Bio-control emerges as a novel and environmentally sustainable method for mitigating soil-borne plant pathogens

Author info »

Introduction

Soil-borne pathogens are responsible for a decline in yield, quality of products; contaminate food grains and other economic parts of the plant with harmful toxic chemicals and causing great economic losses [1]. Pythium spp., Rhizoctonia spp., Fusarium spp., Phytophthora spp., Xanthomonas spp. and Pseudomonas spp. are the most common pathogens of soil affecting most of the crops and causing various diseases like root rot, leaf fall, wilting, damping-off, blight, canker, etc., in plants. Due to climate change these plant pathogens are becoming more aggressive, breaking the plant resistance to various germplasm and predominantly cultivated varieties and inhibit the crop to reach its optimum yield. The current practices for management of these diseases are mostly based on host plant resistance and synthetic chemicals. The continuous overuse of these chemicals like pesticides, insecticides, herbicides and fertilizers in agriculture for controlling diseases directly effect on the health of consumers, disturbing the food chain and food web, biomagnifications of chemicals and economic losses to any country by increasing the cost of food products and other side effect have raised a serious alarm [2,3]. Food grains are important for consumers and to prevent it from the contamination of chemicals, a new approach “biocontrol” has been used in agriculture. The Biocontrol Agents (BCAs) refer to the organism responsible for inhibiting or prevent the growth and development of other harmful pathogens. Some of plant growth-promoting rhizobacteria are studied and used in managing soil-borne diseases in plants as they reduce diseases by acting as biocontrol agents [4]. Biocontrol encompasses a diverse array of eco-friendly microbes, offering a rich source of biologically active compounds. These microbes have the remarkable ability to coexist in the environment as non-dominant species while effectively suppressing plant pathogens. Leveraging biological control serves as a sustainable approach to managing plant pathogens, fostering a deeper understanding of the intricate interactions among pathogens, plants and the environment in the pursuit of sustainable agriculture [5].

Methodology

What are biocontrol agents?

The term ‘biocontrol’ have used in several areas of biology, especially in plant pathology and entomology. The biocontrol in which the living organism such as bacteria, fungi, nematode or predatory insect those suppresses the growth and development of other organism populations. The term biocontrol agents apply to the use of microbial antagonists which suppresses the growth of pathogens included mainly host-specific. The microbial antagonist that used to control the soil-borne plant diseases, by making bio-formulations called bio-pesticides. Bio-pesticides are eco-friendly approaches for the control of soil-borne pathogens in peanut by the mechanisms involved in their antagonistic activity (Figure 1).

Figure 1: Proposed model for a biocontrol research and development program.

Initially, a diverse array of microorganisms is gathered and subjected to screening for biocontrol efficacy. Numerous isolates undergo screening to pinpoint a disease-suppressive strain (illustrated as a yellow rod). However, it's improbable for this strain to exhibit effectiveness across various conditions. A strategy for identifying new strains that collectively demonstrate efficacy across diverse conditions involves unraveling biocontrol mechanisms and discovering additional biocontrol agents sharing these mechanisms. Genetic analyses can unveil biocontrol mechanisms, such as the role of antibiotic X in biocontrol mechanism. Understanding these mechanisms and the associated genes can facilitate the development of nucleic acid probes tailored to identify new strains with identical biocontrol mechanisms, as depicted by a probe for gene anfX. Despite sharing similar biocontrol mechanisms, strains harboring antX may exhibit genetic diversity in significant aspects. This diversity enables some new strains to be effective on different crops across various geographic regions or as part of genetically diverse mixtures. This approach facilitates the identification of extensive collections of disease-suppressive strains, bypassing the necessity to replicate the extensive research [6].

