ArticleMicrobial biotechnology2016
Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR.
Article in Microbial biotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 31 citations in OpenAlex.
- Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations.Molecular ecology resources · 2025Article
- A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes.Environmental microbiology reports · 2023Article
- Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States.Water research · 2023Article
- Study on the hypolipidemic effect ofFood science & nutrition · 2023Article
- Effects of Miao sour soup on hyperlipidemia in high-fat diet-induced obese rats via the AMPK signaling pathway.Food science & nutrition · 2021Article
- Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca.Scientific reports · 2021Article
- Lost in translation: the quest for Nitrosomonas cluster 7-specific amoA primers and TaqMan probes.Microbial biotechnology · 2020Article
- Effects ofFood science & nutrition · 2020Article
- On resolving ambiguities in microbial community analysis of partial nitritation anammox reactors.Scientific reports · 2019Article
- A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.BMC microbiology · 2017Article
- Emerging Technologies for Gut Microbiome Research.Trends in microbiology · 2016Review
- Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR.Microbial biotechnology · 2016Article
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5 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Molecular methods to investigate functional groups in microbial communities rely on the specificity and selectivity of the primer set towards the target. Here, using rapid sand filters for drinking water production as model environment, we investigated the consistency of two commonly used quantitative PCR methods to enumerate ammonia-oxidizing bacteria (AOB): one targeting the phylogenetic gene 16S rRNA and the other, the functional gene amoA. Cloning-sequencing with both primer sets on DNA from two waterworks revealed contrasting images of AOB diversity. The amoA-based approach preferentially recovered sequences belonging to Nitrosomonas Cluster 7 over Cluster 6A ones, while the 16S rRNA one yielded more diverse sequences belonging to three AOB clusters, but also a few non-AOB sequences, suggesting broader, but partly unspecific, primer coverage. This was confirmed by an in silico coverage analysis against sequences of AOB (both isolates and high-quality environmental sequences). The difference in primer coverage significantly impacted the estimation of AOB abundance at the waterworks with high Cluster 6A prevalence, with estimates up to 50-fold smaller for amoA than for 16S rRNA. In contrast, both approaches performed very similarly at waterworks with high Cluster 7 prevalence. Our results highlight that caution is warranted when comparing AOB abundances obtained using different qPCR primer sets.
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