ArticleMycorrhiza2022
Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline.
Article in Mycorrhiza, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 45 citations in OpenAlex.
- Environmental variables associated with Arbuscular Mycorrhizal Fungi diversity in Ohio soybean agricultural systems.Mycorrhiza · 2026Article
- Article
- Molecular markers for the study of arbuscular mycorrhizal fungi.Archives of microbiology · 2026Review
- Host plant phylogeny predicts arbuscular mycorrhizal fungal communities, but plant life history and fungal genetic change predict feedback.PLoS biology · 2026Article
- From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Pharms on farms: Variable impacts of veterinary pharmaceuticals on an arbuscular mycorrhizal symbiosis and soil microorganisms.Plant and soil · 2026Article
- Article
- Catch crop amendments and microbial inoculants differently modulate apple rhizosphere microbiomes and plant responses.FEMS microbiology ecology · 2025Article
- TraitAM, a global spore trait database for arbuscular mycorrhizal fungi.Scientific data · 2025Article
- Synonymization of three species of Rhizophagus based on morphological and molecular evidence and biogeography of Rhizophagus clarus.Mycorrhiza · 2025Article
- Soil microbiome composition is highly responsive to precipitation and plant composition manipulations in a field biodiversity experiment.Frontiers in microbiomes · 2025Article
- Uncovering Diversity within the Glomeromycota: Novel Clades, Family Distributions, and Land Use Sensitivity.Ecology and evolution · 2025Article
- Article
- An updated LSU database and pipeline for environmental DNA identification of arbuscular mycorrhizal fungi.Mycorrhiza · 2024Article
- EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.Database : the journal of biological databases and curation · 2024Article
- Diversity of Arbuscular Mycorrhizal Fungi of the Rhizosphere ofJournal of fungi (Basel, Switzerland) · 2024Article
- Three new species of arbuscular mycorrhizal fungi (Glomeromycota) andFrontiers in microbiology · 2024Article
- Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot.Journal of fungi (Basel, Switzerland) · 2023Article
- Article
- Arbuscular mycorrhizal fungi associated with the rhizosphere of an endemic terrestrial bromeliad and a grass in the Brazilian neotropical dry forest.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
Abstract
Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach to taxa identification is imperative to describe AMF diversity. Further, due to low and biased sampling of AMF taxa, molecular databases do not represent the breadth of AMF diversity, making database matching approaches suboptimal. Therefore, a full description of AMF diversity requires a tool to determine sequence-based placement in the Glomeromycota clade. Nonetheless, commonly used gene regions, including the SSU and ITS, do not enable reliable phylogenetic placement. Here, we present an improved database and pipeline for the phylogenetic determination of AMF using amplicons from the large subunit (LSU) rRNA gene. We improve our database and backbone tree by including additional outgroup sequences. We also improve an existing bioinformatics pipeline by aligning forward and reverse reads separately, using a universal alignment for all tree building, and implementing a BLAST screening prior to tree building to remove non-homologous sequences. Finally, we present a script to extract AMF belonging to 11 major families as well as an amplicon sequencing variant (ASV) version of our pipeline. We test the utility of the pipeline by testing the placement of known AMF, known non-AMF, and Acaulospora sp. spore sequences. This work represents the most comprehensive database and pipeline for phylogenetic placement of AMF LSU amplicon sequences within the Glomeromycota clade.
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Registered trials
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