota, and human health. Environmental Science and Pollution Research30, 67974–67996.

[25] de Vries, F.T., Thébault, E., Liiri, M., Birkhofer, K., Tsiafouli, M.A., Bjørnlund, L., Bracht Jørgensen, H., Brady, M.V., Christensen, S., De Ruiter, P.C., D’Hertefeldt, T., Frouz, J., Hedlund, K., Hemerik, L., Hol, W.H.G., Hotes, S., Mortimer, S.R., Setälä, H., Sgardelis, S.P., Uteseny, K., van der Putten, W.H., Wolters, V., Bardgett, R.D., 2013. Soil food web properties explain ecosystem services across European land use systems. Proceedings of the National Academy of Sciences of the United States of America110, 14296–14301.

[26] Del Signore, A., Hendriks, A.J., Lenders, H.J.R., Leuven, R.S.E.W., Breure, A.M., 2016. Development and application of the SSD approach in scientific case studies for ecological risk assessment. Environmental Toxicology and Chemistry35, 2149–2161.

[27] Du, J.Q., Jia, T., Liu, J.X., Chai, B.F., 2024. Relationships among protozoa, bacteria and fungi in polycyclic aromatic hydrocarbon-contaminated soils. Ecotoxicology and Environmental Safety270, 115904.

[28] Du, S., Li, X.Q., Hao, X.L., Hu, H.W., Feng, J., Huang, Q.Y., Liu, Y.R., 2022. Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems. ISME Communications2, 69.

[29] Du, Y.B., Yu, C.H., Sun, Z.H., Liu, Y.J., Liu, X.X., Feng, Y., Wang, H.T., Zhou, J., Li, X.H., 2025. Soil resource availability regulates the response of micro-food web multitrophic interactions to heavy metal contamination. Environmental Research273, 121222.

[30] Ernst, G., Amorim, M.J.B., Bottoms, M., Brooks, A.C., Hodson, M.E., Kimmel, S., Kotschik, P., Marx, M.T., Natal-da-Luz, T., Pelosi, C., Pieper, S., Schimera, A., Scott-Fordsmand, J., Sharples, A., Sousa, J.P., van Gestel, C.A.M., van Hall, B., Bergtold, M., 2024. Intermediate-tier options in the environmental risk assessment of plant protection products for soil invertebrates—Synthesis of a workshop. Integrated Environmental Assessment and Management20, 780–793.

[31] European Parliament, Council, 2025. Directive (EU) 2025/2360 of the European Parliament and of the Council of 12 November 2025 on Soil Monitoring and Resilience (Soil Monitoring Law). Official Journal of the European Union 2025/2360, 26 November 2025.

[32] Fierer, N., 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology15, 579–590.

[33] Frouz, J., 2018. Effects of soil macro-and mesofauna on litter decomposition and soil organic matter stabilization. Geoderma332, 161–172.

[34] Gao, M.L., Bai, L.S., Xiao, L., Peng, H.C., Chen, Q.T., Qiu, W.W., Song, Z.G., 2024. Micro (nano) plastics and phthalate esters drive endophytic bacteria alteration and inhibit wheat root growth. Science of the Total Environment906, 167734.

[35] Gao, S.H., Fu, Y.B., Peng, X.Y., Ma, S.L., Liu, Y.R., Chen, W.L., Huang, Q.Y., Hao, X.L., 2025. Microplastics trigger soil dissolved organic carbon and nutrient turnover by strengthening microbial network connectivity and cross-trophic interactions. Environmental Science & Technology59, 5596–5606.

[36] Geisen, S., Mitchell, E.A.D., Adl, S., Bonkowski, M., Dunthorn, M., Ekelund, F., Fernández, L.D., Jousset, A., Krashevska, V., Singer, D., Spiegel, F.W., Walochnik, J., Lara, E., 2018. Soil protists: a fertile frontier in soil biology research. FEMS Microbiology Reviews42, 293–323.

[37] Guden, R.M., Haegeman, A., Ruttink, T., Moens, T., Derycke, S., 2024. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: a metatranscriptomic approach. Molecular Ecology33, e17331.

