Coralie Picard, Sylvie Dallot, Kirstyn Brunker, Karine Berthier, Philippe Roumagnac, Samuel Soubeyrand, Emmanuel Jacquot, Gaël Thébaud
{"title":"Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes.","authors":"Coralie Picard, Sylvie Dallot, Kirstyn Brunker, Karine Berthier, Philippe Roumagnac, Samuel Soubeyrand, Emmanuel Jacquot, Gaël Thébaud","doi":"10.1146/annurev-phyto-080516-035616","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035616","url":null,"abstract":"<p><p>During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"139-160"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035616","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35013045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Daniel Debona, Fabrício A Rodrigues, Lawrence E Datnoff
{"title":"Silicon's Role in Abiotic and Biotic Plant Stresses.","authors":"Daniel Debona, Fabrício A Rodrigues, Lawrence E Datnoff","doi":"10.1146/annurev-phyto-080516-035312","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035312","url":null,"abstract":"<p><p>Silicon (Si) plays a pivotal role in the nutritional status of a wide variety of monocot and dicot plant species and helps them, whether directly or indirectly, counteract abiotic and/or biotic stresses. In general, plants with a high root or shoot Si concentration are less prone to pest attack and exhibit enhanced tolerance to abiotic stresses such as drought, low temperature, or metal toxicity. However, the most remarkable effect of Si is the reduction in the intensities of a number of seedborne, soilborne, and foliar diseases in many economically important crops that are caused by biotrophic, hemibiotrophic, and necrotrophic plant pathogens. The reduction in disease symptom expression is due to the effect of Si on some components of host resistance, including incubation period, lesion size, and lesion number. The mechanical barrier formed by the polymerization of Si beneath the cuticle and in the cell walls was the first proposed hypothesis to explain how this element reduced the severity of plant diseases. However, new insights have revealed that many plant species supplied with Si have the phenylpropanoid and terpenoid pathways potentiated and have a faster and stronger transcription of defense genes and higher activities of defense enzymes. Photosynthesis and the antioxidant system are also improved for Si-supplied plants. Although the current understanding of how this overlooked element improves plant reaction against pathogen infections, pest attacks, and abiotic stresses has advanced, the exact mechanism(s) by which it modulates plant physiology through the potentiation of host defense mechanisms still needs further investigation at the genomic, metabolomic, and proteomic levels.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"85-107"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035312","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34995348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aviv Dombrovsky, Lucy T T Tran-Nguyen, Roger A C Jones
{"title":"Cucumber green mottle mosaic virus: Rapidly Increasing Global Distribution, Etiology, Epidemiology, and Management.","authors":"Aviv Dombrovsky, Lucy T T Tran-Nguyen, Roger A C Jones","doi":"10.1146/annurev-phyto-080516-035349","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035349","url":null,"abstract":"<p><p>Cucumber green mottle mosaic virus (CGMMV) was first described in 1935 infecting cucumber, making it one of the first plant viruses to be studied. Its initial distribution occurred out of England to other countries. This was followed by its distribution from England and these other countries to additional countries. This process increased slowly between 1935 and 1985, faster between 1986 and 2006, and rapidly between 2007 and 2016. The discovery that it diminished cucurbit fruit yields and quality, especially of watermelon, prompted a substantial research effort in worst-affected countries. These efforts included obtaining insight into its particle and genome characteristics, evolution, and epidemiology. CGMMV's particle stability, ease of contact transmission, and seed transmissibility, which are typical tobamovirus characteristics, explained its complex disease cycle and its ability to spread locally or over long distances without a vector. Knowledge of its disease etiology and epidemiology enabled development of integrated disease management approaches that rely heavily on diverse phytosanitary measures. Dispersal of seed-borne infection through the international seed trade following cucurbit seed crop production in tropical or subtropical countries explains its recent rapid dispersion worldwide.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"231-256"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035349","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35069882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Adaptation to the Host Environment by Plant-Pathogenic Fungi.","authors":"H Charlotte van der Does, Martijn Rep","doi":"10.1146/annurev-phyto-080516-035551","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035551","url":null,"abstract":"<p><p>Many fungi can live both saprophytically and as endophyte or pathogen inside a living plant. In both environments, complex organic polymers are used as sources of nutrients. Propagation inside a living host also requires the ability to respond to immune responses of the host. We review current knowledge of how plant-pathogenic fungi do this. First, we look at how fungi change their global gene expression upon recognition of the host environment, leading to secretion of effectors, enzymes, and secondary metabolites; changes in metabolism; and defense against toxic compounds. Second, we look at what is known about the various cues that enable fungi to sense the presence of living plant cells. Finally, we review literature on transcription factors that participate in gene expression in planta or are suspected to be involved in that process because they are required for the ability to cause disease.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"427-450"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035551","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35113968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lise N Jørgensen, F van den Bosch, R P Oliver, T M Heick, N D Paveley
{"title":"Targeting Fungicide Inputs According to Need.","authors":"Lise N Jørgensen, F van den Bosch, R P Oliver, T M Heick, N D Paveley","doi":"10.1146/annurev-phyto-080516-035357","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035357","url":null,"abstract":"<p><p>Fungicides should be used to the extent required to minimize economic costs of disease in a given field in a given season. The maximum number of treatments and maximum dose per treatment are set by fungicide manufacturers and regulators at a level that provides effective control under high disease pressure. Lower doses are economically optimal under low or moderate disease pressure, or where other control measures such as resistant cultivars constrain epidemics. Farmers in many countries often apply reduced doses, although they may still apply higher doses than the optimum to insure against losses in high disease seasons. Evidence supports reducing the number of treatments and reducing the applied dose to slow the evolution of fungicide resistance. The continuing research challenge is to improve prediction of future disease damage and account for the combined effect of integrated control measures to estimate the optimum number of treatments and the optimum dose needed to minimize economic costs. The theory for optimizing dose is well developed but requires translation into decision tools because the current basis for farmers' dose decisions is unclear.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"181-203"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035357","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35013043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ikkei Shikano, Cristina Rosa, Ching-Wen Tan, Gary W Felton
