农田土壤生物健康:概念内涵、面临挑战与调控策略

Soil biohealth: concepts, challenges, and management strategies for sustainable agriculture

摘要

土壤是一个孕育着大量生物群落的生命系统，其健康状态关乎绿色农业的可持续发展。近年来，由于集约化农业的快速发展和农化品的大量投入，农田土壤生物健康问题日益突出，具体表现为参与关键元素转化的有益菌(群)缺失引起的土壤生物肥力下降，土传植物病原物积累引起的土壤生物障碍频发以及人畜致病菌在农田系统扩散等引起的土壤生物污染加剧。本文首先介绍了土壤生物健康概念的提出背景与核心内涵，其次从土壤生物肥力、生物障碍和生物污染 3 个方面，系统梳理了农田土壤生物健康的生态功能、作用原理以及调控途径。最后，本文从理论研究、研究方法和应用技术 3 个维度分析了土壤生物健康研究领域的主要瓶颈和未来重点研究方向，为构建高效的土壤生物健康管理和调控体系提供科学依据，促进农业绿色可持续发展。

Abstract

Soil is a living system that harbors diverse biological communities, and its health status is fundamental to the sustainable development of green agriculture. In recent years, the rapid expansion of intensive agriculture and the excessive input of agrochemicals have increasingly exacerbated soil biological health issues in farmlands, manifested as the decline of soil biological fertility due to the loss of beneficial microbial taxa, the frequent occurrence of soil biological obstacles caused by the invasion of soil-borne plant pathogens, and the intensification of soil biological contamination resulting from the dissemination of zoonotic and anthropopathogenic bacteria within agricultural systems. This review first introduces the background and core connotation of the soil biohealth concept. Subsequently, we systematically synthesize the ecological functions, underlying mechanisms, and regulatory approaches of farmland soil biological health from three perspectives: biological fertility, biological obstacles, and biological contamination. Finally, we analyze the major bottlenecks and future research priorities in the field of soil biohealth from three dimensions: theoretical research, methodological development, and applied technology with the aim of providing a scientific basis for establishing efficient soil biological health management and regulation systems, thereby facilitating the transition towards sustainable green agriculture.

关键词

土壤健康 / 生物肥力 / 生物障碍 / 生物污染 / 根际微生物组 / 微生态

Key words

soil health / biological fertility / biological obstacle / biological contamination / rhizosphere microbiome / microecology

参考文献

[1] Lehmann J, Bossio D A, Kögel-Knabner I, et al. The concept and future prospects of soil health[J]. Nature Reviews Earth & Environment, 2020, 1(10): 544-553.

[2] Karlen D L, Mausbach M J, Doran J W, et al. Soil quality:a concept, definition, and framework for evaluation (a guest editorial)[J]. Soil Science Society of America Journal, 1997, 61(1): 4-10.

[3] Doran J W, Sarrantonio M, Liebiger M A. Soil health and sustainability[M]// Advances in agronomy. Amsterdam: Elsevier, 1996: 1-54.

[4] Doran J W, Zeiss M R. Soil health and sustainability: managing the biotic component of soil quality[J]. Applied Soil Ecology, 2000, 15(1): 3-11.

[5] 张江周, 王光州, 李奕赞, 等. 农田土壤健康评价体系构建的若干思考[J]. 土壤学报, 2024, 61(4): 879-891.

[6] Zhang J Z, Wang G Z, Li Y Z, et al. Re-thinking the establishment of the farmland soil health assessment system[J]. Acta Pedologica Sinica, 2024, 61(4): 879-891(in Chinese with English abstract).

[7] 张俊伶, 张江周, 申建波, 等. 土壤健康与农业绿色发展:机遇与对策[J]. 土壤学报, 2020, 57(4): 783-796.

[8] Zhang J L, Zhang J Z, Shen J B, et al. Soil health and agriculture green development: opportunities and challenges[J]. Acta Pedologica Sinica, 2020, 57(4): 783-796(in Chinese with English abstract).

