Candidate Causal Organisms for Apple Replant Disease in the United Kingdom

Continuous planting of apple in the same area leads to reduced growth vigor and subsequent crop losses, i.e., apple replant disease (ARD) syndrome. Several soilborne plant pathogens including Pythium, Fusarium, and Cylindrocarpon spp. are often proposed as candidate causal organisms for ARD. In addition, the presence of root lesion nematodes and the lack of beneficial groups of bacteria are believed to exacerbate or ameliorate the effects of the plant pathogens. The importance of these proposed causal and auxiliary agents seems to vary with site. Using a spatially explicit sampling strategy to minimize spatial variability we collected rhizosphere soil samples from neighboring pairs of healthy and putative ARD trees to identify candidate causal organisms of ARD. Amplicon-based metabarcoding was used to obtain community-level profiles of the bacteria, fungi, oomycetes and nematodes in the soil samples. Total bacterial and fungal biomass in each sample was estimated using qPCR to adjust the raw sequence reads data. The results suggested that ARD is not ameliorated by enhanced rhizosphere biodiversity per se. We identified 25 bacterial operational taxonomic units (OTUs), 16 fungal OTUs, 18 oomycetes OTUs, and one nematode OTU group with differential abundance between healthy and putative ARD trees. All 25 bacterial OTUs had lower abundance in samples from ARD symptomatic trees than from healthy trees. One AMF OTU had lower abundance in samples from ARD symptomatic trees. None of 13 fungal OTUs that had higher abundance in samples from ARD symptomatic trees is a known plant pathogen; but at least one Pythium OTU (probably Pythium intermedium) is a candidate for causing ARD. The abundance of one nematode OTU was much higher in samples from ARD symptomatic trees than in healthy trees. The results suggest that, apart from the use of broad spectrum fumigants, the complexity of ARD may necessitate the combined use of multiple management strategies with the success of these measures expected to vary considerably between sites because of the varying importance of ARD causal agents among sites