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DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi
Article first published online: 8 APR 2009
DOI: 10.1111/j.1469-8137.2009.02835.x
© The Authors (2009). Journal compilation © New Phytologist (2009)
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How to Cite
Krüger, M., Stockinger, H., Krüger, C. and Schüßler, A. (2009), DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytologist, 183: 212–223. doi: 10.1111/j.1469-8137.2009.02835.x
Publication History
- Issue published online: 3 JUN 2009
- Article first published online: 8 APR 2009
- Received: 12 December 2008Accepted: 23 February 2009
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Keywords:
- arbuscular mycorrhizal fungi (AMF);
- DNA barcoding;
- ITS region;
- LSU rRNA gene;
- molecular community analyses;
- rDNA;
- species level resolution;
- specific primers
Summary
- • At present, molecular ecological studies of arbuscular mycorrhizal fungi (AMF) are only possible above species level when targeting entire communities. To improve molecular species characterization and to allow species level community analyses in the field, a set of newly designed AMF specific PCR primers was successfully tested.
- • Nuclear rDNA fragments from diverse phylogenetic AMF lineages were sequenced and analysed to design four primer mixtures, each targeting one binding site in the small subunit (SSU) or large subunit (LSU) rDNA. To allow species resolution, they span a fragment covering the partial SSU, whole internal transcribed spacer (ITS) rDNA region and partial LSU.
- • The new primers are suitable for specifically amplifying AMF rDNA from material that may be contaminated by other organisms (e.g., samples from pot cultures or the field), characterizing the diversity of AMF species from field samples, and amplifying a SSU-ITS-LSU fragment that allows phylogenetic analyses with species level resolution.
- • The PCR primers can be used to monitor entire AMF field communities, based on a single rDNA marker region. Their application will improve the base for deep sequencing approaches; moreover, they can be efficiently used as DNA barcoding primers.