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- Volume 50, 2012
Annual Review of Phytopathology - Volume 50, 2012
Volume 50, 2012
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An Ideal Job
Vol. 50 (2012), pp. 1–14More LessA brief personal history illustrates how fortunate I was to have stumbled into a career in plant pathology, which turned out to be the ideal job for me. Several of the people who steered me or facilitated my development in research on plant diseases are mentioned. Starting with my PhD research, I have had the good fortune to indulge a career-long fascination with epidemiology and genetics of disease resistance in plants, particularly coevolution of gene-for-gene host-pathogen systems. I hope that my example may inspire others of like minds to consider a research career in plant pathology.
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Arthur Kelman: Tribute and Remembrance
Vol. 50 (2012), pp. 15–21More LessWith the death of Professor Arthur Kelman at age 90, the plant sciences, and particularly the field of plant pathology, lost one of its most influential and effective leaders. His long career involved important positions in the Departments of Plant Pathology at North Carolina State University (1949–1965) and the University of Wisconsin (1965–1989). Recognized not only for his achievements in research and his charismatic influence on his numerous students, Arthur was, most of all, an extraordinary teacher. He and his students made significant contributions in the fields of virulence, ecology, and control of bacterial plant pathogens. In addition, he was extremely active in service to professional societies, including the American Phytopathological Society, and a major force in the development of the International Society for Plant Pathology. In addition, he was an influential member of the Council of the National Academy of Sciences, and, after retirement from the University of Wisconsin, he served for two years as Chief Scientist of the Competitive Grants Program of the US Department of Agriculture. He received numerous awards as a teacher and researcher, and felt an intense sense of duty to his profession. He was one of the most influential plant pathologists of the twentieth century and will be remembered for his great intellect and his humanity.
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Stagonospora nodorum: From Pathology to Genomics and Host Resistance
Vol. 50 (2012), pp. 23–43More LessStagonospora nodorum is a major necrotrophic pathogen of wheat that causes the diseases S. nodorum leaf and glume blotch. A series of tools and resources, including functional genomics, a genome sequence, proteomics and metabolomics, host-mapping populations, and a worldwide collection of isolates, have enabled the dissection of pathogenicity mechanisms. Metabolic and signaling genes required for pathogenicity have been defined. Interaction with the host is dominated by interplay of fungal effectors that induce necrosis on wheat lines carrying specific sensitivity loci. As such, the pathogen has emerged as a model for the Pleosporales group of pathogens.
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Apple Replant Disease: Role of Microbial Ecology in Cause and Control
Vol. 50 (2012), pp. 45–65More LessReplant disease of apple is common to all major apple growing regions of the world. Difficulties in defining disease etiology, which can be exacerbated by abiotic factors, have limited progress toward developing alternatives to soil fumigation for disease control. However, the preponderance of data derived from studies of orchard soil biology employing multidisciplinary approaches has defined a complex of pathogens/parasites as causal agents of the disease. Approaches to manipulate microbial resources endemic to the orchard soil system have been proposed to induce a state of general soil suppressiveness to replant disease. Such a long-term strategy may benefit the existing orchard through extending the period of economic viability and reduce overall disease pressure to which young trees are exposed during establishment of successive plantings on the site. Alternatively, more near-term methods have been devised to achieve specific quantitative and qualitative changes in soil biology during the period of orchard renovation that may lead to effective disease suppression.
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Pathogenomics of the Ralstonia solanacearum Species Complex
Vol. 50 (2012), pp. 67–89More LessRalstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network.
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The Genomics of Obligate (and Nonobligate) Biotrophs
Vol. 50 (2012), pp. 91–109More LessBiotrophy is a pervasive trait that evolved independently in plant pathogenic fungi and oomycetes. Comparative genomics of the first sequenced biotrophic pathogens highlight remarkable convergences, including gene losses in the metabolism of inorganic nitrogen, inorganic sulfur, and thiamine, and genes encoding carbohydrate active enzymes and secondary metabolism enzymes. Some biotrophs, but not all, display marked increases in overall genome size because of a proliferation of retrotransposons. I argue here that the release of constraints on transposon activity is driven by the advantages conferred by the genetic variability that results from transposition, in particular by the creation and diversification of broad palettes of effector genes. Increases in genome size and gene losses are the consequences of this trade-off. Genes that are not necessary for growth on a plant disappeared, but we still do not know what lost functions make some of these pathogens obligate.