[38] Guerra, C.A., Bardgett, R.D., Caon, L., Crowther, T.W., Delgado-Baquerizo, M., Montanarella, L., Navarro, L.M., Orgiazzi, A., Singh, B.K., Tedersoo, L., Vargas-Rojas, R., Briones, M.J.I., Buscot, F., Cameron, E.K., Cesarz, S., Chatzinotas, A., Cowan, D.A., Djukic, I., van den Hoogen, J., Lehmann, A., Maestre, F.T., Marín, C., Reitz, T., Rillig, M.C., Smith, L.C., De Vries, F.T., Weigelt, A., Wall, D.H., Eisenhauer, N., 2021. Tracking, targeting, and conserving soil biodiversity. Science371, 239–241.

[39] Guerra, C.A., Heintz-Buschart, A., Sikorski, J., Chatzinotas, A., Guerrero-Ramírez, N., Cesarz, S., Beaumelle, L., Rillig, M.C., Maestre, F.T., Delgado-Baquerizo, M., Buscot, F., Overmann, J., Patoine, G., Phillips, H.R.P., Winter, M., Wubet, T., Küsel, K., Bardgett, R.D., Cameron, E.K., Cowan, D., Grebenc, T., Marín, C., Orgiazzi, A., Singh, B.K., Wall, D.H., Eisenhauer, N., 2020. Blind spots in global soil biodiversity and ecosystem function research. Nature Communications11, 3870.

[40] Haimi, J., Mätäsniemi, L., 2002. Soil decomposer animal community in heavy-metal contaminated coniferous forest with and without liming. European Journal of Soil Biology38, 131–136.

[41] Hale, R.C., Seeley, M.E., La Guardia, M.J., Mai, L., Zeng, E.Y., 2020. A global perspective on microplastics. Journal of Geophysical Research: Oceans125, e2018JC014719.

[42] Han, J., Jiang, Z.Y., Li, P.F., Wang, J., Zhou, X., 2025. Contamination of phthalic acid esters in china's agricultural soils: sources, risk, and control strategies. Agronomy15, 433.

[43] Hickman, Z.A., Reid, B.J., 2008. Increased microbial catabolic activity in diesel contaminated soil following addition of earthworms (Dendrobaena veneta) and compost. Soil Biology and Biochemistry40, 2970–2976.

[44] Huang, C.X., Zhao, W.J., Ren, H.L., Wu, R., Liu, Y., Xu, H.X., Sun, B.H., Shi, J.L., Tian, X.H., Yin, R., 2025. Earthworms mitigate drought effects on microbial decomposition of straw under varying microplastic conditions. Journal of Hazardous Materials495, 139108.

[45] Islam, M.N., Park, J.H., 2025. Predicting PAHs removal from contaminated soil via subcritical water extraction using support vector regression. Environmental Engineering Research30, 240122.

[46] Joimel, S., Potapov, A., Pey, B., Bonfanti, J., Cortet, J., De Almeida, T., Di Lonardo, S., Hackenberger, D.K., Krogh, P.H., Laskowski, R., Loureiro, S., Hedde, M., 2024. Trait concepts, categories, and databases in soil invertebrate ecology–ordering the mess. Soil Organisms96, 151–166.

[47] Kaur, P., Bali, S., Sharma, A., Vig, A.P., Bhardwaj, R., 2017. Effect of earthworms on growth, photosynthetic efficiency and metal uptake in Brassica juncea L. plants grown in cadmium-polluted soils. Environmental Science Pollution Research24, 13452–13465.

[48] Kim, O.H., Chang, E.S., Kang, H.N., Lee, H.J., 2025. Unveiling the impact of microplastics: a perspective on size, shape, and composition in human health. Molecular & Cellular Toxicology21, 997–1006.

[49] Kumari, S., Das, S., 2023. Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations. Environmental Science and Pollution Research30, 79676–79705.

[50] Kuzyakov, Y., Blagodatskaya, E., 2015. Microbial hotspots and hot moments in soil: concept & review. Soil Biology and Biochemistry83, 184–199.

[51] Li, X.L., Wu, S.H., Dong, Y.Z., Fan, H.N., Bai, Z.H., Zhuang, X.L., 2021. Engineering microbial consortia towards bioremediation. Water13, 2928.