[9] Jia J Y, de Goede R, Li Y Z, et al. Unlocking soil health: are microbial functional genes effective indicators?[J]. Soil Biology and Biochemistry, 2025, 204: 109768.

[10] 朱永官, 彭静静, 韦中, 等. 土壤微生物组与土壤健康[J]. 中国科学:生命科学, 2021, 51(1): 1-11.

[11] Zhu Y G, Peng J J, Wei Z, et al. Linking the soil microbiome to soil health[J]. Scientia Sinica Vitae, 2021, 51(1): 1-11(in Chinese with English abstract).

[12] 师玥, 苏铃珺, 刘洋, 等. 基于土壤健康评价的土壤生物指标研究进展[J]. 土壤, 2025, 57(6): 1293-1302.

[13] Shi Y, Su L J, Liu Y, et al. Research progress on soil biological indicators based on soil health assessment[J]. Soils, 2025, 57(6): 1293-1302(in Chinese with English abstract).

[14] 杨晓霞, 周启星, 王铁良. 土壤健康的内涵及生态指示与研究展望[J]. 生态科学, 2007, 26(4): 374-380.

[15] Yang X X, Zhou Q X, Wang T L. Connotation and ecological indicators of soil health and its research prospect[J]. Ecological Science, 2007, 26(4): 374-380(in Chinese with English abstract).

[16] Zwaan R E, Verwijmeren M, Rutgers M, et al. Soil health indices in disagreement: a systematic review and comparison of soil health assessment methods[J]. Soil Biology and Biochemistry, 2026, 220: 110184.

[17] Banerjee S, van der Heijden M G A. Soil microbiomes and one health[J]. Nature Reviews Microbiology, 2023, 21(1): 6-20.

[18] Bardgett R D, van der Putten W H. Belowground biodiversity and ecosystem functioning[J]. Nature, 2014, 515(7528): 505-511.

[19] Hector A, Bagchi R. Biodiversity and ecosystem multifunctionality[J]. Nature, 2007, 448(7150): 188-190.

[20] Delgado-Baquerizo M, Reich P B, Trivedi C, et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes[J]. Nature Ecology & Evolution, 2020, 4(2): 210-220.

[21] Wagg C, Bender S F, Widmer F, et al. Soil biodiversity and soil community composition determine ecosystem multifunctionality[J]. Proc Natl Acad Sci USA, 2014, 111(14): 5266-5270.

[22] Saleem M, Hu J, Jousset A. More than the sum of its parts: microbiome biodiversity as a driver of plant growth and soil health[J]. Annual Review of Ecology, Evolution, and Systematics, 2019, 50: 145-168.

[23] Xu X B, Zhang K L, Zhu Z K, et al. Decoding soil health constraints in regional agroecosystems: machine learning reveals microbial enzymatic thresholds and drivers[J]. Soil and Tillage Research, 2026, 258: 107000.

[24] Yao P W, Lu Q F, Han J, et al. Characteristics of soil respiration and net ecosystem carbon budget from tobacco-planted soil with different organic amendments[J]. Soil and Tillage Research, 2024, 242: 106142.

[25] Radujković D, Portillo-Estrada M, Hendrickx B, et al. Soil biodiversity and ecosystem functions in grasslands: is more always better?[J]. Soil Biology and Biochemistry, 2025, 211: 109988.

[26] Louca S, Polz M F, Mazel F, et al. Function and functional redundancy in microbial systems[J]. Nature Ecology & Evolution, 2018, 2(6): 936-943.

[27] Griffiths B S, Philippot L. Insights into the resistance and resilience of the soil microbial community[J]. FEMS Microbiology Reviews, 2013, 37(2): 112-129.

[28] Ren Y, Xun W B, Yan H, et al. Functional compensation dominates the assembly of plant rhizospheric bacterial community[J]. Soil Biology and Biochemistry, 2020, 150: 107968.

