Biochar immobilized microbes for sustainable soil remediation and agriculture enhancement: from lab to farmland

Abstract

Soil degradation and contamination pose a critical threat to global agricultural sustainability, necessitating innovative remediation strategies. Biochar-immobilized microbes (BIMs), which synergistically integrate physicochemical advantages of biochar with microbial metabolic functions, represent a transformative approach to enhance soil health and crop productivity. This review provides a data-driven analysis, with evidence from 92 published articles to summarize advancements in BIM development from 85 pot experiments and 11 field applications, and to elucidate the underlying mechanisms. Biochar serves as a stable microbial habitat, enhancing colonization through adsorption, entrapment, covalent bonding, and crosslinking. Key factors such as biochar porosity, microbial surface characteristics, and environmental conditions critically influence microbe immobilization efficiency and functional longevity. The compiled data indicate that BIMs can ameliorate soil properties (e.g., elevating pH by 0.5–1.5 units, increasing cation exchange capacity by 12.25–39.05%), and enhance soil enzyme activities (e.g., urease, dehydrogenase). These improvements contribute to effective remediation of contaminated soils, with reported efficiencies up to 95% for heavy metals and 90% for organic pollutants. Furthermore, field applications demonstrate that BIMs can enhance crop yields by up to 45%, primarily through improved nutrient availability and stress resilience. However, scalability challenges persist, as field trials show variable microbial survival under climatic stresses. The transition from predominantly lab-scale research to fewer documented field validations highlights the need for more long-term, on-farm studies. By systematically bridging lab innovations to farmland practicality, BIMs align with the UN Sustainable Development Goals, offering a promising pathway for soil restoration and sustainable agriculture. Future research must prioritize long-term field validations, lifecycle assessments, and farmer-centric optimization to unlock their full potential.

Graphical Abstract

Keywords

Biochar immobilized microbes (BIMs) / Soil remediation / Biochar / Sustainable agriculture / Plant growth-promoting bacteria

References

[1] Azeem M, Ul Hassan T, Tahir MI, et al.. Tea leaves biochar as a carrier of Bacillus cereus improves the soil function and crop productivity. Appl Soil Ecol, 2021, 157: 103732.

[2] Bai K, Wang W, Zhang J, et al.. Effects of phosphorus-solubilizing bacteria and biochar application on phosphorus availability and tomato growth under phosphorus stress. BMC Biol, 2024, 22(1): 211.

[3] Bai X, Bol R, Chen H, et al.. A meta-analysis on crop growth and heavy metals accumulation with PGPB inoculation in contaminated soils. J Hazard Mater, 2024, 471: 134370.

[4] Bekchanova M, Campion L, Bruns S, et al.. Biochar improves the nutrient cycle in sandy-textured soils and increases crop yield: a systematic review. Environ Evid, 2024, 13(1): 3.

[5] Bi F, Jiang Z, Wang M, Lin Q, Liu X, et al.. Enhanced remediation of cadmium-contaminated farmland by smooth vetch (Vicia villosa var.) coupled with phosphorus/sulfur co-doped biochar: synergetic performance and mechanism. J Clean Prod, 2025, 496: 144986.

[6] Bolan N, Kunhikrishnan A, Thangarajan R, et al.. Remediation of heavy metal(loid)s contaminated soils - to mobilize or to immobilize?. J Hazard Mater, 2014, 266: 141-166.

[7] Bolan S, Hou D, Wang L, et al.. The potential of biochar as a microbial carrier for agricultural and environmental applications. Sci Total Environ, 2023, 886: 163968.

[8] Campion L, Bekchanova M, Malina R, et al.. The costs and benefits of biochar production and use: a systematic review. J Clean Prod, 2023, 408: 137138137138.

[9] Carril P, Ghorbani M, Azarnejad N, et al.. Promoting early growth in tomato (Solanum lycopersicum L.) by co-application of biochar and beneficial bacteria. J Soil Sci Plant Nutr, 2025, 25(1): 1493-1503.

