Plants are colonized by a myriad of microorganisms, collectively referred as plant microbiomes or phytomicrobiome, represents a fascinating frontier in sustainable agriculture and ecosystem health. The plant microbiomes including bacteria, fungi, viruses, and archaea inhabit various plant compartments (such as the phyllosphere, rhizosphere and endosphere) and interact with plants in complex ways. These microbial communities can promote plant growth, outcompete with pathogens, and activate plant immune responses. The mechanisms displayed by plant microbiomes can be broadly categorized into direct (including antibiosis, competition for nutrients, and parasitism) and indirect strategies (like induced systemic resistance, immune modulation, and hormone signaling), all of which not only reduces dependency on agrochemicals but also promotes soil health and crop resilience. While the potential of harnessing the plant microbiome for disease suppression is promising, however further research is needed to identify the key metabolites involved in host pathogen interactions and elucidating the molecular mechanisms behind disease suppression. Further, challenges such as variable field efficacy, instability under stress, and limited regulatory frameworks hinder large-scale implementation need to be addressed to effectively translate this strategy into resilient agricultural practices. This chapter pinpoints the multifaceted roles of plant-associated microbiomes in plant health and disease suppression, emphasizing them as potential alternative for securing global food security and promoting sustainable agriculture.
Plant microbiomes, Immune responses, Disease suppression, Sustainable agriculture, Next-generation sequencing
Ajar, N. Y., Priyanka, V., Divjot, K., Kusam, L. R., Vinod, K., Bhanumati, S., Vinay, S. C., Sugitha, T. C. K., Anil, K. S., & Harcharan, S. D. (2017). Plant microbiomes and its beneficial multifunctional plant growth promoting attributes. International Journal of Environmental Science and Natural Resource, 3, 555601.
Arora, N. K., Khare, E., & Maheshwari, D. K. (2010). Plant growth promoting rhizobacteria: constraints in bioformulation, commercialization and future strategies. In: Maheshwari DK (ed) Bacteria and plant health. Springer, Berlin, pp 97–116.
Azevedo, J. L., Maccheroni, W. J., Pereira, J. O., & de Araújo, W. L. (2000). Endophytic microorganism a review on insect control and recent advances on tropical plants. Electronic Journal of Biotechnology, 1, 40–65.
Badri, D. V., & Vivanco, J. M. (2009) Regulation and function of root exudates. Plant Cell and Environment, 32, 666–681.
Baker, K. F. (1987) Evolving concepts of biological control of plant pathogens. Annual Review of Phytopathology, 25, 67–85.
Bashan, Y., & Holguin, G. (1998) Proposal for the division of plant growth-promoting rhizobacteria into two classifications: biocontrol-PGPB (plant growth-promoting bacteria) and PGPB. Soil Biology and Biochemistry, 30, 1225–1228.
Berg, G. & Smalla, K. (2009). Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiology Ecology, 68, 1–13.
Bhatia, S., Dubey, R.C., & Maheshwari, D.K. (2005). Enhancement of plant growth and suppression of collar rot of sunflower caused by Sclerotium rolfsii through fluorescent Pseudomonas. Indian Phytopathology, 58, 17–24.
Bonaterra. A., Camps, J., & Montesinos, E. (2005) Osmotically induced trehalose and glycine betaine accumulation improves tolerance to desiccation, survival and efficacy of the postharvest bio control agent Pantoea agglomerans EPS125. FEMS Microbiology Letter 250, 1–8.
Boraste, A., Vamsi, K. K., Jhadav, A., Khairnar, Y., Gupta, N., Trivedi, S., Patil, P., Gupta, G., Gupta, M., Mujapara, A. K., & Joshi, B. (2009). Biofertilizers: a novel tool for agriculture. International Journal of Microbiology Research, 1, 23–31.
Brar, S.K., Verma, M., Tyagi, R.D., & Valero, J. R. (2006). Recent advances in downstream processing and formulations of Bacillus thuringiensis based biopesticides. Process Biochemistry 41, 323–342.
Bremer, C., Braker, G., Matthies, D., Beierkuhnlein, C., & Conrad, R. (2009) Plant presence and species combination, but not diversity, influence denitrifier activity and the composition of K-type denitrifier communities in grassland soil. FEMS Microbiology Ecology, 70, 377–387.
