ArticleISME communications2021
High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR.
Article in ISME communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 30 citations in OpenAlex.
- Exploring the potential of the COI gene marker for DNA barcoding of planktonic foraminifera.Scientific reports · 2025Article
- The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies.Molecular ecology resources · 2025Article
- Environmental DNA sheds new insight on molecular adaptation of foraminifera to temperature from laboratory-controlled culture experiment.Ecology and evolution · 2024Article
- Directional selection, not the direction of selection, affects telomere length and copy number at ribosomal RNA loci.Scientific reports · 2024Article
- Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms.ISME communications · 2023Article
- Distribution Patterns of Benthic Protist Communities Depending on Depth Revealed by Environmental Sequencing-From the Sublittoral to the Deep Sea.Microorganisms · 2023Article
- Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy.ISME communications · 2023Article
- Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera.PeerJ · 2023Article
- COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies.Ecology and evolution · 2022Article
- Bacteria, Protists, and Fungi May Hold Clues of Seamount Impact on Diversity and Connectivity of Deep-Sea Pelagic Communities.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabarcoding has become the workhorse of community ecology. Sequencing a taxonomically informative DNA fragment from environmental samples gives fast access to community composition across taxonomic groups, but it relies on the assumption that the number of sequences for each taxon correlates with its abundance in the sampled community. However, gene copy number varies among and within taxa, and the extent of this variability must therefore be considered when interpreting community composition data derived from environmental sequencing. Here we measured with single-cell qPCR the SSU rDNA gene copy number of 139 specimens of five species of planktonic foraminifera. We found that the average gene copy number varied between of ~4000 to ~50,000 gene copies between species, and individuals of the same species can carry between ~300 to more than 350,000 gene copies. This variability cannot be explained by differences in cell size and considering all plausible sources of bias, we conclude that this variability likely reflects dynamic genomic processes acting during the life cycle. We used the observed variability to model its impact on metabarcoding and found that the application of a correcting factor at species level may correct the derived relative abundances, provided sufficiently large populations have been sampled.
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Registered trials
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