[29] 韦中, 沈宗专, 杨天杰, 等. 从抑病土壤到根际免疫:概念提出与发展思考[J]. 土壤学报, 2021, 58(4): 814-824.

[30] Wei Z, Shen Z Z, Yang T J, et al. From suppressive soil to rhizosphere immunity: towards an ecosystem thinking for soil-borne pathogen control[J]. Acta Pedologica Sinica, 2021, 58(4): 814-824(in Chinese with English abstract).

[31] Child H T, Friggens N L, Hook C, et al. Land-use driven microbial community legacy shapes soil functionality[J]. Soil Biology and Biochemistry, 2026, 222: 110282.

[32] Ginnan N A, Custódio V, Gopalachan D, et al. Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants[J]. Nature Microbiology, 2025, 10(11): 2823-2844.

[33] Joshi N, Kaur R, Nawaz T. The soil-root nexus: how soil health shapes plant nutrient uptake and food nutritional security[J]. Plant and Soil, 2026, 521(2): 1145-1173.

[34] 孙新, 李琪, 姚海凤, 等. 土壤动物与土壤健康[J]. 土壤学报, 2021, 58(5): 1073-1083.

[35] Sun X, Li Q, Yao H F, et al. Soil fauna and soil health[J]. Acta Pedologica Sinica, 2021, 58(5): 1073-1083(in Chinese with English abstract).

[36] Mueller C W, Baumert V, Carminati A, et al. From rhizosphere to detritusphere-soil structure formation driven by plant roots and their interactions with soil biota[J]. Soil Biology and Biochemistry, 2024, 193: 109396.

[37] Song J J, Haider S, Song J H, et al. Root exudates mediate microorganisms to improve rhizosphere nutrient availability and crop productivity under straw mulching and slow-release nitrogen fertilizer[J]. Functional Ecology, 2026, 40(6): 1725-1739.

[38] Yan Y Y, Zhou X, Liu L L, et al. Soil nutrient enrichment induces trade-offs in bacterial life-history strategies promoting plant productivity[J]. Advanced Science, 2025, 12(45): e10066.

[39] Jian S Y, Li J W, Chen J, et al. Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: a meta-analysis[J]. Soil Biology and Biochemistry, 2016, 101: 32-43.

[40] Smith P, Cotrufo M F, Rumpel C, et al. Biogeochemical cycles and biodiversity as key drivers of ecosystem services provided by soils[J]. Soil, 2015, 1(2): 665-685.

[41] Zhang S X, Kuzyakov Y, Jia Z J, et al. Cascading effects within soil food web amplify fungal biomass and necromass production[J]. Global Change Biology, 2025, 31(5): e70235.

[42] Katan J. Diseases caused by soilborne pathogens: biology, management and challenges[J]. Journal of Plant Pathology, 99(2): 305-315.

[43] Gu Y A, Wei Z, Wang X Q, et al. Pathogen invasion indirectly changes the composition of soil microbiome via shifts in root exudation profile[J]. Biology and Fertility of Soils, 2016, 52(7): 997-1005.

[44] Ren T B, Feng H L, Wan Mahar W A, et al. Biochar and microbial synergy: enhancing tobacco plant resistance and soil remediation under cadmium stress[J]. Biochar, 2025, 7: 119.

[45] Wei Z, Gu Y A, Friman V P, et al. Initial soil microbiome composition and functioning predetermine future plant health[J]. Science Advances, 2019, 5(9): eaaw0759.

[46] You C, Ren P, Guan Y, et al. Forecasting root rot disease through predictive microbial functional profiling[J]. Advanced Science, 2026, 13(23): e22628.

[47] Zhu L, Xu Y C, Li J P, et al. Environmentally persistent microbial contamination in agricultural soils: high risk of pathogenicity and antibiotic resistance[J]. Environment International, 2024, 190: 108902.