The function of prospective bio-control agents in management of soilborne pathogens

Soil-borne pathogens survive in soil as soil inhabitants and saprobes, widely distributed depend upon the cropping and production practices. Soil with poor irrigation facilitates allow the growth of several soil-borne pathogens which included mainly fungal pathogens like Phytophthora, Pythium while, Fusarium and Verticillium wilt occur more frequently in damp soils rather than in dry soils [7]. The usage of Plant Growth-Promoting Rhizobacteria (PGPR) as biocontrol agents, against the soil-borne fungal pathogens, is a complementary strategy [8,9]. The biocontrol provides by PGPR involves competition, parasitism, antibiosis, etc., which act as a natural process [10,11]. Pathogen suppression by PGPR occurs mainly by the activities involved in PGPR rapid growth, multiplication and survival [12]. Biocontrol agents contribute directly to plant growth by production of phytohormones like cytokines, gibberellins and auxin, increase nutrient uptake, siderophore and lytic enzyme production, induction of systemic acquired resistance and reduction the level of ethylene [13].

Mycorrhiza as biocontrol agents

Mycorrhiza is the most prevalent form of symbiotic relationship between plant roots and soil fungi. Symbiosis is so well balance that many of the host cells are invade by the fungal endophyte but there is no visible tissue damage and under certain conditions, it enhances the growth and vigor of the plant. The potential role of mycorrhizal fungi as biocontrol agent for the control of fungal plant diseases has recently received considerable attention [14]. Vesicular Arbuscular (VA)-mycorrhizal infection generally inhibits or sometimes increases and occasionally has no effect on diseases caused by fungal pathogens [15-18]. Arbuscular Mycorrhizal Fungi (AMF) represent a functionally important component of soil microbial community, being of particular significance for plant mineral nutrition in tropical agro ecosystems [19]. Bodker et al., [20] noted the effect of phosphate and the arbuscular mycorrhizal fungus G. intraradices on disease severity of root rot of pea. In Kerala wilt infested area of solanaceous crops, the mycorrhizal fungi (Glomus sp., Acaulospora sp. and Sclerocystis sp.) were the major species and were minimum in tomato and maximum in brinjal [21]. Dai et al., [22] has been reported that in chilli phosphorus content was highest at 150% of organic manure application. Significantly more phosphorus content was observed in mycorrhizal plants than the non-mycorrhizal plants. Oyetunji et al., [23] has been reported that plants inoculated with the G. mosseae has much thickened cell walls particularly at the edges as compare to uninoculated plants. G. mosseae and T. koningii inoculations, controlled Fusarium wilt of pepper. However, these were inoculated at least a week earlier then attack by the pathogen. Tomato roots inoculation with mycorrhizal fungus strains significantly influenced the number of tomato leaves and improved the health status of the plant (Figure 2) [24].

Figure 2: (A): Maintenance of mycorrhizal fungi, maintenance of mycorrhizal fungi on wheat; (B): Arbuscules; (C): Hyphae inside root system; (D): Spore with attachment; (E): Spores inside the root; (F): Entry point of hyphae.

Pseudomonas as biocontrol agents

The genus Pseudomonas belong to the category of non-spore forming, gram-negative and rod-shaped a natural biocontrol agent living in disease suppressive soils and can rapidly grow, colonize and survive in a highly competitive ecosystem for their survival included food and space. Many researchers have been found that fluorescent Pseudomonas strain represents antagonisitic activity against fungal pathogens and abundant in the rhizosphere of different crops. Pseudomonas putida WCS358r, are genetically engineered to produce the phenazine and 2,4-Diacetylphloroglucinol (DAPG), showed modified ability to suppress the plant diseases in wheat [25]. The strains of Pseudomonas can colonize in the root system of several crops, maintaining the control population densities in the rhizosphere [26]. Two isolates of Herbaspirillium spp. and Pseudomonas spp. produced volatile compounds having the potential to inhibit the growth of Fusarium oxysporum f. sp. cubense race 4. The identified compounds were methanethiol, 3-undecene and 2-pentene 3-methyl. Talc-based preparation of P. fluorescens when applied to soil@ 15 g/plant on banana significantly checked wilt disease [27]. The capability in P. fluorescens for suppressing Fusarium depends on its potential to produce antibiotic DAPG. DAPG obtained from P. fluorescens when applied to soil significantly inhibited spore germination and growth of F. oxysporum.

