400 Review TRENDS in Biotechnology Vol.21 No.9 September 2003 Using fungi and yeasts to manage vegetable crop diseases Zamir K. Punja1 and Raj S. Utkhede2 1 Center for Environmental Biology, Dept of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6 2 Pacific Agri-Food Research Center, Agriculture and Agri-Food Canada, PO Box 1000, Agassiz, British Columbia, Canada V0M 1A0 Vegetable crops are grown worldwide as a source of nutrients and fiber in the human diet. Fungal plant pathogens can cause devastation in these crops under appropriate environmental conditions. Vegetable producers confronted with the challenges of managing fungal pathogens have the opportunity to use fungi and yeasts as biological control agents. Several commercially available products have shown significant disease reduction through various mechanisms to reduce pathogen development and disease. Production of hydrolytic enzymes and antibiotics, competition for plant nutrients and niche colonization, induction of plant host defense mechanisms, and interference with pathogenicity factors in the pathogen are the most important mechanisms. Biotechnological techniques are becoming increasingly valuable to elucidate the mechanisms of action of fungi and yeasts and provide genetic characterization and molecular markers to monitor the spread of these agents. Since the domestication of crop plants by humans first began , 10 000 years ago, diseases caused by plant pathogenic fungi have continued to inflict considerable losses in harvestable yield and have reduced the aesthetic value and storage life of agricultural crops. These pathogenic fungi have caused considerable economic losses for producers; on average, annual losses in North America can be up to 10% and are higher in less industrialized regions of the world. Even with recent technological advances in the development of resistant varieties of crop plants using genetic engineering approaches [1], and with new discoveries of novel, sitespecific fungicides [2] and continually evolving crop production practices, fungal plant pathogens continue to find opportunities to destroy crop plants. Management strategies for vegetable crop diseases Vegetable crops are grown and consumed worldwide and leafy vegetables and fruits in particular provide a source of nutrients and fiber in the human diet. These crops might be consumed fresh or after processing and are produced either on farms with conventional or organic agricultural production methods, or under intensively managed environmentally controlled glasshouses. These vegetable crops Corresponding author: Zamir K. Punja ([email protected]). are not spared from destruction by fungal pathogens, which infect roots, stems, leaves, flowers and fruits. The challenges for producers in managing these diseases are ever-increasing, as consumer demand for year-round production of fresh vegetables with reduced or no pesticide residues continues to grow. Concerns over the potential impact of disease management practices – including the use of fungicides – on the environment or on consumer health have prompted producers to examine alternative methods to combat fungal diseases. In this review, we discuss the use of fungi and yeasts to manage fungal diseases on vegetable crops, and highlight recent developments in this area. Emergence of fungi and yeasts as potential disease management agents The plant pathogenic fungi attacking vegetable crops that have been studied from the perspective of using fungi and yeasts for control, range from biotrophs to necrotrophs. Biotrophic fungi, such as powdery mildew fungi, only grow and reproduce on the living host plant (obligate parasites) (Fig. 1), whereas necrotrophs, such as Botrytis cinerea, which causes gray mold disease, are opportunistic fungi that grow and reproduce on plant debris or organic matter but can rapidly invade wounded or senescing plant tissues. In addition, fungi can infect the roots and colonize the vascular tissues of the plant, causing root rots and wilt diseases (Pythium spp. and Fusarium spp., respectively) (Fig. 1). An understanding of the disease cycle (events leading from initial infection to colonization and reproduction of the pathogen) (Fig. 2) and life cycle of the pathogen are crucial to the successful use of any disease management strategy. Most plant pathogens affecting vegetable crop species have been reasonably well-studied and information on their biology is available [3]. The use of fungi and yeasts to manage these diseases requires disruption of some stage of the disease- or life-cycle of the pathogen (Fig. 2) and this has been achieved through several different mechanisms (Fig. 3). Prevention of infection, reduction in colonization of host tissues, or reducing sporulation or survival of the