Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design

Abstract

Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible ‘M26’ apple rootstocks in different substrates combinations (+ARD: apple replant disease soil; -ARD: gamma-irradiated ARD soil; Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil-root continuum (bulk soil, rhizosphere, rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil-root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD, Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.

Importance of microbial communities at the root-soil interface for extracellular polymeric substances and soil aggregation in semiarid grasslands

“…The parent material was the most important driver for microbial community compositions, rather than the studied plant species. To disentangle the effect of the plant species, in the present study rhizoplane and rhizosphere samples were analysed, as the plant-soil interface is known to be most dynamic and largest plant species-specific influences can be expected (Balbín-Suárez et al, 2020). The influence of these two plant species on their root-associated bacterial and archaeal communities (further on microbial communities) and subsequent EPS production has so far been unexplored.…”

Evaluation of Apple Root-Associated Endophytic Streptomyces pulveraceus Strain ES16 by an OSMAC-Assisted Metabolomics Approach

“…The stressful and dysbiotic environment characteristically associated with ARD, not only for apple plants but also for associated microbiota, is well-established (Mazzola and Manici, 2012; Yim et al, 2013Yim et al, , 2015Weiß et al, 2017;Grunewaldt-Stöcker et al, 2019;Radl et al, 2019;Winkelmann et al, 2019;Balbín-Suárez et al, 2020). For example, an increased abundance of environmental stress sensing genes, particularly in the rhizosphere microbiome of ARD soils compared to ARDunaffected soils, was recently unraveled by a metagenomics approach (Radl et al, 2019).…”

“…Interestingly, we found that the increased abundance of Streptomyces in apple roots grown in ARD soils negatively correlated with increased shoot length and fresh mass. Furthermore, gene sequencing revealed that Streptomyces taxa are selectively enriched in the rhizosphere in ARD soils in split-root experiments (Balbín-Suárez et al, 2020). However, whether these observations are causal or correlated remains unclear.…”

Characterization of soils conducive and non-conducive to Prunus replant disease

“…Next generation sequencing (NGS) of marker genes has afforded comparatively deeper and more adaptable approaches to characterizing the microbial communities [11,12]. There are recent examples of NGS applications with high relevance to PRD, including examinations of apple replant disease [13,14], rose replant disease [15], and peach replant suppression [3,16]. However, none of the previous studies using NGS examined PRD incidence or severity among multiple soils or related them to soil physicochemical properties.…”