[52] Liang, Y., Ma, A.Z., Zhuang, G.Q., 2022. Construction of environmental synthetic microbial consortia: based on engineering and ecological principles. Frontiers in Microbiology13, 829717.

[53] Liang, Y., Meggo, R., Hu, D.F., Schnoor, J.L., Mattes, T.E., 2014. Enhanced polychlorinated biphenyl removal in a switchgrass rhizosphere by bioaugmentation with Burkholderia xenovorans LB400. Ecological Engineering71, 215–222.

[54] Lin, D.M., Yang, G.R., Dou, P.P., Qian, S.H., Zhao, L., Yang, Y.C., Fanin, N., 2020. Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment. Proceedings of the Royal Society B: Biological Sciences287, 20201268.

[55] Liu, C., Wang, Y.J., Zhou, Z.Y., Wang, S.M., Wei, Z., Ravanbakhsh, M., Shen, Q.R., Xiong, W., Kowalchuk, G.A., Jousset, A., 2024. Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions. The ISME Journal18, wrae169.

[56] Liu, M.L., Wang, C., Zhu, B., 2023. Drought alleviates the negative effects of microplastics on soil micro-food web complexity and stability. Environmental Science & Technology57, 11206–11217.

[57] Liu, S.J., Chen, J., Gan, W.J., Fu, S.L., Schaefer, D., Gan, J.M., Yang, X.D., 2016. Cascading effects of spiders on a forest-floor food web in the face of environmental change. Basic and Applied Ecology17, 527–534.

[58] Liu, T., Chen, X.Y., Gong, X., Lubbers, I.M., Jiang, Y.Y., Feng, W., Li, X.P., Whalen, J.K., Bonkowski, M., Griffiths, B.S., Hu, F., Liu, M.Q., 2019. Earthworms coordinate soil biota to improve multiple ecosystem functions. Current Biology29, 3420–3429.e5.

[59] Liu, Y.R., Wen, S.H., Singh, B.K., Zhang, W., Liu, Z.W., Hao, X.L., Hao, Y.Y., Delgado-Baquerizo, M., Tan, W.F., Huang, Q.Y., Rillig, M.C., Zhu, Y.G., 2025. Vulnerability of soil food webs to chemical pollution and climate change. Nature Ecology & Evolution9, 1112–1119.

[60] Lu, S.Y., Brown, R.W., Li, M.Y., Chen, M.Y., Huang, C.D., Lian, J.P., Wu, D.H., Jones, D.L., 2025. Soil application of PE and PLA microplastics alter earthworm (Eisenia nordenskioldi) gut bacterial community and soil microbiome-metabolome dynamics. Environmental Pollution383, 126895.

[61] Lu, S.Y., Wei, S.T., Li, M.Y., Chadwick, D.R., Xie, M.M., Wu, D.H., Jones, D.L., 2024. Earthworms alleviate microplastics stress on soil microbial and protist communities. Science of the Total Environment948, 174945.

[62] Lv, J., Wang, L., 2025. Hybrid modeling of adsorption process using mass transfer and machine learning techniques for concentration prediction. Journal of Saudi Chemical Society29, 12.

[63] Lwanga, E.H., Gertsen, H., Gooren, H., Peters, P., Salánki, T., van der Ploeg, M., Besseling, E., Koelmans, A.A., Geissen, V., 2016. Microplastics in the terrestrial ecosystem: implications for Lumbricus terrestris (Oligochaeta, Lumbricidae). Environmental Science & Technology50, 2685–2691.

[64] Maddela, N.R., Ramakrishnan, B., Kakarla, D., Venkateswarlu, K., Megharaj, M., 2022. Major contaminants of emerging concern in soils: a perspective on potential health risks. RSC Advances12, 12396–12415.

[65] Margesin, R., Schinner, F., 2001. Bioremediation (natural attenuation and biostimulation) of diesel-oil-contaminated soil in an alpine glacier skiing area. Applied and Environmental Microbiology67, 3127–3133.