[10] Chen B, Yuan M, Qian L. Enhanced bioremediation of PAH-contaminated soil by immobilized bacteria with plant residue and biochar as carriers. J Soils Sediments, 2012, 12(9): 1350-1359.

[11] Chen H, Min F, Hu X, et al.. Biochar assists phosphate solubilizing bacteria to resist combined Pb and Cd stress by promoting acid secretion and extracellular electron transfer. J Hazard Mater, 2023, 452: 131176.

[12] Chen W, Wu Z, Liu C, et al.. Biochar combined with Bacillus subtilis SL-44 as an eco-friendly strategy to improve soil fertility, reduce Fusarium wilt, and promote radish growth. Ecotoxicol Environ Saf, 2023, 251: 114509.

[13] Chu CH, Zhu LZ. Paving the way toward soil safety and health: current status, challenges, and potential solutions. Front Environ Sci Eng, 2024, 18(6): 74.

[14] Egamberdieva D, Wirth S, Bellingrath-Kimura SD, et al.. Salt-tolerant plant growth promoting rhizobacteria for enhancing crop productivity of saline soils. Front Microbiol, 2019, 10: 2791.

[15] El-Gamal EH, Rashad M, Saleh ME, et al.. Potential bioremediation of lead and phenol by sunflower seed husk and rice straw-based biochar hybridized with bacterial consortium: a kinetic study. Sci Rep, 2023, 13(1): 21901.

[16] Hajieghrari M, Hejazi P. Enhanced biodegradation of n-Hexadecane in solid-phase of soil by employing immobilized Pseudomonas aeruginosa on size-optimized coconut fibers. J Hazard Mater, 2020, 389: 122134.

[17] Hashem AM, Gamal AA, Hassan ME, et al.. Covalent immobilization of Enterococcus faecalis Esawy dextransucrase and dextran synthesis. Int J Biol Macromol, 2016, 82: 905-912.

[18] Huang Y, Liu T, Liu J, et al.. Exceptional anti-toxic growth of water spinach in arsenic and cadmium co-contaminated soil remediated using biochar loaded with Bacillus aryabhattai. J Hazard Mater, 2024, 469: 133966.

[19] Huang Y, Luo Y, Wu C, et al.. Synergistic multi-metal stabilization of lead-zinc smelting contaminated soil by Ochrobactrum EEELCW01-loaded iron-modified biochar: performance and long-term efficacy. Biochar, 2025, 7(1): 58.

[20] Irshad S, Xie Z, Kamran M, et al.. Biochar composite with microbes enhanced arsenic biosorption and phytoextraction by Typha latifolia in hybrid vertical subsurface flow constructed wetland. Environ Pollut, 2021, 291: 118269.

[21] Jafri N, Wong WY, Doshi V, et al.. A review on production and characterization of biochars for application in direct carbon fuel cells. Process Saf Environ Prot, 2018, 118: 152-166.

[22] Jaiswal AK, Alkan N, Elad Y, et al.. Molecular insights into biochar-mediated plant growth promotion and systemic resistance in tomato against Fusarium crown and root rot disease. Sci Rep, 2020, 10(1): 13934.

[23] Jesionowski T, Zdarta J, Krajewska B. Enzyme immobilization by adsorption: a review. Adsorption, 2014, 20(5–6): 801-821.

[24] Jia H, Lv X, Sohail MA, et al.. Control efficiency of biochar loaded with Bacillus subtilis Tpb55 against tobacco black shank. Processes, 2022, 10(12): 2663.

[25] Jiang Y, Yang F, Dai M, et al.. Application of microbial immobilization technology for remediation of Cr (VI) contamination: a review. Chemosphere, 2022, 286: 131721.

[26] Jiang S, Li H, Zhang L, et al.. Generic diagramming platform (GDP): a comprehensive database of high-quality biomedical graphics. Nucleic Acids Res, 2025, 53(D1): D1670-D1676.

