ArticleFrontiers in microbiology2016
Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies.
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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136 citing papers in PubMed, 322 citations in OpenAlex.
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- A bacteria community sequencing data set from pothos (Epipremnum aureum).Scientific data · 2026Article
- Exploring the Algarrobo Decline in the Pómac Forest: Unraveling the Relationship between the Endomicrobiome of Neltuma pallida and Enallodiplosis discordis.Microbial ecology · 2026Article
- A discriminative primer design workflow enables selective metabarcoding, demonstrated using long-read sequencing of endophytic fungi.FEMS microbiology ecology · 2026Article
- An Untargeted Metabolomic Approach to Characterize the Emerging Kernel Disorder "Orange Spot" in Walnut (Metabolites · 2026Article
- Fungicide and warming interact to reduce soil ecosystem functioning.The ISME journal · 2026Article
- Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.Frontiers in microbiology · 2026Article
- Tissue-specific changes in endophytic bacterial and fungal communities of two pine species associated with pine wilt disease.Frontiers in microbiology · 2026Article
- Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community in a cultivar dependent manner.ISME communications · 2026Article
- Fungicides disrupt total and endophytic phyllosphere bacterial communities but a salicylic acid hyperimmune mutant shows microbiome resilience.ISME communications · 2026Article
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- Dual gradient dynamics: morpho-anatomical and symbiotic fungal communities in Fraxinus Mandshurica fine roots across root order and habitats.BMC plant biology · 2025Article
- Influence of Plant Developmental Phase and Irrigation Level on Cultivable Microbiome of Maize Root.Biology · 2025Article
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- Probiotic Bacillus subtilis enhances silkworm (Bombyx mori) growth performance and silk production via modulating gut microbiota and amino acid metabolism.Animal microbiome · 2025Article
- Soil bacteria and fungi diversity analysis reveals effects of sesame (Sesamum indicum L.) under waterlogging stress.BMC microbiology · 2025Article
- Soil Properties Induced Changes in the Microbial Communities Associated With Potato Tubers Grown in Different Lowland Fields of Northern Thailand.MicrobiologyOpen · 2025Article
76 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high-resolution community 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 × 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.
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