[66] Mazzola, M., de Bruijn, I., Cohen, M.F., Raaijmakers, J.M., 2009. Protozoan-induced regulation of cyclic lipopeptide biosynthesis is an effective predation defense mechanism for Pseudomonas fluorescens. Applied and Environmental Microbiology75, 6804–6811.

[67] Megharaj, M., Ramakrishnan, B., Venkateswarlu, K., Sethunathan, N., Naidu, R., 2011. Bioremediation approaches for organic pollutants: a critical perspective. Environment International37, 1362–1375.

[68] Meng, K., Lwanga, E.H., van der Zee, M., Munhoz, D.R., Geissen, V., 2023. Fragmentation and depolymerization of microplastics in the earthworm gut: a potential for microplastic bioremediation. Journal of Hazardous Materials447, 130765.

[69] Meyer, H., Pebesma, E., 2022. Machine learning-based global maps of ecological variables and the challenge of assessing them. Nature Communications13, 2208.

[70] Mishra, B., Varjani, S., Kumar, G., Awasthi, M.K., Awasthi, S.K., Sindhu, R., Binod, P., Rene, E.R., Zhang, Z.Q., 2021. Microbial approaches for remediation of pollutants: innovations, future outlook, and challenges. Energy & Environment32, 1029–1058.

[71] Pace, R., Schiano Di Cola, V., Monti, M.M., Affinito, A., Cuomo, S., Loreto, F., Ruocco, M., 2025. Artificial intelligence in soil microbiome analysis: a potential application in predicting and enhancing soil health-a review. Discover Applied Sciences7, 85.

[72] Panagos, P., Jones, A., Lugato, E., Ballabio, C., 2025. A soil monitoring law for Europe. Global Challenges9, 2400336.

[73] Potapov, A.M., 2022. Multifunctionality of belowground food webs: resource, size and spatial energy channels. Biological Reviews97, 1691–1711.

[74] Potapov, A.M., Beaulieu, F., Birkhofer, K., Bluhm, S.L., Degtyarev, M.I., Devetter, M., Goncharov, A.A., Gongalsky, K.B., Klarner, B., Korobushkin, D.I., Liebke, D.F., Maraun, M., Mc Donnell, R.J., Pollierer, M.M., Schaefer, I., Shrubovych, J., Semenyuk, I.I., Sendra, A., Tuma, J., Tůmová, M., Vassilieva, A.B., Chen, T.W., Geisen, S., Schmidt, O., Tiunov, A.V., Scheu, S., 2022. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biological Reviews97, 1057–1117.

[75] Quintella, C.M., Mata, A.M.T., Lima, L.C.P., 2019. Overview of bioremediation with technology assessment and emphasis on fungal bioremediation of oil contaminated soils. Journal of Environmental Management241, 156–166.

[76] Ray, P., Lakshmanan, V., Labbé, J.L., Craven, K.D., 2020. Microbe to microbiome: a paradigm shift in the application of microorganisms for sustainable agriculture. Frontiers in Microbiology11, 622926.

[77] Roeben, V., Oberdoerster, S., Rakel, K.J., Liesy, D., Capowiez, Y., Ernst, G., Preuss, T.G., Gergs, A., Oberdoerster, C., 2020. Towards a spatiotemporally explicit toxicokinetic–toxicodynamic model for earthworm toxicity. Science of the Total Environment722, 137673.

[78] Salminen, J., van Gestel, C.A.M., Oksanen, J., 2001. Pollution-induced community tolerance and functional redundancy in a decomposer food web in metal-stressed soil. Environmental Toxicology and Chemistry20, 2287–2295.

[79] Sánchez-Moreno, S., Ferris, H., 2007. Suppressive service of the soil food web: effects of environmental management. Agriculture Ecosystems & Environment119, 75–87.

[80] Sandhu, M., Paul, A.T., Jha, P.N., 2022. Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil. PLoS One17, e0266808.

[81] Saravanan, A., Kumar, P.S., Vo, D.V.N., Jeevanantham, S., Karishma, S., Yaashikaa, P.R., 2021. A review on catalytic-enzyme degradation of toxic environmental pollutants: microbial enzymes. Journal of Hazardous Materials419, 126451.

