Soil has abundant microbial population and species diversity. Coexistence and interaction of these different species of soil microorganism with plant root affect plant development and soil microbial structure. Plant disease caused by plant pathogen can be controlled by biological control agents. Biocontrol may operate through antibiosis or competition for space or nutrients in the rhizosphere and parasitism. Antibiotic production is a mode of action for suppression of disease. Inhibition of pathogens by antimicrobial compound is known as antibiosis. Different volatile and non-volatile secondary metabolite have been characterized in biocontrol agents. Soil microorganisms such as fungi, bacteria and actinomycetes can produce natural bioactive compound the antibiotic.
Antibiosis is a biological interaction between organisms. During antagonistic interaction the secondary metabolite is released by one organisms that inhibits the growth of the other organisms. Biocontrol agent act through antibiosis, substrate competition, mycoparasitism and produce cell wall degrading enzyme (glucanases and chitinases) and diverse antibiotic (gliotoxin, peptaibols or gliovirin.) against the fungal phytopathogen (Howell 2003). Patulin a mycotoxin inhibits three important rice pathogen Pyricularia oryzae, Drechslera oryzae and Gerlachia oryzae (Okeke et al., 1993). Patulin is produced by Aspergillus, Penicillium and Byssochlamys (Puel et al., 2010). The species producing patulin are:
- Aspergillus clavatus and giganteus (Varga et al., 2007).
- Penicillium carneum, P. clavigerum, P. concentricum, P. coprobium, P. dipodomyicola, P. expansum, P. glandicola, P. gladioli, P. griseofulvum, P. marinum, P. paneum, P. sclerotigenum, P. vulpinum (Frisvad et al., 2004).
- Byssochlamys nivea and some strains of Paecilomyces saturatus (Samson et al., 2009).
Most of the plant disease is caused by fungus and many soil borne biocontrol agent have the potential of controlling these plant pathogen. A few example of antagonists, target pathogen and host plant (Ghisalberti 2000) are:
- Chaetomium globosum inhibits Pythium ultimum and Sclerotium cepivorum that infect sugarbeet and onion respectively.
- Gliocladium roseum suppresses Fusarium culmorum infecting wheat, Bipolaris sorokiniana that infects barley and Fusarium monoliformae that infects maize.
- Idriella bolleys controls pathogen Fusarium culmorum infecting wheat.
- Paecilomyces lilacinus suppresses fungi Macrophomina phaesolina infecting mungbean and sunflower.
- Trichoderma virens (“Q”) produce the antibiotic, gliotoxin, that is active against Rhizoctonia solani, but less active against Pythium ultimum (Howell et al., 1993), other strains (“P”) of fungus produce antibiotic gliovirin which is highly active against ultimum but has no effect on R. solani (Howell and Stipanovic, 1983). Gliocladium virens produce phytotoxin, viridiol (Howell and Stipanovic, 1984). Howell and Puckhaber (2005) studied the efficacy of the “P” and “Q” strains of Trichoderma virens. “P” Strains of T. virens are ineffective biocontrol agents of seedling disease in cotton but are pathogenic to susceptible seed lots. While the “Q” strain with high level of phytoalexins are effective biocontrol agents of cotton seedling disease and are not pathogenic to cotton.
The antagonistic potential of Trichoderma species makes it the best biocontrol agent. This involves production of extracellular cell wall degrading enzyme β-1,3-glucanases and chitinases by Trichoderma harzianum which suppresses the fungal pathogen showing antibiosis (Chet and Inbar 1994).
Antifungal metabolites produced by bacteria include ammonia, butyrolactones, 2,4-diacetylphloroglucinol, HCN, kanosamine, Oligomycin A, Oomycin A, phenazine-1-carboxylic acid, pyoluterin, pyrrolnitrin, viscosinamide, xanthobaccin, zwittermycin A and several other uncharacterized moieties (Laville et al., 1992; Milner et al., 1996; Nielson et al., 1998; Kang et al., 1998; Kim et al., 1999; Thrane et al., 1999; Nakayama et al., 1999). Fluorescent Pseudomonas population produce antifungal metabolite 2,4-diacetylphloroglucinol (Weller et al., 2002). Streptomyces synthesize many siderophores and degradative enzymes (e.g., chitinases) to break down complex substrates (Chater et al., 2010; Hjort et al., 2010) and have the ability to produce a vast array of antibiotic compounds which can inhibit the growth of competitors (Watve et al., 2001).
Suppressive soil provide information about natural microbe based plant defense. Indigenous soil microorganisms can reduce disease (Schlatter et al., 2017). Multiple microbial interactions in the rhizosphere are shown to provide enhanced biocontrol in many cases as compared to the biocontrol agents used singly (Whipps 2001). Diverse soil microorganisms producing range of antimicrobial molecules serve to be a better biopesticide.