Application of Trichoderma for control of soil-borne pathogens

The most commonly used bio pesticide in living form namely Trichoderma spp. have been found effective in suppressing the soil-borne plant pathogens [28]. Trichoderma a genus was first proposed by Persoon 1794 in Germany and described it as fungi having mealy powder-like appearance enclosed by a hairy covering. Some species of the genus Trichoderma have been used as effective biocontrol agents against soil-borne, foliar and postharvest fungal pathogens in several plant crops, including peanut [29]. Trichoderma species such as T. viride and T. harzianum reduced the incidence of collar rot disease in groundnut caused by Aspergillus niger in a screen house study (Figure 3) [30].

Figure 3: Trichoderma culture on Potato Dextrose Agar (PDA).

The fungus occurs worldwide and is associated with plant roots, plant debris, temperate and tropical soils in 10¹-10³ culturable propagules per gram [31]. Trichoderma species have good agricultural importance due to antagonistic abilities against soil born plant pathogens by the mechanisms of antagonism: The production of antifungal metabolites, competition for space and nutrients, induction of defense responses in the plant, mycoparasitism, ability to promote plant growth such as increase plant height, leaf area, dry weight, stronger root growth, nutrient uptake and other yield attributes. Direct effects of Trichoderma on plant growth and development are significantly important for agricultural uses and for understanding the roles of Trichoderma in natural and managed ecosystems (Figure 4) [32-35].

Figure 4: Coiling of hyphae around the pathogen, vacuolization, penetration by haustoria and lysis.

Results and Discussion

Mechanisms of action of biocontrol agents

The biological control may have resulted from many different types of interactions among the organisms (Table 1). In the mechanism of biocontrol, the pathogens are antagonized by the presence and activities of antagonists. Direct antagonist results from the direct contact or highly selective for the pathogens expressed by the antagonists, while in case of indirect antagonisms results from the activities that do not directly target the pathogens. Many of the biocontrol agent viz. Trichoderma spp., Bacillus spp., Pseudomonas fluorescens and Agrobacterium radiobacter (K84) strain [36-38].

Table 1: Progression of bacterial blight on clusterbean in relation to weather parameters epiphytotic conditions during Kharif 2023.

Antibiosis

Antibiosis is a biological interaction between microorganisms, in which the organic substance of low molecular weight produced by microorganisms that affect the metabolic activity and growth of other microbes. A variety of antibiotics have been identified, including compounds such as 2,4-Diacetylphloroglucinol (DAPG), amphisin, oomycin A, hydrogen cyanide, pyoluteorin, phenazine, tensin, pyrrolnitrin, cyclic lipopeptides and troplone produced by pseudomonads and kanosamine, oligomycin A, xanthobaccin and zwittermicin A produced by Streptomyces, Bacillus and Stenotrophomonas spp. (Table 2).

Table 2: Antibiotics producing bio-control agents against diseases.

Hyperparasitism

• The hyperparasitism means that the pathogens which are directly parasitized or attack with specific BCAs. Generally, mycoparsitism involves four steps:

• Chemotropic growth, where the biocontrol agent can grow toward the target fungus.

• The recognition includes specific interaction between lectin of pathogen or carbohydrates receptors on the biocontrol agent surface.

• Attachment by cell wall degradation such as chitinases and 1,3-glucanases.

• Penetration, where the biocontrol agent could produce a structure like appressoria for penetrating the cell wall of pathogenic fungus [39].

In some cases, multiple hyper parasites attack a single fungus such as Acremonium alternatum, Cladosporium oxysporum and Gliocladium virens can parasitize the powdery mildew fungi [40]. A classic example is the hypovirus, a hypoparasitic virus on Cryptonectria parasitica, a fungus causing chestnut blight. The hypovirulence of hypovirus reduces the diseases-producing capacity of C. parasitica [41].

Competition

Biocontrol agents and pathogens engage in competitive interactions for nutrients and space within the environment. This competition represents an indirect confrontation, wherein pathogens are excluded through resource depletion and physical occupation by biocontrol agents [42]. Filamentous fungi rely on iron uptake to regulate growth and metabolic processes. Under iron-deficient conditions, Trichoderma sp. produce siderophores, low molecular weight iron chelators, which sequester iron molecules, thereby inhibiting the growth of other fungi [43]. Additionally, carbon competition plays a significant role in suppressing Fusarium wilt, where non-pathogenic strains of F. oxysporum outcompete pathogenic ones [44]. This competition extends to the rhizosphere, where rhizobacteria effectively compete with Pythium ultimum for carbon sources, providing efficient biocontrol against seedling damping-off in various crops.

