Soilborne Plant Diseases Caused by Pythium spp.: Ecology,Epidemiology, and Prospects for Biological Control

Soilborne root diseases caused by plant pathogenic Pythium species cause serious losses in a number of agricultural production systems, which has led to a considerable effort devoted to the development of biological agents for disease control. In this article we review information on the ecology and biological control of these pathogens with the premise that a clear understanding of the ecology of the pathogen will assist in the development of efficacious biocontrol agents. The lifecycles of the pathogens and etiology of host infection also are reviewed, as are epidemiological concepts of inoculum-disease relationships and the influence of environmental factors on pathogen aggressiveness and host susceptibility. A number of fungal and bacterial biocontrol agents are discussed and parallels between their ecology and that of the target pathogens highlighted. The mechanisms by which these microbial agents suppress diseases caused by Pythium spp., such as interference with pathogen survival, disruption of the process of plant infection, and induced host resistance, are evaluated. The possibilities for enhancement of efficacy of specific biological control agents by genetic manipulation or deployment tactics are discussed, as are conceptual suggestions for consideration when developing screening programs for antagonists.     

Combinations of Biocontrol Agents for Management of Plant-Parasitic Nematodes and Soilborne Plant-Pathogenic Fungi

Numerous microbes are antagonistic to plant-parasitic nematodes and soilborne plant-pathogenic fungi, but few of these organisms are commercially available for management of these pathogens. Inconsistent performance of applied biocontrol agents has proven to be a primary obstacle to the development of successful commercial products. One of the strategies for overcoming inconsistent performance is to combine the disease-suppressive activity of two (or more) beneficial microbes in a biocontrol preparation. Such combinations have potential for more extensive colonization of the rhizosphere, more consistent expression of beneficial traits under a broad range of soil conditions, and antagonism to a larger number of plant pests or pathogens than strains applied individually. Conversely, microbes applied in combination also may have antagonistic interactions with each other. Increased, decreased, and unaltered suppression of the target pathogen or pest has been observed when biocontrol microbes have been applied in combination. Unfortunately, the ecological basis for increased or decreased suppression has not been determined in many cases and needs further consideration. The complexity of interactions involved in the application of multiple organisms for biological control has slowed progress toward development of successful formulations. However, this approach has potential for overcoming some of the efficacy problems that occur with application of individual biocontrol agents.     

Minor effects of two elicitors of insect and pathogen resistance on volatile emissions and parasitism of Spodoptera frugiperda in Mexican maize fields

Synthetic elicitors can be used to induce resistance in plants against pathogens and arthropod herbivores. Such compounds may also change the emission of herbivore-induced plant volatiles, which serve as important cues for parasitic wasps to locate their hosts. Therefore, the use of elicitors in the field may affect biological control of insect pests. To test this, we treated maize seedlings growing in a subtropical field in Mexico with methyl jasmonate (MeJA), an elicitor of defense responses against many insects, and benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), an elicitor of resistance against certain pathogens. Volatile emission, herbivore infestation, pathogen infection, and plant performance (growth and grain yield) of treated and untreated maize plants were measured. Application of BTH slightly reduced volatile emission in maize, while MeJA increased the emission compared to control treatments. Despite the apparent changes in volatile emissions, the elicitor application did not consistently affect infestation by Spodoptera frugiperda larvae, the main insect pest found on the maize seedlings, and had only marginal effects on parasitism rates. Similarly, there were no treatment effects on infestation by other herbivores and pathogens. Results for the six replications that stretched over one summer and one winter season were highly variable, with parasitism rates and the species composition of the parasitoids differing significantly between seasons. This variability, as well as the severe biotic and abiotic stresses on young seedlings might explain why we measured only slight effects of elicitor application on pest incidence and biological control in this specific field study. Indeed, an additional field experiment under milder and more standardized conditions revealed that BTH induced significant resistance against Bipolaris maydis, a major pathogen in the experimental maize fields. Similar affects can be expected for herbivory and parasitism rates.     

Geographical variation and sexual dimorphism of phenoloxidase levels in Japanese beetles (Popillia japonica)

Phenoloxidase (PO) production can be used as an indicator of pathogen defence in insects. The geographical mosaic of coevolution implies that traits associated with pathogen defence will vary across a geographical range. Bateman's principle implies that the benefit of increased defence levels is greater for females than males. To test both of these hypotheses, we sampled four populations of Japanese beetles, Popillia japonica, across Vermont: two were from locations using biological pest control, and two locations did not use biocontrol. We quantified defence levels (PO) and parasite resistance in males and females from each population. Populations from areas with biocontrol exhibited greater PO production, females produced more PO, populations with higher levels of PO suffered less mortality from pathogen exposure, and PO levels positively correlate with increased mortality in the absence of parasitism. Results support the geographical mosaic of coevolution and the implications of Bateman's principle.     

Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere?

Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays; however, they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.     

Ecological,practical, and political inputs into selection of weed targets: What makes a good biological control target?

The topic of ecological, practical, and political considerations in the selection of weed targets for biological control has been widely discussed during the past two decades, mostly from the perspective of insect herbivores. For conceptual and practical purposes, plant pathogens have been treated in these discussions as if they are a subset of inoculative biocontrol agents, with little said about the inherent differences between pathogens and insects as biocontrol agents or the selection of weed targets for control by the inundative, bioherbicide strategy. Herein, I attempt to address the question of what makes a good biological control target for plant pathogens used as inoculative as well as inundative agents, basing my analysis on examples from the past three decades. Despite the small number of examples available for this analysis, the following generalizations can be made: (1) Weeds with robust capacity for vegetative regeneration are more difficult to control with pathogens than those that lack this trait. (2) A plant’s growth habit is not a reliable guide for target selection; weeds that have been successfully controlled include annual and biennial herbs, perennial shrubs, perennial vines, and trees, while numerous failures have been reported irrespective of the target’s growth habit or reproductive mode. (3) It is more challenging to control species with genetic heterogeneity and capacity for introgression than genetically homogeneous and reproductively conserved species. (4) Matching the target host’s susceptibility with the candidate pathogen’s virulence is of utmost importance for biocontrol success since host–pathogen interactions at the species and subspecies levels are often governed by single-gene differences (e.g., varietal specificity). (5) Practical and political considerations are central to the selection of targets for control with pathogens. (6) Demand from influential stakeholders for control and/or for a nonchemical or economically sustainable control typically drives the initiative as well as the continuance of biocontrol projects to their completion. (7) In the case of inundative, bioherbicide agents, the continuity and ultimate implementation of a project will be dictated by the prospects of economic returns from developing and using a pathogen. (8) The stakeholders’ perceptions of the effectiveness of a biocontrol program can be unpredictable, leading to conflicting views of “success.” In the final analysis, a good weed target for control by a pathogen is one that has strong stakeholder backing and the list of available pathogens for the target suggests a possibility of acceptable control at a cost that is competitive with those of other control options. While this conclusion is also applicable to target selection for insect biocontrol agents, it is more relevant for pathogens because of limited funding and personnel available for development of pathogens and the added cost and technological complexity of implementing bioherbicides compared to classical biocontrols.     

Constraints on the evolution of tolerance to herbicide in the common morning glory: resistance and tolerance are mutually exclusive

Evolutionary biologists explain the maintenance of intermediate levels of defense in plant populations as being due to trade-offs, or negative genetic covariances among ecologically important traits. Attempts at detecting trade-offs as constraints on the evolution of defense have not always been successful, leading some to conclude that such trade-offs rarely explain current levels of defense in the population. Using the agricultural pest Ipomoea purpurea, we measured correlations between traits involved in defense to glyphosate, the active ingredient in Roundup, a widely used herbicide. We found significant allocation costs of tolerance, as well as trade-offs between resistance and two measures of tolerance to glyphosate. Selection on resistance and tolerance exhibited differing patterns: tolerance to leaf damage was under negative directional selection, whereas resistance was under positive directional selection. The joint pattern of selection on resistance and tolerance to leaf damage indicated the presence of alternate peaks in the fitness landscape such that a combination of either high tolerance and low resistance, or high resistance and low tolerance was favored. The widespread use of this herbicide suggests that it is likely an important selective agent on weed populations. Understanding the evolutionary dynamics of herbicide defense traits is thus of increasing importance in the context of human-mediated evolution.     

Safety of Microorganisms Intended for Pest and Plant Disease Control: A Framework for Scientific Evaluation