[82] Schwarz, B., Barnes, A.D., Thakur, M.P., Brose, U., Ciobanu, M., Reich, P.B., Rich, R.L., Rosenbaum, B., Stefanski, A., Eisenhauer, N., 2017. Warming alters energetic structure and function but not resilience of soil food webs. Nature Climate Change7, 895–900.

[83] Shen, Q.H., Fu, W., Chen, B.D., Zhang, X.M., Xing, S.P., Ji, C.N., Zhang, X., 2023. Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant. Frontiers in Microbiology14, 1143742.

[84] Shi, Z.M., Li, W.W., Shi, S.Y., Zhao, Y.H., Wang, C.Y., 2023. Effects of cadmium and pyrene on earthworm-associated bacterial communities: unveiling new perspectives for soil pollution management. Journal of Environmental Management346, 119037.

[85] Shi, Z.M., Yan, J., Su, R., Shi, S.Y., Li, W.W., Zhao, Y.H., Zhang, J., Wang, C.Y., 2024. Cadmium and pyrene in the soil modify the properties of earthworm-mediated soil. Science of the Total Environment949, 174878.

[86] Sigmund, G., Ågerstrand, M., Antonelli, A., Backhaus, T., Brodin, T., Diamond, M.L., Erdelen, W.R., Evers, D.C., Hofmann, T., Hueffer, T., Lai, A., Torres, J.P.M., Mueller, L., Perrigo, A.L., Rillig, M.C., Schaeffer, A., Scheringer, M., Schirmer, K., Tlili, A., Soehl, A., Triebskorn, R., Vlahos, P., vom Berg, C., Wang, Z.Y., Groh, K.J., 2023. Addressing chemical pollution in biodiversity research. Global Change Biology29, 3240–3255.

[87] Singh, V., Sable, H., Vaishali, 2024. Bioremediation of emerging pollutants: a sustainable remediation approach. In: Kumari, A., Rajput, V.D., Mandzhieva, S.S., Minkina, T., van Hullebusch, E., eds. Emerging Contaminants. Amsterdam: Elsevier, 335–361.

[88] Soliveres, S., van der Plas, F., Manning, P., Prati, D., Gossner, M.M., Renner, S.C., Alt, F., Arndt, H., Baumgartner, V., Binkenstein, J., Birkhofer, K., Blaser, S., Blüthgen, N., Boch, S., Böhm, S., Börschig, C., Buscot, F., Diekötter, T., Heinze, J., Hölzel, N., Jung, K., Klaus, V.H., Kleinebecker, T., Klemmer, S., Krauss, J., Lange, M., Morris, E.K., Müller, J., Oelmann, Y., Overmann, J., Pašalić, E., Rillig, M.C., Schaefer, H.M., Schloter, M., Schmitt, B., Schöning, I., Schrumpf, M., Sikorski, J., Socher, S.A., Solly, E.F., Sonnemann, I., Sorkau, E., Steckel, J., Steffan-Dewenter, I., Stempfhuber, B., Tschapka, M., Türke, M., Venter, P.C., Weiner, C.N., Weisser, W.W., Werner, M., Westphal, C., Wilcke, W., Wolters, V., Wubet, T., Wurst, S., Fischer, M., Allan, E., 2016. Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality. Nature536, 456–459.

[89] Song, C.X., Mazzola, M., Cheng, X., Oetjen, J., Alexandrov, T., Dorrestein, P., Watrous, J., van der Voort, M., Raaijmakers, J.M., 2015. Molecular and chemical dialogues in bacteria-protozoa interactions. Scientific Reports5, 12837.

[90] Song, Y., Yao, S., Li, X.N., Wang, T., Jiang, X., Bolan, N., Warren, C.R., Northen, T.R., Chang, S.X., 2024. Soil metabolomics: deciphering underground metabolic webs in terrestrial ecosystems. Eco-Environment & Health3, 227–237.

[91] Sünnemann, M., Barnes, A.D., Amyntas, A., Ciobanu, M., Jochum, M., Lochner, A., Potapov, A.M., Reitz, T., Rosenbaum, B., Schädler, M., Zeuner, A., Eisenhauer, N., 2024. Sustainable land use strengthens microbial and herbivore controls in soil food webs in current and future climates. Global Change Biology30, e17554.

