ArticleISME communications2024
Amplicon sequencing with internal standards yields accurate picocyanobacteria cell abundances as validated with flow cytometry.
Article in ISME communications, 2024. 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.
- Bacterial Community Expansion and Nutrient Activation Underlie Yield Improvement Following Diazotrophic Inoculant Application in Paddy Soil.Microorganisms · 2026Article
- The dynamic mesoscale sink and source niches for eukaryotic phytoplankton in a subtropical gyre.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Induced pathogenicity toward open-ocean diatoms by a filterable bacterium Ekhidna algicida sp. nov.The ISME journal · 2026Article
- Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.ISME communications · 2026Article
- Evaluating the role of microplastics and wastewater in shaping Vibrio spp. and antibiotic resistance gene abundance in urban freshwaters.Scientific reports · 2025Article
- Cervicovaginal Microbiome and HPV: A Standardized Approach to 16S/ITS NGS and Microbial Community Profiling for Viral Association.International journal of molecular sciences · 2025Article
- Characterizing organisms from three domains of life with universal primers from throughout the global ocean.Scientific data · 2025Article
- Quantitative microbial taxonomy across particle size, depth, and oxygen concentration.Frontiers in microbiology · 2025Article
- Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes.ISME communications · 2025Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To understand ecosystem state and function, marine microbial ecologists seek measurements of organismal abundance and diversity at high taxonomic resolution. Conventional flow cytometry accurately estimates microbial cell abundance but only discerns broad groups with distinct optical properties. While amplicon sequencing resolves more comprehensive diversity within microbiomes, it typically only provides relative organismal abundances within samples, not absolute abundance changes. Internal genomic standards offer a solution for absolute amplicon-based measures. Here, we spiked genomic standards into plankton samples from surface seawater, gathered at 46-km intervals along a cruise transect spanning the southern California Current System and the oligotrophic North Pacific Subtropical Gyre. This enabled evaluation of the absolute volumetric gene copy abundances of 16S rRNA amplicon sequence variants (amplified with 515Y-926R universal primers, quantitatively validated with mock communities) and cell abundances of picocyanobacteria with known genomic 16S copy numbers. Comparison of amplicon-derived cell abundances of
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