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Advances continue to be made by plant pathologists on topics in plant health, environmental protection and food security. Many advances have been made for individual crops, pathogens and diseases that in many cases have led to their successful management. A wider impact of research depends on recognition of the multifaceted challenges posed by plant diseases and the need to integrate studies in a systems level approach. The adoption of high‐throughput sequencing for diagnosis and detection is widespread but impact depends upon the agricultural and ecological context combined with improved surveillance. Deployment of host resistance in the field needs to be aligned with a greater appreciation of plant genetic diversity and the complementary contribution made by tolerance of disease. Epidemiological understanding of the spatiotemporal spread of plant diseases has improved through population dynamic and genetic analyses. Research emphasis on the plant microbiome has invigorated soil microbial studies, especially for disease complexes and declines, but the challenge is to move to interventions that benefit plant health. Analysis of the impacts of climate change has been made for single‐crop disease studies, but seldom have these been placed in the context of pathogen adaptation, new crops, wild plants, vectors and soil microbes. Advances in informatic analysis illustrate not only the global impacts of plant disease introductions, but also the challenges inherent in marshalling and integrating information. Advances have been made in applying artificial intelligence technologies across many areas of plant pathology but have yet to be integrated within any coordinated research agenda. [ABSTRACT FROM AUTHOR]

Aim We assessed the effect of exposing apple orchard soil to different temperatures and CO2 levels on the resident microbiome of soils from a conventionally managed and an organically managed apple orchard. The key difference between these two orchards was that synthetic fertilizers and pesticides are routinely used in the former one. Methods and results To investigate the effect of CO2 and temperature, soil samples from each site at two depths were exposed to either elevated temperature (29°C) at either 5000 or 10 000 ppm for five weeks or control conditions (25°C + 400 ppm). Both bacterial and fungal communities were profiled with amplicon-sequencing. The differences between the two orchards were the most significant factor affecting the bacterial and fungal communities, contributing to 53.7–14.0% of the variance in Bray–Curtis β diversity, respectively. Elevated CO2 concentration and increased temperature affected organic orchard microbial diversity more than the conventionally managed orchard. A number of candidate beneficial and pathogenic microorganisms had differential abundances when temperature and CO2 were elevated, but their effect on the plant is unclear. Conclusions This study has highlighted that microbial communities in bulk soils are most significantly influenced by crop management practices compared to the climate conditions used in the study. The studied climate conditions had a more limited effect on microbial community diversity in conventionally managed soil samples than in organically managed soils. [ABSTRACT FROM AUTHOR]

European apple canker, caused by Neonectria ditissima , is a severe disease of apple. Achieving effective control is difficult with the currently available pesticides. Specific apple endophytes associated with cultivars may partially contribute to the cultivar response to the pathogen and thus could be used for disease management. We sought to determine whether the overall endophyte community differed among cultivars differing in their susceptibility to N. ditissima and to identify specific microbial groups associated with the susceptibility. Using Illumina MiSeq meta-barcoding, we profiled apple tree endophytes in 16 scion–rootstock combinations at two locations and quantified the relative contribution of scion, rootstock and location to the observed variability in the endophyte communities. Endophyte diversity was primarily affected by the orchard location (accounting for 29.4% and 85.9% of the total variation in the PC1 for bacteria and fungi, respectively), followed by the scion genotype (24.3% and 19.5% of PC2), whereas rootstock effects were small (<3% of PC1 and PC2). There were significant differences in the endophyte community between canker-resistant and -susceptible cultivars. Several bacterial and fungal endophyte groups had different relative abundance between susceptible and resistant cultivars. These endophyte groups included putative pathogen antagonists as well as plant pathogens. Their possible ecological roles in the N. ditissima pathosystem are discussed. [ABSTRACT FROM AUTHOR]