[48] 陈保冬, 赵方杰, 张莘, 等. 土壤生物与土壤污染研究前沿与展望[J]. 生态学报, 2015, 35(20): 6604-6613.

[49] Chen B D, Zhao F J, Zhang X, et al. Soil pollution and soil organisms: an overview of research progress and perspectives[J]. Acta Ecologica Sinica, 2015, 35(20): 6604-6613(in Chinese with English abstract).

[50] Mather A E, Gilmour M W, Reid S W J, et al. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world[J]. Nature Reviews Microbiology, 2024, 22(9): 543-555.

[51] Savary S, Willocquet L, Pethybridge S J, et al. The global burden of pathogens and pests on major food crops[J]. Nature Ecology & Evolution, 2019, 3(3): 430-439.

[52] Xie S T, Ding L J, Huang F Y, et al. VFG-Chip: a high-throughput qPCR microarray for profiling virulence factor genes from the environment[J]. Environment International, 2023, 172: 107761.

[53] Zhu L, Lian Y L, Lin D, et al. Insights into microbial contamination in multi-type manure-amended soils: the profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes[J]. Journal of Hazardous Materials, 2022, 437: 129356.

[54] Karkman A, Pärnänen K, Larsson D G J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments[J]. Nature Communications, 2019, 10: 80.

[55] Liu Z T, Ma R A, Zhu D, et al. Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome[J]. Nature Communications, 2024, 15: 5168.

[56] Zhao Y X, Li L G, Huang Y, et al. Global soil antibiotic resistance genes are associated with increasing risk and connectivity to human resistome[J]. Nature Communications, 2025, 16: 7141.

[57] Forsberg K J, Reyes A, Wang B, et al. The shared antibiotic resistome of soil bacteria and human pathogens[J]. Science, 2012, 337(6098): 1107-1111.

[58] Munck C, Albertsen M, Telke A, et al. Limited dissemination of the wastewater treatment plant core resistome[J]. Nature Communications, 2015, 6: 8452.

[59] Jones H N, Bebber D P, Chaloner T M, et al. Threats to global food security from emerging fungal and oomycete crop pathogens[J]. Nature Food, 2020, 1(6): 332-342.

[60] Emmenegger B, Massoni J, Pestalozzi C M, et al. Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning[J]. Nature Communications, 2023, 14: 7983.

[61] Singh B K, Hu H W, MacDonald C A, et al. Microbiome-facilitated plant nutrient acquisition[J]. Cell Host & Microbe, 2025, 33(6): 869-881.

[62] Chen X L, Ma X Z, Liu Z X, et al. Organic fertilizers increase microbial community diversity and stability slowing down the transformation process of nutrient cycling[J]. Environmental Microbiome, 2025, 20: 130.

[63] Ma W M, Tang S H, Dengzeng Z M, et al. Root exudates contribute to belowground ecosystem hotspots: a review[J]. Frontiers in Microbiology, 2022, 13: 937940.

[64] Hamza A, Karčauskienė D, Ali Tahir M, et al. Root-soil interactions a key driver of aggregate formation and stability: a trait-based and mechanistic review[J]. Plant and Soil, 2026, 521(2): 1037-1066.

[65] Liang X W, Yu S P, Ju Y F, et al. Integrated management practices foster soil health, productivity, and agroecosystem resilience[J]. Agronomy, 2025, 15(8): 1816.

[66] Steinauer K, Thakur M P, Hannula S E, et al. Root exudates and rhizosphere microbiomes jointly determine temporal shifts in plant-soil feedbacks[J]. Plant, Cell & Environment, 2023, 46(6): 1885-1899.

[67] 王光州, 申建波, 张俊伶, 等. 植物-土壤反馈驱动的土壤健康机制与调控策略[J/OL]. 土壤学报, 2025-09-24. https://link.cnki.net/urlid/32.1119.P.20250924.1218.002.

