Skip to main navigation menu Skip to main content Skip to site footer

Review Articles

Vol. 13 No. sp1 (2026): Recent Advances in Agriculture

Microbial biofilms and their role in sustainable agriculture and climate-smart farming

DOI
https://doi.org/10.14719/pst.12853
Submitted
21 November 2025
Published
21-01-2026

Abstract

Microbial biofilms are organised populations of microbes covered with a self-made extracellular polymeric matrix and are at the core of climate-smart farming and sustainable agriculture. Biofilms enhance soil health by stabilising soil structures, enhancing microbial diversity and promoting nutrient cycling and thereby naturally supporting plant growth and resilience. One way biofilm-forming plant growth promoting rhizobacteria (PGPR) might be helping plants is by making them better able to take up nutrients through the solubilization of elements such as nitrogen, phosphorus and potassium; at the same time, they release phytohormones and compounds that alleviate stress to make plants resistant to abiotic stresses like salinity and drought. Root colonisation becomes more durable and pathogen biocontrol can be done more efficiently by biofilm matrices, which protect microorganisms from environmental stresses. Rhizospheric interactions exemplified by cross-kingdom biofilms with fungi are the most effective ways to exchange nutrients and enhance ecosystem resilience. The growth of stable biofilm communities and their microbial diversity can be supported by agricultural techniques such as the use of organic additives and conservation tillage. Recent developments emphasise the use of biofilm-based inoculants as biofertilizers, bio-stimulants and biocontrol agents in an effort to lower chemical inputs and greenhouse gas emissions in agroecosystems. More research and innovative applications like multi-strain consortia and biofilm-enhanced seed coating provide promising ways of harnessing microbial biofilms for increased agricultural productivity and soil quality, as well as environmental sustainability in the face of climate change.

