Microbial indication of soil health in apple orchards affected by replant disease

The aim of this study was to describe the interactions between soil physico-chemical parameters, plant growth, and soil microbial diversity under different fertilisation regimes in apple orchards affected by replant disease. The hypothesis was that fertiliser type and application, as well as tillage technique, could exert a shift in the soil chemical and biological parameters linked to soil sickness. Two apple orchards affected by ARD and located at different sites in South Tyrol, Italy, were selected as representatives of perennial crops affected by replant disease. The effects of application of six different amendments to the soil, at both sites, were investigated. Physicochemical and ecophysiological properties, along with soil microbial communities (evaluated with PCR-Denaturing gradient gel electrophoresis and high throughput sequencing of the V1-V3 region of the bacterial 16S rRNA gene) were analysed. High-throughput sequencing resulted in 1,590,042 sequence reads, classified in 326,371 operational taxonomic units (OTUs). Considering a threshold of 1% relative abundance of OTUs for each sample, 39 bacterial phyla and 197 genera were detected. The phyla Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes comprised between 24% and 71% of all sequences. Plant growth parameters were correlated with physico-chemical and ecophysiological parameters as well as with bacterial genus abundances. Findings revealed that in this study, Rhodanobacter, Blastocatella, Arenimonas, Variovorax, Ferruginobacter, Demequina and Schlesneria were the genera most affected by treatment type in terms of abundance. Furthermore, Ferruginobacter, Demequina and Schlesneria, genera not commonly described as involved in biocontrol, were strongly correlated with plant growth by a positive association. Treatments were found to exert contradictory effects on the bacterial communities and on the ecophysiological parameters at the different sites. These findings indicate not only a high complexity in the interaction between environmental and biological entities, but also that changes in environmental parameters result in changes in the interactions within bacterial communities. High-throughput sequencing confirmed the hypothesis that soil bacterial communities at the two sites were diverse and differed significantly, while they did not differ significantly according to treatment type. The dominant genera detected were not directly related to the treatment or to the growth of apple plants, suggesting that minor populations and unclassified sequences could be involved in replant disease. High-throughput sequencing can be proposed as a suitable method to deeply describe the soil microbiota found in ARD soils.