Advantages of biocontrol strategies

• Safety from hazards of chemicals.

• It can be used in organic form.

• Reduces the excessive use of pesticides.

• Reduces legal, environmental and public issues.

• Commercially available in the market.

• Environmental eco-friendly.

Disadvantages of biocontrol strategies

• Requires skilled and expertise.

• Time-consuming in disease control and does not achieve immediately.

• Take more intensive management and future planning.

• Peoples are not aware of this phenomenon.

Conclusion

Soil-borne plant diseases like wilt, damping-off, root rot and collar rot, etc. cause a hazardous impact on the yield loss in the agricultural and ornamental ecosystem. The soil-borne pathogens such as Rhizoctonia solani, Phytophthora, Pythium, Sclerotium rolfsii, Fusarium and Verticillium have a wide range of host and destroy many vegetables, ornamental and agricultural plants. In the past few years, the management of the soil-borne diseases was often based on the application of chemical mainly soil fumigants which was successful in managing the disease, but side effects of these chemicals on the environment, human and animals, turned into biggest diversified problems for whole ecosystem. Antagonistic bacteria and fungi are widely used to manage soil-borne diseases. In comparison with chemicals, biocontrol is a healthier and safer mechanism to control harmful pathogens and toxic microorganisms. Biocontrol agents also use as plant growth-promoting factors and biotic stimulation induce the Systemic Acquired Resistance (SAR) of plants against soil-borne pathogens. However, a better understanding of the factors involved and signaling interaction among antagonists and pathogens, soil and plants are yet revealed to promote the bio-control agents as wide applicable bio pesticides in a sustainable agricultural ecosystem.

References

1. Zaidi A, Ahmad E, Khan MS, et al. Role of phosphate-solubilizing microbes in the management of plant diseases. Phosphate Solubilizing Microorganisms. 2014:225-256.

   [Google Scholar]

2. Tandon S, Vats S. Microbial biosynthesis of Cadmium sulfide (Cds) nanoparticles and their characterization. Eur J Pharm Med Res. 2016;3(9):545-550.

   [Google Scholar]

3. Kaur A, Vats S, Rekhi S, et al. Physico-chemical analysis of the industrial effluents and their impact on the soil microflora. Procedia Environ Sci. 2010;2:595-599.

   [Crossref] [Google Scholar]

4. Shaikh SS, Sayyed RZ. Role of plant growth-promoting rhizobacteria and their formulation in biocontrol of plant diseases. Plant Microbes Symbiosis.

   [Crossref] [Google Scholar]

5. Sharma M, Tarafdar A, Ghosh R, et al. Biological control as a tool for eco-friendly management of plant pathogens. Adv Soil Microbiol. 2017:153-88.

   [Crossref] [Google Scholar]

6. Handelsman J, Stabb EV. Biocontrol of soilborne plant pathogens. Plant cell. 1996;8(10):1855.

   [Crossref] [Google Scholar] [PubMed]

7. Deketelaere S, Franca SC, Hofte M, et al. Desirable traits of a good biocontrol agent against Verticillium wilt. Front Microbiol. 2017;8:276684.

   [Crossref] [Google Scholar] [PubMed]

8. Haas D, Defago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol. 2005;3(4):307-319.

   [Crossref] [Google Scholar] [PubMed]

9. Weller DM. Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu Rev Phytopathol. 1988;26(1):379-407.

   [Google Scholar]

10. Weller DM, Raaijmakers JM, Gardener BB, et al. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol. 2002;40(1):309-348.

    [Crossref] [Google Scholar] [PubMed]

11. Weller DM, Landa BB, Mavrodi OV, et al. Role of 2, 4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in the defense of plant roots. Plant Biol. 2006:4-20.