pathogen, can each provide a level of disease control using biological control agents (Fig. 2). Many of these fungi and yeasts exist naturally on or near plant leaves, roots and other structures as epiphytes or saprophytes, using nutrients available in various http://tibtec.trends.com 0167-7799/$ - see front matter q 2003 Elsevier Ltd. All rights reserved. doi:10.1016/S0167-7799(03)00193-8 Review TRENDS in Biotechnology (a) (b) 401 Vol.21 No.9 September 2003 Pathogen development and biocontrol activity Survival Germination and infection (c) Tissue colonization (d) Biocontrol agent Growth and sporulation Fig. 1. Using fungi and yeasts to control fungal pathogens on cucumber. (a) Blastospores of the yeast Tilletiopsis pallescens from a 72-h-old liquid broth culture. Scale bar, 20 mm. (b) Cucumber leaf heavily infected with powdery mildew [Podosphaera (Sect. Sphaerotheca) xanthi ] growth and sporulation. (c). Two applications – made one-week apart – of the yeast suspension shown in (a) to leaves shown in (b) provided a significant reduction in growth and development of the mildew pathogen. This was caused, in part, by the production of antifungal compounds by the yeast [10]. Photograph taken one week after the second application of yeast spores. (d) Application of the biocontrol agent Gliocladium catenulatum (Prestop Mix) to cucumber seed at the time of planting followed by inoculation 10 days later with Pythium aphanidermatum provided significant protection and improved growth (plant on left) compared with the control plant (plant on right), which did not receive the biocontrol agent. Photograph taken three weeks after seeds were planted. niches. Research to elucidate whether these organisms could potentially be used as biological control agents to combat diseases has intensified over the past 20 years, and this has led to the commercial development of several registered microbial agents for vegetable crop disease management, as well as for diseases on other crops (Table 1). Following their initial discovery, the development Spread and infection TRENDS in Biotechnology Fig. 2. The various stages of the development of a pathogen and resulting plant disease can be reduced by the application of fungi and yeast biological control agents. Different agents can target single or multiple stages of pathogen development as indicated. of these biological control agents from a research laboratory to a commercial product is quite a daunting task. Information needs to be gathered on the efficacy and mode(s) of action of the agent, as well as on the survival and spread and potential toxicity to non-target species [4– 6]. Furthermore, formulation, product stability and shelf-life studies are also required [4– 6]. The quest to identify biological control agents for plant diseases has, however, provided tremendous opportunities for plant pathologists, mycologists, geneticists, biochemists and Table 1. Commercially available fungi and yeast biological control products to manage vegetable crop diseasesa Product trade name Microorganism(s) contained Fungal disease target Manufacturer or distributor AQ 10 Binab Biofox C Ampelomyces quisqualis M-10 Trichoderma spp. Fusarium oxysporum (non-pathogenic) Trichoderma spp. Coniothyrium minitans Fusarium oxysporum (nonpathogenic) Coniothyrium minitans Pythium oligandrum Gliocladium catenulatum Trichoderma harzianum T. harzianum T-22 Powdery mildews Root rot, wilt Wilt Ecogen, USA Binab, Sweden S.I.A.P.A., Italy Root rot, wilt Root rot Wilt Bioplant, Denmark Prophyta Biologischer, Germany Natural Plant Protection, France Root rot Root rot Root rot, wilt Root rot Root rot Bioved, Hungary Biopreparaty, Czech Republic Verdera Oy, Finland Efal Agri, Israel Bioworks, USA Root rot Certis, USA Powdery mildews Grey mold Root rot Root rot, wilt Plant Products, Canada Makhteshim Chemical Works, Israel Agrimm Technologies, New Zealand Ecosense Laboratories, India Biofungus, Superesivit Contans WG, Intercept WG Fusaclean KONI Polyversum Primastop (Prestop Mix) Root Pro Root Shield, Plant Shield, T-22 Planter box Soil Gard Sporodex Trichodex Trichopel Trieco a Trichoderma (Gliocladium) virens GL-21 Pseudozyma flocculosa T. harzianum Trichoderma spp. Trichoderma viride For more details, visit http://www.oardc.ohio-state.edu/apsbcc/productlist.htm. See also [76]. http://tibtec.trends.com 402 Review TRENDS in Biotechnology Vol.21 No.9 September 2003 Fungal or yeast biological control agent Production of antibotic compounds Secretion of enzymes Parasitism of pathogen Competition for nutrients and infections sites Interference with pathogenicity factors Induced resistance in host plant Inhibition of fungal pathogen growth, destruction of hyphae and spores and reduced development of disease TRENDS in Biotechnology Fig. 