ArticleFrontiers in microbiology2023
Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils.
Article in Frontiers in microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.BMC bioinformatics · 2026Article
- Harnessing indigenous bacterial defenders to improve disease resistance and plant health in vegetableSustainable microbiology · 2026Review
- Responses of Soil Microbial Communities and Anthracnose Dynamics to Different Planting Patterns inMicroorganisms · 2025Article
- Dietary modulation of gut microbiota and functional enzymes in savannah honey bees (Apis mellifera scutellata Lepeletier).Applied microbiology and biotechnology · 2025Article
- Advancing time-since-interval estimation for clandestine graves: a forensic ecogenomics perspective into burial and translocation timelines using massively parallel sequencing.Frontiers in microbiology · 2025Review
- Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation.Microorganisms · 2024Article
- Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review.Microorganisms · 2024Review
- Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management.Frontiers in microbiology · 2024Article
- Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil.The ISME journal · 2023Article
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Authors and funding
3 authors.
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Abstract
The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to
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