Showing papers in "Annual Review of Phytopathology in 2011"

Hormone Crosstalk in Plant Disease and Defense: More Than Just JASMONATE-SALICYLATE Antagonism

Abstract: Until recently, most studies on the role of hormones in plant-pathogen interactions focused on salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). It is now clear that pathogen-induced modulation of signaling via other hormones contributes to virulence. A picture is emerging of complex crosstalk and induced hormonal changes that modulate disease and resistance, with outcomes dependent on pathogen lifestyles and the genetic constitution of the host. Recent progress has revealed intriguing similarities between hormone signaling mechanisms, with gene induction responses often achieved by derepression. Here, we report on recent advances, updating current knowledge on classical defense hormones SA, JA, and ET, and the roles of auxin, abscisic acid (ABA), cytokinins (CKs), and brassinosteroids in molding plant-pathogen interactions. We highlight an emerging theme that positive and negative regulators of these disparate hormone signaling pathways are crucial regulatory targets of hormonal crosstalk in disease and defense.

Hidden Fungi, Emergent Properties: Endophytes and Microbiomes

Abstract: Endophytes are microorganisms that live within plant tissues without causing symptoms of disease. They are important components of plant microbiomes. Endophytes interact with, and overlap in function with, other core microbial groups that colonize plant tissues, e.g., mycorrhizal fungi, pathogens, epiphytes, and saprotrophs. Some fungal endophytes affect plant growth and plant responses to pathogens, herbivores, and environmental change; others produce useful or interesting secondary metabolites. Here, we focus on new techniques and approaches that can provide an integrative understanding of the role of fungal endophytes in the plant microbiome. Clavicipitaceous endophytes of grasses are not considered because they have unique properties distinct from other endophytes. Hidden from view and often overlooked, endophytes are emerging as their diversity, importance for plant growth and survival, and interactions with other organisms are revealed.

Emerging Virus Diseases Transmitted by Whiteflies

Abstract: Virus diseases that have emerged in the past two decades limit the production of important vegetable crops in tropical, subtropical, and temperate regions worldwide, and many of the causal viruses are transmitted by whiteflies (order Hemiptera, family Aleyrodidae). Most of these whitefly-transmitted viruses are begomoviruses (family Geminiviridae), although whiteflies are also vectors of criniviruses, ipomoviruses, torradoviruses, and some carlaviruses. Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes in the vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants. The role of humans in increasing the emergence of virus diseases is obvious, and the effect that climate change may have in the future is unclear.

The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production

Abstract: Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat.

Reactive Oxygen Species in Phytopathogenic Fungi: Signaling, Development, and Disease

Abstract: Reactive oxygen species (ROS) play a major role in pathogen-plant interactions: recognition of a pathogen by the plant rapidly triggers the oxidative burst, which is necessary for further defense reactions. The specific role of ROS in pathogen defense is still unclear. Studies on the pathogen so far have focused on the importance of the oxidative stress response (OSR) systems to overcome the oxidative burst or of its avoidance by effectors. This review focuses on the role of ROS for fungal virulence and development. In the recent years, it has become obvious that (a) fungal OSR systems might not have the predicted crucial role in pathogenicity, (b) fungal pathogens, especially necrotrophs, can actively contribute to the ROS level in planta and even take advantage of the host's response, (c) fungi possess superoxide-generating NADPH oxidases similar to mammalian Nox complexes that are important for pathogenicity; however, recent data indicate that they are not directly involved in pathogen-host communicati...

Understanding and exploiting late blight resistance in the age of effectors

Abstract: Potato (Solanum tuberosum) is the world's third-largest food crop. It severely suffers from late blight, a devastating disease caused by Phytophthora infestans. This oomycete pathogen secretes host-translocated RXLR effectors that include avirulence (AVR) proteins, which are targeted by resistance (R) proteins from wild Solanum species. Most Solanum R genes appear to have coevolved with P. infestans at its center of origin in central Mexico. Various R and Avr genes were recently cloned, and here we catalog characterized R-AVR pairs. We describe the mechanisms that P. infestans employs for evading R protein recognition and discuss partial resistance and partial virulence phenotypes in the context of our knowledge of effector diversity and activity. Genome-wide catalogs of P. infestans effectors are available, enabling effectoromics approaches that accelerate R gene cloning and specificity profiling. Engineering R genes with expanded pathogen recognition has also become possible. Importantly, monitoring eff...

