Review of Plant Beneficial Microorganisms and Their Biocontrol Mechanism in Controlling Plant Disease

doi:10.16409/j.cnki.2095-039x.2025.02.059

Abstract

Abstract: Plant beneficial microorganisms have functions such as inhibiting pathogenic bacteria, enhancing plant disease resistance, promoting plant growth, and improving plant stress tolerance. Currently, plant beneficial microorganisms have become a research hotspot in the field of biological control, achieving significant development and progress. To better understand and utilize plant beneficial microorganisms, the types of plant beneficial microorganisms, their functions beneficial to plants, their interactions with plants, and the mechanism of action in biological control were reviewed in this paper, based on research progress both domestically and internationally. Additionally, it will present considerations and prospects for utilizing plant beneficial microorganisms in biological control. This will help to comprehensively understand the role of beneficial microorganisms in plants and provide new strategies for the development and utilization of beneficial microorganisms in plants.

Key words: plant beneficial microorganisms, biological control, plant disease

CLC Number:

S476

CHEN Feifei, XU Shiyi, KONG Jiahui, MIN Ziquan, WANG Yahui, PAN Yuemin. Review of Plant Beneficial Microorganisms and Their Biocontrol Mechanism in Controlling Plant Disease[J]. Chinese Journal of Biological Control, 2025, 41(5): 1263-1275.

References

[1] He D C, Burdon J J, Xie L H, et al. Triple bottom-line consideration of sustainable plant disease management: From economic, sociological and ecological perspectives[J]. Journal of Integrative Agriculture, 2021, 20(10): 2581-2591.
[2] 康振生. 聚焦小麦赤霉病，助力国家粮食安全[J]. 生物技术进展, 2021, 11(5): 553.
[3] Mishra S, Srivastava S, Dewangan J, et al. Global occurrence of deoxynivalenol in food commodities and exposure risk assessment in humans in the last decade: a survey[J]. Critical Reviews in Food Science and Nutrition, 2020, 60(8): 1346-1374.
[4] Chakraborty S, Newton A C. Climate change, plant diseases and food security: an overview[J]. Plant Pathology, 2011, 60(1): 2-14.
[5] Gould F, Brown Z S, Kuzma J. Wicked evolution: Can we address the sociobiological dilemma of pesticide resistance?[J]. Science, 2018, 360(6390): 728-732.
[6] Gunstone T, Cornelisse T, Klein K, et al. Pesticides and soil invertebrates: A hazard assessment[J]. Frontiers in Environmental Science, 2021, 9(3): 161-176.
[7] Li C J, Zhu H M, Li C Y, et al. The present situation of pesticide residues in China and their removal and transformation during food processing[J]. Food Chemistry, 2021, 354: 129552.
[8] Pandit M A, Kumar J, Gulati S, et al. Major biological control strategies for plant pathogens[J]. Pathogens, 2022, 11(2): 237.
[9] Niu J Z, Hull-Sanders H, Zhang Y X, et al. Biological control of arthropod pests in citrus orchards in China[J]. Biological Control, 2014, 68: 15-22.
[10] Migunova V D, Sasanelli N. Bacteria as biocontrol tool against phytoparasitic nematodes[J]. Plants-Basel, 2021, 10(2): 389.
[11] Karthika S, Varghese S, Jisha M S. Exploring the efficacy of antagonistic rhizobacteria as native biocontrol agents against tomato plant diseases[J]. 3 Biotech, 2020, 10(7): 320.
[12] Diaz-Siefer P, Olmos-Moya N, Fonturbel F E, et al. Bird-mediated effects of pest control services on crop productivity: a global synthesis[J]. Journal of Pest Science, 2022, 95(2): 567-576.
[13] Rizvi S A H, George J, Reddy G V P, et al. Latest developments in insect sex pheromone research and its application in agricultural pest management[J]. Insects, 2021, 12(6): 484.
[14] 袁善奎, 王以燕, 师丽红, 等. 我国生物源农药标准制定现状及展望[J]. 中国生物防治学报, 2018, 34(1): 1-7.
[15] 崔佳佳, 张雪洪. 微生物源农用抗生素的研发与高产策略[J]. 生物工程学报, 2021, 37(3): 1032-1041.