{"title":"Tritrophic Interactions: Microbe-Mediated Plant Effects on Insect Herbivores.","authors":"Ikkei Shikano, Cristina Rosa, Ching-Wen Tan, Gary W Felton","doi":"10.1146/annurev-phyto-080516-035319","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035319","url":null,"abstract":"<p><p>It is becoming abundantly clear that the microbes associated with plants and insects can profoundly influence plant-insect interactions. Here, we focus on recent findings and propose directions for future research that involve microbe-induced changes to plant defenses and nutritive quality as well as the consequences of these changes for the behavior and fitness of insect herbivores. Insect (herbivore and parasitoid)-associated microbes can favor or improve insect fitness by suppressing plant defenses and detoxifying defensive phytochemicals. Phytopathogens can influence or manipulate insect behavior and fitness by altering plant quality and defense. Plant-beneficial microbes can promote plant growth and influence plant nutritional and phytochemical composition that can positively or negatively influence insect fitness. Lastly, we suggest that entomopathogens have the potential to influence plant defenses directly as endophytes or indirectly by altering insect physiology.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"313-331"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035319","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35069885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Stephen Parnell, Frank van den Bosch, Tim Gottwald, Christopher A Gilligan
{"title":"Surveillance to Inform Control of Emerging Plant Diseases: An Epidemiological Perspective.","authors":"Stephen Parnell, Frank van den Bosch, Tim Gottwald, Christopher A Gilligan","doi":"10.1146/annurev-phyto-080516-035334","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035334","url":null,"abstract":"<p><p>The rise in emerging pathogens and strains has led to increased calls for more effective surveillance in plant health. We show how epidemiological insights about the dynamics of disease spread can improve the targeting of when and where to sample. We outline some relatively simple but powerful statistical approaches to inform surveillance and describe how they can be adapted to include epidemiological information. This enables us to address questions such as: Following the first report of an invading pathogen, what is the likely incidence of disease? If no cases of disease have been found, how certain can we be that the disease was not simply missed by chance? We illustrate the use of spatially explicit stochastic models to optimize targeting of surveillance and control resources. Finally, we discuss how modern detection and diagnostic technologies as well as information from passive surveillance networks (e.g., citizen science) can be integrated into surveillance strategies.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"591-610"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035334","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35108251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Ecology and Genomic Insights into Plant-Pathogenic and Plant-Nonpathogenic Endophytes.","authors":"Günter Brader, Stéphane Compant, Kathryn Vescio, Birgit Mitter, Friederike Trognitz, Li-Jun Ma, Angela Sessitsch","doi":"10.1146/annurev-phyto-080516-035641","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035641","url":null,"abstract":"<p><p>Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathogens. The outcome of these plant-microbe interactions depends on biotic and abiotic environmental factors and on the genotype of the host and the interacting microorganism. In addition, endophytic microbiota and the manifold interactions between members, including pathogens, have a profound influence on the function of the system plant and the development of pathobiomes. In this review, we elaborate on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. We furthermore discuss environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathobiome.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"61-83"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035641","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34981791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fusarium oxysporum and the Fusarium Wilt Syndrome.","authors":"Thomas R Gordon","doi":"10.1146/annurev-phyto-080615-095919","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080615-095919","url":null,"abstract":"<p><p>The Fusarium oxysporum species complex (FOSC) comprises a multitude of strains that cause vascular wilt diseases of economically important crops throughout the world. Although sexual reproduction is unknown in the FOSC, horizontal gene transfer may contribute to the observed diversity in pathogenic strains. Development of disease in a susceptible crop requires F. oxysporum to advance through a series of transitions, beginning with spore germination and culminating with establishment of a systemic infection. In principle, each transition presents an opportunity to influence the risk of disease. This includes modifications of the microbial community in soil, which can affect the ability of pathogen propagules to survive, germinate, and infect plant roots. In addition, many host attributes, including the composition of root exudates, the structure of the root cortex, and the capacity to recognize and respond quickly to invasive growth of a pathogen, can impede development of F. oxysporum.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"23-39"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080615-095919","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34981793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Scientific, Economic, and Social Impacts of the New Zealand Outbreak of Bacterial Canker of Kiwifruit (Pseudomonas syringae pv. actinidiae).","authors":"Joel L Vanneste","doi":"10.1146/annurev-phyto-080516-035530","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080516-035530","url":null,"abstract":"<p><p>The introduction of Pseudomonas syringae pv. actinidiae (Psa) severely damaged the New Zealand kiwifruit industry, which in 2010 was based on only two cultivars. Despite an extraordinarily quick and strong response by industry, government, and scientists to minimize the economic and social impacts, the economic consequences of this outbreak were severe. Although our understanding of Psa epidemiology and control methods increased substantively over the past six years, the kiwifruit industry largely recovered because of the introduction of a less-susceptible yellow-fleshed cultivar. The New Zealand population of Psa is clonal but has evolved rapidly since its introduction by exchanging mobile genetic elements, including integrative conjugative elements (ICEs), with the local bacterial populations. In some cases, this has led to copper resistance. It is currently believed that the center of origin of the pathogen is Japan or Korea, but biovar 3, which is responsible for the global outbreak, originated in China.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"55 ","pages":"377-399"},"PeriodicalIF":10.2,"publicationDate":"2017-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080516-035530","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35087474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}