Plant-parasite coevolution: bridging the gap between genetics and ecology.

Abstract: We review current ideas about coevolution of plants and parasites, particularly processes that generate genetic diversity. Frequencies of host resistance and parasite virulence alleles that interact in gene-for-gene (GFG) relationships coevolve in the familiar boom-and-bust cycle, in which resistance is selected when virulence is rare, and virulence is selected when resistance is common. The cycle can result in stable polymorphism when diverse ecological and epidemiological factors cause negative direct frequency-dependent selection (ndFDS) on host resistance, parasite virulence, or both, such that the benefit of a trait to fitness declines as its frequency increases. Polymorphism can also be stabilized by overdominance, when heterozygous hosts have greater resistance than homozygotes to diverse pathogens. Genetic diversity can also persist in the form of statistical polymorphism, sustained by random processes acting on gene frequencies and population size. Stable polymorphism allows alleles to be long-lived and genetic variation to be detectable in natural populations. In agriculture, many of the factors promoting stability in host-parasite interactions have been lost, leading to arms races of host defenses and parasite effectors.

Diverse Targets of Phytoplasma Effectors: From Plant Development to Defense Against Insects

Abstract: Phytoplasma research begins to bloom (75). Indeed, this review shows that substantial progress has been made with the identification of phytoplasma effectors that alter flower development, induce witches' broom, affect leaf shape, and modify plant-insect interactions. Phytoplasmas have a unique life cycle among pathogens, as they invade organisms of two distinct kingdoms, namely plants (Plantae) and insects (Animalia), and replicate intracellularly in both. Phytoplasmas release effectors into host cells of plants and insects to target host molecules, and in plants these effectors unload from the phloem to access distal tissues and alter basic developmental processes. The effectors provide phytoplasmas with a fitness advantage by modulating their plant and insect hosts. We expect that further research on the functional characterization of phytoplasma effectors will generate new knowledge that is relevant to fundamental aspects of plant sciences and entomology, and for agriculture by improving yields of crops affected by phytoplasma diseases.

A Coevolutionary Framework for Managing Disease-Suppressive Soils

Abstract: This review explores a coevolutionary framework for the study and management of disease-suppressive soil microbial communities. Because antagonistic microbial interactions are especially important to disease suppression, conceptual, theoretical, and empirical work on antagonistic coevolution and its relevance to disease suppression is reviewed. In addition, principles of coevolution are used to develop specific predictions regarding the drivers of disease-suppressive potential in soil microbial communities and to highlight important areas for future research. This approach brings an evolutionary perspective to microbial community management and emphasizes the role of species interactions among indigenous nonpathogenic microbes in developing and maintaining disease-suppressive activities in soil.

Diversity of Puccinia striiformis on Cereals and Grasses

Abstract: Yellow (stripe) rust is a common fungal disease on cereals and grasses. It is caused by Puccinia striiformis sensu lato, which is biotrophic and heteroecious. The pathogen is specialized on the primary host at both species and cultivar levels, whereas several Berberis spp. may serve as alternate hosts. One lineage infects mainly cereals and at least two lineages are restricted to grasses. P. striiformis on cereals has a typical clonal population structure in many areas, resulting from asexual reproduction, but high diversity, suggesting frequent recombination, has been observed in certain areas in Asia. Yellow rust is spreading by airborne spores potentially across long distances, which may contribute to sudden disease epidemics in new areas. This has been the case since 2000, where large-scale epidemics in warmer wheat-growing areas have been ascribed to the emergence of two closely related yellow rust strains with increased aggressiveness and tolerance to warm temperatures.

Revision of the nomenclature of the differential host-pathogen interactions of Venturia inaequalis and Malus.

Abstract: The apple scab (Venturia inaequalis–Malus) pathosystem was one of the first systems for which Flor’s concept of gene-for-gene (GfG) relationships between the host plant and the pathogen was demonstrated. There is a rich resource of host resistance genes present in Malus germplasm that could potentially be marshalled to confer durable resistance against this most important apple disease. A comprehensive understanding of the host-pathogen interactions occurring in this pathosystem is a prerequisite for effectively manipulating these host resistance factors. An accurate means of identification of specific resistance and consistent use of gene nomenclature is critical for this process. A set of universally available, differentially resistant hosts is described, which will be followed by a set of defined pathogen races at a later stage. We review pertinent aspects of the history of apple scab research, describe the current status and future directions of this research, and resolve some outstanding issues.