[16] 刘艳潇, 祝一鸣, 周而勋. 植物免疫诱抗剂的作用机理和应用研究进展[J]. 分子植物育种, 2020, 18(3): 1020-1026.
[17] Rodriguez P A, Rothballer M, Chowdhury S P, et al. Systems biology of plant-microbiome interactions[J]. Molecular Plant, 2019, 12(6): 804-821.
[18] Trivedi P, Leach J E, Tringe S G, et al. Plant-microbiome interactions: from community assembly to plant health[J]. Nature Reviews Microbiology, 2020, 18(11): 607-621.
[19] Yu Y Y, Gui Y, Li Z J, et al. Induced systemic resistance for improving plant immunity by beneficial microbes[J]. Plants-Basel, 2022, 11(3): 386.
[20] Ku Y S, Liao Y J, Chiou S P, et al. From trade-off to synergy: microbial insights into enhancing plant growth and immunity[J]. Plant Biotechnology Journal, 2024, 22(9): 2461-2471.
[21] Mandal S D, Jeon J. Phyllosphere microbiome in plant health and disease[J]. Plants-Basel, 2023, 12(19): 3481.
[22] 潘建刚, 呼庆, 齐鸿雁, 等. 叶际微生物研究进展[J]. 生态学报, 2011, 31(2): 583-592.
[23] 陈招荣, 刘新悦, 赵欣迪, 等. 植物内生菌群落组成及其功能研究进展[J]. 生命科学, 2023, 35(2): 132-139.
[24] Petrini O. Fungal endophytes of tree leaves[C]// Andrews J H, Hirano S S. Microbial Ecology of Leaves. New York, US: Springer New York, NY, 1991, 179-197.
[25] Kharwar R N, Mishra A, Gond S K, et al. Anticancer compounds derived from fungal endophytes: their importance and future challenges[J]. Natural Product Reports, 2011, 28(7): 1208-1228.
[26] McKinney. Mosaic diseases in the Canary Islands, West Africa and Gibraltar[J]. Journal of Agricultural Research, 1929, 39: 577-578.
[27] 张瑞福. 根际微生物:农业绿色发展中大有作为的植物第二基因组[J]. 生物技术通报, 2020, 36(9): 1-2.
[28] Kloepper J W, Schroth M N. Plant growth promoting rhizobacteria on radishes[C]//Proceedings of the 4th international conference on plant pathogenic bacteria II, Station de Pathologie Vegetale et Phytobacteriologie. Angers, France: INRA, 1978: 879-882.
[29] Latef A, Abu Alhmad M F, Kordrostami M, et al. Inoculation with Azospirillum lipoferum or Azotobacter chroococcum reinforces maize growth by improving physiological activities under saline conditions[J]. Journal of Plant Growth Regulation, 2020, 39(3): 1293-1306.
[30] Wang H T, Wu C F, Zhang H Q, et al. Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease[J]. World Journal of Microbiology & Biotechnology, 2022, 38(9): 155.
[31] Harley J L. The significance of mycorrhiza[J]. Mycological Research, 1989, 92(2): 129-139.
[32] Ivanov S, Austin J, Berg R H, et al. Extensive membrane systems at the host-arbuscular mycorrhizal fungus interface[J]. Nature Plants, 2019, 5(2): 194-203.
[33] 聂建华, 张理航, 张明明, 等. 真菌病毒减弱寄主致病性机理及其生防应用[J]. 中国生物防治学报, 2022, 38(4): 951-958.
[34] Ge H J, Fu S S, Guo H M, et al. Application and challenge of bacteriophage in the food protection[J]. International Journal of Food Microbiology, 2022, 380: 109872.
[35] Strathdee S A, Hatfull G F, Mutalik V K, et al. Phage therapy: From biological mechanisms to future directions[J]. Cell, 2023, 186(1): 17-31.
[36] Hsueh Y P, Mahanti P, Schroeder F C, et al. Nematode-trapping fungi eavesdrop on nematode pheromones[J]. Current Biology, 2013, 23(1): 83-86.
