The Largest Subunit of RNA Polymerase II as a New Marker Gene to Study Assemblages of Arbuscular Mycorrhizal Fungi in the Field

• Published in: PloS one Vol. 9; no. 10; p. e107783
• Main Authors: Stockinger, Herbert, Peyret-Guzzon, Marine, Koegel, Sally, Bouffaud, Marie-Lara, Redecker, Dirk
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02.10.2014; Public Library of Science (PLoS)
• Subjects: Agricultural practices; Agricultural production; Agriculture; Arbuscular mycorrhizas; Biology and Life Sciences; Cloning; Deoxyribonucleic acid; DNA; DNA Barcoding, Taxonomic; DNA-directed RNA polymerase; Ecology and Environmental Sciences; Environmental Sciences; Exons - genetics; Fungi; Gene polymorphism; Gene sequencing; Genes; Genes, Fungal; Genetic polymorphisms; Glomeromycota; Glomeromycota - enzymology; Glomeromycota - genetics; Life Sciences; Molecular Sequence Data; Morphology; Multiculturalism & pluralism; Mycorrhizae - enzymology; Mycorrhizae - genetics; Next-generation sequencing; Phylogenetics; Phylogeny; Plant growth; Polymerase chain reaction; Polymorphism; Primers; Principal Component Analysis; Protein Subunits - genetics; Resolution; Ribonucleic acid; RNA; RNA polymerase; RNA polymerase II; RNA Polymerase II - genetics; Soil improvement; Soil management; Soil management (Agronomy); Soil properties; Soil quality; Studies; Tillage; Tillage effects; Vegetal Biology; Zea mays - microbiology; France; United States > US; Switzerland; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0107783

Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.