Water relations in the interaction of foliar bacterial pathogens with plants.

Abstract: This review examines the many ways in which water influences the relations between foliar bacterial pathogens and plants. As a limited resource in aerial plant tissues, water is subject to manipulation by both plants and pathogens. A model is emerging that suggests that plants actively promote localized desiccation at the infection site and thus restrict pathogen growth as one component of defense. Similarly, many foliar pathogens manipulate water relations as one component of pathogenesis. Nonvascular pathogens do this using effectors and other molecules to alter hormonal responses and enhance intercellular watersoaking, whereas vascular pathogens use many mechanisms to cause wilt. Because of water limitations on phyllosphere surfaces, bacterial colonists, including pathogens, benefit from the protective effects of cellular aggregation, synthesis of hygroscopic polymers, and uptake and production of osmoprotective compounds. Moreover, these bacteria employ tactics for scavenging and distributing water to overcome water-driven barriers to nutrient acquisition, movement, and signal exchange on plant surfaces.

The Clavibacter michiganensis Subspecies: Molecular Investigation of Gram-Positive Bacterial Plant Pathogens

Abstract: Clavibacter michiganensis subspecies are actinomycete plant pathogens residing mainly in the xylem vessels that infect economically important host plants In the Clavibacter subspecies michiganensis and sepedonicus, infecting tomato and potato, respectively, essential factors for disease induction are plasmid encoded and loss of the virulence plasmids converts these biotrophic pathogens into endophytes The genes responsible for successful colonization of the host plant, including evasion/suppression of plant defense reactions, are chromosomally encoded Several serine proteases seem to be involved in colonization They are secreted by Clavibacter, but their targets remain unknown A type 3 secretion system (T3SS) translocating effectors into the plant cells is absent in these gram-positive pathogens With the development of the modern ‘omics technologies for RNA and proteins based on the known genome sequences, a new phase in the investigation of the mechanisms of plant pathogenicity has begun to allow the genome-wide investigation of the Clavibacter-host interaction

Phytophthora Beyond Agriculture

Abstract: Little is known about indigenous Phytophthora species in natural ecosystems. Increasing evidence, however, suggests that a diverse, trophically complex Phytophthora community is important in many forests. The number of described species has steadily increased, with a dramatic spike in recent years as new species have been split from old and new species have been discovered through exploration of new habitats. Forest soil, streams, and the upper canopies of trees are now being explored for Phytophthora diversity, and a new appreciation for the ecological amplitude of the genus is emerging. Ten to twenty species are regularly identified in temperate forest surveys. Half or more of this Phytophthora diversity comes from species described since 2000. Taxa in internal transcribed spacer (ITS) Clade 6 are especially numerous in forest streams and may be saprophytic in this habitat. Three ecological assemblages of forest Phytophthora species are hypothesized: aquatic opportunists, foliar pathogens, and soilborne fine-root and canker pathogens. Aggressive invasive species are associated with all three groups.

RNA-RNA Recombination in Plant Virus Replication and Evolution

Abstract: RNA-RNA recombination is one of the strongest forces shaping the genomes of plant RNA viruses. The detection of recombination is a challenging task that prompted the development of both in vitro and in vivo experimental systems. In the divided genome of Brome mosaic virus system, both inter- and intrasegmental crossovers are described. Other systems utilize satellite or defective interfering RNAs (DI-RNAs) of Turnip crinkle virus, Tomato bushy stunt virus, Cucumber necrosis virus, and Potato virus X. These assays identified the mechanistic details of the recombination process, revealing the role of RNA structure and proteins in the replicase-mediated copy-choice mechanism. In copy choice, the polymerase and the nascent RNA chain from which it is synthesized switch from one RNA template to another. RNA recombination was found to mediate the rearrangement of viral genes, the repair of deleterious mutations, and the acquisition of nonself sequences influencing the phylogenetics of viral taxa. The evidence fo...

