DNA‐based species level detection of <i>Glomeromycota</i>: one PCR primer set for all arbuscular mycorrhizal fungi

Krüger, Manuela; Stockinger, Herbert; Krüger, Claudia; Schüßler, Arthur

doi:10.1111/j.1469-8137.2009.02835.x

Cited by 350 publications

(293 citation statements)

References 54 publications

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“…The community structure of root-colonizing AM fungi was determined by terminal-restriction fragment length polymorphism (T-RFLP) analyses of the fragments of the LSU rRNA gene [57,58]. This procedure involves nested PCR with the primer pair LR1-FLR2 and a nested reaction with the AM fungal-specific primer pair FLR3-FLR4 [59], which were labelled with fluorescent dyes 6-FAM (FLR3) and NED (FLR4).…”

Section: Methodsmentioning

confidence: 99%

Mutualism breakdown in breadfruit domestication

et al. 2011

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During the process of plant domestication, below-ground communities are rarely considered. Some studies have attempted to understand the changes in root symbionts owing to domestication, but little is known about how it influences mycorrhizal response in domesticated crops. We hypothesized that selection for above-ground traits may also result in decreased mycorrhizal abundance in roots. Breadfruit (Artocarpus sp.) has a long domestication history, with a strong geographical movement of cultivars from west to east across the Melanesian and Polynesian islands. Our results clearly show a decrease in arbuscular mycorrhizas (AMs) along a domestication gradient from wild to recently derived cultivars. We showed that the vesicular and arbuscular colonization rate decreased significantly in more recently derived breadfruit cultivars. In addition, molecular analyses of breadfruit roots indicated that AM fungal species richness also responded along the domestication gradient. These results suggest that human-driven selection for plant cultivars can have unintended effects on below-ground mutualists, with potential impacts on the stress tolerance of crops and long-term food security.

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Section: Methodsmentioning

confidence: 99%

Mutualism breakdown in breadfruit domestication

et al. 2011

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“…The second primer set used (28G1/28G2), amplifying a region of the LSU rDNA, was chosen because this region is claimed to exhibit a higher phylogenetic resolution than the SSU, and it has recently been used to design new primer sets for AMF species-level identification (Krüger et al 2009). Even though this primer set also amplifies Diversisporales (da Silva et al 2006), we only amplified sequences from fungi belonging toGlomerales, probably due to a major affinity of the primers towards this group of AMF.…”

Section: Each Primer Combination Contributes To Amf Diversity Descripmentioning

confidence: 99%

Effects of different management practices on arbuscular mycorrhizal fungal diversity in maize fields by a molecular approach

et al. 2012

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Effects of different management practices on arbuscular mycorrhizal fungal diversity in maize fields by a molecular approach / R. Borriello; E. Lumini; M. Girlanda; P. Bonfante; V. Bianciotto. AbstractAs obligate mutualistic symbionts, arbuscular mycorrhizal fungi (AMF) colonize the roots of many agricultural crops, and it is often claimed that agricultural practices are detrimental to AMF. As a result, agroecosystems impoverished in AMF may not get the fully expected range of benefits from these fungi. Using molecular markers on DNA extracted directly from soil and roots, we studied the effects of different management practices (tillage and N fertilization) on the AMF communities colonizing an experimental maize field in Central Italy. Our molecular analysis based on three different nuclear rRNA regions (18S, 28S and ITS) allowed us to assess AMF biodiversity. Glomeraceae members were the main colonizer, and they co-occurred with Gigasporaceae and Paraglomus regardless of the management practices applied. Diversisporaceae and Entrophosporaceae members were instead detected in the N-fertilized soils and in the untreated soil, respectively. The results obtained indicated that the general AMF assemblages structure and composition in the maize field plots appear to be primarily influenced by N fertilization and, to a lesser extent, by tillage. This study also validates the usefulness of multiple molecular markers to consolidate and refine the assessment of the environmental AMF diversity.

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“…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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DNA‐based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi

Cited by 350 publications

References 54 publications

Mutualism breakdown in breadfruit domestication

Mutualism breakdown in breadfruit domestication

Effects of different management practices on arbuscular mycorrhizal fungal diversity in maize fields by a molecular approach

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

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