Exploring soil microbial and plant parasitic nematode communities involved in the apple replant disease complex in...

Apple replant disease (ARD) is incited by a complex of causal agents including various fungi, oomycetes, and plant parasitic nematodes. These causal agents can differ significantly in abundance between orchard sites within a geographic region. Knowledge of the specific etiology of ARD is required in order to develop commercially viable soil management strategies to combat specific/individual components of the pathogen complex. In this study, we analyzed soil from six ARD affected orchard sites to assess the presence and composition of fungal, bacterial and oomycetes communities, as well as the prevalence of plant parasitic nematodes. Five fungal, and 17 bacterial classes were differentially represented in the soil microbiomes across the different locations. Mortierellomycetes was the most abundant fungal taxa represented followed by Sordariomycetes. Mortierella exigua, a fungal endophyte, was the most abundant fungal amplicon sequence variant (ASV) in the core microbiome. Among bacteria, Proteobacteria was the most prevalent phylum identified in these orchard soils. Several potential phytopathogenic fungi associated with ARD, as well as endophytes including Fusarium oxysporum, F. solani, Nectria ramulariae, Ilyonectria robusta and Nectriaceae, were identified in ARD soils. Among oomycetes, Pythium attrantheridium (Globisporangium attrantheridium), and P. irregulare (Globisporangium irregulare) were the most abundant taxa. Additionally, six different groups of plant-parasitic nematodes were found across the ARD orchard soils. Root-lesion nematodes, Pratylenchus spp., which are commonly associated with ARD, were identified in all orchard soils at population densities range from 12 to 33/100 cm³ soil. This research enhances our understanding of the ARD pathogen complex and provide important insights for developing alternative disease management strategies in the apple industry.