[92] Trap, J., Bonkowski, M., Plassard, C., Villenave, C., Blanchart, E., 2016. Ecological importance of soil bacterivores for ecosystem functions. Plant and Soil398, 1–24.

[93] Tso, S.F., Taghon, G.L., 2006. Protozoan grazing increases mineralization of naphthalene in marine sediment. Microbial Ecology51, 460–469.

[94] UNEP, 2021. Global Assessment of Soil Pollution. Rome: UNEP.

[95] Urich, T., Lanzén, A., Qi, J., Huson, D.H., Schleper, C., Schuster, S.C., 2008. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One3, e2527.

[96] Ventura, E., Marín, A., Gámez-Pérez, J., Cabedo, L., 2024. Recent advances in the relationships between biofilms and microplastics in natural environments. World Journal of Microbiology and Biotechnology40, 220.

[97] Wan, B.B., Liu, T., Gong, X., Zhang, Y., Li, C.J., Chen, X.Y., Hu, F., Griffiths, B.S., Liu, M.Q., 2022. Energy flux across multitrophic levels drives ecosystem multifunctionality: evidence from nematode food webs. Soil Biology and Biochemistry169, 108656.

[98] Wang, F., Wang, Y., Xiang, L.L., Redmile-Gordon, M., Gu, C.G., Yang, X.L., Jiang, X., Barceló, D., 2022a. Perspectives on ecological risks of microplastics and phthalate acid esters in crop production systems. Soil Ecology Letters4, 97–108.

[99] Wang, Q.L., Adams, C.A., Wang, F.Y., Sun, Y.H., Zhang, S.W., 2022b. Interactions between microplastics and soil fauna: a critical review. Critical Reviews in Environmental Science & Technology52, 3211–3243.

[100] Wang, X.H., Dai, Z.M., Lin, J.H., Zhao, H.C., Yu, H.D., Ma, B., Hu, L.F., Shi, J.C., Chen, X.Y., Liu, M.Q., Ke, X., Yu, Y.J., Dahlgren, R.A., Xu, J.M., 2023. Heavy metal contamination collapses trophic interactions in the soil microbial food web via bottom-up regulation. Soil Biology and Biochemistry184, 109058.

[101] Wang, Y.F., Xu, J.Y., Liu, Z.L., Cui, H.L., Chen, P., Cai, T.G., Li, G., Ding, L.J., Qiao, M., Zhu, Y.G., Zhu, D., 2024. Biological interactions mediate soil functions by altering rare microbial communities. Environmental Science & Technology58, 5866–5877.

[102] Wardle, D.A., Bardgett, R.D., Klironomos, J.N., Setälä, H., van der Putten, W.H., Wall, D.H., 2004. Ecological linkages between aboveground and belowground biota. Science304, 1629–1633.

[103] Wei, T., Zhen, Z., Luo, S.W., Chen, Y.J., Li, J., Liang, Y.Q., Song, M.K., Li, J.C., Lin, Z., Zhang, D.Y., 2025. Earthworm-assisted shift and enrichment of the active di (2-ethylhexyl) phthalate degraders in farmland soils by DNA-stable isotope probing. Journal of Hazardous Materials498, 139916.

[104] Windsor, F.M., Pereira, M.G., Morrissey, C.A., Tyler, C.R., Ormerod, S.J., 2020. Environment and food web structure interact to alter the trophic magnification of persistent chemicals across river ecosystems. Science of the Total Environment717, 137271.

[105] Xu, A.M., Zhang, X.X., Wu, S.L., Xu, N., Huang, Y., Yan, X., Zhou, J., Cui, Z.L., Dong, W.L., 2021. Pollutant degrading enzyme: catalytic mechanisms and their expanded applications. Molecules26, 4751.

[106] Xu, X.H., Jiang, J.D., 2024. Engineering microbiomes for enhanced bioremediation. PLoS Biology22, e3002951.