References

  1. 1. Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. Sci Tot Environ. 2023;900:165801. https://doi.org/10.1016/j.scitotenv.2023.165801
  2. 2. Wu Y, Cai P, Jing X, Niu X, Ji D, Ashry NM, et al. Soil biofilm formation enhances microbial community diversity and metabolic activity. Environ Intl. 2019;132:105116. https://doi.org/10.1016/j.envint.2019.105116
  3. 3. Zhang M, Wu Y, Qu C, Huang Q, Cai P. Microbial extracellular polymeric substances (EPS) in soil: from interfacial behaviour to ecological multifunctionality. Geo-bio Interfaces. 2024;1:e4. https://doi.org/10.1180/gbi.2024.4
  4. 4. Ajijah N, Fiodor A, Pandey AK, Rana A, Pranaw K. Plant growth promoting bacteria (PGPB) with biofilm-forming ability: a multifaceted agent for sustainable agriculture. Diversity. 2023;15(1):112. https://doi.org/10.3390/d15010112
  5. 5. Fu B, Yan Q. Exopolysaccharide is required for motility, stress tolerance and plant colonization by the endophytic bacterium Paraburkholderia phytofirmans PsJN. Front Microbiol. 2023;14:1218653.
  6. 6. Naveen S, Balachandar D. Extracellular polymeric substances of plant-growth-promoting rhizobacteria modulate the positive plantsoil feedback in maize via soil conditioning. Sci Tot Environ. 2025;975:179256. https://doi.org/10.1016/j.scitotenv.2025.179256
  7. 7. Altaf MM, Ahmad I. Plant growth promoting activities, biofilm formation and root colonization by Bacillus sp. isolated from rhizospheric soils. J Pure Appl Microbiol. 2016;10(1):109–20.
  8. 8. Coenye T, Ahonen M, Anderson S, Cámara M, Chundi P, Fields M, et al. Global challenges and microbial biofilms: identification of priority questions in biofilm research, innovation and policy. Biofilm. 2024;8:100210. https://doi.org/10.1016/j.bioflm.2024.100210
  9. 9. Karygianni L, Ren Z, Koo H, Thurnheer T. Biofilm Matrixome: extracellular components in structured microbial communities. Trends Microbiol. 2020;28(8):668–81. https://doi.org/10.1016/j.tim.2020.03.01
  10. 10. Flemming HC, Wingender J. The biofilm matrix. Nat Rev Microbiol. 2010;8(9):623–33. https://doi.org/10.1038/nrmicro2415
  11. 11. Rather MA, Gupta K, Mandal M. Microbial biofilm: formation, architecture, antibiotic resistance and control strategies. Braz J Microbiol. 2021;52(4):1701–18. https://doi.org/10.1007/s42770-021-00624-x
  12. 12. Perez JJ, Oseguera FA, Monnappa AK, Santos JI, Bianco V, Nie P, et al. Self-adaptation of Pseudomonas fluorescens biofilms to hydrodynamic stress. arXiv. 2021. https://doi.org/10.48550/arXiv.2101.02542
  13. 13. Luo A, Wang F, Sun D, Liu X, Xin B. Formation, development and cross-species interactions in biofilms. Front Microbiol. 2022;12:757327. https://doi.org/10.3389/fmicb.2021.757327
  14. 14. Zhang N, Yang D, Wang D, Miao Y, Shao J, Zhou X, et al. Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates. BMC Genomics. 2015;16(1):685. https://doi.org/10.1186/s12864-015-1825-5
  15. 15. Fan B, Li L, Chao Y, Förstner K, Vogel J, Borriss R, et al. dRNA-Seq reveals genome wide TSSs and noncoding RNAs of plant beneficial rhizobacterium Bacillus amyloliquefaciens FZB42. PLoS ONE. 2015;10(11):e0142002. https://doi.org/10.1371/journal.pone.0142002
  16. 16. Haque MdM, Mosharaf MK, Khatun M, Haque MdA, Biswas MdS, Islam MdS, et al. Biofilm producing rhizobacteria with multiple plant growth-promoting traits promote growth of tomato under water-deficit stress. Front Microbiol. 2020;11:542053. https://doi.org/10.3389/fmicb.2020.542053
  17. 17. Wang X, Liu M, Yu C, Li J, Zhou X. Biofilm formation: mechanistic insights and therapeutic targets. Mol Biomed. 2023;4(1):49. https://doi.org/10.1186/s43556-023-00164-w
  18. 18. Rajewska M, Maciąg T, Narajczyk M, Jafra S. Carbon source and substrate surface affect biofilm formation by the plant-associated bacterium Pseudomonas donghuensis P482. IJMS. 2024;25(15):8351. https://doi.org/10.3390/ijms25158351
  19. 19. Liaqat F, Ansar W, Muhammad N, Tariq M, Nazir Z, Qamar HMG, et al. Development of microbial biofilms and their role in device, non device and organ system level infections. BioSci Rev. 2025;7(2):32–53. https://doi.org/10.32350/bsr.72.04
