Arbuscular mycorrhizal fungal species isolated from commercial mixture and apple roots. Metagenome

Arbuscular mycorrhizal fungi (AMF) are promoted as commercial biofertilizers (bioinoculants) for sustainable agriculture. Little is known, however, about the survival of AMF inoculants in soil and their impacts on native or pre-established AMF communities in root tissue. The current study was designed to assess the stability of pre-existing/nursery-derived AMF in apple rootstocks after being planted into soil containing a known community of AMF with a limited number of species. In orchard systems, root-associated endophytic communities (bacteria and fungi) are known to differ depending on apple rootstock genotype and soil-type. Thus, an additional aim of this study was to explore the effect of apple rootstock genotype on AMF community structure. A greenhouse experiment was conducted in which a variety of apple rootstock genotypes (G.890, G.935, M.26 and M.7) were inoculated with a commercially available, multi-species AMF consortium. Nursery-derived AMF communities were sequenced and changes to AMF community structure following cultivation in pasteurized soil (inoculated and non-inoculated) were assessed. In order to accurately assign high throughput sequencing data to the species level, a Glomermycota-specific phylogenetic tree was constructed. Phylogenetic analysis showed that inoculant colonization potential was limited and that the rootstock serves as a significant source of nursery-derived AMF inoculum. Claroideoglomus spp. contained in the inoculant were, however, capable of infecting both M.26 and M.7 rootstocks. It was also found that the inoculant caused alterations (taxa suppression and/or stimulation) to the resident AMF communities of both Geneva and Malling rootstocks, regardless of colonization success. The impact on specific members of the resident AMF communities varied according to rootstock genotype. The rootstock most sensitive to changes in AMF community structure was M.26. Phylogenetic analysis also revealed that the commercial inoculant contained a very different consortium of AMF than expected. Tree-based analysis identified a unique, well-supported clade of unknown taxonomy, highlighting the importance of using phylogenetic-based classification for accurate characterization of AMF communities.