[37] Boukaew S, Cheirsilp B, Yossan S, et al. Utilization of palm oil mill effluent as a novel substrate for the production of antifungal compounds by Streptomyces philanthi RM-1-138 and evaluation of its efficacy in suppression of three strains of oil palm pathogen[J]. Journal of Applied Microbiology, 2022, 132(3): 1990-2003.
[38] Zhang H Z, Zhang C H, Xiang X L, et al. Uptake and transport of antibiotic kasugamycin in castor bean (Ricinus communis L.) seedlings[J]. Frontiers in Microbiology, 2022, 13: 948171.
[39] Li Z J, Tang S Y, Gao H S, et al. Plant growth-promoting rhizobacterium Bacillus cereus AR156 induced systemic resistance against multiple pathogens by priming of camalexin synthesis[J]. Plant Cell and Environment, 2024, 47(1): 337-353.
[40] Olaniyan F T, Alori E T, Adekiya A O, et al. The use of soil microbial potassium solubilizers in potassium nutrient availability in soil and its dynamics[J]. Annals of Microbiology, 2022, 72(1): 45.
[41] Soumare A, Diedhiou A G, Thuita M, et al. Exploiting biological nitrogen fixation: A route towards a sustainable agriculture[J]. Plants-Basel, 2020, 9(8): 1011.
[42] 吕俊, 于存. 一株高效溶磷伯克霍尔德菌的筛选鉴定及对马尾松幼苗的促生作用[J]. 应用生态学报, 2020, 31(9): 2923-2934.
[43] Ma Y, Prasad M N V, Rajkumar M, et al. Plant growth promoting rhizobacteria and endophytes accelerate phytoremediation of metalliferous soils[J]. Biotechnology Advances, 2011, 29(2): 248-258.
[44] Afzal I, Shinwari Z K, Sikandar S, et al. Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants[J]. Microbiological Research, 2019, 221: 36-49.
[45] 刘婉慧, 陈飞飞, 叶建仁, 等. 吡咯伯克霍尔德氏菌JK-SH007吲哚-3-乙酰胺IAA合成功能及其依赖途径鉴定[J]. 林业科学, 2019, 55(9): 121-129.
[46] 马莹, 曹梦圆, 石孝均, 等. 植物促生菌的功能及在可持续农业中的应用[J]. 土壤学报, 2023, 60(6): 1555-1568.
[47] Bernabeu P R, Pistorio M, Torres-Tejerizo G, et al. Colonization and plant growth-promotion of tomato by Burkholderia tropica[J]. Scientia Horticulturae, 2015, 191: 113-120.
[48] El-Hadad M E, Mustafa M I, Selim S M, et al. The nematicidal effect of some bacterial biofertilizers on Meloidogyne incognita in sandy soil[J]. Brazilian Journal of Microbiology, 2011, 42(1): 105-113.
[49] Sattar A, Naveed M, Ali M, et al. Perspectives of potassium solubilizing microbes in sustainable food production system: A review[J]. Applied Soil Ecology, 2019, 133: 146-159.
[50] Singh T B, Sahai V, Goyal D, et al. Identification, characterization and evaluation of multifaceted traits of plant growth promoting rhizobacteria from soil for sustainable approach to agriculture[J]. Current Microbiology, 2020, 77(11): 3633-3642.
[51] Verbon E H, Liberman L M. Beneficial microbes affect endogenous mechanisms controlling root development[J]. Trends in Plant Science, 2016, 21(3): 218-229.
[52] 范美玉, 黎妮, 贾雨田, 等. 耐镉阿氏芽孢杆菌缓解水稻受镉胁迫的研究[J]. 农业环境科学学报, 2021, 40(2): 279-286.
[53] 王亚军, 冯炬威, 李雅倩, 等. 高产铁载体菌Burkholderia vietnamiensis YQ9促生特性研究及其对重金属胁迫条件下种子萌发的影响[J]. 环境科学学报, 2022, 42(2): 430-437.
[54] Eljounaidi K, Lee S K, Bae H. Bacterial endophytes as potential biocontrol agents of vascular wilt diseases - review and future prospects[J]. Biological Control, 2016, 103: 62-68.
[55] Liu Y P, Xu Z H, Chen L, et al. Root colonization by beneficial rhizobacteria[J]. Fems Microbiology Reviews, 2024, 48(1): fuad066.