3. Mechanisms by which fungi and yeasts reduce growth and development of fungal plant pathogens and reduce disease. molecular biologists to interact, work together, and gain a better understanding of how these microbes can reduce fungal pathogen development and disease. Here, we summarize recent scientific developments and illustrate how modern research techniques are being applied to better understand the way in which biological control of vegetable diseases using fungi and yeasts is achieved. Efficacy data on these biocontrol agents are summarized elsewhere [7]. There is no single unifying feature that can be identified among the biological control agents listed in Table 1 that would explain how they manifest themselves as antagonists to disease-causing fungi. However, several important features have emerged from scientific investigations concerning their modes of action (Fig. 3), and these are discussed later. Role of mycoparasitism in pathogen biocontrol Reports dating back to the 1930s first showed that fungal pathogens could be infected or parasitized by other fungi (mycoparasites) [8]. The most widely studied fungi in this regard were different species of Trichoderma. In the late 1980s, yeasts were discovered that could reduce the growth and spore production of plant pathogenic fungi [9,10]. These interactions between plant pathogen and mycoparasite require that they be in close physical proximity to each other. As a result, most observations have been made from Petri dishes or detached plant tissues under controlled conditions. For example, Ampelomyces quisqualis (AQ 10) was shown to be parasitic on powdery mildew hyphae and conidia [11], whereas Coniothyrium minitans (Contans) is mycoparasitic on sclerotia of Sclerotinia spp. [12,13], and Pythium oligandrum (Polyversum) is mycoparasitic on other Pythium spp. and some other fungi [14,15]. These findings have now been extended outside the confines of the laboratory to vegetable crops grown under glasshouse and field conditions, and these specific microbial agents have been shown to reduce disease development significantly and are now registered products (Table 1). In many cases, however, the importance of mycoparasitism is difficult to demonstrate conclusively in situ, even though it is evident under experimental conditions. http://tibtec.trends.com For example, although Trichoderma spp. were among the first mycoparasites to be described, their role in reducing infection and colonization of host tissues through mycoparasitism has been difficult to confirm [8]. There are technical difficulties in making microscopic observations to demonstrate mycoparasitic activity in situ, such as at the soil – root interface, even with the availability of fluorescence imaging and differential staining methods. The recent development of a monoclonal antibody, prepared against a b-1, 3-glucanase enzyme, specific to the genus Trichoderma and related species, showed use in staining the cell walls of the mycoparasite but not the fungal pathogen Rhizoctonia solani, and could therefore be used to study dual interactions [16]. The antibody could also be used in a combined baitingELISA technique to detect Trichoderma spp. in composts. Such techniques should significantly facilitate an understanding of the role of mycoparasitism in biological control studies. Production of antibiotic compounds by fungi and yeasts The production of antibiotic compounds is characteristic of many effective fungal and yeast biocontrol agents, and can be shown both in vitro and in vivo. Species of Trichoderma and Gliocladium, as well as the yeast Pseudozyma, which are currently all registered biological control products (Table 1), are known to produce several secondary metabolites with broad-spectrum antimicrobial activity. For example, gliotoxin and gliovirin are well-described antibiotics (among others) produced by Trichoderma (Gliocladium) virens [8]. The antibiotics produced by Pseudozyma flocculosa are a mixture of fatty acid-containing derivatives that affect membrane permeability of the target organisms, thereby inhibiting their growth [9]. Conclusive evidence for the role of antibiotics in biocontrol-mediated disease suppression has required the development of antibiotic-minus mutant strains with a subsequent evaluation of their efficacy. Mutants of T. virens unable to synthesize gliotoxin and gliovirin were shown to have lost their capacity to control root-infecting fungi such as Pythium [8]. In some instances, disease-suppressive activity was directly correlated with the timing and Review TRENDS in Biotechnology amount of antibiotic produced [17]. However, not all studies aimed at generating antibiotic-minus mutants have provided clear results, as there are reports of T. virens mutants lacking gliotoxin