Chater, K. F., Biro, S., Lee, K. J., Palmer, T. and Schrempf, H. 2010 The Complex Extracellular Biology of Streptomyces. FEMS Microbiol. Rev. 34(2): 171-198
Chet, I. and Inbar, J. 1994 Biological Control of Fungal Pathogens. Appl. Biochem. Biotechnol. 48(1): 37 – 43
Frisvad, J. C., Smedsgaard, J., Larsen, T. O. and Samson, R. A. 2004 Mycotoxins Drugs and Other Extrolites Produced by Species in Penicillium Subgenus Penicillium. Stud. Mycol. 49: 201–242
Ghisalberti, E. L. 2000 Bioactive Metabolite From Soil Fungi: Natural Fungicides and Biocontrol Agents in “ Studies in Natural Products Chemistry” Volume 21 Bioactive Natural Products (Part B). Atta-ur-Rahman (ed.) Elsevier Science B. V. 21: 181
Howell, C. R. 2003 Mechanisms Employed by Trichoderma Species in the Biological Control of Plant Diseases: The History and Evolution of Current Concepts. Plant Disease 87(1): 4-10
Howell, C. R. and Puckhaber, L. S. 2005 A Study of the Characteristics of “P” and “Q” Strains of Trichoderma virens to Account for Differences in Biological Control Efficacy Against Cotton Seedling Diseases. Biological Control 33: 217–222
Howell, C. R. and Stipanovic, R. D. 1983 Gliovirin, A New Antibiotic From Gliocladium Virens and Its Role in the Biological Control of Pythium ultimum. Can. J. Microbiol. 29(3): 321–324
Howell, C. R. and Stipanovic, R. D. 1984 Phytotoxicity to Crop Plants and Herbicidal Effects on Weeds of Viridiol Produced by Gliocladium virens. Phytopathol. 74(11):1346–1349
Howell, C., Stipanovic, R. and Lumsden, R. 1993 Antibiotic Production by Strains of Gliocladium virens and its Relation to Biocontrol of Cotton Seedling Diseases. Biocontrol Sci Technol. 3(4): 435–441
Hjort, K., Bergström, M., Adesina, M. F., Jansson, J. K., Smalla, K. and Sjöling, S. 2010 Chitinase Genes Revealed and Compared in Bacterial Isolates, DNA Extracts and a Metagenomic Library From a Phytopathogen-Suppressive Soil. FEMS Microbiol. Ecol. 71(2): 197-207
Kang, Y., Carlson, R., Tharpe, W. and Schell, M. A. 1998 Characterization of Genes Involved in Biosynthesis of a Novel Antibiotic from Burkholderia cepacia BC11 and their Role in Biological Control of Rhizoctonia solani. Appl. Environ. Microbiol. 64: 3939–3947
Kim, B. S., Moon, S. S. and Hwang, B. K. 1999. Isolation, Identification and Antifungal Activity of a Macrolide Antibiotic, Oligomycin A, Produced by Streptomyces libani. Can. J. Bot. 77 (6): 850–858
Laville, J., Voisard, C., Keel, C., Maurhofer, M., Défago, G. and Haas, D. 1992 Global Control in Pseudomonas fluorescens Mediating Antibiotic Synthesis and Suppression of Black Root Rot of Tobacco. Proc. Natl. Acad. Sci. U S A. 89(5): 1562–1566
Milner, J. L., Silo-Suh, L., Lee, J. C., He, H., Clardy, J. and Handelsman, J. 1996 Production of Kanosamine by Bacillus cereus UW85. Appl. Environ. Microbiol. 62: 3061–3065
Nakayama, T., Homma, Y., Hashidoko, Y., Mizutani, J. and Tahara, S. 1999 Possible Role of Xanthobaccins Produced by Stenotrophomonas sp. strain SB-K88 in Suppression of Sugar Beet Damping-Off Disease. Appl. Environ. Microbiol. 65: 4334–4339
Nielsen, M. N., Sørensen, J., Fels, J. and Pedersen, H. C. 1998 Secondary Metabolite- and Endochitinase-Dependent Antagonism Toward Plant-Pathogenic Microfungi of Pseudomonas fluorescens Isolates From Sugar Beet Rhizosphere. Appl. Environ. Microbiol. 64: 3563–3569
Okeke, B., Seigle-Murandi, F., Steiman, R., Benoit-Guyod, J. L. and Kaouadji, M. 1993 Identification of Mycotoxin-Producing Fungal Strains: A Step in the Isolation of Compounds Active Against Rice Fungal Diseases. J. Agric. Food Chem. 41(10): 1731–1735
Puel, O., Galtier, P. and Oswald, I. P. 2010 Biosynthesis and Toxicological Effects of Patulin. Toxins (Basel). 2(4): 613-631
Samson, R. A., Houbraken, J., Varga, J. and Frisvad, J. C. 2009 Polyphasic Taxonomy of the Heat Resistant Ascomycete Genus Byssochlamys and its Paecilomyces anamorphs. Persoonia 22: 14–27
Schlatter, D., Kinkel, L., Thomashow, L., Weller, D. and Paulitz, T. 2017 Disease Suppressive Soils: New Insights from the Soil Microbiome. Phytopathol. 107(11): 1284-1297
Thrane, C., Olsson, S., Nielsen, T. H. and Sörensen, J. 1999 Vital Fluorescent Stains for Detection of Stress in Pythium ultimum and Rhizoctonia solani Challenged with Viscosinamide from Pseudomonas fluorescens DR54. FEMS Microbiol. Ecol. 30(1): 11–23
Varga, J., Due, M., Frisvad, J. C. and Samson, R. A. 2007 Taxonomic Revision of Aspergillus section Clavati Based on Molecular, Morphological and Physiological Data. Stud. Mycol. 59: 89–106
Watve, M. G., Tickoo, R., Jog, M. M. and Bhole, B. D. 2001. How Many Antibiotics are Produced by the Genus Streptomyces? Arch. Microbiol. 176(5): 386 – 390
Weller, D. M., Raaijmakers, J. M., McSpadden Gardener, B. B., and Thomashow, L. S. 2002 Microbial Populations Responsible for Specific Soil Suppressiveness to Plant Pathogens. Annu. Rev. Phytopathol. 40:309-348
Whipps, J. M. 2001 Microbial Interactions and Biocontrol in the Rhizosphere. J. Exp. Bot. 52 (1): 487 – 511