[56] Janisiewicz W J, Tworkoski T J, Sharer C. Characterizing the mechanism of biological control of postharvest diseases on fruits with a simple method to study competition for nutrients[J]. Phytopathology, 2000, 90(11): 1196-1200.
[57] Shen N K, Li S Y, Li S Y, et al. The siderophore-producing bacterium, Bacillus siamensis Gxun-6, has an antifungal activity against Fusarium oxysporum and promotes the growth of banana[J]. Egyptian Journal of Biological Pest Control, 2022, 32(1): 34.
[58] Spence C, Alff E, Johnson C, et al. Natural rice rhizospheric microbes suppress rice blast infections[J]. Bmc Plant Biology, 2014, 14: 130.
[59] 林福呈, 李德葆. 枯草芽孢杆菌（ Bacillus subtilis） S9对植物病原真菌的溶菌作用[J]. 植物病理学报, 2003(2): 174-177.
[60] R W. Trichoderma lignorumas a parasite of other soil fungi[J]. Phytopathology, 1932(22): 837-845.
[61] Zhang H X, Xie J T, Fu Y P, et al. A 2-kb mycovirus converts a pathogenic fungus into a beneficial endophyte for Brassica protection and yield enhancement[J]. Molecular Plant, 2020, 13(10): 1420-1433.
[62] 黄显德, 王玉, 闫志勇, 等. 番木瓜环斑病毒西瓜株系弱毒突变体的筛选与应用[J]. 植物保护学报, 2019, 46(4): 738-744.
[63] Huang C J, Liu Y H, Yang K H, et al. Physiological response of Bacillus cereus C1L-induced systemic resistance in lily against Botrytis leaf blight[J]. European Journal of Plant Pathology, 2012, 134(1): 1-12.
[64] Torres-Rodriguez J A, Reyes-Perez J J, Quinones-Aguilar E E, et al. Actinomycete potential as biocontrol agent of phytopathogenic fungi: Mechanisms, source, and applications[J]. Plants-Basel, 2022, 11(23): 3201.
[65] Carrión V J, Perez-Jaramillo J, Cordovez V, et al. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome[J]. Science, 2019, 366(6465): 606-612.
[66] Wonglom P, Ito S, Sunpapao A. Volatile organic compounds emitted from endophytic fungus Trichoderma asperellum T1 mediate antifungal activity, defense response and promote plant growth in lettuce (Lactuca sativa)[J]. Fungal Ecology, 2020, 43: 100867.
[67] 程笑笑, 冯自力, 冯鸿杰, 等. 真菌源几丁质酶在植物抗真菌病害中的应用[J]. 植物保护, 2017, 43(3): 29-35.
[68] Zhang L L, Bao L L, Li S Y, et al. Substances derived from myxobacteria that prevent and control plant pathogenic diseases and their prevention and control principles[J]. Frontiers in Microbiology, 2024, 14: 1294854.
[69] Perrot T, Pauly M, Ramírez V. Emerging roles of β-glucanases in plant development and adaptative responses[J]. Plants-Basel, 2022, 11(9): 1119.
[70] Fira D, Dimkic I, Beric T, et al. Biological control of plant pathogens by Bacillus species[J]. Journal of Biotechnology, 2018, 285: 44-55.
[71] Cochrane S A, Vederas J C. Lipopeptides from Bacillus and Paenibacillus spp.: A gold mine of antibiotic candidates[J]. Medicinal Research Reviews, 2016, 36(1): 4-31.
[72] Park E J, Jang H J, Park J Y, et al. Efficacy evaluation of Streptomyces nigrescens KA-1 against the root-knot nematode Meloidogyne incognita[J]. Biological Control, 2023, 179: 105150.
[73] Dimopoulou A, Theologidis I, Benaki D, et al. Direct antibiotic activity of bacillibactin broadens the biocontrol range of Bacillus amyloliquefaciens MBi600[J]. Msphere, 2021, 6(4): e00376-00321.
[74] Phoka N, Suwannarach N, Lumyong S, et al. Role of volatiles from the endophytic fungus Trichoderma asperelloides PSU-P1 in biocontrol potential and in promoting the plant growth of Arabidopsis thaliana[J]. Journal of Fungi, 2020, 6(4): 341.