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Genome-Enabled Perspectives on the Composition, Evolution, and Expression of Virulence Determinants in Bacterial Plant Pathogens
Vol. 50 (2012), pp. 111–132More LessGenome sequence analyses of bacterial plant pathogens are revealing important insights into the molecular determinants of pathogenicity and, through transcript characterization, responses to environmental conditions, evidence for small RNAs, and validation of uncharacterized genes. Genome comparison sheds further light on the processes impacting pathogen evolution and differences in gene repertoire among isolates contributing to niche specialization. Information derived from pathogen genome analysis is providing tools for use in diagnosis and interference with host-pathogen interactions for the purpose of disease control. However, the existing information infrastructure fails to adequately integrate the increasing numbers of sequence data sets, bioinformatic analyses, and experimental characterization, as required for effective systems-level analysis. Enhanced standardization of data formats at the point of publication is proposed as a possible solution.
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Suppressive Composts: Microbial Ecology Links Between Abiotic Environments and Healthy Plants
Vol. 50 (2012), pp. 133–153More LessSuppressive compost provides an environment in which plant disease development is reduced, even in the presence of a pathogen and a susceptible host. Despite the numerous positive reports, its practical application is still limited. The main reason for this is the lack of reliable prediction and quality control tools for evaluation of the level and specificity of the suppression effect. Plant disease suppression is the direct result of the activity of consortia of antagonistic microorganisms that naturally recolonize the compost during the cooling phase of the process. Thus, it is imperative to increase the level of understanding of compost microbial ecology and population dynamics. This may lead to the development of an ecological theory for complex ecosystems as well as favor the establishment of hypothesis-driven studies.
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Plant Defense Compounds: Systems Approaches to Metabolic Analysis
Vol. 50 (2012), pp. 155–173More LessSystems biology attempts to answer biological questions by integrating across diverse genomic data sets. With the increasing ability to conduct genomics experiments, this integrative approach is being rapidly applied across numerous biological research communities. One of these research communities investigates how plants utilize secondary metabolites or defense metabolites to defend against attack by pathogens and other biotic organisms. This use of systems biology to integrate across transcriptomics, metabolomics, and genomics is significantly enhancing the rate of discovery of genes, metabolites, and bioactivities for plant defense compounds as well as extending our knowledge of how these compounds are regulated. Plant defense compounds are also providing a unique proving platform to develop new approaches that enhance the ability to conduct systems biology with existing and previously unforseen genomics data sets. This review attempts to illustrate both how systems biology is helping the study of plant defense compounds and vice versa.
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Role of Nematode Peptides and Other Small Molecules in Plant Parasitism
Vol. 50 (2012), pp. 175–195More LessMolecular, genetic, and biochemical studies are demonstrating an increasingly important role of peptide signaling in nematode parasitism of plants. To date, the majority of nematode-secreted peptides identified share similarity with plant CLAVATA3/ESR (CLE) peptides, but bioinformatics analyses of nematode genomes have revealed sequences homologous to other classes of plant peptide hormones that may be utilized by these pests. Extracellular host receptors for secreted nematode peptides are beginning to be identified and their roles in parasitism elucidated. Here, we outline recent advances from studies of biologically active nematode-secreted peptides that function as molecular mimics of endogenous plant peptides to promote parasitism. Several strategies are being used to exploit this information to provide new targets for engineering nematode resistance.
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New Grower-Friendly Methods for Plant Pathogen Monitoring*
Vol. 50 (2012), pp. 197–218More LessAccurate plant disease diagnoses and rapid detection and identification of plant pathogens are of utmost importance for controlling plant diseases and mitigating the economic losses they incur. Technological advances have increasingly simplified the tools available for the identification of pathogens to the extent that, in some cases, this can be done directly by growers and producers themselves. Commercially available immunoprinting kits and lateral flow devices (LFDs) for detection of selected plant pathogens are among the first tools of what can be considered grower-friendly pathogen monitoring methods. Research efforts, spurned on by point-of-care needs in the medical field, are paving the way for the further development of on-the-spot diagnostics and multiplex technologies in plant pathology. Grower-friendly methods need to be practical, robust, readily available, and cost-effective. Such methods are not restricted to on-the-spot testing but extend to laboratory services, which are sometimes more practicable for growers, extension agents, regulators, and other users of diagnostic tests.
