Reanalysis of microbiomes in soils affected by apple replant disease (ARD): Old foes and novel suspects lead to the proposal of extended model of disease development

Abstract

The aim of this study was to identify the presumed microbiological drivers in soils affected by apple replant disease (ARD) based on reanalysis of a larger cohort of molecular data. A literature search was conducted to identify the relevant deep-sequencing datasets from ARD-affected soil microbiomes next to the data on environmental variables and molecular techniques. The sequencing datasets of bacteria and fungi were analyzed using a taxonomic approach in mothur, using SILVA and UNITE databases, respectively. Variation partitioning and network analysis were used to identify the extent of variability related to environmental, spatial, spatially structured environmental or methodological sources.The structure of bacterial and fungal microbial communities in ARD-affected differed significantly from healthy soils and revealed a pool of microbial OTUs co-occurring in ARD-affected soils. Available meta-data explained most of the genetic variability in bacterial communities, in addition to the different molecular methods that accounted for 25% of the variability. Most of the variability in fungal communities remained unexplained and was not related to the differences in molecular methods among the studies. The variables that affected most both bacterial and fungal microbial communities were the presence of ARD, the types of soil treatments and the plant rootstock. In addition, the lack of congruency in reporting standards of measured soil characteristics precluded the inclusion of numerous measured soil parameters recorded in published literature, hence hampering the depth of reanalysis.In conclusion, this large-scale reanalysis indicated that ARD can be defined as an opportunistic microbial infectious disease, created by certain prevailing environmental conditions affecting microbial metabolism and their interaction with the plant host. A call for a united standard for reporting soil parameters is also issued.