Microorganisms are enormous but largely untapped natural resources for biological control of pests and diseases. There are two primary reasons for their underployment for pest or disease control: (1) the technical difficulties of using microorganisms for biological control, owing to a lack of fundamental information on them and their ecology, and (2) the costs of product development and regulatory approvals required for each strain, formulation, and use. Agriculture and forestry benefit greatly from the resident communities of microorganisms responsible for naturally occurring biological control of pest species, but additional benefits are achieved by introducing/applying them when or where needed. This can be done as (1) an inoculative release, (2) an augmentative application, or (3) an inundative application. Because of their specificity, different microbial biocontrol agents typically are needed to control different pests or the same pest in different environments. Four potential adverse effects are identified as safety issues (hazards) associated with the use of microorganisms for the biological control of plant pests and diseases. These are: (1) displacement of nontarget microorganisms, (2) allergenicity to humans and other animals, (3) toxigenicity to nontarget organisms, and (4) pathogenicity to nontarget organisms. Except for allergenicity, these are the same attributes that contribute to the efficacy of microbial biocontrol agents toward the target pest species. The probability of occurrence of a particular adverse nontarget effect of a microbial biocontrol agent may be a function of geographic origin or a specific trait genetically added or modified, but the safety issues are the still the same, including whether the microorganism intended for pest or disease control is indigenous, nonindigenous (imported and released), or genetically modified by traditional or recombinant DNA (rDNA) technology. Likewise, the probability of occurrence of a particular adverse nontarget effect may vary with method of application, e.g., whether as an aerosol, soil treatment, baits, or seed treatment, and may increase with increased scale of use, but the safety issues are still the same, including whether the microorganism is used for an inoculative release or augmentative or inundative application. Existing practices for managing microorganisms in the environment (e.g., plant pathogens,Rhizobium,plant inoculants) provide experience and options for managing the risks of microorganisms applied for pest and disease control. Moreover, experience to date indicates that any adverse nontarget effects, should they occur, are likely to be short-term or transitory effects that can, if significant, be eliminated by terminating use of the microbial biocontrol agent. In contrast, production agriculture as currently practiced, such as the use of tillage and crop rotations, has significant and long-term effects on nontarget organisms, including the intentional and unintentional displacement of microorganisms. Even the decision to leave plant pests and diseases unmanaged could have significant long-term environmental effects on nontarget organisms. Potential safety issues associated with the use of microbial biocontrol must therefore be properly identified and compared with the impact of other options for managing the pest or leaving the pest unmanaged. This paper provides a scientific framework for this process.     

Molecular evolution of plant immune system genes

Molecular population genetic studies are providing new perspectives on the evolution of genes that confer resistance to pathogens and herbivores. Here, we compare the evolutionary history of different components of the defense response (detection, signaling and response) and of genes with parallel function in plants and Drosophila. A review of the literature indicates that the dominant form of selection acting on defense genes (balancing, positive and purifying) differs among components of defense. Sampling of particular classes of genes and genes from non-model organisms, however, remains limited. Future studies combining molecular evolutionary analyses with ecological genetic and functional analyses should better reveal how natural selection has shaped defense gene evolution.     

Exploring the evolution of diversity in pathogen populations

Pathogen biodiversity is an under-exploited source of inference regarding disease processes and the evolution of pathogens and pathogenesis. In addition, the structure of pathogen populations, especially for diverse organisms such as the meningococcus, has implications for public health interventions including vaccination and antibiotic use. The predominant paradigm for interpreting bacterial diversity has been the clonal population structure, which has been modified by the incorporation of the effects of horizontal genetic exchange. Multilocus models of variable antigens, which explore the effects of immune selection, provide alternative explanations for structured diversity in pathogen populations.     

The evolutionary strategies of plant defenses have a dynamic impact on the adaptations and interactions of vectors and pathogens

Plants have evolved and diversified to reduce the damages imposed by infectious pathogens and herbivorous insects. Living in a sedentary lifestyle, plants are constantly adapting to their environment. They employ various strategies to increase performance and fitness. Thus, plants developed cost‐effective strategies to defend against specific insects and pathogens. Plant defense, however, imposes selective pressure on insects and pathogens. This selective pressure provides incentives for pathogens and insects to diversify and develop strategies to counter plant defense. This results in an evolutionary arms race among plants, pathogens and insects. The ever‐changing adaptations and physiological alterations among these organisms make studying plant–vector–pathogen interactions a challenging and fascinating field. Studying plant defense and plant protection requires knowledge of the relationship among organisms and the adaptive strategies each organism utilize. Therefore, this review focuses on the integral parts of plant–vector–pathogen interactions in order to understand the factors that affect plant defense and disease development. The review addresses plant–vector–pathogen co‐evolution, plant defense strategies, specificity of plant defenses and plant–vector–pathogen interactions. Improving the comprehension of these factors will provide a multi‐dimensional perspective for the future research in pest and disease management.     

