Apple rhizosphere microbiome in relation to soil microbial amendment at planting and subsequent tree development
Apple Replant Disease (ARD) symptoms usually appear shortly after planting when apple trees are replanted in soils where the same or a closely related species has grown previously. In an orchard study in which arbuscular mycorrhizal fungi (AMF), biocontrols and plant growth-promoting rhizobacteria (PGPR) were added to soils at the time of planting, we showed that amendment with AMF and biocontrols resulted in significantly better tree development. In the same experiment, rhizosphere soils were sampled three times and subjected to 16S and ITS amplicon sequencing. In this paper, we report the long-term effects of microbial amendment on rhizosphere community structure and relative abundance of specific microbial taxa. Apple rhizosphere microbial communities varied greatly with spatial locations and sampling time. There was a lack of long-term effects of microbial soil amendment on the overall microbial structure in the apple rhizosphere. Microbial amendment significantly affected relative abundance of many microbial taxa, most of which had very low abundance. This finding implies that improved girth expansion associated with AMF and biocontrol amendments are likely attributable to changes in specific taxa within the rhizosphere rather than community-wide changes. Predominance of spatial and temporal effects on the rhizosphere microbiome indicates the importance of controlling spatial heterogeneity and temporal dynamics in soil microbial communities when designing microbiome field experiments.
Apple Replant Disease (ARD) symptoms usually appear shortly after planting when apple trees are replanted in soils where the same or a closely related species has grown previously. In an orchard study in which arbuscular mycorrhizal fungi (AMF), biocontrols and plant growth-promoting rhizobacteria (PGPR) were added to soils at the time of planting, we showed that amendment with AMF and biocontrols resulted in significantly better tree development. In the same experiment, rhizosphere soils were sampled three times and subjected to 16S and ITS amplicon sequencing. In this paper, we report the long-term effects of microbial amendment on rhizosphere community structure and relative abundance of specific microbial taxa. Apple rhizosphere microbial communities varied greatly with spatial locations and sampling time. There was a lack of long-term effects of microbial soil amendment on the overall microbial structure in the apple rhizosphere. Microbial amendment significantly affected relative abundance of many microbial taxa, most of which had very low abundance. This finding implies that improved girth expansion associated with AMF and biocontrol amendments are likely attributable to changes in specific taxa within the rhizosphere rather than community-wide changes. Predominance of spatial and temporal effects on the rhizosphere microbiome indicates the importance of controlling spatial heterogeneity and temporal dynamics in soil microbial communities when designing microbiome field experiments.
East Malling Research