    [Crossref] [Google Scholar] [PubMed]

12. Pathak R, Shrestha A, Lamichhane J, et al. PGPR in biocontrol: Mechanisms and roles in disease suppression. Int J Agron Agri R. 2017;11(1):69-80.

    [Google Scholar]

13. Bhattacharyya PN, Jha DK. Plant Growth-Promoting Rhizobacteria (PGPR): Emergence in agriculture. World J Microbiol Biotechnol. 2012;28:1327-50.

    [Crossref] [Google Scholar] [PubMed]

14. Kumar R, Mehta S, Sharma L, et al. Effect of different levels of mycorrhization on the growth parameters and nutrient content of chilli. Int J Plant Sci. 2022;34(20):464-472.

    [Crossref] [Google Scholar]

15. Chu EY, Endo T, Sten RL, et al. Evaluation of arbuscular mycorrhizal fungi inoculation on the incidence of Fusarium root rot of black pepper. Fitopatol Bras. 1997;22(2):205-208.

    [Google Scholar]

16. Rabie GH. Induction of fungal disease resistance in Vicia faba by dual inoculation with Rhizobium leguminosarum and vesicular-arbuscular mycorrhizal fungi. Mycopathologia. 1998;141(3):159-166.

    [Crossref] [Google Scholar] [PubMed]

17. Jayaraman J, Kumar D. VAM fungi pathogen-Fungicide interactions in gram. Indian Phytopathol. 1995;48(3):294-299.

    [Google Scholar]

18. Batcho M, Kane A, Thiam ML, et al. Effects of four endomycorrhizal inocula and Basamid on the development of onion roots (Allium cepa L.) cultivated in soil infected by Pyrenochaeta terrestris (Hansen) Gorenz, Walker & Larson. 1994;47:11-32.

    [Google Scholar]

19. Sakha MA, Jefwa J, Gweyi-Onyango JP, et al. Effects of arbuscular mycorrhizal fungal inoculation on growth and yield of two sweet potato varieties. J Agric Ecol. 2019;18(3):1-8.

    [Google Scholar]

20. Bodker L, Kjoller R, Rosendahl S. Effect of phosphate and the arbuscular mycorrhizal fungus glomus intraradices on disease severity of root rot of peas (Pisum sativum) caused by Aphanomyces euteiches. Mycorrhiza. 1998;8:169-174.

    [Crossref] [Google Scholar]

21. Gopal S, Otta SK, Kumar S, et al. The occurrence of Vibrio species in tropical shrimp culture environments; implications for food safety. Int J Food Microbiol. 2005;102(2):151-159.

    [Crossref] [Google Scholar] [PubMed]

22. Dai O, Singh RK, Nimasow G, et al. Effect of Arbuscular Mycorrhizal (AM) inoculation on growth of chili plant in organic manure amended soil. Afr J Microbiol Res. 2011;5(28):5004-51112.

    [Google Scholar]

23. Oyetunji OJ, Salami AO. Study on the control of Fusarium wilt in the stems of mycorrhizal and trichodermal inoculated pepper (Capsicum annum L.). J Appl Biosci. 2011;45:3071-3080.

    [Google Scholar]

24. Jamiolkowska A, Thanoon AH, Skwarylo-Bednarz B, et al. Mycorrhizal inoculation as an alternative in the ecological production of tomato (Lycopersicon esculentum Mill.). Inte Agrophysics. 2020;34(2):48.

    [Crossref] [Google Scholar]

25. Glandorf DC, Verheggen P, Jansen T, et al. Effect of genetically modified Pseudomonas putida WCS358r on the fungal rhizosphere microflora of field-grown wheat. Appl Environ Microbiol. 2001;67(8):3371-3378.

    [Crossref] [Google Scholar] [PubMed]

26. Rosas SB, Pastor NA, Guinazu LB, et al. Efficacy of Pseudomonas chlororaphis subsp. aurantiaca SR1 for improving productivity of several crops. Crop Prod Technolo. 2012:178-270.

    [Google Scholar]

27. Ting AS, Mah SW, Tee CS, et al. Detection of potential volatile inhibitory compounds produced by endobacteria with biocontrol properties towards Fusarium oxysporum f. sp. cubense race 4. World J Microbiol Biotechnol. 2011;27(2):229-235.