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Somatic Hybridization in the Uredinales
Vol. 50 (2012), pp. 219–239More LessRust fungi are cosmopolitan in distribution and parasitize a wide range of plants, including economically important crop species such as wheat. Detailed regional, national, and continental surveys of pathogenic variability in wheat-attacking rust pathogens over periods of up to 90 years have shown that in the absence of sexual recombination, genetic diversity is generated by periodic introduction of exotic isolates, single-step mutation, and somatic hybridization. Laboratory studies have provided evidence for somatic hybridization between many rust species and formae speciales, and there is evidence for the process in nature within and between rust species on Linum, poplar, Senecio, wheat, and several grass species. Although the mechanisms involved in somatic hybridization are not well understood, they are thought to involve the fusion of dikaryotic vegetative hyphae, nuclear exchange, and possibly exchange of whole chromosomes between nuclei or parasexuality via the fusion of the two haploid nuclei, followed by mitotic crossing over and vegetative haploidization. In three cases, hybrid isolates rendered resistant plant genotypes susceptible because of new combinations of virulence. Implications for resistance breeding and future prospects in understanding the process are discussed.
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Interrelationships of Food Safety and Plant Pathology: The Life Cycle of Human Pathogens on Plants
Vol. 50 (2012), pp. 241–266More LessBacterial food-borne pathogens use plants as vectors between animal hosts, all the while following the life cycle script of plant-associated bacteria. Similar to phytobacteria, Salmonella, pathogenic Escherichia coli, and cross-domain pathogens have a foothold in agricultural production areas. The commonality of environmental contamination translates to contact with plants. Because of the chronic absence of kill steps against human pathogens for fresh produce, arrival on plants leads to persistence and the risk of human illness. Significant research progress is revealing mechanisms used by human pathogens to colonize plants and important biological interactions between and among bacteria in planta. These findings articulate the difficulty of eliminating or reducing the pathogen from plants. The plant itself may be an untapped key to clean produce. This review highlights the life of human pathogens outside an animal host, focusing on the role of plants, and illustrates areas that are ripe for future investigation.
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Plant Immunity to Necrotrophs
Vol. 50 (2012), pp. 267–294More LessPlants inhabit environments crowded with infectious microbes that pose constant threats to their survival. Necrotrophic pathogens are notorious for their aggressive and wide-ranging virulence strategies that promote host cell death and acquire nutrients for growth and reproduction from dead cells. This lifestyle constitutes the axis of their pathogenesis and virulence strategies and marks contrasting immune responses to biotrophic pathogens. The diversity of virulence strategies in necrotrophic species corresponds to multifaceted host immune response mechanisms. When effective, the plant immune system disarms the infectious necrotroph of its pathogenic arsenal or attenuates its effect, restricting further ingress and disease symptom development. Simply inherited resistance traits confer protection against host-specific necrotrophs (HSNs), whereas resistance to broad host-range necrotrophs (BHNs) is complex. Components of host genetic networks, as well as the molecular and cellular processes that mediate host immune responses to necrotrophs, are being identified. In this review, recent advances in our understanding of plant immune responses to necrotrophs and comparison with responses to biotrophic pathogens are summarized, highlighting common and contrasting mechanisms.
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Mechanisms and Evolution of Virulence in Oomycetes
Vol. 50 (2012), pp. 295–318More LessMany destructive diseases of plants and animals are caused by oomycetes, a group of eukaryotic pathogens important to agricultural, ornamental, and natural ecosystems. Understanding the mechanisms underlying oomycete virulence and the genomic processes by which those mechanisms rapidly evolve is essential to developing effective long-term control measures for oomycete diseases. Several common mechanisms underlying oomycete virulence, including protein toxins and cell-entering effectors, have emerged from comparing oomycetes with different genome characteristics, parasitic lifestyles, and host ranges. Oomycete genomes display a strongly bipartite organization in which conserved housekeeping genes are concentrated in syntenic gene-rich blocks, whereas virulence genes are dispersed into highly dynamic, repeat-rich regions. There is also evidence that key virulence genes have been acquired by horizontal transfer from other eukaryotic and prokaryotic species.
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Variation and Selection of Quantitative Traits in Plant Pathogens
Vol. 50 (2012), pp. 319–338More LessThe first section presents the quantitative traits of pathogenicity that are most commonly measured by plant pathologists, how the expression of those traits is influenced by environmental factors, and why the traits must be taken into account for understanding pathogen evolution in agricultural systems. Particular attention is given to the shared genetic control of these traits by the host and the pathogen. Next, the review discusses how quantitative traits account for epidemic development and how they can be related to pathogen fitness. The main constraints that influence the evolution of quantitative traits in pathogen populations are detailed. Finally, possible directions for research on the management of pathogen virulence (as defined by evolutionists) and host quantitative resistance are presented. The review evaluates how the theoretical corpus developed by epidemiologists and evolutionists may apply to plant pathogens in the context of agriculture. The review also analyzes theoretical papers and compares the modeling hypotheses to the biological characteristics of plant pathogens.