[27] Jorge P, Ángela M, Carmen F, et al.. The use of biochar for plant pathogen control. Phytopathology, 2021, 111(9): 1490-1499.

[28] Kamyab H, Chelliapan S, Khalili E, et al.. Biochar as a carrier for plant growth-promoting bacteria in phytoremediation of pesticides. J Hazard Mater Adv, 2025, 18: 100673.

[29] Kong Z, Liu H. Modification of rhizosphere microbial communities: a possible mechanism of plant growth promoting rhizobacteria enhancing plant growth and fitness. Front Plant Sci, 2022, 13: 920813.

[30] Lehmann J, Joseph S. Biochar for environmental management: science, technology and implementation, 2009. London, Taylor and Francis.

[31] Li Z, Wang P, Yue X, et al.. Effects of Bacillus thuringiensis HC-2 combined with biochar on the growth and Cd and Pb accumulation of radish in a heavy metal-contaminated farmland under field conditions. Int J Environ Res Public Health, 2019, 16(19): 3676.

[32] Li X, Wang Y, Luo T, et al.. Remediation potential of immobilized bacterial strain with biochar as carrier in petroleum hydrocarbon and Ni co-contaminated soil. Environ Technol, 2022, 43(7): 1068-1081.

[33] Li W, Zhu Y, Li K, et al.. Synergistic remediation of phenanthrene-cadmium co-contaminants by an immobilized acclimated bacterial-fungal consortium and its community response. Chemosphere, 2023, 336: 139234-139234.

[34] Li J, Yang D, Zou W, et al.. Mechanistic insights into the synergetic remediation and amendment effects of zeolite/biochar composite on heavy metal-polluted red soil. Front Environ Sci Eng, 2024, 18(9): 114.

[35] Li J, Sun W, Lichtfouse E, et al.. Life cycle assessment of biochar for sustainable agricultural application: a review. Sci Total Environ, 2024, 951: 175448.

[36] Li Y, Zhang M, Wang X, et al.. Synergistic enhancement of cadmium immobilization and soil fertility through biochar and artificial humic acid-assisted microbial-induced calcium carbonate precipitation. J Hazard Mater, 2024, 476: 135140.

[37] Li H, Wang Y, Zhao Y, et al.. Struvite-loaded biochar beads fertilizer for different soils: nutrient slow release, soil properties improvement and heavy metal remediation. Front Environ Sci Eng, 2025, 19(6): 73.

[38] Liu J, Ding Y, Ma L, et al.. Combination of biochar and immobilized bacteria in cypermethrin-contaminated soil remediation. Int Biodeterior Biodegrad, 2017, 120: 15-20.

[39] Liu J, Zhang J, Zhu M, et al.. Effects of plant growth promoting rhizobacteria (PGPR) strain Bacillus licheniformis with biochar amendment on potato growth and water use efficiency under reduced irrigation regime. Agronomy, 2022, 12(5): 1031.

[40] Liu Q, Wang Y, Sun S, et al.. A novel chitosan-biochar immobilized microorganism strategy to enhance bioremediation of crude oil in soil. Chemosphere, 2023, 313: 137367.

[41] Liu W, Xiao X, Li L, et al.. Biochar-based metal tolerating plant growth promoting bacterial inoculants enhanced the ability of ryegrass for phytostabilization. Environ Res, 2025, 265: 120389.

[42] Lu J, Peng W, Lv Y, et al.. Application of cell immobilization technology in microbial cocultivation systems for biochemicals production. Ind Eng Chem Res, 2020, 59(39): 17026-17034.

[43] Luo D, Huang H, Wang J, et al.. Inoculations of phosphorus-solubilizing bacteria alter soil properties, microbial communities, and improve crop yield and fruit quality in the tomato production system. Appl Soil Ecol, 2025, 207: 105944.

[44] Ma L, Hu T, Liu Y, et al.. Combination of biochar and immobilized bacteria accelerates polyacrylamide biodegradation in soil by both bio-augmentation and bio-stimulation strategies. J Hazard Mater, 2021, 405: 124086.