Broeckling, C. D., Broz, A.K., Bergelson, J., Manter, D. K., & Vivanco, J. M. (2008) Root exudates regulate soil fungal community composition and diversity. Applied and Environmental Microbiology, 74, 738–744.
Brown, M., & Burlingham, S.K. (1968) Production of plant growth substances by Azotobacter chroococcum. Journal of General Microbiology, 53, 135–144.
Broz, A. K., Manter, D. K., & Vivanco, J. M. (2007). Soil fungal abundance and diversity: another victim of the invasive plant Centaurea maculosa. International Society for Microbial Ecology Journal, 1, 763–765.
Bulgarelli, D., Schlaeppi, K., Spaepen, S., van Themaat, E. V. L., & Schulze-Lefert, P. (2013). Structure and functions of the bacterial microbiota of plants. Annual Review of Plant Biology, 64, 807–838.
Burges, H. D., & Jones, K. A. (1998). Formulation of microbial biopesticides: beneficial microorganisms, nematodes and seed treatments. Kluwer Academic, Dordrecht, p 411
Callaghan, M. O., & Gerard, F. M. (2005). Establishment of Serratia entomophila in soil from a granular formulation. New Zealand Plant Protection, 58, 122–125.
Cassán, F., Vanderleyden, J., & Spaepen, S. (2013). Physiological and agronomical aspects of phytohormone production by model plant-growth-promoting rhizobacteria (PGPR) belonging to the genus Azospirillum. Journal of Plant Growth Regulators, 33, 440–459. https://doi.org/10.1007/ s00344-013-9362-4
Cheng, W., & Gershenson, A. (2007). Carbon fluxes in the rhizosphere. In: Cardon ZG, Whitbeck JL (eds) The rhizosphere—an ecological perspective. Academic, San Diego, pp 31–56.
DeBach, P. (1964). The scope of biological control. In: Paul DeBach, Evert I Schlinger. Biological control of insect pests and weeds. Reinhold Publishing Corporation, New York, pp 3–20.
Dennis, P. G., Miller, A. J., & Hirsch, P. R. (2010). Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiology Ecology, 72, 313–327.
Dey, R., Sarkar, K., Dutta, S., Murmu, S., & Mandal, N. (2017). Role of Azotobacter sp. isolates as a plant growth promoting agent and their antagonistic potentiality against soil borne pathogen (Rhizoctonia solani) under in vitro condition. International Journal of Current Microbiology and Applied Science 6, 2830–2836.
Dimpka, C. (2016). Microbial siderophores: production, detection and application in agriculture and environment. Endocytobiosis Cell Research, 27, 7–16.
Doornbos, R., van Loon, L., & Bakker, P. (2012). Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. Agronomy for Sustainable Development, 32, 227–234.
Dutta, S., & Khurana, S. P. (2015). Plant growth-promoting rhizobacteria for alleviating abiotic stresses in medicinal plants. In: Plant-growth-promoting rhizobacteria (PGPR) and medicinal plants. Springer, Cham, pp 167–200.
Evans, J., Wallace, C., & Dobrowolski, N. (1993) Interaction of soil type and temperature on the survival of Rhizobium leguminosarum bv. viciae. Soil Biology and Biochemistry, 25, 1153–1160.
Falk, S. P., Gadoury, D. M., Cortesi, P., Pearson, R. C., & Seem, R. C. (1995). Partial control of grape powdery mildew by the mycoparasite Ampelomyces quisqualis. Plant Disease, 79, 483–490.
Farzaneh, M., Vierheilig, H., Lössl, A., & Kaul, H. P. (2011). Arbuscular mycorrhiza enhances nutrient uptake in chickpea. Plant, Soil and Environment, 57, 465–470.
Franken, P. (2012) The plant strengthening root endophyte Piriformospora indica: potential application and the biology behind. Applied Microbiology and Biotechnology, 96, 1455–1464.
Geetanjali, & Jain, P. (2016). Antibiotic production by rhizospheric soil microflora—a review. International Journal of Pharmaceutical Sciences and Research, 7, 4304–4314.
Grunsven, R. H. A., Putten, W. H., Bezemer, T. M., & Veenendaal, E. M. (2009). Plant-soil feedback of native and range expanding plant species is insensitive to temperature. Oecologia 162, 1059–1069.
Gupta, A., & Gopal, M. (2008). Siderophore production by plant growth promoting rhizobacteria. Indian Journal of Agricultural Research, 42, 153–156.
