Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

No abstract is available for this paper.

• Publication year

  2012

• Venue

  The ISME Journal

• Publication date

  2012-10-04

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/ismej.2012.106PMID 23038176PMCID PMC3554406
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Utility of genetic markers and morphology for species discrimination within the order Tintinnida (Ciliophora, Spirotrichea).

  2013cited by this paper
• Two decades of describing the unseen majority of aquatic microbial diversity

  2012cited by this paper
• Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments.

  2012cited by this paper
• Molecular phylogeny of tintinnid ciliates (Tintinnida, Ciliophora).

  2012influential reference
• Redescription of Rhizodomus tagatzi (Ciliophora: Spirotrichea: Tintinnida), Based on Morphology and Small Subunit Ribosomal RNA Gene Sequence

  2012cited by this paper
• Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.

  2012cited by this paper
• Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

  2011cited by this paper
• Removing Noise From Pyrosequenced Amplicons

  2011influential reference
• 24. Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere”

  2011cited by this paper
• Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.

  2011cited by this paper
• Diversity and Vertical Distribution of Microbial Eukaryotes in the Snow, Sea Ice and Seawater Near the North Pole at the End of the Polar Night

  2011cited by this paper
• WebMGA: a customizable web server for fast metagenomic sequence analysis

  2011influential reference
• Diversity in a hidden world: potential and limitation of next‐generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

  2010cited by this paper
• The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

  2010cited by this paper
• Experimental factors affecting PCR-based estimates of microbial species richness and evenness

  2010cited by this paper
• 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.

  2010cited by this paper
• Ironing out the wrinkles in the rare biosphere through improved OTU clustering

  2010influential reference
• Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

  2010cited by this paper
• Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

  2009cited by this paper
• Accurate determination of microbial diversity from 454 pyrosequencing data

  2009cited by this paper
• Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.

  2009cited by this paper
• ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

  2009cited by this paper
• Microbial community structure in the North Pacific ocean

  2009cited by this paper
• The 'rare biosphere': a reality check

  2009cited by this paper
• Dynamics of core and occasional species in the marine plankton: tintinnid ciliates in the north‐west Mediterranean Sea

  2009cited by this paper
• Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure.

  2009cited by this paper
• FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

  2009cited by this paper
• Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

  2009influential reference
• Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata).

  2008cited by this paper
• Unveiling new microbial eukaryotes in the surface ocean.

  2008cited by this paper
• Accuracy and quality of massively parallel DNA pyrosequencing

  2007cited by this paper
• BMC Evolutionary Biology BioMed Central Research article

  2007cited by this paper
• Culture-independent assessment of planktonic ciliate diversity in coastal northwest Atlantic waters

  2007cited by this paper
• Picobiliphytes: A Marine Picoplanktonic Algal Group with Unknown Affinities to Other Eukaryotes

  2007cited by this paper
• Vertical distribution of picoeukaryotic diversity in the Sargasso Sea.

  2007cited by this paper
• Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSrRNA gene sequences.

  2007cited by this paper
• Ecology. Dipping into the rare biosphere.

  2007cited by this paper
• Dipping into the Rare Biosphere

  2007cited by this paper
• Probing diversity in the plankton: using patterns in Tintinnids (planktonic marine ciliates) to identify mechanisms

  2006cited by this paper
• Microbial diversity in the deep sea and the underexplored “rare biosphere”

  2006cited by this paper
• Genome sequencing in microfabricated high-density picolitre reactors

  2005cited by this paper
• Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge

  2003cited by this paper
• Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci.

  2002cited by this paper
• MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

  2002influential reference
• Microzooplankton diversity : relationships of tintinnid ciliates with resources , competitors and predators from the Atlantic Coast of Morocco to the Eastern Mediterranean

  2002cited by this paper
• Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity

  2001cited by this paper
• Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity

  2001cited by this paper
• Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton

  2001cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997influential reference
• Global biogeography of marine tintinnids

  1993cited by this paper
• MUST, a computer package of Management Utilities for Sequences and Trees.

  1993cited by this paper
• A conspectus of the marine and fresh-water ciliata belonging to suborder Tintinnoinea, with descriptions of new species principally from the Agassiz expedition to the Eastern Tropical Pacific 1904-1905

  year unknowncited by this paper

• Testing the waters: A comparison of DNA extraction methods for the metabarcoding of microbial communities.