[45] Ma Y, Zhang F, Cheng L, et al.. Remediation potential of biochar for As and Cd by modifying soil physicochemical properties: a conceptual model elucidating stabilization mechanism based on conditional probability theory. Biochar, 2025, 7(1): 63.

[46] Mei C, Wang H, Cai K, et al.. Characterization of soil microbial community activity and structure for reducing available Cd by rice straw biochar and Bacillus cereus RC-1. Sci Total Environ, 2022, 839: 156202.

[47] Nguyen Thi Hai H, Nguyen Chi T, Kajitvichyanukul P. Enhanced paraquat removal from contaminated water using cell-immobilized biochar. Clean Technol Environ Policy, 2022, 24(4): 1073-1085.

[48] Noureen S, Iqbal A, Muqeet HA. Potential of drought tolerant rhizobacteria amended with biochar on growth promotion in wheat. Plants Basel, 2024, 13(9): 1183.

[49] Patel K, Amaresan N. Amaresan N, Dharumadurai D, Cundell DR. Mass multiplication, production cost analysis, and marketing of cellulase. Industrial microbiology based entrepreneurship. Microorganisms for sustainability, 2022. Singapore, Springer

[50] Pathak HK, Chauhan PK, Seth CS, et al.. Mechanistic and future prospects in rhizospheric engineering for agricultural contaminants removal, soil health restoration, and management of climate change stress. Sci Total Environ, 2024, 927: 172116.

[51] Peng Y, Zhang H, Li G, et al.. Microbial inoculum improved soil aggregate formation and increased cucumber yield in a greenhouse under secondary salinization conditions. J Environ Manag, 2025, 376: 124576.

[52] Prum C, Dolphen R, Thiravetyan P. Enhancing arsenic removal from arsenic-contaminated water by Echinodorus cordifolius−endophytic Arthrobacter creatinolyticus interactions. J Environ Manag, 2018, 213: 11-19.

[53] Qi X, Gou J, Chen X, et al.. Application of mixed bacteria-loaded biochar to enhance uranium and cadmium immobilization in a co-contaminated soil. J Hazard Mater, 2021, 401: 123823.

[54] Qu JH, Wang SQ, Li ZW, et al.. Highly efficient recovery of phosphate from water using Cerium Carbonate Hydroxide-decorated magnetic biochar: a slow-release phosphate fertilizer for agricultural reuse. ACS ES T Eng, 2024, 4(12): 3045-3056.

[55] Qu JH, Yu R, Wang MN, et al.. Tailoring sponge-like nitrogen-enriched biochar: a green and sustainable remediation technology for Pb and Cu contaminated soil. Chem Eng J, 2025, 522: 167603.

[56] Rasool M, Akhter A, Haider MS. Molecular and biochemical insight into biochar and Bacillus subtilis induced defense in tomatoes against Alternaria solani. Sci Hortic, 2021, 285: 110203.

[57] Ren H, Deng Y, Ma L, et al.. Enhanced biodegradation of oil-contaminated soil oil in shale gas exploitation by biochar immobilization. Biodegradation, 2022, 33(6): 621-639.

[58] Ren W, Liu H, Mao T, et al.. Enhanced remediation of PAHs-contaminated site soil by bioaugmentation with graphene oxide immobilized bacterial pellets. J Hazard Mater, 2022, 433: 128793.

[59] Russi A, Granada CE, Schwambach J. Bacillus velezensis S26-loaded biochar boosts plant growth, alleviates copper stress and suppresses black foot disease in SO4 vine rootstock. Appl Soil Ecol, 2024, 202: 105550.

[60] Saravanan A, Swaminaathan P, Kumar PS, et al.. A comprehensive review on immobilized microbes - biochar and their environmental remediation: mechanism, challenges and future perspectives. Environ Res, 2023, 236: 116723.