[75] Lin L, Shao X L, Yang Y C, et al. Lysobacter enzymogenes: A fully armed biocontrol warrior[J]. Journal of Integrative Agriculture, 2025, 24(1): 23-35.
[76] Lin L, Shen D Y, Shao X L, et al. Soil microbiome bacteria protect plants against filamentous fungal infections via intercellular contacts[J]. Proceedings of The National Academy of Sciences of The United States of America, 2025, 122(3): e2418766122.
[77] 许沛冬, 易剑锋, 陈迪, 等. 贝莱斯芽孢杆菌生防次级代谢产物研究进展[J]. 生物技术通报, 2024, 40(3): 75-88.
[78] Sehrawat A, Sindhu S S, Glick B R. Hydrogen cyanide production by soil bacteria: Biological control of pests and promotion of plant growth in sustainable agriculture[J]. Pedosphere, 2022, 32(1): 15-38.
[79] Kremer R J, Souissi T. Cyanide production by rhizobacteria and potential for suppression of weed seedling growth[J]. Current Microbiology, 2001, 43: 182-186.
[80] Li Y Q, Zhou X L, Zhang X J, et al. A myxobacterial GH19 lysozyme with bacteriolytic activity on both gram-positive and negative phytopathogens[J]. Amb Express, 2022, 12(1): 54.
[81] Druzhinina I S, Seidl-Seiboth V, Herrera-Estrella A, et al. Trichoderma: the genomics of opportunistic success[J]. Nature Reviews Microbiology, 2011, 9(12): 749-759.
[82] Weindling R. Trichoderma lignorumas a parasite of other soil fungi[J]. Phytopathology, 1932, 22: 837-845.
[83] Barnett H L, Binder F L. The fungal host-parasite relationship[J]. Annual Review of Phytopathology, 1973, 11(1): 273-292.
[84] 李利. 白粉菌重寄生真菌的分离鉴定及生物学特性研究[D]. 杨凌: 西北农林科技大学, 2016.
[85] Chen Y Y, Chen P C, Tsay T T. The biocontrol efficacy and antibiotic activity of Streptomyces plicatus on the oomycete Phytophthora capsici[J]. Biological Control, 2016, 98: 34-42.
[86] Wu J N, Xin R L, Jiang Y C, et al. Botrytis cinerea type II inhibitor of apoptosis BcBIR1 enhances the biocontrol capacity of Coniothyrium minitans[J]. Microbial Biotechnology, 2024, 17(2): e14402.
[87] Wang Y, Yu H, Xu Y, et al. Expression of a mycoparasite protease in plant petals suppresses the petal-mediated infection by necrotrophic pathogens[J]. Cell Reports, 2023, 42(11): 113290.
[88] Casadevall A, Pirofski L A. Host-pathogen interactions: redefining the basic concepts of virulence and pathogenicity[J]. Infection and immunity, 1999, 67(8): 3703-3713.
[89] Hillman B I, Suzuki N. Viruses of the chestnut blight fungus, Cryphonectria parasitica [M]. Advances in Virus Research. Academic Press. 2004: 423-472.
[90] Rajesha G, Nakkeeran S, Hubballi M, et al. Endophytic bacterial biocontrol agents degrade a putative toxin of Alternaria macrospora responsible for the severity of cotton leaf blight[J]. Journal of Plant Pathology, 2021, 103(4): 1283-1293.
[91] Shen M, Xia D, Yin Z F, et al. Bacillus pumilus WP8 exhibits biocontrol efficacy against tomato bacterial wilt via attenuation of the virulence of the pathogenic bacterium[J]. ACTA Agriculturae Scandinavica Section B-Soil and Plant Science, 2018, 68(5): 379-387.
[92] Zhu X X, Chen W J, Bhatt K, et al. Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review[J]. Frontiers in Plant Science, 2023, 13: 1063393.
[93] Sason G, Yedidia I, Nussinovitch A, et al. Self-demise of soft rot bacteria by activation of microbial predators by pectin-based carriers[J]. Microbial Biotechnology, 2023, 16(7): 1561-1576.