  2026cites this paper
• Revisiting chlorophyll a thresholds for San Francisco Bay: insights from observations of phytoplankton molecular abundance

  2026cites this paper
• Dynamics of aboveground vegetation-soil fauna/microorganism interactions along karst terrestrial ecosystem degradation

  2026cites this paper
• Internal transcribed spacers enable species-level Metataxonomic analysis of ciliated protozoa

  2025cites this paper
• Tubifex tubifex reduces antibiotic stress on nitrogen removal in constructed wetlands by reshaping microbial networks

  2025cites this paper
• Morphological differences and statistical validation of tintinnid lorica traits at a global scale

  2025cites this paper
• Paracolpoda steinii (Ciliophora, Colpodida) from ancient Siberian permafrost: insights into cryptic diversity

  2025cites this paper
• Comprehensive metabolomic and microbial analysis of tobacco rhizosphere soil responses to crop rotation and fertilization

  2025cites this paper
• Comparative Profiling of the Fecal Bacteriome, Mycobiome, and Protist Community in Wild Versus Captive (Cervus canadensis)

  2025cites this paper
• Comparison of Metabarcoding and Shotgun Sequencing Confirms the Relevance of Chloroplastic rRNA Genes to Assess Community Structure of Lake Phytoplankton

  2025cites this paper
• Diversity and distribution of small-sized planktonic ciliate communities in the East China Sea

  2024cites this paper
• Ciliate diversity in rodrigo de freitas lagoon (Rio de Janeiro, Brazil) from an integrative standpoint

  2024cites this paper
• Herbicide leakage into seawater impacts primary productivity and zooplankton globally

  2024cites this paper
• How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation.

  2024cites this paper
• A pilot restoration of Enhalus acoroides by transplanting dislodged rhizome fragments and its effect on the microbial diversity of submarine sediments.

  2024cites this paper
• Effects of cotton peanut rotation on crop yield soil nutrients and microbial diversity

  2024cites this paper
• An assessment of the species diversity and disease potential of Pythium communities in Europe

  2024cites this paper
• Flourishing in Darkness: Protist Communities of Water Sites in Shulgan-Tash Cave (Southern Urals, Russia)

  2024cites this paper
• Comparative analysis of size-fractional eukaryotic microbes in subtropical riverine systems inferred from 18S rRNA gene V4 and V9 regions.

  2024cites this paper
• Comparative assessment of the intragenomic variations of dinoflagellate Tripos species through single-cell sequencing.

  2024cites this paper
• Assessment of DNA extraction methods for human gut mycobiome analysis

  2024cites this paper
• Global diversity and biogeography of Lyophyllum inferred from amplicon datasets

  2024cites this paper
• Internal Transcribed Spacers as Phylogenetic Markers Enable Species-level Metataxonomic Analysis of Ciliated Protozoa

  2024cites this paper
• Interspecies relationships of wild amoebae and bacteria with C. elegans create environments propitious for multigenerational diapause

  2024cites this paper
• Integration of DNA barcoding and nanotechnology in drug delivery.

  2023cites this paper
• Geographical distribution and driving force of micro-eukaryotes in the seamount sediments along the island arc of the Yap and Mariana trenches

  2023cites this paper
• Improved phyllosphere microbiome composition of tea plant with the application of small peptides in combination with rhamnolipid

  2023cites this paper
• Eukaryotic food sources analysis in situ of tropical common sea cucumber Holothuria leucospilota based on 18S rRNA gene high-throughput sequencing

  2023influential citation
• Impacts of three feeding modes on the diet composition and contribution ratios for juvenile Chinese mitten crab Eriocheir sinensis

  2023cites this paper
• Evolution of Phytoplankton as Estimated from Genetic Diversity

  2022cites this paper
• Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

  2022cites this paper
• ITS3/ITS4 outperforms other ITS region and 18S rRNA gene primer sets for amplicon sequencing of soil fungi

  2022cites this paper
• Spatiotemporal distribution of protists in the Yarlung Zangbo River, Tibetan Plateau

  2022cites this paper
• Nutrient loading decreases blue carbon by mediating fungi activities within seagrass meadows.

  2022cites this paper
• First Insights into the Diet Composition of Madeiran and Monteiro's Storm Petrels (Hydrobates castro and H. monteiroi) Breeding in the Azores

  2022cites this paper
• Filter-Feeding Bivalve Weakens Food Competition Between Crustaceans (Portunus trituberculatus, Marsupenaeus japonicus) in Integrated Culture Ponds: Evidence From 18S rDNA Barcoding and Stable Isotope Analysis

  2022cites this paper
• Dietary Analysis Based on 18S rDNA, and Stable Carbon and Nitrogen Isotopes in Juvenile Eriocheir sinensis Crabs Reared Under Three Feeding Modes

  2021influential citation
• Intra‐genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing

  2021influential citation
• Use of High-Throughput Sequencing to Identify Fungal Communities on the Surface of Citri Reticulatae Pericarpium During the 3-Year Aging Process

  2021cites this paper
• A robust approach to estimate relative phytoplankton cell abundances from metagenomes

  2021influential citation
• Ciliate microzooplankton from the Northeastern Gulf of Mexico

  2021cites this paper
• Diversity and Seasonality Dynamics of Ciliate Communities in Four Estuaries of Shenzhen, China (South China Sea)

  2021cites this paper
• Microzooplankton diversity and potential role in carbon cycling of contrasting Southern Ocean productivity regimes

  2021cites this paper
• Genetic Diversity in Marine Planktonic Ciliates (Alveolata, Ciliophora) Suggests Distinct Geographical Patterns – Data From Chinese and European Coastal Waters

  2021cites this paper
• CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

  2021cites this paper
• Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing

  2020cites this paper
• Endangerment of Ostrya rehderiana Chun and its relationship with rhizosphere soil microflora

  2020cites this paper
• Assessing the impact of taxon resolution on network structure.