[107] Yang, Z.N., Liu, Z.S., Wang, K.H., Liang, Z.L., Abdugheni, R., Huang, Y., Wang, R.H., Ma, H.L., Wang, X.K., Yang, M.L., Zhang, B.G., Li, D.F., Jiang, C.Y., Corvini, P.F.X., Liu, S.J., 2022. Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites. Environmental Science and Ecotechnology10, 100169.

[108] Yin, R., Siebert, J., Eisenhauer, N., Schädler, M., 2020. Climate change and intensive land use reduce soil animal biomass via dissimilar pathways. eLife9, e54749.

[109] Yu, X.M, Pan, D.Q., Long, Q.Y., Chen, X.Y., 2022. Degradation of organic pollutants using a photo-enzymatic cascade process. Food Machinery38, 70–73.

[110] Zhai, Y.J., Hunting, E.R., Liu, G., Baas, E., Peijnenburg, W.J.G.M., Vijver, M.G., 2019. Compositional alterations in soil bacterial communities exposed to TiO₂ nanoparticles are not reflected in functional impacts. Environmental Research178, 108713.

[111] Zhang, B.W., Wang, X., Liu, C.X., 2024. Screening and optimization of soil remediation strategies assisted by machine learning. Processes12, 1157.

[112] Zhang, T., Zhang, H.J., 2022. Microbial consortia are needed to degrade soil pollutants. Microorganisms10, 261.

[113] Zhang, Y.X., Jing, M.Y., Lyu, L.H., Nie, L., Xu, X.H., Sun, R., Xu, X.Y., Chen, S.Y., He, S.B., Zhang, Y.M., Huang, P., Luo, W.J., Liang, J.J., Gao, G.F., Fan, K.K., Yang, T., Zhang, L.Y., Fu, X., Allard, S.M., Gilbert, J.A., Zhang, J.B., Chu, H.Y., 2026. Principles for rigorous design and application of synthetic microbial communities. Advanced Science13, e14750.

[114] Zhao, S., Yuan, X.T., Wang, X.H., Ai, Y.J., Li, F.P., 2024. Research progress and hotspots in microbial remediation for polluted soils. Sustainability16, 7458.

[115] Zhao, S.Y., Wang, B.H., Zhong, Z., Liu, T.Q., Liang, T.K., Zhan, J.J., 2020. Contributions of enzymes and gut microbes to biotransformation of perfluorooctane sulfonamide in earthworms (Eisenia fetida). Chemosphere238, 124619.

[116] Zheng, J., Dini-Andreote, F., Luan, L., Geisen, S., Xue, J.R., Li, H.X., Sun, B., Jiang, Y.J., 2022a. Nematode predation and competitive interactions affect microbe-mediated phosphorus dynamics. mBio13, e03293–21.

[117] Zheng, W.K., Cui, T., Li, H., 2022b. Combined technologies for the remediation of soils contaminated by organic pollutants. A review. Environmental Chemistry Letters20, 2043–2062.

[118] Zhou, H.T., Zhuang, W.L., Shi, Z.J., Liu, Z.Q., Wei, H., Zhang, J.E., 2026. Differential responses of soil micro-food web components to global change factors: a meta-analysis. Basic and Applied Ecology90, 62–72.

[119] Zhou, Q.Q., Chen, H.F., Liu, G.J., Wang, X.H., 2024. Occurrence, sustainable treatment technologies, potential sources, and future prospects of emerging pollutants in aquatic environments: a review. Frontiers in Environmental Science12, 1455377.

[120] Zhu, L., Liu, J.B., Zhou, J.Y., Wu, X.T., Yang, K.J., Ni, Z., Liu, Z., Jia, H.Z., 2022. The overlooked toxicity of environmentally persistent free radicals (EPFRs) induced by anthracene transformation to earthworms (Eisenia fetida). Science of the Total Environment853, 158571.

[121] Zhu, L.Y., Chen, Y., Sun, R.B., Zhang, J.B., Hale, L., Dumack, K., Geisen, S., Deng, Y., Duan, Y.H., Zhu, B., Li, Y., Liu, W.Z., Wang, X.Y., Griffiths, B.S., Bonkowski, M., Zhou, J.Z., Sun, B., 2023. Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability. Microbiome11, 95.

RIGHTS & PERMISSIONS

Higher Education Press