  20. 20. Zhang B, Hu X, Zhao D, Wang Y, Qu J, Tao Y, et al. Harnessing microbial biofilms in soil ecosystems: enhancing nutrient cycling, stress resilience and sustainable agriculture. J Environ Manage. 2024;370:122973. https://doi.org/10.1016/j.jenvman.2024.122973
  21. 21. Li Y, Narayanan M, Shi X, Chen X, Li Z, Ma Y. Biofilms formation in plant growth-promoting bacteria for alleviating agroenvironmental stress. Sci Tot Environ. 2024;907:167774. https://doi.org/10.1016/j.scitotenv.2023.167774
  22. 22. Chen Q, Song Y, An Y, Lu Y, Zhong G. Soil microorganisms: their role in enhancing crop nutrition and health. Diversity. 2024;16(12):734. https://doi.org/10.3390/d1612073421
  23. 23. Rafique M, Naveed M, Mumtaz MZ, Niaz A, Alamri S, Siddiqui MH, et al. Unlocking the potential of biofilm-forming plant growth promoting rhizobacteria for growth and yield enhancement in wheat (Triticum aestivum L.). Sci Rep. 2024;14(1):15546. https://doi.org/10.1038/s41598-024-66562-4
  24. 24. Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. Methods Microbiol. 2023;3–48. https://doi.org/10.1016/bs.mim.2023.05.006
  25. 25. Nair BM, Vijayaraghavan R. Biofilm chronicles: unravelling quorum secrets for disease management. J Adv Biol Biotechnol. 2025;28(10):840–63. https://doi.org/10.9734/jabb/2025/v28i103108
  26. 26. Riseh RS, Fathi F, Vazvani MG, Tarkka MT. Plant colonization by biocontrol bacteria and improved plant health: a review. Front Biosci. 2025;30(1):23223. https://doi.org/10.31083/FBL23223
  27. 27. Chen Y, Yan F, Chai Y, Liu H, Kolter R, Losick R, et al. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation. Environ Microbiol. 2013;15(3):848–64. https://doi.org/10.1111/j.1462-2920.2012.02860.x
  28. 28. Rudrappa T, Biedrzycki ML, Bais HP. Causes and consequences of plant-associated biofilms. FEMS Microbiol Ecol. 2008;64(2):153–66. https://doi.org/10.1111/j.1574-6941.2008.00465.x
  29. 29. Zhang C, Van Der Heijden MGA, Dodds BK, Nguyen TB, Spooren J, Valzano-Held A, et al. A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization. Microbiome. 2024;12(1):13. https://doi.org/10.1186/s40168-023-01726-4
  30. 30. Pandit A, Adholeya A, Cahill D, Brau L, Kochar M. Microbial biofilms in nature: unlocking their potential for agricultural applications. J Appl Microbiol. 2020;129(2):199–211. https://doi.org/10.1111/jam.14609
  31. 31. Abdian PL, Cámara M, Cassan FD, Castrillo G, Díaz M, Gonzalez Anta G, et al. Creating pathways for collaboration between Argentina and the UK to utilise microbial biofilms in sustainable agriculture. CABI Agric Biosci. 2024;23. https://doi.org/10.1186/s43170-024-00227-0
  32. 32. Haque MdM, Biswas MdS, Mosharaf MK, Haque MdA, Islam MdS, Nahar K, et al. Halotolerant biofilm-producing rhizobacteria mitigate seawater-induced salt stress and promote growth of tomato. Sci Rep. 2022;12(1):5599. https://doi.org/10.1038/s41598-022-09519-9
  33. 33. Hidri R, Mahmoud OMB, Zorrig W, Mahmoudi H, Smaoui A, Abdelly C, et al. Plant growth-promoting rhizobacteria alleviate high salinity impact on the halophyte Suaeda fruticosa by modulating antioxidant defense and soil biological activity. Front Plant Sci. 2022;13:821475. https://doi.org/10.3389/fpls.2022.821475
  34. 34. Gupta G, Parihar SS, Ahirwar NK, Snehi SK, Singh V. Plant growth promoting rhizobacteria (PGPR): current and future prospects for development of sustainable agriculture. J Microb Biochem Technol. 2015;7(2):96–102. http://dx.doi.org/10.4172/1948-5948.1000188
  35. 35. Miquel Guennoc C, Rose C, Labbé J, Deveau A. Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls? FEMS Microbiol Ecol. 2018;94(7). https://doi.org/10.1093/femsec/fiy093
  36. 36. Dos Santos AJ, Shen H, Lanza MRV, Li Q, Garcia-Segura S. Electrochemical oxidation of surfactants as an essential step to enable greywater reuse. Environ Technol Innov. 2024;34:103563. https://doi.org/10.1016/j.eti.2024.103563
  37. 37. Karimi E, Aliasgharzad N, Esfandiari E, Hassanpouraghdam MB, Neu TR, Buscot F, et al. Biofilm-forming rhizobacteria affect the physiological and biochemical responses of wheat to drought. AMB Expr. 2022;12(1):93. https://doi.org/10.1186/s13568-022-01432-8