Haas, D., & Défago, G. (2005). Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiology, 3(4), 307.
Hardoim, P. R., van Overbeek, L. S., Berg, G., Pirttilä, A. M., Compant, S., Campisano, A., Döring, M., & Sessitsch, A. (2015). The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiology and Molecular Biology Reviews, 79(3), 293–320.
Harris, J., & Dent, D. (2000). Priorities in biopesticide research and development in developing coun tries. CAB International Centre, Wallingford
Heyadri, A., & Pessarakli, M. (2010). A review on biological control of fungal plant pathogens using microbial antagonists. Journal of Biological Sciences, 10, 273–290.
Hiltner, L. (1904) Über neuere Erfahrungen und Probleme auf dem Gebiet der Bodenbakteriologie und unter besonderer Berücksichtigung der Grüdungen und Brache. Arbeiten der Deutschen Landwirtschafts-Gesellschaft H 98, 59–78.
Hirano, S. S., & Upper, C. D. (2000). Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae—a pathogen, ice nucleus, and epiphyte. Microbiology and Molecular Biology Reviews, 64(3), 624–653.
Hwang, S. F., Ahmed, H. U., Gossen, B. D., Kutcher, H. R., Brandt, S. A., Strelkov, S. E., Chang, K. F., & Turnbull, G. D. (2009). Effect of crop rotation on the soil pathogen population dynamics and canola seed ling establishment. Plant Pathology Journal, 8, 106–112.
Hynes, R. K., & Boyetchko, S. M. (2006) Research initiatives in the art and science of biopesticide formulations. Soil Biology and Biochemistry, 38, 845–849.
Jeyarajan, R., & Nakkeeran, S. (2000) Exploitation of microorganisms and viruses as biocontrol agents for crop disease management. In: RK Upadhyay et al. (eds) Biocontrol potential and their exploitation in sustainable agriculture. Kluwer Academic/Plenum, New York, pp 95–116.
Jones, D. L., Hodge, A., & Kuzyakov, Y. (2004). Plant and mycorrhizal regulation of rhizo deposition. New Phytologist, 163, 459–480.
Kabi, M. C. (1997) Impact of biofertilizer on rural development. In: Proceedings of National Conference on Impact of Biotechnology and Modern Horticulture in Rural Development, Jadavpur.
Kandel, S. L., Joubert, P. M., & Doty, S. L. (2017). Bacterial endophyte colonization and distribution within plants. Microorganisms, 5, 77.
Knowles, A. (2008) Recent developments of safer formulations of agrochemicals. Environmentalist, 28, 35–44.
Kosanke, J. W., Osburn, R. M., Shuppe, G. I., & Smith, R.S. (1992). Slow rehydration improves the recovery of dried bacterial populations. Canadian Journal of Microbiology, 38, 520–525.
Kumar, V. V. (2018). Biofertilizers and biopesticides in sustainable agriculture. In: Meena VS (ed) Role of rhizospheric microbes in soil. Springer, Singapore, pp 377–398.
Laatsch, H., & AntiBase. (2010), A data base for rapid structural determination of microbial natural products, and annual updates, chemical concepts, Weinheim, Germany; see http://wwwuser. gwdg.de/~ucoc/laatsch/AntiBase.htm
Lambers, H., Mougel, C., Jaillard, B., & Hinsinger, P. (2009). Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective. Plant Soil, 321, 83–115.
Lindermann, R. G. (1988). Mycorrhizal interactions with the rhizosphere microflora: the mycorrhizal effect. Phytopathology, 78, 366–371.
Lindow, S. E., & Brandl, M. T. (2003). Microbiology of the phyllosphere. Applied Environmental Microbiology, 69(4), 1875–1883.
Mbarga, J. B., Begoude, B. A. D., Ambang, Z., Meboma, M., Kuate, J., Schiffers, B., & Hoopen, G. M. T. (2014). A new oil-based formulation of Trichoderma asperellum for the biological control of cacao black pod disease caused by Phytophthora megakarya. Biological Control, 77, 15–22.
Mendes, R., Kruijt, M., De Bruijn, I., Dekkers, E., Van der Voor, T. M., Schneider, J. H., Piceno, Y. M., De Santis, T. Z., Andersen, G. L., Bakker, P. A., & Raaijmakers, J. M. (2011). Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science, 332, 1097–1100.