Evolution of host resistance: looking for coevolutionary hotspots at small spatial scales

Natural plant populations are often found to be extremely diverse in their resistance to pathogens. While the potential of pathogens in driving the evolution of resistance in hosts has been widely recognized, empirical evidence linking disease dynamics to host population genetic structure has remained scarce. Here I show that current coevolutionary selection for resistance can be divergent even on a very fine spatial scale. In a natural plant-pathogen metapopulation, disease occurrence patterns were highly aggregated over space and time within host populations. A laboratory inoculation experiment showed higher resistance within areas of the host populations where encounter rates with the pathogen have been high. Higher resistance to sympatric than to allopatric strains of the pathogen suggests that this change has taken place as a response to local selection. These results constitute evidence of adaptive microevolution of resistance resulting from disease epidemics in natural plant-pathogen associations, and highlight the importance of finding the relevant scale at which to address questions of current coevolutionary selection.     

Evolution of Drosophila resistance against different pathogens and infection routes entails no detectable maintenance costs

Pathogens exert a strong selective pressure on hosts, entailing host adaptation to infection. This adaptation often affects negatively other fitness‐related traits. Such trade‐offs may underlie the maintenance of genetic diversity for pathogen resistance. Trade‐offs can be tested with experimental evolution of host populations adapting to parasites, using two approaches: (1) measuring changes in immunocompetence in relaxed‐selection lines and (2) comparing life‐history traits of evolved and control lines in pathogen‐free environments. Here, we used both approaches to examine trade‐offs in Drosophila melanogaster populations evolving for over 30 generations under infection with Drosophila C Virus or the bacterium Pseudomonas entomophila, the latter through different routes. We find that resistance is maintained after up to 30 generations of relaxed selection. Moreover, no differences in several classical life‐history traits between control and evolved populations were found in pathogen‐free environments, even under stresses such as desiccation, nutrient limitation, and high densities. Hence, we did not detect any maintenance costs associated with resistance to pathogens. We hypothesize that extremely high selection pressures commonly used lead to the disproportionate expression of costs relative to their actual occurrence in natural systems. Still, the maintenance of genetic variation for pathogen resistance calls for an explanation.     

Ecological, practical, and political inputs into selection of weed targets: What makes a good biological control target?

The topic of ecological, practical, and political considerations in the selection of weed targets for biological control has been widely discussed during the past two decades, mostly from the perspective of insect herbivores. For conceptual and practical purposes, plant pathogens have been treated in these discussions as if they are a subset of inoculative biocontrol agents, with little said about the inherent differences between pathogens and insects as biocontrol agents or the selection of weed targets for control by the inundative, bioherbicide strategy. Herein, I attempt to address the question of what makes a good biological control target for plant pathogens used as inoculative as well as inundative agents, basing my analysis on examples from the past three decades. Despite the small number of examples available for this analysis, the following generalizations can be made: (1) Weeds with robust capacity for vegetative regeneration are more difficult to control with pathogens than those that lack this trait. (2) A plant’s growth habit is not a reliable guide for target selection; weeds that have been successfully controlled include annual and biennial herbs, perennial shrubs, perennial vines, and trees, while numerous failures have been reported irrespective of the target’s growth habit or reproductive mode. (3) It is more challenging to control species with genetic heterogeneity and capacity for introgression than genetically homogeneous and reproductively conserved species. (4) Matching the target host’s susceptibility with the candidate pathogen’s virulence is of utmost importance for biocontrol success since host–pathogen interactions at the species and subspecies levels are often governed by single-gene differences (e.g., varietal specificity). (5) Practical and political considerations are central to the selection of targets for control with pathogens. (6) Demand from influential stakeholders for control and/or for a nonchemical or economically sustainable control typically drives the initiative as well as the continuance of biocontrol projects to their completion. (7) In the case of inundative, bioherbicide agents, the continuity and ultimate implementation of a project will be dictated by the prospects of economic returns from developing and using a pathogen. (8) The stakeholders’ perceptions of the effectiveness of a biocontrol program can be unpredictable, leading to conflicting views of “success.” In the final analysis, a good weed target for control by a pathogen is one that has strong stakeholder backing and the list of available pathogens for the target suggests a possibility of acceptable control at a cost that is competitive with those of other control options. While this conclusion is also applicable to target selection for insect biocontrol agents, it is more relevant for pathogens because of limited funding and personnel available for development of pathogens and the added cost and technological complexity of implementing bioherbicides compared to classical biocontrols.     

