ArticleMolecular ecology2010
Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms.
Article in Molecular ecology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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117 citing papers in PubMed.
- From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR.Molecular ecology resources · 2026Article
- Response of Benthic Foraminifera to Cadmium Pollution Assessed via Morphological and Metabarcoding Analyses.Microorganisms · 2026Article
- Endolithic fungal diversity is present in the unique phosphatized rocks of an environmentally extreme equatorial archipelago revealed by DNA amplicon metagenomics.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Article
- Dynamic changes in protist community composition along a surface water-groundwater transect in the Danube wetland Lobau, Vienna, Austria.Frontiers in microbiology · 2026Article
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- Fungal diversity present in ornithogenic soils of extreme equatorial Atlantic São Pedro and São Paulo archipelago using DNA metabarcoding.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Metagenomic Analysis Reveals the Characteristics of Cecal Microbiota in Chickens with Different Levels of Resistance During Recovery fromAnimals : an open access journal from MDPI · 2025Article
- Genetic variability in microbial eukaryotes reshapes marine biodiversity assessment in the age of amplicon sequencing.PloS one · 2025Article
- Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning.FEMS microbiology ecology · 2024Article
- Endolithic Fungal Diversity in Antarctic Oligocene Rock Samples Explored Using DNA Metabarcoding.Biology · 2024Article
- Ciliate diversity in rodrigo de freitas lagoon (Rio de Janeiro, Brazil) from an integrative standpoint.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- A Review of the Rumen Microbiota and the Different Molecular Techniques Used to Identify Microorganisms Found in the Rumen Fluid of Ruminants.Animals : an open access journal from MDPI · 2024Review
- Fungal diversity present in snow sampled in summer in the north-west Antarctic Peninsula and the South Shetland Islands, Maritime Antarctica, assessed using metabarcoding.Extremophiles : life under extreme conditions · 2024Article
- A full-length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing.Ecology and evolution · 2024Article
- eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea.BMC ecology and evolution · 2024Article
- Insights into freshwater ciliate diversity through high throughput DNA metabarcoding.FEMS microbes · 2024Article
- Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration.Microbial ecology · 2023Article
- Cryptic fungal diversity revealed by DNA metabarcoding in historic wooden structures at Whalers Bay, Deception Island, maritime Antarctic.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
- Article
57 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
With the delivery of millions of sequence reads in a single experiment, next-generation sequencing (NGS) is currently revolutionizing surveys of microorganism diversity. In particular, when applied to Eukaryotes, we are still lacking a rigorous comparison of morphological and NGS-based diversity estimates. In this report, we studied the diversity and the seasonal community turnover of alveolates (Ciliophora and Dinophyceae) in an oligotrophic freshwater lake by SSU amplicon sequencing with NGS as well as by classical morphological analysis. We complemented the morphological analysis by single-cell PCR followed by Sanger sequencing to provide an unambiguous link to the NGS data. We show that NGS and morphological analyses generally capture frequency shifts of abundant taxa over our seasonal samples. The observed incongruencies are probably largely due to rDNA copy number variation among taxa and heterogeneity in the efficiency of cell lysis. Overall, NGS-based amplicon sequencing was superior in detecting rare species. We propose that in the absence of other nuclear markers less susceptible to copy number variation, rDNA-based diversity studies need to be adjusted for confounding effects of copy number variation.
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