[68] Wang G Z, Shen J B, Zhang J L, et al. Soil health mechanism and regulation strategy driven by plant-soil feedback[J/OL]. China Industrial Economics, 2025-09-24. https://link.cnki.net/urlid/32.1119.P.20250924.1218.002(in Chinese with English abstract).

[69] Zhou Y Y, Yang Z, Liu J G, et al. Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease[J]. Nature Communications, 2023, 14: 8126.

[70] Zhang H L, Guo D S, Lei Y T, et al. Cover crop rotation suppresses root-knot nematode infection by shaping soil microbiota[J]. New Phytologist, 2025, 245(1): 363-377.

[71] Wang X F, Wang S, Huang M C, et al. Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness[J]. mBio, 2024, 15(6): e03016-e03023.

[72] Wang X F, Wei Z, Yang K M, et al. Phage combination therapies for bacterial wilt disease in tomato[J]. Nature Biotechnology, 2019, 37(12): 1513-1520.

[73] Yang K M, Fu R X, Feng H C, et al. RI enhances plant disease resistance via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota[J]. Molecular Plant, 2023, 16(9): 1379-1395.

[74] You C, Zhang W Q, Guan Y, et al. Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot[J]. Microbiome, 2026, 14: 157.

[75] Jiang G F, Zhang Y L, Gan G Y, et al. Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation[J]. ISME Communications, 2022, 2: 10.

[76] Singh B K, Jiang G F, Wei Z, et al. Plant pathogens, microbiomes, and soil health[J]. Trends in Microbiology, 2025, 33(8): 887-902.

[77] Liu L L, Kong J J, Cui H L, et al. Relationships of decomposability and C/N ratio in different types of organic matter with suppression of Fusarium oxysporum and microbial communities during reductive soil disinfestation[J]. Biological Control, 2016, 101: 103-113.

[78] Pieterse C M J, Zamioudis C, Berendsen R L, et al. Induced systemic resistance by beneficial microbes[J]. Annual Review of Phytopathology, 2014, 52: 347-375.

[79] Liao H P, Lu X M, Rensing C, et al. Hyperthermophilic composting accelerates the removal of antibiotic resistance genes and mobile genetic elements in sewage sludge[J]. Environmental Science & Technology, 2018, 52(1): 266-276.

[80] Zhu N, Long Y J, Kan Z X, et al. Reduction of mobile genetic elements determines the removal of antibiotic resistance genes during pig manure composting after thermal pretreatment[J]. Bioresource Technology, 2023, 387: 129672.

[81] Xie T, Lin D, et al. Nano-biochar regulates phage-host interactions, reducing antibiotic resistance genes in vermicomposting systems[J]. Proc Natl Acad Sci USA, 2025, 122(34): e2511986122.

[82] Li Q, Zhang L Y, et al. Positive contribution of antimicrobial biodegradation in mitigating conjugative transfer of antibiotic resistance genes[J]. Environmental Science & Technology, 2025, 59(40): 21645-21656.

[83] Xu Y, Fu T H, You G X, et al. Niche differentiation shaped the evolution of rhizobacterial antibiotic resistance in paddy fields: evidences from spatial-temporal and chemical-biological scaling[J]. Journal of Hazardous Materials, 2025, 491: 137924.

[84] Citorik R J, Mimee M, Lu T K. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases[J]. Nature Biotechnology, 2014, 32(11): 1141-1145.

[85] Zheng F, Bi Q F, Giles M, et al. Fates of antibiotic resistance genes in the gut microbiome from different soil fauna under long-term fertilization[J]. Environmental Science & Technology, 2021, 55(1): 423-432.

[86] Zhu D, Xiang Q, Yang X R, et al. Trophic transfer of antibiotic resistance genes in a soil detritus food chain[J]. Environmental Science & Technology, 2019, 53(13): 7770-7781.

基金资助

国家自然科学基金项目(42542018)

教育部基础学科和交叉学科突破计划生物肥药学科突破先导项目(JYB2025XDXM703)

江苏省自然科学基金项目(BK20230988, BK20230194)