Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution?

Kohout, Petr; Sudová, Radka; Janoušková, Martina; Čtvrtlíková, Martina; Hejda, Martin; Pánková, Hana; Slavíková, Renata; Štajerová, Kateřina; Vosátka, Miroslav; Sýkorová, Zuzana

doi:10.1016/j.soilbio.2013.08.027

Cited by 150 publications

(122 citation statements)

References 63 publications

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“…(VTX00064). This result would seem to indicate that the two pairs of primers cover different taxa, and it offers an indication of the AMF community that lives in a truffle-ground, but it also reveals, as recently pointed out by Kohout et al (2014), that it is difficult to amplify AMF communities with the common primer pair and that bias appears. In spite of this, discrepancy was here observed between the number of clones that were sequenced and that of the effective Glomeromycota sequences that were obtained, irrespectively of what pair of primers was used.…”

Section: Discussionsupporting

confidence: 60%

Arbuscular mycorrhizal fungal diversity in the Tuber melanosporum brûlé

et al. 2015

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The development of the fruiting body (truffle) of the ectomycorrhizal fungus Tuber melanosporum is associated with the production of an area (commonly referred to with the French word brûlé) around its symbiotic plant that has scanty vegetation. As truffles produce metabolites that can mediate fungal-plant interactions, the authors wondered whether the brûlé could affect the arbuscular mycorrhizal fungi (AMF) that colonize the patchy herbaceous plants inside the brûlé. A morphological evaluation of the roots of plants collected in 2009 from a T. melanosporum/Quercus pubescens brûlé in France has shown that the herbaceous plants are colonized by AMF to a great extent. An analysis of the 18S rRNA sequences obtained from roots and soil inside the brûlé has shown that the AMF community structure seemed to be affected in the soil inside the brûlé, where less richness was observed compared to outside the brûlé.

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Section: Discussionsupporting

confidence: 60%

Arbuscular mycorrhizal fungal diversity in the Tuber melanosporum brûlé

et al. 2015

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“…This approach yielded an estimate of 34 AMF taxa detected in roots on the basis of SSU-DGGE banding that has been shown, via individual band sub-cloning and sequencing, to underestimate AMF diversity (Öpik et al 2003), although it assumes we did not have any nonspecific amplification from other fungal phyla (see Kohout et al 2014). The clearest relationship between soil nutrients and AMF taxa representation was seen for soil N. A related study in species rich tropical montane forest found reduced AMF species richness in bulked root samples in response to N and P addition (Camenzind et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Arbuscular mycorrhizal community structure on co-existing tropical legume trees in French Guiana

et al. 2016

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Aims: We aimed to characterise the arbuscular mycorrhizal fungal (AMF) community structure and potential edaphic determinants in the dominating, but poorly described, root-colonizing Paris-type AMF community on co-occurring Amazonian leguminous trees. Methods:We targeted three highly productive leguminous trees Results: Classical approaches targeting abundant SSU ampliconshighlighted a diverse root-colonizing symbiotic AMF community dominated by members of the Glomeraceae. DGGE profiling indicated that, of the edaphic factors investigated, soil nitrogen was most important in influencing the AMF community and this was more important than any host tree species effect. Conclusions: Dominating Paris-type mycorrhizal leguminous trees inAmazonian soils host diverse and novel taxa within the Glomeraceae that appear under edaphic selection in the investigated tropical forests.Linking symbiotic diversity of identified AMF taxa to ecological processes is the next challenge ahead.

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“…Some primer combinations discriminate against certain AMF lineages (Gamper et al 2009), while others result in high non-specific amplification (Alguacil et al 2009). The region that we amplified in the first PCR offers species resolution power (Stockinger et al 2010) and the primers used (Krüger et al 2009) allow the widest taxon coverage compared to other commonly used primers targeting a single nuclear rDNA marker (Kohout et al 2014). It may be mentioned that Kohout et al (2014) reported chimera formation when using these primers.…”

Section: Taxonomic Coverage and Species Diversitymentioning

confidence: 99%

“…The SSU-ITS-LSU rRNA gene region used was defined as an extended DNA barcode resolving closely related AMF species (Stockinger et al 2010;Schoch et al 2012). Importantly, it can be amplified from field samples using AMF specific PCR primers (Krüger et al 2009), which recently were confirmed to have the broadest taxonomic coverage among other PCR primers frequently applied for AMF detection (Kohout et al 2014). The primers amplify approx.…”

Section: Introductionmentioning

confidence: 99%

A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes

Senés‐Guerrero

Schüßler

2015

Fungal Diversity

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Plant-symbiotic arbuscular mycorrhizal fungi (AMF) are of high global ecological and economic importance, but describing environmental communities of AMF at the species level remains a challenge, despite the need to understand AMF-plant preferences and to apply AMF in sustainable agriculture. Here, the potato-associated AMF species community composition was assessed for three Andean countries along an altitudinal gradient and at different plant stages, by using 454 GS-FLX+ sequencing of a 760 bp LSU rRNA gene PCR amplicon. Two methods were compared: defining OTUs based on a simple sequence similarity threshold, or affiliating reference sequences to species based on a high throughput phylogenetic annotation approach using an evolutionary placement algorithm (EPA). The EPA-based approach was not only more precise, but also fundamental to robustly unveil the AMF species community composition. The principal advantage of this approach was also demonstrated by using artificially constructed datasets based on validated public database sequences. The affiliation of sequence reads to species using phylogenetic annotation revealed a surprisingly conserved AMF core-species community structure in Andean potatoes, regardless of different plant stages and environmental factors. In total, 41 species were detected and in some cases more than 25 species were found colonizing an individual root system. Acaulospora species were identified as dominant colonizers, co-occurring with Cetraspora nodosa and certain Claroideoglomus and Rhizophagus species in most potato root samples.

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Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution?

Cited by 150 publications

References 63 publications

Arbuscular mycorrhizal fungal diversity in the Tuber melanosporum brûlé

Arbuscular mycorrhizal fungal diversity in the Tuber melanosporum brûlé

Arbuscular mycorrhizal community structure on co-existing tropical legume trees in French Guiana

A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes

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