Molecular community analysis of arbuscular mycorrhizal fungi-Contributions of PCR primer and host plant selectivity to the detected community profiles

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12310%2F16%3A43890761" target="_blank" >RIV/60076658:12310/16:43890761 - isvavai.cz</a>

Alternative codes found

RIV/61388971:_____/16:00463541 RIV/44555601:13440/16:43887747

Result on the web

<a href="http://www.sciencedirect.com/science/article/pii/S0031405616300129" target="_blank" >http://www.sciencedirect.com/science/article/pii/S0031405616300129</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.pedobi.2016.04.002" target="_blank" >10.1016/j.pedobi.2016.04.002</a>

Result language

angličtina

Original language name

Molecular community analysis of arbuscular mycorrhizal fungi-Contributions of PCR primer and host plant selectivity to the detected community profiles

Original language description

Various primers targeting different regions of nuclear ribosomal DNA (rDNA) are commonly used in studies addressing diversity of soil- or root-associated fungi including the arbuscular mycorrhizal fungi (AMF) from the phylum Glomeromycota. Nevertheless, direct comparisons of the different primers remain rare. In this study, AMF community profiles were generated by 454 pyrosequencing of amplicons resulting from direct (i.e., single) PCR amplification with three commonly used primer pairs. Root DNA extracts from four different plant species growing in the same field soil were included into the study to address the following aspects: (1) specificity of the primers for Glomeromycota, (2) structure of the detected AMF communities, and (3) efficiency of the different primers for detecting specific AMF genera. The magnitude of the effect due to PCR selectivity was then compared with the well documented effect of host plant identity on the structure of AMF communities. The primers targeting the small ribosomal subunit (SSU) yielded almost exclusively glomeromycotan sequences. The primers targeting the large ribosomal subunit (LSU) were reasonably selective for Glomeromycota (75% of the operational taxonomic units [OTUs] detected), whereas only about 25% of the OTUs obtained by the primers targeting the internal transcribed region (ITS) of the rDNA belonged to the Glomeromycota. There was good agreement in detecting AMF community dominants between the different PCR primers. In comparison to the AMF selectivity due to host plant identity, the variation due to PCR primer choice was even larger. This was partly due to a large fraction of (mainly ITS) sequences that could not be assigned to validly described AMF taxa. The community profiles generated by the SSU and LSU primers also differed significantly from each other, mainly due to considerable SSU primer selectivity.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

EF - Botany

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Pedobiologia

ISSN

0031-4056

e-ISSN

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Volume of the periodical

59

Issue of the periodical within the volume

4

Country of publishing house

DE - GERMANY

Number of pages

9

Pages from-to

179-187

UT code for WoS article

000382339100002

EID of the result in the Scopus database

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