Candidate Organisms for Apple Replant Disease

Continuous plantation of apple in the same area can lead to reduced growth vigour and subsequent crop losses, referred to as apple replant disease (ARD). In addition to decreased populations of beneficial bacteria, several soil-borne pathogens, including Pythium, Fusarium and Cylindrocarpon spp., are often proposed as candidate causal organisms for ARD, whereas nematodes may exacerbate ARD development. Previous ARD studies have used fumigants to create “healthy” soils, or compared trees from different sites. This limits the identification of ARD causal agents owing to the wide-ranging effects of the fumigants and the high spatial heterogeneity of soil microbial communities. In a novel sampling approach, we collected rhizosphere soil samples from neighbouring pairs of healthy and ARD trees to identify candidate organisms of ARD, thereby minimising the effects of spatial variability. Amplicon-based metabarcoding of the ITS region and 16S rRNA gene was used to profile samples for archaea, bacteria, fungi, oomycetes and nematodes. Total bacterial and fungal biomass in each sample was estimated using qPCR to adjust raw sequence reads data. This sampling scheme considerably reduced the total number of microorganism groups with differential abundances between healthy and ARD tree samples: 25 bacterial OTUs, 16 fungal OTUs, 18 oomycetes OTUs and one nematode OTU. All 25 bacterial OTUs were less abundant in ARD samples than in healthy samples. None of the 13 fungal OTUs that were more prevalent in ARD samples were known plant pathogens, although one AMF OTU had a significantly lower abundance in ARD soils. Of the 11 oomycete OTUs enriched in ARD soils, four were members of the genus Pythium (including P. intermedium). Aside from the use of broad spectrum fumigants, the ARD complexity may necessitate combined use of alternative management strategies, with effectiveness likely to vary considerably between sites owing to the spatial variance of ARD causal agents.