Apple endophyte community in relation to location, scion and rootstock genotypes and susceptibility to European canker

Abstract

European apple canker, caused by Neonectria ditissima, is a severe disease of apple. Achieving effective control is difficult with the currently available pesticides. Specific apple endophytes associated with cultivars may partially contribute to the cultivar response to the pathogen and thus could be used for disease management. We sought to determine whether the overall endophyte community differed among cultivars differing in their susceptibility to N. ditissima and to identify specific microbial groups associated with the susceptibility. Using Illumina MiSeq meta-barcoding, we profiled apple tree endophytes in 16 scion-rootstock combinations at two locations, and quantified the relative contribution of scion, rootstock and location to the observed variability in the endophyte communities. Endophyte diversity was primarily affected by the orchard location (accounting for 29.4% and 85.9% of the total variation in the PC1 for bacteria and fungi, respectively), followed by the scion genotype (24.3% and 19.5% of PC2), whereas rootstock effects were small (<3% of PC1 and PC2). There were significant differences in the endophyte community between canker resistant and susceptible cultivars. Several bacterial and fungal endophyte groups had different relative abundance between susceptible and resistant cultivars. These endophyte groups included putative pathogen antagonists as well as plant pathogens. Their possible ecological roles in the N. ditissima pathosystem are discussed.

Characterization and Antagonistic Effect of Culturable Apple-Phyllosphere Endophytic Bacteria from the Cold Plateau in Yunnan, China

“…Liu et al (2020) and our study proved that the site was the main driver shaping the endophytic community in apple, but not the region [12]. Leone Olivieri et al (2021) studied and found that the apple endophyte community in relation to location, and scion and rootstock genotypes was susceptible to European canker [40]. Liu Jia et al (2018) stated that the mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known [41].…”

“…In China, Li et al (2020) isolated and identified four strains of B. subtilis, two strains of B. velezensis, and one strain of B. amyloliquefaciens from a wild apple (Malus sieversii) [39]. Therefore, it is suggested that differences in the distribution of endophytic bacteria communities in apple leaves may depend upon the external environmental conditions, or upon different cultivation methods such as the use of pesticides [12,40,41]. Liu et al (2020) and our study proved that the site was the main driver shaping the endophytic community in apple, but not the region [12].…”

Apple Endophytic fungi and their antagonism against apple scab disease

“…Further, scab disease management had an effect on the abundance of some taxa depending on bark age, orchard location, and sampling time ( Arrigoni et al, 2020 ). Interestingly, Olivieri et al (2021) mentioned the presence of significant differences between canker-resistant and susceptible apple cultivars with respect to the endophyte community.…”

“…Several studies have assessed the endophytic fungal communities of apple (e.g., Camatti-Sartori et al, 2005;Alijani et al, 2016a;Liu et al, 2017;Muresan, 2017;Afandhi et al, 2018;Liu et al, 2018;Arrigoni et al, 2020;Olivieri et al, 2021), some of which have focused on the biological control potential of the endophytes against apple fungal diseases. Alijani et al (2016a) purified about 350 isolates from the shoots, leaves, and barks of endemic and commercial apple trees in West Azerbaijan province, Iran and identified 24 species belonging to 10 genera of Ascomycota.…”

“…Several studies have assessed the endophytic fungal communities of apple (e.g., Camatti-Sartori et al, 2005 ; Alijani et al, 2016a ; Liu et al, 2017 ; Muresan, 2017 ; Afandhi et al, 2018 ; Liu et al, 2018 ; Arrigoni et al, 2020 ; Olivieri et al, 2021 ), some of which have focused on the biological control potential of the endophytes against apple fungal diseases. Based on the results, apple tissues are colonized by a diverse array of fungal taxa (e.g., Alternaria Nees, Arthrinium Kunze, Aspergillus P. Micheli ex Haller, Biscogniauxia Kuntze, Botryosphaeria Ces.…”