production, which provided significant control of Rhizoctonia root rot [8]. Therefore, other attributes of the biological control agent Trichoderma clearly also play a significant role. A recent report by Cheng et al. [18] using insertional mutagenesis showed that strains of Pseudozyma that lacked production of the glycolipid flocculosin had significantly reduced biocontrol activity against powdery mildew. Role of extracellular enzyme production by fungi and yeasts Secretion of hydrolytic enzymes, particularly chitinases and glucanases, is a feature common to many effective biological control agents. Strains of Trichoderma, for example, are efficient producers of lytic enzymes, and many are used in commercial enzyme manufacturing. Using molecular biology techniques, the genes encoding chitinases, glucanases and proteinases have been cloned and sequenced from Trichoderma species. Mutant strains with disrupted activity of ech 42, a chitinase-encoding gene, were shown to be less effective as biocontrol agents against Rhizoctonia solani and Botrytis cinerea compared with wild-type strains [19,20]. Conversely, the overexpression of several genes encoding enzymes such as chitinase (ech 42, chit 33) [19,21], endoglucanase (egl1) [22], and proteinase ( prb1) [23], in transformed Trichoderma spp. improved the antagonistic potential of the agent against pathogens such as Rhizoctonia and Pythium, both in vitro and in vivo. A mutant strain of T. harzianum with an enhanced ability to hydrolyze pustulan (a polymer of b-1, 6-glucans) showed enhanced production of chitinase and b-1, 3- and b-1, 6-glucanases, and produced more extracellular proteins and other compounds [24]. This strain provided a significantly increased inhibitory activity against Botrytis cinerea in vitro. There is probably a complex sequential time-course of induction of these enzymes, and interactions with other compounds are possible (e.g. with antibiotics to achieve optimal biological activity). In T. harzianum, differential expression of a series of chitin-degrading enzymes was reported during mycoparasitism, which varied with time and the fungal pathogen host [25]. Specificity of hydrolytic enzyme activity was also suggested in a study by Woo et al. [20], where an endochitinase-deficient mutant displayed differing levels of biocontrol activity against different pathogens. Secretion of an exo- b-1, 3-glucanase by Ampelomyces quisqualis was found to play a role during the later stages of hyperparasitism of powdery mildew [11]. The importance of hydrolytic enzyme production in the biocontrol activity of yeasts can vary with the organism, with Candida producing biologically relevant levels for Botrytis control [26] and Tilletiopsis spp. producing insignificant enzyme activity against powdery mildews [10]. In situ localization of various lytic enzymes during interactions between a specific biocontrol agent and pathogen remains a challenge, but microscopic observations have revealed that pathogen hyphae – in addition http://tibtec.trends.com Vol.21 No.9 September 2003 403 to other pathogen structures – were disintegrated and collapsed [11,27– 29]. The attachment of yeasts to pathogen hyphae is an important factor for biocontrol activity [30], enabling cell wall degrading enzymes to have an effect. Taken together, recent research on extracellular enzyme production by fungal and yeast biocontrol agents convincingly demonstrate their involvement in reducing pathogen growth and infection. Predictably, synergies between these enzymes and antibiotic compounds have also been reported. For example, hydrolytic enzymes in the presence of gliotoxin, peptaibols or other antifungal compounds significantly suppressed the growth of B. cinerea and Fusarium oxysporum compared with either one alone [31,32]. Biocontrol agents can affect pathogenicity of fungal pathogens There are several pathogenicity factors that influence the degree and extent to which a fungal organism can invade host plant tissues [33]. Disruption of any of these through site-directed mutagenesis, for example, can render a plant pathogen unable to infect. One interesting aspect of biocontrol agent-induced suppression of disease is the reported affect of T. harzianum on development of gray mold disease caused by B. cinerea through a reduction in its pathogenicity [34,35]. Production of cystein protease enzymes by Trichoderma was reported to inhibit the activities of hydrolytic enzymes – especially polygalacturonases – in the pathogen, which are important pathogenicity factors in Botrytis and many other fungi [34,35]. The proteases inactivated the pathogen enzyme by cleaving the molecule. Reduction in disease was also demonstrated with extracts containing proteases from Trichoderma culture filtrates and from infected