Inter-Row Cropping and Rootstock Genotype Selection as a Management Strategy for Apple Replant Disease in a UK Cider Orchard.

Abstract

Purpose Apple rootstock genotypes confer different levels of tolerance to apple replant disease (ARD) and vigour to a newly replanted apple tree. A hybrid management system of rotating the rootstock genotype planted between successive generations and inter-row planting in the alleyways of orchards may minimise the severity of ARD symptoms by altering the communities in the rhizosphere microbiome. Methods High-throughput sequencing of the fungal ITS and bacterial 16S regions was used to investigate the diversity, and differential taxa present in soils displaying symptoms of ARD. Candidate pathogens and beneficial microorganisms were correlated with the above-ground establishment of each rootstock genotype in a U.K. cider orchard. Results Our results suggest rootstocks that are more closely genetically related to the previous rootstock had more severe ARD. Planting in the alleyway appeared an effective strategy to minimise the severity of symptoms irrespective of rootstock genotype. The planting location effect had a higher contribution to the variation in rhizosphere microbiome than the rootstock genotype contribution. No causal agents for ARD could be identified to a taxonomic level to predict their function but two taxa associated with mycorrhizae, Pteridiospora spinosispora and Paraglomus laccatum were identified to be beneficial for the plant to minimise ARD severity. Conclusions Our findings suggest a hybrid management approach of rotating rootstock genotype to a rootstock dissimilar to those previously planted, planting rootstocks in the alleyway, and biological amendment with beneficial microorganisms could be an effective strategy to minimise severity of ARD.