    [Google Scholar]

28. De RK, Dwivedi RP, Narain U. Biological control of lentil wilt caused by Fusarium oxysporum f. sp. lends. Ann Plant Sci. 2003;11(1):46-52.

    [Google Scholar]

29. Cortes C, Gutierrez A, Olmedo V, et al. The expression of genes involved in parasitism by Trichoderma harzianum is triggered by a diffusible factor. Mol Gen Genet. 1998;260:218-225.

    [Crossref] [Google Scholar] [PubMed]

30. Gajera H, Rakholiya K, Vakharia D, et al. Bioefficacy of Trichoderma isolates against Aspergillus niger Van Tieghem inciting collar rot in groundnut (Arachis hypogaea L.). J Plant Prot Res. 2011.

    [Crossref] [Google Scholar]

31. Harman GE, Howell CR, Viterbo A, et al. Trichoderma species-opportunistic, avirulent plant symbionts. Nat Rev Microbiol. 2004;2(1):43-56.

    [Crossref] [Google Scholar] [PubMed]

32. Howell CR. Mechanisms employed by Trichoderma species in the biological control of plant diseases: The history and evolution of current concepts. Plant Dis. 2003;87(1):4-10.

    [Crossref] [Google Scholar] [PubMed]

33. Topolovec-Pintaric S. Trichoderma: Invisible partner for visible impact on agriculture. 2019:15.

    [Google Scholar]

34. Kerr A. Biological control of crown gall through production of agrocin 84. Plant Dis. 1980;64(1):24-30.

    [Google Scholar]

35. Smith KP, Havey MJ, Handelsman J, et al. Suppression of cottony leak of cucumber with Bacillus cereus strain UW85. Plant Dis. 1993;77(2):139-142.

    [Crossref] [Google Scholar]

36. Shanahan P, O'Sullivan DJ, Simpson P, et al. Isolation of 2, 4-diacetylphloroglucinol from a fluorescent pseudomonad and investigation of physiological parameters influencing its production. Appl Environ Microbiol. 1992;58(1):353-358.

    [Crossref] [Google Scholar] [PubMed]

37. Howell CR, Stipanovic RD. Suppression of Pythium ultimum-induced damping-off of cotton seedlings by Pseudomonas fluorescens and its antibiotic, pyoluteorin. Phytopathology. 1980;70(8):712-715.

    [Google Scholar]

38. Wilhite SE, Lumsden RD, Straney DC, et al. Peptide synthetase gene in Trichoderma virens. Appl Environ Microbiol. 2001;67(11):5055-5062.

    [Crossref] [Google Scholar] [PubMed]

39. Lorito M, Harman GE, Hayes CK, et al. Chitinolytic enzymes produced by Trichoderma harzianum: Antifungal activity of purified endochitinase and chitobiosidase. Phytopathology. 1993;83(3):302-307.

    [Google Scholar]

40. Heydari A, Pessarakli M. A review on biological control of fungal plant pathogens using microbial antagonists. J Biol Sci. 2010;10(4):273-290.

    [Crossref] [Google Scholar]

41. Tjamos EC, Tjamos SE, Antoniou PP, et al. Biological management of plant diseases: Highlights on research and application. Plant Pathol J. 2010;92:17-21.

    [Google Scholar]

42. Lorito M, Hayes CK, Zoina A, et al. Potential of genes and gene products from Trichoderma sp. and Gliocladium sp. for the development of biological pesticides. Mol Biotechnol. 1994;2:209-217.

    [Crossref] [Google Scholar] [PubMed]

43. Benítez T, Rincon AM, Limon MC, et al. Biocontrol mechanisms of Trichoderma strains. Int Microbiol. 2004;7(4):249-260.

    [Google Scholar] [PubMed]

44. Alabouvette C, Olivain C, Migheli Q, et al. Microbiological control of soil-borne phytopathogenic fungi with special emphasis on wilt-inducing Fusarium oxysporum. New Phytol. 2009;184(3):529-544.

    [Crossref] [Google Scholar] [PubMed]