Candidate Causal Organisms for Apple Replant Disease in the United Kingdom

Abstract

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.

Effect of fungal, oomycete and nematode interactions on apple root development in replant soil

“…However, it is in the early stages of the experiment, when the roots of young plants are assumed to have been most susceptible to pathogen attack, that differences in pathogenic groups would have had the greatest impact on the observed differences in root necrosis and abundance. The majority of bacterial OTUs where relative abundance was increased, compared with the untreated control, were obtained from treatments containing the fungicide and/or oomycete biocide, which agrees with our recent finding that the relative bacterial OTU abundance is generally greater in the rhizosphere of healthy trees, than in ARD-affected trees (Tilston et al 2018). In contrast, the treatment which resulted in the fewest changes in abundance within the bacterial community was the nematicide only treatment.…”

Global challenges facing plant pathology: multidisciplinary approaches to meet the food security and environmental challenges in the mid-twenty-first century

“…Secondly, an OTU table from amplicon sequences only represents the relative frequencies of OTUs in each sample, when absolute microbial biomass/ counts may possibly be more important. It is possible that qPCR could be used to estimate the total microbial biomass via the generic fungal ITS and bacterial 16S primers (e.g., Tilston et al 2018). Alternatively, each environmental sample may be spiked with a known amount of a synthetic DNA fragment to estimate absolute abundance (Tkacz et al 2018).…”

Isolation, Identification, and Antibacterial Mechanisms of Bacillus amyloliquefaciens QSB-6 and Its Effect on Plant Roots

“…Apple replant disease has been attributed to a variety of biotic and abiotic causal factors, but current studies suggest that biotic factors such as fungi ( Rhizoctonia , Fusarium , and Cylindrocarpon ), Oomycetes ( Pythium , Humicola , and Phytophthora ), and nematodes ( Pratylenchus ) play a leading role in disease development ( Utkhede et al, 1992 ; Van Schoor et al, 2009 ; Tewoldemedhin et al, 2011a , b ; Kelderer et al, 2012 ; Tilston et al, 2018 , 2020 ; Yim et al, 2020 ). This has been widely demonstrated in other studies via soil pasteurization and the application of biocides ( Weller et al, 2002 ; Garbeva et al, 2004 ).…”