Morales, S. E., & Holben, W. E. (2011). Linking bacterial identities and ecosystem processes: can “omic” analyses be more than the sum of their parts? FEMS Microbiology Ecology 75, 2–16.
Morel, M. A., Brana, V., & Castro-Sowinski, S. (2012). Legume crops, importance and use of bacterial inoculation to increase the production. In: Goyal A (ed) Crop plant. InTech, Rijeka, pp 217–240.
Morel, M. A., Cagide, C., Minteguiaga, M. A., Dardanelli, M. S., & Castro-Sowinski, S. (2015). The pattern of secreted molecules during the co-inoculation of alfalfa plants with Sinorhizobium meliloti and Delftia sp. strain JD2: an interaction that improves plant yield. Molecular Plant-Microbe Interaction, 28, 134–142.
Morel, M. A., & Castro-Sowinski, S. (2013) The complex molecular signaling network in microbe–plant interaction. In: Arora NK (ed) Plant microbe symbiosis: fundamentals and advances. Springer, New Delhi, pp 169–199.
Naher, L., Yusuf, U. K., Ismail, A., & Hossain, A. (2014). Trichoderma spp.: a biocontrol agent for sustain able management of plant diseases. Pakistan Journal of Botanicals, 46, 1489–1493.
Nguyen, C. (2003). Rhizodeposition of organic C by plant: mechanisms and controls. In: Lichtfouse E, Navarrete M, Debaeke P, Véronique S, Alberola C (eds) Sustainable agriculture. Springer, Dordrecht, pp 97–123.
Nongkhlaw, F. M. W., & Joshi, S. R. (2014). Distribution pattern analysis of epiphytic bacteria on ethnomedicinal plant surfaces: a micrographical and molecular approach. Journal of Microscopy and Ultrastructure, 2, 34–40.
Pal, K. K., & Gardener, B. M. (2006). Biological control of plant pathogens. The Plant Health Instructor, 2, 1117–1142.
Patel, M. V., & Patel, R. K. (2014). Indole-3-acetic acid (IAA) production by endophytic bacteria isolated from saline dessert, the little Runn of Kutch. CIBTech Journal of Microbiology, 3, 17–28.
Paul, E., Fages, J., Blanc, P., Goma, G., & Pareilleux, A. (1993). Survival of alginate-entrapped cells of Azospirillum lipoferum during dehydration and storage in relation to water properties. Applied Microbiology and Biotechnology, 40, 34–39.
Pieterse, C. M., Zamioudis, C., Berendsen, R. L., Weller, D. M., Van Wees, S. C., & Bakker, P. A. (2014) Induced systemic resistance by beneficial microbes. Annual Review of Phytopathology, 52.
Prashar, P., Kapoor, N., & Sachdeva, S. (2014). Rhizosphere: its structure, bacterial diversity and significance. Reviews in Environmental Science and Bio-Technology, 13(1), 63–77.
Pundir, R. K., & Jain, P. (2015). Mechanism of prevention and control of medicinal plant-associated diseases. In: Plant growth promoting rhizobacteria (PGPR) and medicinal plants. Springer, Cham, pp 231–246.
Rangaswamy, V. (2012). Improved production of gibberellic acid by Fusarium moniliforme. Journal of Microbiology Research, 2, 51–55.
Rani, T. U., Naidu, N. V., Ramalaxmi, C.S., Kumar, V.V., & Sreelatha, T. (2011). Bioefficacy of mycorrhizae on yield and quality of sugarcane. Journal of Soils and Crops, 21, 1–8.
Robin, A., Vansuyt, G., Hinsinger, P., Meyer, J. M., Briat, J. F., & Lemanceau, P. (2008). Iron dynamics in the rhizosphere: consequences for plant health and nutrition. Advances in Agronomy, 99, 183–225.
Roesch, L. F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H., Camargo, F. A., Farmerie, W. G., & Triplett, E. W. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. International Society for Microbial Ecology Journal, 1, 283–290.
Rout, M. E., & Southworth, D. (2013) The root microbiome influences scales from molecules to ecosystems: the unseen majority. American Journal of Botany, 100, 1689–1691.
Santoro, M. V., Cappellari, L., Giordano, W., & Banchio, E. (2015). Systemic induction of secondary metabolite biosynthesis in medicinal aromatic plants mediated by rhizobacteria. In: Plant- growth- promoting rhizobacteria (PGPR) and medicinal plants. Springer, Cham, pp 263–285.