The Pathogen-Actin Connection: A Platform for Defense Signaling in Plants

Abstract: The cytoskeleton, a dynamic network of cytoplasmic polymers, plays a central role in numerous fundamental processes, such as development, reproduction, and cellular responses to biotic and abiotic stimuli. As a platform for innate immune responses in mammalian cells, the actin cytoskeleton is a central component in the organization and activation of host defenses, including signaling and cellular repair. In plants, our understanding of the genetic and biochemical responses in both pathogen and host that are required for virulence and resistance has grown enormously. Additional advances in live-cell imaging of cytoskeletal dynamics have markedly altered our view of actin turnover in plants. In this review, we outline current knowledge of host resistance following pathogen perception, both in terms of the genetic interactions that mediate defense signaling, as well as the biochemical and cellular processes that are required for defense signaling.

Evolution of Plant Pathogenesis in Pseudomonas syringae: A Genomics Perspective

Abstract: The phytopathogenic bacterium Pseudomonas syringae causes serious diseases in a wide range of important crop plants, with recent severe outbreaks on the New Zealand kiwifruit crop and among British horse chestnut trees. Next-generation genome sequencing of over 25 new strains has greatly broadened our understanding of how this species adapts to a diverse range of plant hosts. Not unexpectedly, the genomes were found to be highly dynamic, and extensive polymorphism was found in the distribution of type III secreted effectors (T3SEs) and other virulence-associated genes, even among strains within the same pathovar. An underexplored area brought to light by these data is the specific metabolic adaptations required for growth on woody hosts. These studies provide a tremendous wealth of candidates for more refined functional characterization, which is greatly enhancing our ability to disentangle the web of host-pathogen interactions that determine disease outcomes.

Detection of Diseased Plants by Analysis of Volatile Organic Compound Emission

Abstract: This review focuses on the detection of diseased plants by analysis of volatile organic compound (VOC) emissions. It includes an overview of studies that report on the impact of infectious and noninfectious diseases on these emissions and discusses the specificity of disease-induced emissions. The review also provides an overview of processes that affect the gas balance of plant volatiles, including their loss processes. These processes are considered as important because they contribute to the time-dynamic concentration profiles of plant-emitted volatiles. In addition, we describe the most popular techniques currently in use to measure volatiles emitted from plants, with emphasis on agricultural application. Dynamic sampling coupled with gas chromatography and followed by an appropriate detector is considered as the most appropriate method for application in agriculture. It is recommended to evaluate the state-of-the-art in the fields concerned with this method and to explore the development of a new instrument based on the specific needs for application in agricultural practice. However, to apply such an instrument in agriculture remains a challenge, mainly due to high costs.

Cuticle surface coat of plant-parasitic nematodes.

Abstract: The surface coat (SC) of the plant-parasitic nematode cuticle is an understudied area of current research, even though it likely plays key roles in both nematode-plant and nematode-microbe interactions. Although in several ways Caenorhabditis elegans is a poor model for plant-parasitic nematodes, it is a useful starting point for investigations of the cuticle and its SC, especially in the light of recent work using this species as a model for innate immunity and the generic biology underpinning much host-parasite biology. We review the research focused on the involvement of the SC of plant-parasitic nematodes. Using the insights gained from animal-parasitic nematodes and other sequenced nematodes, we discuss the key roles that the SC may play.

Evolution and Population Genetics of Exotic and Re-Emerging Pathogens: Novel Tools and Approaches

Abstract: Given human population growth and accelerated global trade, the rate of emergence of exotic plant pathogens is bound to increase. Understanding the processes that lead to the emergence of new pathogens can help manage emerging epidemics. Novel tools for analyzing population genetic variation can be used to infer the evolutionary history of populations or species, allowing for the unprecedented reconstruction of the demographic history of pathogens. Specifically, recent advances in the application of coalescent, maximum likelihood (ML), and Bayesian methods to population genetic data combined with increasing availability of affordable sequencing and parallel computing have created the opportunity to apply these methods to a broad range of questions regarding the evolution of emerging pathogens. These approaches are particularly powerful when used to test multiple competing hypotheses. We provide several examples illustrating how coalescent analysis provides critical insights into understanding migration pa...

What can plant autophagy do for an innate immune response

Abstract: Autophagy plays an established role in the execution of senescence, starvation, and stress responses in plants. More recently, an emerging role for autophagy has been discovered during the plant innate immune response. Recent papers have shown autophagy to restrict, and conversely, to also promote programmed cell death (PCD) at the site of pathogen infection. These initial studies have piqued our excitement, but they have also revealed gaps in our understanding of plant autophagy regulation, in our ability to monitor autophagy in plant cells, and in our ability to manipulate autophagic activity. In this review, we present the most pressing questions now facing the field of plant autophagy in general, with specific focus on autophagy as it occurs during a plant-pathogen interaction. To begin to answer these questions, we place recent findings in the context of studies of autophagy and immunity in other systems, and in the context of the mammalian immune response in particular.

