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

Kód výsledku v 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>

Nalezeny alternativní kódy

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

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

EF - Botanika

OECD FORD obor

—

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

Pedobiologia

ISSN

0031-4056

e-ISSN

—

Svazek periodika

59

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

DE - Spolková republika Německo

Počet stran výsledku

9

Strana od-do

179-187

Kód UT WoS článku

000382339100002

EID výsledku v databázi Scopus

—