  38. 38. Latif M, Bukhari SAH, Alrajhi AA, Alotaibi FS, Ahmad M, Shahzad AN, et al. Inducing drought tolerance in wheat through exopolysaccharide producing rhizobacteria. Agronomy. 2022;12(5):1140. https://doi.org/10.3390/agronomy12051140
  39. 39. Liu Y, Dai Z, Wang D, Ma Y, Guo P. Root surface microbial biofilms in phytoremediation: formation processes, regulatory mechanisms, influencing factors and roles. Environ Technol Innov. 2025;40:104406. https://doi.org/10.1016/j.eti.2025.104406
  40. 40. Takeuchi K, Ogiso M, Ota A, Nishimura K, Nishino C, Omori Y, et al. Pseudomonas rhodesiae HAI-0804 suppresses Pythium damping-off and root rot in cucumber by its efficient root colonization promoted by amendment with glutamate. Front Microbiol. 2024;15:1485167. https://doi.org/10.3389/fmicb.2024.1485167
  41. 41. Maan H, Gilhar O, Porat Z, Kolodkin-Gal I. Bacillus subtilis colonization of Arabidopsis thaliana roots induces multiple biosynthetic clusters for antibiotic production. Front Cell Infect Microbiol. 2021;11. https://doi.org/10.3389/fcimb.2021.722778
  42. 42. Montes-Osuna N, Gómez-Lama Cabanás C, Valverde-Corredor A, Berendsen RL, Prieto P, Mercado-Blanco J. Assessing the involvement of selected phenotypes of Pseudomonas simiae PICF7 in olive root colonization and biological control of Verticillium dahliae. Plants. 2021;10(2):412. https://doi.org/10.3390/plants10020412
  43. 43. Timmusk S, Copolovici D, Copolovici L, Teder T, Nevo E, Behers L. Paenibacillus polymyxa biofilm polysaccharides antagonise Fusarium graminearum. Sci Rep. 2019;9(1):662. https://doi.org/10.1038/s41598-018-37718-w
  44. 44. Guan Y, Bak F, Hennessy RC, Horn Herms C, Elberg CL, Dresbøll DB, et al. The potential of Pseudomonas fluorescens SBW25 to produce viscosin enhances wheat root colonization and shapes root associated microbial communities in a plant genotype-dependent manner in soil systems. In: McMahon K, editor. mSphere. 2024;9(7):e00294-24. https://doi.org/10.1128/msphere.00294-24
  45. 45. Valente IDL, Wancura JHC, Zabot GL, Mazutti MA. Endophytic and rhizospheric microorganisms: an alternative for sustainable, organic and regenerative bioinput formulations for modern agriculture. Microorganisms. 2025;13(4):813. https://doi.org/10.3390/microorganisms13040813
  46. 46. Yaron S, Römling U. Biofilm formation by enteric pathogens and its role in plant colonization and persistence. Microb Biotechnol. 2014;7(6):496–516. https://doi.org/10.1111/1751-7915.12186
  47. 47. Morris CE, Monier J, Jacques M. Methods for observing microbial biofilms directly on leaf surfaces and recovering them for isolation of culturable microorganisms. Appl Environ Microbiol. 1997;63(4):1570–6. https://doi.org/10.1128/aem.63.4.1570-1576.1997
  48. 48. Peredo EL, Simmons SL. Leaf-FISH: microscale imaging of bacterial taxa on phyllosphere. Front Microbiol. 2018;8:2669. https://doi.org/10.3389/fmicb.2017.02669
  49. 49. Cordero-Bueso G, Vigentini I, Foschino R, Maghradze D, Ruiz-Muñoz M, Benitez-Trujillo F, et al. Culturable yeast diversity of grape berriesfrom Vitis vinifera ssp. sylvestris (Gmelin) Hegi. J Fungi. 2022;8(4):410. https://doi.org/10.3390/jof8040410
  50. 50. Sabaghian S, Braschi G, Vannini L, Patrignani F, Samsulrizal NH, Lanciotti R. Isolation and identification of wild yeast from Malaysian grapevine and evaluation of their potential antimicrobial activity against grapevine fungal pathogens. Microorganisms. 2021;9(12):2582. https://doi.org/10.3390/microorganisms9122582
  51. 51. Kushwaha P, Kashyap PL, Srivastava AK, Tiwari RK. Plant growth promoting and antifungal activity in endophytic Bacillus strains from pearl millet (Pennisetum glaucum). Braz J Microbiol. 2020;51(1):229–41. https://doi.org/10.1007/s42770-019-00172-5
  52. 52. Amaya-Gómez CV, Porcel M, Mesa-Garriga L, Gómez-Álvarez MI. A framework for the selection of plant growth-promoting rhizobacteria based on bacterial competence mechanisms. Appl Environ Microbiol. 2020;86(14):e00760–20. https://doi.org/10.1128/AEM.00760-20
  53. 53. Ahmad Ansari F, Ahmad I, Pichtel J. Synergistic effects of biofilm producing PGPR strains on wheat plant colonization, growth and soil resilience under drought stress. Saudi J Biol Sci. 2023;30(6):103664. https://doi.org/10.1016/j.sjbs.2023.103664
