ArticleEnvironmental microbiology2014
A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology.
Article in Environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR.Molecular ecology resources · 2026Article
- Phytoplankton Diversity in the Northern Adriatic Sea: Insights and Inconsistencies from Microscopy and Metabarcoding.Biology · 2026Article
- Article
- A protozoan perspective on climate change and biosafety threats: differences in testate amoebae in lakes in forest-swamp and forest-steppe zones in Western Siberia.Applied and environmental microbiology · 2025Article
- New lineage of scuticociliates dominates the ciliate community and bacterivory in hypolimnetic waters of a freshwater reservoir.The ISME journal · 2025Article
- Article
- Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism.Environmental microbiome · 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
- Insights into freshwater ciliate diversity through high throughput DNA metabarcoding.FEMS microbes · 2024Article
- Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding.Scientific reports · 2023Article
- Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters.Microorganisms · 2022Review
- Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes.Scientific reports · 2022Article
- Impact of Nutrients on Protozoa Community Diversity and Structure in Litter of Two Natural Grass Species in a Copper Tailings Dam, China.Microorganisms · 2021Article
- Finding needles in a haystack-Extensive diversity in the eustigmatophyceae revealed by community metabarcode analysis targeting the rbcL gene using lineage-directed primers.Journal of phycology · 2021Article
- Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids.Environmental microbiology · 2021Article
- Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea.Microorganisms · 2021Article
- Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.Microbial ecology · 2021Article
- An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea).Scientific reports · 2021Article
- CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology.Frontiers in microbiology · 2021Review
- Molecular Data Reveal a Cryptic Diversity in the GenusFrontiers in microbiology · 2021Article
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6 authors.
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Abstract
Analyses of high-throughput environmental sequencing data have become the 'gold-standard' to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive 'rare microbial biosphere' and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes.
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