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Gall Midges (Hessian Flies) as Plant Pathogens
Vol. 50 (2012), pp. 339–357More LessGall midges constitute an important group of plant-parasitic insects. The Hessian fly (HF; Mayetiola destructor), the most investigated gall midge, was the first insect hypothesized to have a gene-for-gene interaction with its host plant, wheat (Triticum spp.). Recent investigations support that hypothesis. The minute larval mandibles appear to act in a manner that is analogous to nematode stylets and the haustoria of filamentous plant pathogens. Putative effector proteins are encoded by hundreds of genes and expressed in the HF larval salivary gland. Cultivar-specific resistance (R) genes mediate a highly localized plant reaction that prevents the survival of avirulent HF larvae. Fine-scale mapping of HF avirulence (Avr) genes provides further evidence of effector-triggered immunity (ETI) against HF in wheat. Taken together, these discoveries suggest that the HF, and other gall midges, may be considered biotrophic, or hemibiotrophic, plant pathogens, and they demonstrate the potential that the wheat-HF interaction has in the study of insect-induced plant gall formation.
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Phytophthora Beyond Agriculture
Vol. 50 (2012), pp. 359–378More LessLittle 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.
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Landscape Epidemiology of Emerging Infectious Diseases in Natural and Human-Altered Ecosystems
Vol. 50 (2012), pp. 379–402More LessA central challenge to studying emerging infectious diseases (EIDs) is a landscape dilemma: Our best empirical understanding of disease dynamics occurs at local scales, whereas pathogen invasions and management occur over broad spatial extents. The burgeoning field of landscape epidemiology integrates concepts and approaches from disease ecology with the macroscale lens of landscape ecology, enabling examination of disease across spatiotemporal scales in complex environmental settings. We review the state of the field and describe analytical frontiers that show promise for advancement, focusing on natural and human-altered ecosystems. Concepts fundamental to practicing landscape epidemiology are discussed, including spatial scale, static versus dynamic modeling, spatially implicit versus explicit approaches, selection of ecologically meaningful variables, and inference versus prediction. We highlight studies that have advanced the field by incorporating multiscale analyses, landscape connectivity, and dynamic modeling. Future research directions include understanding disease as a component of interacting ecological disturbances, scaling up the ecological impacts of disease, and examining disease dynamics as a coupled human-natural system.
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Diversity and Natural Functions of Antibiotics Produced by Beneficial and Plant Pathogenic Bacteria
Vol. 50 (2012), pp. 403–424More LessSoil- and plant-associated environments harbor numerous bacteria that produce antibiotic metabolites with specific or broad-spectrum activities against coexisting microorganisms. The function and ecological importance of antibiotics have long been assumed to yield a survival advantage to the producing bacteria in the highly competitive but resource-limited soil environments through direct suppression. Although specific antibiotics may enhance producer persistence when challenged by competitors or predators in soil habitats, at subinhibitory concentrations antibiotics exhibit a diversity of other roles in the life history of the producing bacteria. Many processes modulated by antibiotics may be inherently critical to the producing bacterium, such as the acquisition of substrates or initiation of developmental changes that will ensure survival under stressful conditions. Antibiotics may also have roles in more complex interactions, including in virulence on host plants or in shaping the outcomes of multitrophic interactions. The innate functions of antibiotics to producing bacteria in their native ecosystem are just beginning to emerge, but current knowledge already reveals a breadth of activities well beyond the historical perspective of antibiotics as weaponry in microbial conflicts.
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The Role of Secretion Systems and Small Molecules in Soft-Rot Enterobacteriaceae Pathogenicity
Amy Charkowski, Carlos Blanco, Guy Condemine, Dominique Expert, Thierry Franza, Christopher Hayes, Nicole Hugouvieux-Cotte-Pattat, Emilia López Solanilla, David Low, Lucy Moleleki, Minna Pirhonen, Andrew Pitman, Nicole Perna, Sylvie Reverchon, Pablo Rodríguez Palenzuela, Michael San Francisco, Ian Toth, Shinji Tsuyumu, Jacquie van der Waals, Jan van der Wolf, Frédérique Van Gijsegem, Ching-Hong Yang, and Iris YedidiaVol. 50 (2012), pp. 425–449More LessSoft-rot Enterobacteriaceae (SRE), which belong to the genera Pectobacterium and Dickeya, consist mainly of broad host-range pathogens that cause wilt, rot, and blackleg diseases on a wide range of plants. They are found in plants, insects, soil, and water in agricultural regions worldwide. SRE encode all six known protein secretion systems present in gram-negative bacteria, and these systems are involved in attacking host plants and competing bacteria. They also produce and detect multiple types of small molecules to coordinate pathogenesis, modify the plant environment, attack competing microbes, and perhaps to attract insect vectors. This review integrates new information about the role protein secretion and detection and production of ions and small molecules play in soft-rot pathogenicity.