[61] Shan T, Wang B, Tu W, et al.. Adsorption and biodegradation of butyl xanthate in mine water by Pseudomonas sp. immobilized on yak dung biochar. Environ Res, 2025, 264: 120300.

[62] Sharma L, Shukla SK, Jaiswal VP, et al.. Novel strains of Pseudomonas fluorescens and Bacillus cereus and their integrated use with inorganic fertilizers enhancing P availability, crop growth parameters, and sugarcane yield in subtropical India. Sugar Tech, 2023, 25(6): 1467-1485.

[63] Sher Y, Baker NR, Herman D, et al.. Microbial extracellular polysaccharide production and aggregate stability controlled by switchgrass (Panicum virgatum) root biomass and soil water potential. Soil Biol Biochem, 2020, 143: 107742.

[64] Shi A, Hu Y, Zhang X, et al.. Biochar loaded with bacteria enhanced Cd/Zn phytoextraction by facilitating plant growth and shaping rhizospheric microbial community. Environ Pollut, 2023, 327: 121559.

[65] Shyam S, Ahmed S, Joshi SJ, et al.. Biochar as a soil amendment: implications for soil health, carbon sequestration, and climate resilience. Discov Soil, 2025.

[66] Shyam S, Daimary M, Narayan M, et al.. Biochar-based electroanalytical materials: towards sustainable, high-performance electrocatalysts and sensors. Next Mater, 2025, 8: 100873.

[67] Sun T, Miao J, Saleem M, et al.. Bacterial compatibility and immobilization with biochar improved tebuconazole degradation, soil microbiome composition and functioning. J Hazard Mater, 2020, 398: 122941.

[68] Tallur PN, Mulla SI, Megadi VB, et al.. Biodegradation of cypermethrin by immobilized cells of Micrococcus sp strain CPN 1. Braz J Microbiol, 2015, 46(3): 667-672.

[69] Tao R, Ding W, Zhang K, et al.. Biochar and Bacillus subtilis boost cut chrysanthemum growth via intensified microbial interkingdom interactions. Biochar, 2025, 7(1): 75.

[70] Tu C, Wei J, Guan F, et al.. Biochar and bacteria inoculated biochar enhanced Cd and Cu immobilization and enzymatic activity in a polluted soil. Environ Int, 2020, 137: 105576.

[71] Wahla AQ, Anwar S, Mueller JA, et al.. Immobilization of metribuzin degrading bacterial consortium MB3R on biochar enhances bioremediation of potato vegetated soil and restores bacterial community structure. J Hazard Mater, 2020, 390: 121493.

[72] Wang T, Sun H, Ren X, et al.. Evaluation of biochars from different stock materials as carriers of bacterial strain for remediation of heavy metal-contaminated soil. Sci Rep, 2017, 7: 12114.

[73] Wang L, Li Z, Wang Y, et al.. Performance and mechanisms for remediation of Cd(II) and As(III) co-contamination by magnetic biochar-microbe biochemical composite: competition and synergy effects. Sci Total Environ, 2021, 750: 141672.

[74] Wang X, Cai D, Ji M, et al.. Isolation of heavy metal-immobilizing and plant growth-promoting bacteria and their potential in reducing Cd and Pb uptake in water spinach. Sci Total Environ, 2022, 819: 153242.

[75] Wang N, Wang T, Chen Y, et al.. Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize. Nat Commun, 2024, 15(1): 839.

[76] Wen M, Ma Z, Gingerich DB, et al.. Heavy metals in agricultural soil in China: a systematic review and meta-analysis. Eco-Environ Health, 2022, 1(4): 219-228.

[77] Woo J-I, Adhikari A, Gam H-J, et al.. Integrated role of biochar and PGPR (Leclercia adecarboxylata HW04) in enhancing cadmium phytoremediation and stress tolerance in Glycine max L. Plant Physiol Biochem, 2025, 220: 109489.

