Climate change and plant health: designing research spillover from plant genomics for understanding the role of microbial communities

Abstract

Climate change presents new challenges for managing plant health. Simultaneously, the revolution in sequencing technologies offers an exciting new perspective on whole microbial communities -and on both microbial responses to climate and microbial effects on plant health. There is still the need for a comparable revolution in experimental approaches to understand the functional roles of microbial taxa within these communities. Two approaches leveraging advances in genomics tools and analyses may contribute. First, new soil mixing experiments may be developed, where analyses of quantitative trait taxa (QTT) may be analogous to analyses of quantitative trait loci (QTL). Second, new approaches for characterizing the extended phenotype or phenome of soil microbial communities may be developed, leveraging genomic tools for Arabidopsis and other model plant species through the construction of plant genotype panels in an 'Arabidopsitron'. Résumé:Les changements climatiques posent de nouveaux défis quant à la gestion de la santé des plantes. Simultanément, la révolution dans les technologies de séquençage offre une nouvelle perspective passionnante quant à des communautés microbiennes entières, et ce, tant sur le plan des réactions des microorganismes aux changements climatiques que sur celui des effets de ces microorganismes sur la santé des plantes. Le besoin d'une révolution similaire quant aux approches expérimentales demeure essentiel pour comprendre les rôles fonctionnels des taxons au sein de ces communautés. Deux approches qui optimisent les avancées dans le domaine des outils génomiques et des analyses peuvent y contribuer. Premièrement, de nouvelles expériences sur le mélange des sols peuvent être conçues alors que les analyses des taxons à caractère quantitatif (QTT) peuvent être analogues aux analyses des locus à caractère quantitatif (QTL). Deuxièmement, de nouvelles approches permettant de caractériser le phénome (phénotype élargi) des communautés bactériennes terricoles peuvent être développées, optimisant les outils génomiques pour Arabidopsis et d'autres espèces modèles de plantes par la constitution de panels de génotypes de plantes dans un « Arabidopsitron ».

Meta-Analysis and Other Approaches for Synthesizing Structured and Unstructured Data in Plant Pathology

“…The amount of new scientific data generated every day will increase even faster with the application of high-throughput 'omics and phenotyping technologies at the population or field levels (6,49), leading to significant analytical bottlenecks. At the same time, informal information in the form of digital traces (112) left behind in cyberspace by the protagonists in our disciplinegrowers, consultants, extension agents, industry personnel, and university scientists-as a result of daily use of digital media and networks will escalate even more.…”

Response to Temperature and Virulence Assessment of Fusarium circinatum Isolates in the Context of Climate Change

“…In the future, a larger number of outbreaks and possible pathogenic variants may be expected as new environmental conditions resulting from climate change may favor survival and fitness of some pathogens. In contrast, plant disease management strategies under new climate conditions are lagging [35].The USDA Forest Service Resistance Screening Center (RSC) in Asheville, North Carolina has been screening seedlings of pine and other forest tree species for genetically-controlled resistance or tolerance to diseases like pitch canker, fusiform rust, dogwood anthracnose, chestnut blight, white pine blister rust brown spot needle blight, and butternut canker [36]. The RSC has screened plant material for over 20 industrial, governmental, non-profit, and academic institutions.…”

“…In the future, a larger number of outbreaks and possible pathogenic variants may be expected as new environmental conditions resulting from climate change may favor survival and fitness of some pathogens. In contrast, plant disease management strategies under new climate conditions are lagging [35].…”