[94] Xu L, Zhang W, Liu S, et al. Transcriptome analysis of the synergistic mechanisms between two strains of potato virus Y in Solanum tuberosum L.[J]. Virology, 2024, 594: 110032.
[95] Liu Y, Zhang H, Wang J, et al. Nonpathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant "cry for help" response to assemble disease suppressing and growth promoting rhizomicrobiome[J]. Nature Communications, 2024, 15(1): 1907.
[96] Liu X Y, Matsumoto H, Lv T X, et al. Phyllosphere microbiome induces host metabolic defence against rice false-smut disease[J]. Nature Microbiology, 2023, 8(8): 1419-1433.
[97] Liu H, Wang J, Sun H M, et al. Transcriptome profiles reveal the growth-promoting mechanisms of Paenibacillus polymyxa YC0136 on tobacco (Nicotiana tabacum L.)[J]. Frontiers in Microbiology, 2020, 11: 584174.
[98] Castrillo G, Teixeira P, Paredes S H, et al. Root microbiota drive direct integration of phosphate stress and immunity[J]. Nature, 2017, 543(7646): 513-518.
[99] Garrido-Oter R, Nakano R T, Dombrowski N, et al. Modular traits of the rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia[J]. Cell Host & Microbe, 2018, 24(1): 155-167.
[100] Yi J C, Zhang D J, Cheng Y J, et al. The impact of Paenibacillus polymyxa HY96-2 luxS on biofilm formation and control of tomato bacterial wilt[J]. Applied Microbiology and Biotechnology, 2019, 103: 9643-9657.
[101] Abedon S T. Ecology of anti-biofilm agents II: Bacteriophage exploitation and biocontrol of biofilm bacteria[J]. Pharmaceuticals (Basel, Switzerland), 2015, 8(3): 559-589.
[102] Vasic T, Andjelkovic S, Radovic J, et al. Alfalfa inoculation: the effect on root growth and number of rhizospheric microorganisms[J]. Romanian Biotechnological Letters, 2014, 19(4): 9457-9464.
[103] Huang X Q, Zhang N, Yong X Y, et al. Biocontrol of Rhizoctonia solani damping-off disease in cucumber with Bacillus pumilus SQR-N43[J]. Microbiological Research, 2012, 167(3): 135-143.
[104] Ballaré C L, Austin A T. Recalculating growth and defense strategies under competition: key roles of photoreceptors and jasmonates[J]. Journal of Experimental Botany, 2019, 70(13): 3425-3434.
[105] 李法喜, 段廷玉. AM真菌和其他4类有益微生物联合防治植物病害研究进展[J]. 中国草地学报, 2021, 43(8): 93-105.
[106] Neeraj, Singh K. Organic amendments to soil inoculated arbuscular mycorrhizal fungi and Pseudomonas fluorescens treatments reduce the development of root-rot disease and enhance the yield of Phaseolus vulgaris L.[J]. European Journal of Soil Biology, 2011, 47(5): 288-295.
[107] Singh P, Singh R K, Guo D J, et al. Whole genome analysis of sugarcane root-associated endophyte Pseudomonas aeruginosa b18-a plant growth-promoting bacterium with antagonistic potential against Sporisorium scitamineum[J]. Frontiers in Microbiology, 2021, 12: 628376.
[108] Tahir H A S, Gu Q, Wu H J, et al. Bacillus volatiles adversely affect the physiology and ultra-structure of Ralstonia solanacearum and induce systemic resistance in tobacco against bacterial wilt[J]. Scientific Reports, 2017, 7: 40481.
[109] Eida A A, Bougouffa S, L'Haridon F, et al. Genome insights of the plant-growth promoting bacterium Cronobacter muytjensii JZ38 with volatile-mediated antagonistic activity against Phytophthora infestans[J]. Frontiers in Microbiology, 2020, 11: 369.
[110] Tian B, Xie J, Fu Y, et al. A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases[J]. The ISME Journal, 2020, 14(12): 3120-3135.
[111] Yu X, Li B, Fu Y P, et al. A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus[J]. Proceedings of The National Academy of Sciences of the United States of America, 2010, 107(18): 8387-8392.