[78] Wu P, Wang Z, Bhatnagar A, et al.. Microorganisms-carbonaceous materials immobilized complexes: synthesis, adaptability and environmental applications. J Hazard Mater, 2021, 416: 125915.

[79] Wu C, Zhi D, Yao B, et al.. Immobilization of microbes on biochar for water and soil remediation: a review. Environ Res, 2022, 212: 113226.

[80] Wu J, Fu X, Zhao L, et al.. Biochar as a partner of plants and beneficial microorganisms to assist in-situ bioremediation of heavy metal contaminated soil. Sci Total Environ, 2024, 923: 171442.

[81] Wu C, Wang Y, Clarke JL, et al.. Biochar enhances the sorption and degradation of fluridone and its main metabolite in soil: insights into biodegradation potential and remediation of microbial communities. Biochar, 2025, 7(1): 81.

[82] Xiong B, Zhang Y, Hou Y, et al.. Enhanced biodegradation of PAHs in historically contaminated soil by M. gilvum inoculated biochar. Chemosphere, 2017, 182: 316-324.

[83] Xiong X, Liu J, Xiao T, et al.. Remediation of uranium-contaminated water and soil by biochar-based materials: a review. Biochar, 2025, 7(1): 41.

[84] Yang H, Kerner P, Liang X, et al.. Biochar amendment modulates root metabolome and rhizosphere microbiome of wheat. Biochar, 2025, 7(1): 46.

[85] Yin C, Yan H, Cao Y, et al.. Enhanced bioremediation performance of diesel-contaminated soil by immobilized composite fungi on rice husk biochar. Environ Res, 2023, 226: 115663.

[86] Yu K, Wang Z, Yang W, et al.. Application of biochar-immobilized Bacillus megaterium for enhancing phosphorus uptake and growth in rice. Plants Basel, 2025, 14(2): 214.

[87] Zeng Y, Wen M, Li S, et al.. Role of Fe-based nanoparticles introduced into soil-plant systems or contaminated soil-plant systems: toxic substance or remediation agent?. Front Environ Sci Eng, 2025, 19(3): 27.

[88] Zhai Q, Chen X, Zhang M, et al.. Immobilization of Klebsiella jilinsis strain 2N3 by corn straw biochar enhanced the degradation of nicosulfuron and restores the soil microbiome function and composition. Appl Soil Ecol, 2023, 189: 104917.

[89] Zhang B, Zhang L, Zhang X. Bioremediation of petroleum hydrocarbon-contaminated soil by petroleum-degrading bacteria immobilized on biochar. RSC Adv, 2019, 9(60): 35304-35311.

[90] Zhang Z, Fan Z, Zhang G, et al.. Application progress of microbial immobilization technology based on biomass materials. Bioresour, 2021, 16(4): 8509-8524.

[91] Zhang M, Liu Y, Wei Q, et al.. The co-application of PGPR and biochar enhances the production capacity of continuous cropping peppers in the Karst Yellow Soil Region of Southwest China. Horticulturae, 2023, 9(10): 1104.

[92] Zhang S, Shen Y, Zheng C, et al.. Recent advances, challenges, and perspectives on carbon capture. Front Environ Sci Eng, 2024, 18(6): 2095-2201.

[93] Zhong JC, Xie CJ, Yan KJ, et al.. Optimizing biochar-microbe immobilization for formaldehyde removal: synergistic adsorption and phytoremediation enhancement. J Environ Chem Eng, 2025, 13(5): 118964.

[94] Zou Q, Zhao L, Guan L, et al.. The synergistic interaction effect between biochar and plant growth-promoting rhizobacteria on beneficial microbial communities in soil. Front Plant Sci, 2024, 15: 1501400.

Funding

National Key Research and Development Program of China(2022YFD1700700)

National Natural Science Foundation of China(No. 52279051)

China Agriculture Research System of MOF and MARA(CARS-23-B12)

2115 Talent Development Program of China Agricultural University(No. 109018)

RIGHTS & PERMISSIONS

The Author(s)