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Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of  c . 80% of land plants, having enormous ecological and economic impact, as they often improve crop plant nutrition and yield. DNA-based identification with molecular markers is used to analyze AM fungal communities in the field, but reaching species level taxonomic resolution remains challenging. Thus, currently there is no consensus on how to analyze high-throughput sequences and assign them into species. Here, a new sequencing strategy combined with taxonomic affiliations implemented with an evolutionary placement algorithm (EPA) was established. It is based on sequencing a  c . 450 bp region of the large subunit (LSU) ribosomal rRNA gene with the MiSeq-Illumina platform. The method is suitable for the discrimination of closely related AMF species and was used to study host-AMF preferences in roots of Pequin pepper, soybean and orange at one location in the arid northeast of Mexico. Twenty AM fungal species from 13 genera were detected. Phylogenetic affiliation of reads to species revealed crop preferential associations. In Pequin pepper roots, several  Rhizophagus  species represented most of the community,  Rhizophagus clarus  being the most abundant. The soybean AM fungal community was dominated by  Rhizophagus irregularis  and  Funneliformis mosseae  and that of orange by several species of  Dominikia,  some of them only found in this crop. Unraveling the AMF-plant preferences of important crops by an affordable and robust sequencing method, combined with phylotaxonomic AMF species resolution, is an important tool to obtain taxonomic units that are meaningful in both biological and ecological studies.

New MiSeq based strategy exposed plant-preferential arbuscular mycorrhizal fungal communities in arid soils of Mexico