bean leaves, and was reversed by adding protease inhibitors [35]. For such an interaction to be evoked on the plant leaf surface infected with B. cinerea, the interacting organisms must spatially and temporally occupy the same niche and be in close proximity to one another, providing localized protection. Induction of host plant defenses by fungi and yeasts Higher plants are able to defend themselves against potential pathogens through the induction of a diverse array of chemical compounds whose production is triggered by elicitor molecules or inducing agents [36]. An interesting area of biocontrol agent-induced suppression of plant diseases is the induction of host defense responses (Fig. 4). Following their application to plants, Trichoderma spp., Pythium oligandrum and nonpathogenic Fusarium oxysporum (Table 1) have all been reported to enhance structural and biochemical changes, which increased resistance to disease [14,37 – 40]. These changes included enhanced deposition of plant cell wall materials (e.g. callose) at the infection site, as well as increased activity of several enzymes (e.g. peroxidase and chitinases) and other pathogenesis-related proteins [14,38 – 42]. In some of these reports, however, the biochemical changes might provide only correlative and not confirmatory evidence for their role in induced resistance. In one report, biocontrol activity of T. virens was highly correlated with 404 Review TRENDS in Biotechnology Vol.21 No.9 September 2003 Fungal or yeast biological control agent Production of elicitors Production of signaling compounds Colonization of tissues Induction of defense responses in the plant Production of growthpromoting substances Stimulation of growth of plant Reduced pathogen development TRENDS in Biotechnology Fig. 4. Induction of plant host responses by fungal and yeast biological control agents that can lead to biological control of disease. induction of terpenoid synthesis and peroxidase activity in plant roots, which were shown to be inhibitory to R. solani [43]. Yeast biocontrol agents have also been reported to induce host defense responses following their application to plant tissues [44]. A transposon-mediated insertional mutagenesis approach has been used to create mutants of nonpathogenic F. oxysporum Fo47 that were altered in their biocontrol activity [45] and could be used to further study the mechanism of action. Induction of plant defense responses through signaling pathways is well-described for plant growth-promoting rhizobacteria, which use several mechanisms to achieve induced systemic resistance in the plant [46]. However, it is unclear whether specific or general elicitors are produced by the fungal and yeast biocontrol agents, and whether a host recognition system is triggered to initiate the defense mechanism similar to that occurring in incompatible pathogen – host interactions [1]. Interestingly, as all of these inducing biocontrol agents have been reported to colonize root tissues internally (mainly epidermal and cortical cells) without causing noticeable cell damage [14,40 – 42], host plant defenses could have been induced as a result (Fig. 4). The release of fungal pathogen elicitor molecules (e.g. oligosaccharides) is known to trigger host defense responses against pathogens [46] and biocontrol agents could potentially act in the same way. In addition, T. harzianum has been reported to produce growth-promoting substances that enhanced root and shoot growth following application in the absence of pathogens [4,47]. Production of diffusible metabolites capable of solubilizing phosphates and micronutrients was demonstrated [48], and enhanced micronutrient levels in plants treated with T. harzianum was reported [49]. Competition for nutrients and niche colonization by fungi and yeasts Fungal pathogens require entry points to gain access into plant tissues. For obligate parasites, this is usually achieved by direct penetration of hyphae through the cuticle and epidermis of the plant. For facultative parasites that are mostly saprophytic, entry can be through wounds, senescing host tissues, or natural openings such as stomates and lenticels. These areas are http://tibtec.trends.com generally nutrient-rich owing to exudation of sugars and amino acids. Biological control agents that can compete effectively with the pathogen to occupy these infection sites and use the nutrients can effectively displace the pathogen by preventing germination of propagules or infection (Fig. 2). Biocontrol agents such as Trichoderma and Gliocladium spp. can outgrow and outcompete the pathogen, especially if applied before pathogen arrival. Colonization of roots by Trichoderma (rhizosphere competence) is an important aspect contributing to its biocontrol efficacy [4]. Nonpathogenic