The effect of plant cultivar on the degree of mycorrhization and the benefits mediated by arbuscular mycorrhizal fungi (AMF) have been documented in many crops. In apple, a wide variety of rootstocks are commercially available; however, it is not clear whether some rootstock genotypes are more susceptible to mycorrhization than others and/or whether AMF species identity influences rootstock compatibility. This study addresses these questions by directly testing the ability/efficacy of four different AMF species (Rhizophagus irregularis, Septoglomus deserticola, Claroideoglomus claroideum or Claroideoglomus etunicatum) to colonize a variety of commercially available Geneva apple rootstock genotypes (G.11, G.41, G.210, G.969, and G.890). Briefly, micropropagated plantlets were inoculated with individual species of AMF or were not inoculated. The effects of the rootstock genotype/AMF interaction on mycorrhization, plant growth, and/or leaf nutrient concentrations were assessed. We found that both rootstock genotype and the identity of the AMF are significant sources of variation affecting the percentage of colonization. However, these factors largely operate independently in terms of the extent of root colonization. Among the AMF tested, C. etunicatum and R. irregularis represented the most compatible fungal partners, regardless of apple rootstock genotype. Among the rootstocks tested, semi-dwarfing rootstocks appeared to have an advantage over dwarfing rootstocks in regard to establishing and maintaining associations with AMF. Nutrient uptake and plant growth outcomes were also influenced in a rootstock genotype/AMF species-specific manner. Our findings suggest that matching host genetics with compatible AMF species has the potential to enhance agricultural practices in nursery and orchard systems.

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. High-throughput sequencing of the fungal ITS and bacterial 16S rDNA 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 UK cider orchard. Our results suggest that the same rootstock or rootstock with closely related parentage to the previous rootstock had more severe ARD symptoms. 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 the rhizosphere microbiome than that of the rootstock genotype. No predicted causal agents for ARD could be identified to a taxonomic level to predict their function but two species associated with mycorrhizae, Pteridiospora spinosispora and Paraglomus laccatum were identified as inversely correlated with ARD severity and could be candidate beneficial species for apple, warranting further investigation and research. Our findings suggest that planting in the alleyways and planting rootstocks genetically dissimilar to the previously planted rootstock can be beneficial for tree establishment. We have also identified species inversely associated with ARD severity, making candidates for future research to test the antagonistic effect of the species against ARD pathogens in apple roots.

Currently, there are no standard management practices to counteract the adverse effects of fumigation on the soil microbiome. In this study, a variety of pre-plant soil amendments were examined for their ability to recruit and maintain apple rhizosphere microbiomes that are suppressive to pathogen re-infestation of fumigated orchard soils. The capacity of these amendments to improve other characteristics of soil productivity was also evaluated. Results suggest that composted chicken manure and liquid chitin are likely to be detrimental to plant and soil health when used as a post-fumigation soil amendment. In comparison, insect frass (IF) resulted in a significant increase in tree trunk diameter relative to the fumigated control. Following pathogen re-infestation of fumigated soil, however, IF induced a significant increase in Pythium ultimum in the rhizosphere. Therefore, IF can benefit the growth of young apple trees in fumigated soil but may stimulate pathogen activity upon re-infestation. To date, the possibility of using soil amendments to suppress pathogen re-infestation of fumigated soils has not been tested. Results from this study ground support the use of soil amendments as an intervention strategy for “steering” the soil and rhizosphere microbiome in more beneficial and/or prophylactic directions following fumigation.

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.