Apple replant disease (ARD) is a complex issue caused by various fungal, oomycetes pathogens and parasites which can differ in their abundance between sites within a geographic region. Knowledge of the specific etiology of ARD at a particular site is required in order to develop commercially viable soil management strategies to combat specific/individual components of the disease. In this study we analyzed the soil from six ARD sites for the presence of fungal, bacterial and oomycetes communities and plant parasitic nematodes. Five fungal, and 17 bacterial classes were differentially represented in the microbiomes from 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. Proteobacteria was the most prevalent phylum identified in orchard soils. Several potential phytopathogenic fungi involved in ARD and endophytes including Fusarium oxysporum, F. solani, Nectria ramulariae, Ilyonectria robusta and Nectriaceae were identfied in the orchard soil. Pythium attrantheridium (Globisporangium attrantheridium), P. monospermum and P. ultimum (Globisporangium ultimum) were the most abundant oomycete taxa identified in these soil samples. Six different groups of plant-parasitic nematodes were found across the six orchards soil. Root-lesion nematodes, Pratylenchus spp., which are commonly associated with ARD, were identified in all orchards soil at population densities ranging from 12 to 33/100 cm3 soil. This research contributes valuable understanding of the ARD complex as the apple industry needs alternative approaches to combat the disease.

Apple replant disease (ARD) is a severe problem in orchards and tree nurseries caused by yet unknown soil biota that accumulate over replanting cycles. This study tested the contribution of nematodes to ARD, and cultivation of Tagetes as a control option. In a pot experiment, Tagetes patula or Tagetes tenuifolia were grown in ARD soil, incorporated or removed. Nematodes extracted from untreated ARD soil and washed on 20 µm-sieves induced ARD symptoms when inoculated to apple saplings growing in a sterile substrate. In contrast, nematodes from Tagetes treated ARD soil did not reduce root growth compared to uninoculated plants, irrespective of Tagetes species and incorporation. In plots of five apple tree nurseries or orchards, either Tagetes or grass was grown on ARD soil. Nematodes extracted from the grass plots and inoculated to apple saplings significantly reduced plant growth compared to nematodes from Tagetes plots for all five farms. Apple rootstocks showed overall a significantly higher increase in shoot base diameter when grown on Tagetes-treated plots compared to grass plots, while this effect differed among farms. Plant-parasitic nematodes were too low in abundance to explain plant damage. In conclusion, the free-living nematodes involved in ARD can be controlled by Tagetes.

Apple replant disease is a severe problem in orchards and tree nurseries. Evidence for the involvement of a nematode-microbe disease complex was reported. To search for this complex, plots with a history of apple replanting, and control plots cultivated for the first time with apple were sampled in two fields in two years. Shoot weight drastically decreased with each replanting. Nematodes were extracted from soil samples by floatation-centrifugation, washed on a 20 µm-sieve, and used for DNA extraction. Nematode communities and co-extracted fungi and bacteria were analyzed by high-throughput sequencing of amplified ribosomal fragments. The nematode community and co-extracted fungal and bacterial communities significantly differed between replanted and control plots. Free-living nematodes of the genera Aphelenchus, Cephalenchus, and an unidentified Dorylaimida were associated with replanted plots, as indicated by linear discriminant analysis effect size. Among the co-extracted fungi and bacteria, Mortierella was most indicative of replanting. Some genera, mostly Rhabditis, indicated healthy control plots. Isolating and investigating the putative disease complexes will help to understand and alleviate stress-induced root damage of apple in replanted soil.