F. oxysporum strains can also compete with pathogenic strains for infection sites and nutrients (e.g. carbon on the roots) [50]. Competition for nutrients is also a mechanism by which many yeast biocontrol agents that colonize wounds or senescing tissues can prevent infection by pathogens [51]. Treatment of wounds, germinating seeds, or flower blossoms can therefore provide opportunities to establish biocontrol agents that can then outcompete pathogens. There is some evidence that biocontrol fungi such as Clonastachys (Gliocladium) roseum can enter the host tissues and reside as an endophyte [52], subsequently colonizing the tissues or potentially inducing host defenses to reduce further development of the pathogen. Such endophytes are receiving increasing interest from the perspective of their role(s) in plants [53]. Other fungi and yeasts show biocontrol potential Many reports have described the biocontrol potential of other saprophytic fungi and yeasts to reduce diseases on vegetable crops; this information is summarized elsewhere [7]. The mechanisms of action of these agents fall into the same categories as those described here. Further research on these organisms and their advancement through the microbial registration process should increase their chances of being used as biocontrol agents in the future, thereby adding to the list of current products summarized in Table 1. Applications of molecular methods to biocontrol fungi and yeasts Several fungi and yeasts that have the potential to reduce the development of vegetable crop diseases have recently Review TRENDS in Biotechnology been characterized using molecular methods. Mitochondrial DNA, internal transcribed spacers of rDNA (ITS1 and ITS2 regions), and nuclear DNA have been evaluated using techniques such as restriction fragment length polymorphisms (RFLP), arbitrarily primed polymerase chain reaction (AP-PCR), random amplified polymorphic DNA (RAPD), sequence-characterized amplified region (SCAR) and other molecular approaches. These studies were used to distinguish between species and among strains of the biocontrol fungi Trichoderma [54 – 59], Gliocladium [60], Ampelomyces [61], and the yeasts Pseudozyma [62] and Tilletiopsis [63]. In addition to resolving taxonomic affinities, the molecular tools provided strain-specific markers to track the movement of strains [57,64,65] and to test the genetic stability over successive generations of propagation [66]. Molecular tools will prove to be valuable in monitoring the survival and environmental fate following release of these biocontrol agents as well as in ensuring product quality and stability during large-scale production of inoculum. Genetic transformation techniques have been applied to Trichoderma and nonpathogenic F. oxysporum. Transformation of T. harzianum with the b-glucuronidase (uid A, gus) gene and the hygromycin B (hyg B) gene provided markers for use in population dynamic studies [67– 69]. Co-transformation with genes encoding b-glucuronidase and green fluorescent protein (GFP) has also been described [70]. Similar markers (gus, hyg B) were developed for nonpathogenic F. oxysporum strains [42,50,71] and used to study the role of competition for infection sites on plant roots and to estimate fungal biomass on roots in relation to the pathogenic strains. Techniques of protoplast fusion were used to create strain T-22 of T. harzianum by fusing a mutant strain capable of colonizing plant roots with a strain able to compete with bacteria under iron-limiting conditions [4]. This new strain had the enhanced ability to colonize the root system of host plants, resulting in greater efficacy as a biological control agent for long-term root protection [4]. Yeasts with biocontrol potential have also been transformed with the GFP, which was used to track movement [72]. Transformation of Saccharomyces to express a cecropin-A based peptide with antifungal activity was recently described [73] that enhanced the ability of the strain to reduce decay when applied to tomato fruits. Expression of novel antimicrobial compounds in biological control agents through genetic transformation provides a new approach for disease control. Finally, the use of antimicrobial genes from biocontrol fungi, such as Trichoderma, when expressed in transgenic plants, has also opened up new opportunities to enhance resistance to pathogens [74,75]. Several crop species have now been engineered with genes expressing chitinases; these transgenic plants were shown to express resistance to many different fungal pathogens [1]. Concluding remarks Techniques in biotechnology are becoming increasingly applicable to studies on the biological control of plant diseases using fungi and yeasts. 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