Once studies (e.g. Kohout et al. 2014) have shown strong bias towards the Glomeraceae in the LSU and SSU primer systems and some differences in the composition of AMF communities based on the "Redecker" primer system (Redecker 2000) and, finally, the "Krüger" primer system (Krüger 2009) can produce some chimeric sequences.
So, once some AMF primer systems suffer from co-amplification of other fungal groups or plants DNA, I am asking if there are an primer system (or primers) that I could use to best characterize AMF communities from soil (not from roots)?
Question's references:
Kohout, P.; Sudová, R.; Janousková, M.; Ctvrtlíková, M.; Hejda, M.; Pánková, H.; Slavíková, R.; Stajerová, K.; Vosátka, M. & Sýkorová, Z. 2014. Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution? Soil Biology & Biochemistry, 68: 482-493.
Krüger, M.; Stockinger, H.; Krüger, C. & Schüßler, A. 2009. DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytologist, 183: 212–223.
Redecker, D. 2000. Specific PCR primers to identify arbuscular mycorrhizal fungi within colonized roots. Mycorrhiza, 10 :73–80.
http://www.ncbi.nlm.nih.gov/pubmed/18631176
I found this paper useful, May it helps you too. All the best.
Here is a link to the publication that used nested pcr with Glo1/NS31 and AM1/NS31GC primers:
https://ulir.ul.ie/bitstream/handle/10344/4259/Schmalenberger_Noll_2014.pdf?sequence=3
98
Hi Francisco
There are many references in attachment 1
http://www.nature.com/ismej/journal/v8/n11/full/ismej201472a.html
3
https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2006.01799.x/pdf
4
http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1095&context=plantpathpapers
5
https://bio.kuleuven.be/eebcs/plant-conservation-and-population-biology/in-the-picture-2016/de-beenhouwer-et-al-2015-sb-biochem.pdf
6
https://bio.kuleuven.be/eebcs/plant-conservation-and-population-biology/in-the-picture-2016/de-beenhouwer-et-al-2015-sb-biochem.pdf
7
https://iris.unito.it/retrieve/handle/2318/100878/15767/APERTO_780020_Effects%20of%20different%20management%20practices.pdf
9
http://journals.im.ac.cn/actamicrocn/ch/reader/create_pdf.aspx?file_no=201507-13&year_id=2015&quarter_id=7&falg=1
10
https://iris.unito.it/retrieve/handle/2318/1622925/291612/Bouffaud%20Bragalini%20Mycorrhiza%202016.pdf
13
https://www.academia.edu/22549381/Comparison_of_commonly_used_primer_sets_for_evaluating_arbuscular_mycorrhizal_fungal_communities_Is_there_a_universal_solution
14
http://mpgranch.com/upload/site-assets/published%20papers_need_63/Appoloni%20et%20al.%20Microbial%20Ecology%202008.pdf
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