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Performance of 16s rDNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies

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Biotechnology for a sustainable economy (Bio-Economy)
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.
Keywords
DNA, COMMUNITIES, DIVERSITY, RARE BIOSPHERE, ROOT MICROBIOTA, ONLINE RESOURCE, LIGNIN BIOSYNTHESIS, RIBOSOMAL-RNA, POLYMERASE-CHAIN-REACTION, RNA GENE DATABASE, endophytes, chloroplast DNA, plant microbiome, 454 pyrosequencing, 16S rDNA metabarcoding

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Chicago
Beckers, Bram, Michiel Op De Beeck, Sofie Thijs, Sascha Truyens, Nele Weyens, Wout Boerjan, and Jaco Vangronsveld. 2016. “Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies.” Frontiers in Microbiology 7.
APA
Beckers, B., Op De Beeck, M., Thijs, S., Truyens, S., Weyens, N., Boerjan, W., & Vangronsveld, J. (2016). Performance of 16s rDNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies. FRONTIERS IN MICROBIOLOGY, 7.
Vancouver
1.
Beckers B, Op De Beeck M, Thijs S, Truyens S, Weyens N, Boerjan W, et al. Performance of 16s rDNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies. FRONTIERS IN MICROBIOLOGY. 2016;7.
MLA
Beckers, Bram, Michiel Op De Beeck, Sofie Thijs, et al. “Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies.” FRONTIERS IN MICROBIOLOGY 7 (2016): n. pag. Print.
@article{7756487,
  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.},
  articleno    = {650},
  author       = {Beckers, Bram and Op De Beeck, Michiel and Thijs, Sofie and Truyens, Sascha and Weyens, Nele and Boerjan, Wout and Vangronsveld, Jaco},
  issn         = {1664-302X},
  journal      = {FRONTIERS IN MICROBIOLOGY},
  keyword      = {DNA,COMMUNITIES,DIVERSITY,RARE BIOSPHERE,ROOT MICROBIOTA,ONLINE RESOURCE,LIGNIN BIOSYNTHESIS,RIBOSOMAL-RNA,POLYMERASE-CHAIN-REACTION,RNA GENE DATABASE,endophytes,chloroplast DNA,plant microbiome,454 pyrosequencing,16S rDNA metabarcoding},
  language     = {eng},
  pages        = {15},
  title        = {Performance of 16s rDNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies},
  url          = {http://dx.doi.org/10.3389/fmicb.2016.00650},
  volume       = {7},
  year         = {2016},
}

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