Schenkeveld, Y., Schindlegger, Y., Oburger E., Puschenreiter, M., Hann, S., & Kraemer, S. M. (2014). Geochemical processes constraining iron uptake in strategy II Fe acquisition. Environmental Science and Technology, 48, 12662–12670.
Schlaeppi, K., & Bulgarelli, D. (2015). The plant microbiome at work. Molecular Plant-Microbe Interaction, 28, 212–217.
Seneviratne, G., & Kulasooriya, S. A. (2013). Reinstating soil microbial diversity in agroecosystems: the need of the hour for sustainability and health. Agriculture, Ecosystems & Environment, 164, 181–182.
Shah-Smith, D. A., & Burns, R. G. (1997) Shelf-life of a biocontrol Pseudomonas putida applied to sugarbeet seeds using commercial coating. Biocontrol Science and Technology, 7, 65–74.
Sharma, A., Diwevidi, V. D., Singh, S., Pawar, K. K., Jerman, M., Singh, M., Singh, S., & Srivastawa, D. (2013) Biological control and its important in agriculture. The International Journal of Biotechnology and Bioengineering Research, 4, 175–180.
Sharma, S., & Kaur, M. (2017). Plant hormones synthesized by microorganisms and their role in biofertilizer—a review article. International Journal of Advanced Research, 5(12), 1753–1762.
Showkat, S., Murtaza, I., Laila, O., & Ali, A. (2012). Biological control of Fusarium oxysporum and Aspergillus sp. by Pseudomonas fluorescens isolated from wheat rhizosphere soil of Kashmir. IOSR Journal of Pharmacy and Biological Sciences, 1, 24–32.
Singh, K. N., & Merchant, K. (2012). The agrochemical industry. In: Kent JA (ed) Handbook of industrial chemistry and biotechnology. Springer, New York, pp 643–699.
Singh, S. K., & Pathak, R. (2015) Ecological manipulations of rhizobacteria for curbing medicinal plant diseases. In: Plant-growth-promoting rhizobacteria (PGPR) and medicinal plants. Springer, Cham, pp 217–230.
Sivasakthi, S., Saranraj, P., & Sivasakthivelan, P. (2017). Biological nitrogen fixation by Azotobacter sp.—a review. Indo-Asian journal of multi-disciplinary research, 3, 1274–1284.
Steyaert, J. M., Ridgway, H. J., Elad, Y., & Stewart, A. (2003) Genetic basis of mycoparasitism: a mechanism of biological control by species of Trichoderma. New Zealand Journal of Crop and Horticultural Science, 31, 281–291.
Tadros, T. (2013). Suspension concentrates. In: Tadros T (ed) Encyclopedia of colloid and interface science. Springer, Berlin/Heidelberg, 1334–1334.
Takagi, S., Kamei, S., & Yu, M. H. (2008). Efficiency of iron extraction from soil by mugineic acid family phytosiderophores. Journal of Plant Nutrition, 11, 643–651.
Tien, T. M., Gaskins, M. H., & Hubbell, D. H. (1979). Plant growth substances produced by Azospirillum brasilense and their effect on the growth of pearl millet (Pennisetum americanum L.). Applied and Environmental Microbiology, 37, 1016–1024.
Torsvik, V., Goksøyr, J., & Daae, F. L. (1990). Comparison of phenotypic diversity and DNA heterogenecity in a population of soil bacteria. Applied and Environmental Microbiology, 56, 776–781.
Tripathi, S., Kamal, S., & Sheramati, I. (2008) Mycorrhizal fungi and other root endophytes as biocontrol agents against root pathogens. Mycorrhiza, 3, 281–306.
Vinalea, F., Sivasithamparamb, K., Ghisalbertic, E. L., Marraa, R., Wooa, S. L., & Loritoa, M. (2008). Trichoderma plant pathogen interactions. Soil Biology and Biochemistry, 40, 1–10.
Vorholt, J. (2012). Microbial life in the phyllosphere. Nature Review of Microbiology, 10, 828–840.
Waghunde, R. R., Shelake, R. M., Shinde, M. S., & Hayashi, H. (2017). Endophyte microbes: a weapon for plant health management. In: Microorganisms for green revolution. Springer, Singapore, pp 303–325.