A Successful Bacterial Coup d' ´ Etat: How Rhodococcus fascians Redirects Plant Development

Abstract: Rhodococcus fascians is a gram-positive phytopathogen that induces differentiated galls, known as leafy galls, on a wide variety of plants, employing virulence genes located on a linear plasmid. The pathogenic strategy consists of the production of a mixture of six synergistically acting cytokinins that overwhelm the plant's homeostatic mechanisms, ensuring the activation of a signaling cascade that targets the plant cell cycle and directs the newly formed cells to differentiate into shoot meristems. The shoots that are formed upon infection remain immature and never convert to source tissues resulting in the establishment of a nutrient sink that is a niche for the epiphytic and endophytic R. fascians subpopulations. Niche formation is accompanied by modifications of the transcriptome, metabolome, physiology, and morphology of both host and pathogen. Here, we review a decade of research and set the outlines of the molecular basis of the leafy gall syndrome.

Application of High-Throughput DNA Sequencing in Phytopathology

Abstract: The new sequencing technologies are already making a big impact in academic research on medically important microbes and may soon revolutionize diagnostics, epidemiology, and infection control. Plant pathology also stands to gain from exploiting these opportunities. This manuscript reviews some applications of these high-throughput sequencing methods that are relevant to phytopathology, with emphasis on the associated computational and bioinformatics challenges and their solutions. Second-generation sequencing technologies have recently been exploited in genomics of both prokaryotic and eukaryotic plant pathogens. They are also proving to be useful in diagnostics, especially with respect to viruses.

Not As They Seem

Abstract: I recount the early influences that directed me toward a career in research and then describe some efforts investigating Cowpea mosaic virus and the satellite RNA of Tobacco ringspot virus. These descriptions have a common theme of surprise, how things often can be not as they are expected to be. Finally, I examine the widely held belief that a plant transgene derived from a distant taxonomic source presents a greater risk than a transgene derived from a closely related plant and contend that this also is a situation in which things may not be as they initially seem.

Norman Borlaug: the man I worked with and knew.

Abstract: Much has been written about Norman Borlaug the agricultural scientist and humanitarian whose achievements are recognized with many accolades; to add to those writings is a difficult task. This brief paper is an attempt to provide a personal perspective on Norman Borlaug that can come only from someone who has worked closely with him throughout his professional life. I have endeavored to recollect my early impressions of working with Borlaug as a wheat breeder in Mexico and to highlight his innovative approach to wheat breeding, as well as his views on global population and food security, fertilizers, organic agriculture, biotechnology, and conventional academia. His work ethic was instrumental in his vision for the international agricultural system as an instrument of change in the world. His spirit serves as a reminder to future agricultural scientists that the battle must be vigorously engaged and can be won.

Chris Lamb: A Visionary Leader in Plant Science

Abstract: Christopher John Lamb (1950-2009) made major contributions to the field of plant defense gene activation, particularly through his studies on signal transduction mechanisms. Between 1994 and 2004, he published a series of seminal papers that outlined the involvement of hydrogen peroxide, nitric oxide, lipid transfer proteins, and aspartic proteases as critical components of local and/or systemic resistance during plant-microbe interactions. Prior to this, he had been one of the first to establish the fact that induced defense responses resulted from transcriptional activation of sets of coordinately regulated genes. Chris obtained his B.S and PhD degrees in biochemistry from the University of Cambridge, United Kingdom, moving to the Botany School at the University of Oxford as a postdoctoral fellow in 1975 and to the Biochemistry Department in Oxford as a Departmental Demonstrator in 1978. He was appointed founding director of the Plant Biology Laboratory at the Salk Institute for Biological Studies in La Jolla, California in 1982, and occupied the last ten years of his life as Director of the John Innes Center, Norwich, United Kingdom. In spite of spending most of his career as a director at two of the world's most prestigious institutes, formal recognition of his achievements came late in life, with election to the Royal Society of London in 2008 and endowment of the honor of Commander of the British Empire (CBE) for his contributions to British plant science by Queen Elizabeth II in 2009. Sadly, Chris did not live to attend the official ceremony at which he would receive his CBE.