New MiSeq based strategy exposed plant-preferential arbuscular mycorrhizal fungal communities in arid soils of Mexico
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New MiSeq based strategy exposed plant-preferential arbuscular mycorrhizal fungal communities in arid soils of Mexico Carolina Senés-Guerrero 1,2 Arthur Schüßler 3
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Salvador Giménez 1 & Adriana Pacheco 1
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Misael Sebastián Gradilla-Hernández 2
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Received: 5 April 2020 / Accepted: 16 July 2020 # The Author(s) 2020
Abstract 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. Keywords Arbuscular mycorrhizal fungi . DNA-based species monitoring . Citrus . Evolutionary placement algorithm . Pepper . Soybean
1 Introduction Arbuscular mycorrhizal fungi (AMF, abbreviation also used for ‘arbuscular mycorrhizal fungal’) have received great attention because they form symbiotic relations with the most relevant Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13199-020-00698-5) contains supplementary material, which is available to authorized users. * Carolina Senés-Guerrero [email protected] 1
Tecnologico de Monterrey, Centro de Biotecnologia-FEMSA, Escuela de Ingenieria y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey 64849, N.L., Mexico
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Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jal, Mexico
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SYMPLANTA GmbH und Co. KG, Graupnerweg 42, 64287 Darmstadt, Germany
food crops for human consumption (FAO 2018). AMF are obligate symbionts of c. 80% of land plants, providing them with a wide range of be
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