  54. 54. Ansari FA, Ahmad I. Biofilm development, plant growth promoting traits and rhizosphere colonization by Pseudomonas entomophila FAP1: a promising PGPR. Adv Microbiol. 2018;8(3):235–51. https://doi.org/10.4236/aim.2018.83016
  55. 55. Ansari FA, Ahmad I. Fluorescent Pseudomonas FAP2 and Bacillus licheniformis interact positively in biofilm mode enhancing plant growth and photosynthetic attributes. Sci Rep. 2019;9(1):4547. https://doi.org/10.1038/s41598-019-40864-4
  56. 56. Cai Y, Tao H, Gaballa A, Pi H, Helmann JD. The extracytoplasmic sigma factor σX supports biofilm formation and increases biocontrol efficacy in Bacillus velezensis 118. Sci Rep. 2025;15(1):5315. https://doi.org/10.1038/s41598-025-89284-7
  57. 57. Zhu ML, Wu XQ, Wang YH, Dai Y. Role of biofilm formation by Bacillus pumilus HR10 in biocontrol against pine seedling damping-off disease caused by Rhizoctonia solani. Forests. 2020;11(6):652. https://doi.org/10.3390/f11060652
  58. 58. Lahlali R, Ezrari S, Radouane N, Kenfaoui J, Esmaeel Q, El Hamss H, et al. Biological control of plant pathogens: a global perspective. Microorganisms. 2022;10(3):596. https://doi.org/10.3390/microorganisms10030596
  59. 59. Ashry NM, Alaidaroos BA, Mohamed SA, Badr OAM, El-Saadony MT, Esmael A. Utilization of drought-tolerant bacterial strains isolated from harsh soils as a plant growth-promoting rhizobacteria (PGPR). Saudi J Biol Sci. 2022;29(3):1760–9. https://doi.org/10.1016/j.sjbs.2021.10.054
  60. 60. Kaushal M, Wani SP. Plant-growth-promoting rhizobacteria: drought stress alleviators to ameliorate crop production in drylands. Ann Microbiol. 2016;66(1):35–42. https://doi.org/10.1007/s13213-015-1112-3
  61. 61. Naseem H, Bano A. Role of plant growth-promoting rhizobacteria and their exopolysaccharide in drought tolerance of maize. J Plant Interact. 2014;9(1):689–701. https://doi.org/10.1080/17429145.2014.902125
  62. 62. Shankar A, Prasad V. Potential of desiccation-tolerant plant growth promoting rhizobacteria in growth augmentation of wheat (Triticum aestivum L.) under drought stress. Front Microbiol. 2023;14:1017167. https://doi.org/10.3389/fmicb.2023.1017167
  63. 63. Oliva RL, Khadka UB, Camenzind T, Dyckmans J, Joergensen RG. Constituent of extracellular polymeric substances (EPS) produced by a range of soil bacteria and fungi. BMC Microbiol. 2025;25(1):298. https://doi.org/10.1186/s12866-025-04034-z
  64. 64. Khan MH, Liu H, Zhu A, Khan MH, Hussain S, Cao H. Conservation tillage practices affect soil microbial diversity and composition in experimental fields. Front Microbiol. 2023;14:1227297. https://doi.org/10.3389/fmicb.2023.1227297
  65. 65. Reddy PN, Mounika C, Kashyap S, Chandravanshi M, Reddy MS, Raigar BL. Role of biofilms for enhancing nutrient use efficiency: a review. Int J Res Agron. 2024;7(9):39–46.
  66. 66. Velmourougane K, Thapa S, Prasanna R. Prospecting microbial biofilms as climate smart strategies for improving plant and soil health: a review. Pedosphere. 2023;33(1):129–52. https://doi.org/10.1016/j.pedsph.2022.06.037
  67. 67. Khan N, Bano A. Exopolysaccharide producing rhizobacteria and their impact on growth and drought tolerance of wheat grown under rainfed conditions. PLoS ONE. 2019;14(9):e0222302. https://doi.org/10.1371/journal.pone.0222302
  68. 68. Olagoke FK, Bettermann A, Nguyen PTB, Redmile-Gordon M, Babin D, Smalla K, et al. Importance of substrate quality and clay content on microbial extracellular polymeric substances production and aggregate stability in soils. Biol Fertil Soils. 2022;58(4):435–57. https://doi.org/10.1007/s00374-022-01632-1
  69. 69. Kim JY, Cho KS. Inoculation effect of Pseudomonas sp. TF716 on N2O emissions during rhizoremediation of diesel-contaminated soil. Sci Rep. 2022;12(1):13018. https://doi.org/10.1038/s41598-022-17356-z
  70. 70. Kaur J, Mudgal G, Chand K, Singh GB, Perveen K, Bukhari NA, et al. An exopolysaccharide-producing novel Agrobacterium pusense strain JAS1 isolated from snake plant enhances plant growth and soil water retention. Sci Rep. 2022;12(1):21330. https://doi.org/10.1038/s41598-022-25225-y

Downloads

Download data is not yet available.