THE ORIGIN OF SPECIFICITY BY MEANS OF NATURAL SELECTION: EVOLVED AND NONHOST RESISTANCE IN HOST–PATHOGEN INTERACTIONS

Most species seem to be completely resistant to most pathogens and parasites. This resistance has been called “nonhost resistance” because it is exhibited by species that are considered not to be part of the normal host range of the pathogen. A conceptual model is presented suggesting that failure of infection on nonhosts may be an incidental by‐product of pathogen evolution leading to specialization on their source hosts. This model is contrasted with resistance that results from hosts evolving to resist challenge by their pathogens, either as a result of coevolution with a persistent pathogen or as the result of one‐sided evolution by the host against pathogens that are not self‐sustaining on those hosts. Distinguishing evolved from nonevolved resistance leads to contrasting predictions regarding the relationship between resistance and genetic distance. An analysis of cross‐inoculation experiments suggests that the resistance is often the product of pathogen specialization. Understanding the contrasting evolutionary origins of resistance is critical for studies on the genetics and evolution of host–pathogen interactions in human, agricultural, and natural populations. Research on human infectious disease using animal models may often study resistances that have quite contrasting evolutionary origins, and therefore very different underlying genetic mechanisms.     

Environmental variation enables invasions of environmental opportunist pathogens

Emerging infectious diseases are a persistent threat to humans and food production but the mechanisms promoting the emergence of novel pathogens are not fully understood. The widely discussed explanations for pathogen emergence include range shifts, coincidental evolution of virulence, and host immunity variation. Here we propose a novel mechanism of virulence evolution that relies on environmental variability. Our model combines an environmental community experiencing random or periodic variability, to a classical SIR epidemiological model. We assume that environmentally growing, potentially infective variants arise at low frequency from a resident, non‐infective (benign microbial) strain through random variation on genetic material. We found that environmental perturbations commonly promote establishment of sporadic infections or persistent epidemics, by creating transient periods of low competition, which can in turn be exploited by an infective strain. Given the ubiquitous nature of potentially pathogenic environmental micro‐organisms and environmental variability, this mechanism provides a plausible explanation for emerging diseases.     

Theory of catastrophic diseases of cultivated plants

Genetically homogeneous plant populations generate selective pressures for pathogens to overcome host resistance. Once a pathogen strain has evolved which overcomes host resistance, a catastrophic collapse of genetically h homogeneous host population can result. The dynamics of such a collapse are discussed by means of a mathematical model. Also, a gametheoretical model shows that high density of the host population may lead to selection for maximum pathogen virulence rather than host-parasite commensalism. The evolution of mutant pathogens is compared with the evolution of insecticide resistance. While time frame estimates are intrinsically difficult to obtain, it is argued that industrial pollution may speed up the evolution of mutant pathogens and may have been responsible for a number of agricultural and horticultural epidemics. The theory may have implications for the clonal propagation of forests.     

Biological control of fungal plant diseases

Research has demonstrated the agricultural potential of biological control. For airborne pathogens as well as for soilborne pathogens similar strategies based on different targets in the life cycle of the pathogen can be distinguished, viz. (1) microbial protection of the host against infection, (2) microbial reduction of pathogen sporulation and (3) microbial interference with pathogen survival. Some successes and failures with respect to these targets will be discussed and include (1) biocontrol of seedling diseases, root pathogens, and post-harvest diseases (2) biocontrol of powdery mildew and Botrytis cinerea (3) biocontrol of sclerotial pathogens. Despite of a lot of research on biological control of plant diseases, the number of products available is limited and their market size is marginal. The market for biological control products is not only determined by agricultural aspects such as the number of diseases controlled by one biocontrol product in different crops but also by economic aspects as cost-effective mass production, easy registration and the availability of competing means of control including fungicides. The future development of low-chemical input sustainable agriculture and organic farming will determine the eventual role of biological control in agriculture.     

Complex genetics control natural variation in Arabidopsis thaliana resistance to Botrytis cinerea

The genetic architecture of plant defense against microbial pathogens may be influenced by pathogen lifestyle. While plant interactions with biotrophic pathogens are frequently controlled by the action of large-effect resistance genes that follow classic Mendelian inheritance, our study suggests that plant defense against the necrotrophic pathogen Botrytis cinerea is primarily quantitative and genetically complex. Few studies of quantitative resistance to necrotrophic pathogens have used large plant mapping populations to dissect the genetic structure of resistance. Using a large structured mapping population of Arabidopsis thaliana, we identified quantitative trait loci influencing plant response to B. cinerea, measured as expansion of necrotic lesions on leaves and accumulation of the antimicrobial compound camalexin. Testing multiple B. cinerea isolates, we identified 23 separate QTL in this population, ranging in isolate-specificity from being identified with a single isolate to controlling resistance against all isolates tested. We identified a set of QTL controlling accumulation of camalexin in response to pathogen infection that largely colocalized with lesion QTL. The identified resistance QTL appear to function in epistatic networks involving three or more loci. Detection of multilocus connections suggests that natural variation in specific signaling or response networks may control A. thaliana-B. cinerea interaction in this population.