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Receptor Kinase Signaling Pathways in Plant-Microbe Interactions
Vol. 50 (2012), pp. 451–473More LessPlant receptor-like kinases (RLKs) function in diverse signaling pathways, including the responses to microbial signals in symbiosis and defense. This versatility is achieved with a common overall structure: an extracytoplasmic domain (ectodomain) and an intracellular protein kinase domain involved in downstream signal transduction. Various surfaces of the leucine-rich repeat (LRR) ectodomain superstructure are utilized for interaction with the cognate ligand in both plant and animal receptors. RLKs with lysin-motif (LysM) ectodomains confer recognitional specificity toward N-acetylglucosamine-containing signaling molecules, such as chitin, peptidoglycan (PGN), and rhizobial nodulation factor (NF), that induce immune or symbiotic responses. Signaling downstream of RLKs does not follow a single pattern; instead, the detailed analysis of brassinosteroid (BR) signaling, innate immunity, and symbiosis revealed at least three largely nonoverlapping pathways. In this review, we focus on RLKs involved in plant-microbe interactions and contrast the signaling pathways leading to symbiosis and defense.
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Fire Blight: Applied Genomic Insights of the Pathogen and Host
Vol. 50 (2012), pp. 475–494More LessThe enterobacterial phytopathogen Erwinia amylovora causes fire blight, an invasive disease that threatens a wide range of commercial and ornamental Rosaceae host plants. The response elicited by E. amylovora in its host during disease development is similar to the hypersensitive reaction that typically leads to resistance in an incompatible host-pathogen interaction, yet no gene-for-gene resistance has been described for this host-pathogen system. Comparative genomic analysis has found an unprecedented degree of genetic uniformity among strains of E. amylovora, suggesting that the pathogen has undergone a recent genetic bottleneck. The genome of apple, an important host of E. amylovora, has been sequenced, creating new opportunities for the study of interactions between host and pathogen during fire blight development and for the identification of resistance genes. This review includes recent advances in the genomics of both host and pathogen.
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Previous Volumes
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Volume 62 (2024)
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Volume 61 (2023)
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Volume 60 (2022)
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Volume 59 (2021)
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Volume 58 (2020)
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Volume 57 (2019)
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Volume 56 (2018)
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Volume 55 (2017)
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Volume 54 (2016)
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Volume 53 (2015)
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Volume 52 (2014)
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Volume 51 (2013)
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Volume 50 (2012)
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Volume 49 (2011)
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Volume 48 (2010)
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Volume 47 (2009)
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Volume 46 (2008)
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Volume 45 (2007)
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Volume 44 (2006)
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Volume 43 (2005)
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Volume 42 (2004)
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Volume 41 (2003)
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Volume 40 (2002)
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Volume 39 (2001)
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Volume 38 (2000)
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Volume 37 (1999)
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Volume 36 (1998)
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Volume 35 (1997)
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Volume 34 (1996)
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Volume 33 (1995)
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Volume 32 (1994)
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Volume 31 (1993)
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Volume 30 (1992)
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Volume 29 (1991)
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Volume 28 (1990)
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Volume 27 (1989)
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Volume 26 (1988)
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Volume 25 (1987)
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Volume 24 (1986)
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Volume 23 (1985)
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Volume 22 (1984)
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Volume 21 (1983)
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Volume 20 (1982)
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Volume 19 (1981)
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Volume 18 (1980)
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Volume 17 (1979)
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Volume 16 (1978)
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Volume 15 (1977)
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Volume 14 (1976)
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Volume 13 (1975)
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Volume 12 (1974)
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Volume 11 (1973)
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Volume 10 (1972)
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Volume 9 (1971)
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Volume 8 (1970)
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Volume 7 (1969)
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Volume 6 (1968)
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Volume 5 (1967)
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Volume 4 (1966)
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Volume 3 (1965)
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Volume 2 (1964)
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Volume 1 (1963)
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Volume 0 (1932)