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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/21640

Title: Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies
Authors: Beckers, Bram
Op De Beeck, Michiel
Thijs, Sofie
Truyens, Sascha
Weyens, Nele
Boerjan, Wout
Vangronsveld, Jaco
Issue Date: 2016
Publisher: FRONTIERS MEDIA SA
Citation: FRONTIERS IN MICROBIOLOGY, 7
Abstract: Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high resolutioncommunity profiling. However, the use of these technologies in unraveling the plant microbiome remains challenging. Many bacterial 16S rDNA primer pairs also exhibit high affinity for non-target DNA such as plastid (mostly chloroplast) DNA and mitochondrial DNA. Therefore, we experimentally tested a series of commonly used primers for the analysis of plant associated bacterial communities using 454 pyrosequencing. We evaluated the performance of all selected primer pairs in the study of the bacterial microbiomes present in the rhizosphere soil, root, stem and leaf endosphere of field-grown poplar trees (Populus tremula x Populus alba) based on (a) co-amplification of non-target DNA, (b) low amplification efficiency for pure chloroplast DNA (real-time PCR), (c) high retrieval of bacterial 16S rDNA, (d) high operational taxonomic unit (OTU) richness and Inverse Simpson diversity and (e) taxonomic assignment of reads. Results indicate that experimental evaluation of primers provide valuable information that could contribute in the selection of suitable primer pairs for 16S rDNA metabarcoding studies in plant-microbiota research. Furthermore, we show that primer pair 799F-1391R outperforms all other primer pairs in our study in the elimination of non target DNA and retrieval of bacterial OTUs.
Notes: [Beckers, Bram; De Beeck, Michiel Op; Thijs, Sofie; Truyens, Sascha; Weyens, Nele; Vangronsveld, Jaco] Hasselt Univ, Ctr Environm Sci, Diepenbeek, Belgium. [Boerjan, Wout] Flanders Inst Biotechnol VIB, Dept Plant Syst Biol, Ghent, Belgium. [Boerjan, Wout] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9000 Ghent, Belgium. [De Beeck, Michiel Op] Lund Univ, Dept Biol, Lund, Sweden.
URI: http://hdl.handle.net/1942/21640
DOI: 10.3389/fmicb.2016.00650
ISI #: 000375998700001
ISSN: 1664-302X
Category: A1
Type: Journal Contribution
Validation: ecoom, 2017
Appears in Collections: Research publications

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