  2020cites this paper
• Litter decomposition, microbial community dynamics and their relationships under seasonal snow cover

  2020cites this paper
• Enhanced organic matter decomposition in sediment by Tubifex tubifex and its pathway.

  2020cites this paper
• Progress in studies on the diversity and distribution of planktonic ciliates (Protista, Ciliophora) in the South China Sea

  2020cites this paper
• Characteristics of fungal community structure during the decomposition of mixed foliage litter from Pinus massoniana and broadleaved tree species in southwestern China

  2020cites this paper
• Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients

  2020cites this paper
• Temporal and spatial pattern of endophytic fungi diversity of Camellia Sinensis (cv. Shu Cha Zao) CURRENT

  2020cites this paper
• Identification of Fungal Dynamics Associated With Black Locust Leaves Mineralization and Their Correlations With Physicochemical Factors

  2020cites this paper
• Soil protist communities in burrowing and casting hotspots of different earthworm species

  2020cites this paper
• Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

  2020cites this paper
• Metabarcoding, stables isotopes, and tracking: unraveling the trophic ecology of a winter-breeding storm petrel (Hydrobates castro) with a multimethod approach

  2020cites this paper
• Temporal and spatial pattern of endophytic fungi diversity of Camellia sinensis (cv. Shu Cha Zao)

  2020cites this paper
• Comparing Morphological and Molecular Estimates of Species Diversity in the Freshwater Genus Synura (Stramenopiles): A Model for Understanding Diversity of Eukaryotic Microorganisms

  2020cites this paper
• Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts?

  2019cites this paper
• Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding

  2019cites this paper
• Current practice in plankton metabarcoding: optimization and error management

  2019cites this paper
• High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere of Ginkgo biloba

  2019cites this paper
• Abundance and seasonal variability of aloricate ciliates and tintinnids in a eutrophic coastal lagoon system of the Gulf of California, Mexico

  2019cites this paper
• Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea

  2019cites this paper
• Diversity of oligotrich ciliates (Ciliophora, Spirotrichea) in the northern coast of South China Sea as revealed in LSU rDNA sequences

  2019cites this paper
• Comparison of Microscopic and PCR Amplicon and Shotgun Metagenomic Approaches Applied to Marine Diatom Communities

  2019cites this paper
• Marine Metagenomics: Technological Aspects and Applications

  2019influential citation
• Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants.

  2019cites this paper
• A novel approach for tracing mycophagous small mammals and documenting their fungal diets

  2019cites this paper
• Vertical distribution of planktonic ciliates in the oceanic and slope areas of the western Pacific Ocean

  2019cites this paper
• High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere of [i]Ginkgo biloba[i]

  2019cites this paper
• Are We Overestimating Protistan Diversity in Nature?

  2019cites this paper
• funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model

  2019cites this paper
• Techniques and tools for species identification in ciliates: a review.

  2019cites this paper
• A census-based estimate of Earth's bacterial and archaeal diversity

  2019cites this paper
• Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities

  2018cites this paper
• Cryptophyta as major bacterivores in freshwater summer plankton

  2018cites this paper
• The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean

  2018cites this paper
• Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms

  2018cites this paper
• Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

  2018cites this paper
• Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding

  2018cites this paper
• EukRef‐Ciliophora: a manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates

  2018cites this paper
• Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota

  2018cites this paper
• Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe.

  2018cites this paper
• Conventional and molecular analysis of the diet of gentoo penguins: contributions to assess scats for non-invasive penguin diet monitoring

  2018cites this paper
• What Can Environmental Sequences Tell Us About the Distribution of Low‐Rank Taxa? The Case of Euplotes (Ciliophora, Spirotrichea), Including a Description of Euplotes enigma sp. nov.

  2018cites this paper
• Composition and Genetic Diversity of the Nicotiana tabacum Microbiome in Different Topographic Areas and Growth Periods

  2018cites this paper
• Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment

  2018cites this paper
• Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy

  2018cites this paper
• Global and local DNA (meta)barcoding reveal new biogeography patterns in tintinnid ciliates

  2018influential citation
• Molecular analyses of protists in long-term observation programmes—current status and future perspectives

  2018cites this paper
• Studying safe storage time of orange peel (Citrus reticulata) using high‐throughput sequencing and conventional pure culture

  2018cites this paper
• A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA

  2018cites this paper
• A fundamental difference between macrobiota and microbial eukaryotes: protistan plankton has a species maximum in the freshwater‐marine transition zone of the Baltic Sea

  2018cites this paper
• Assessing the impact of taxon resolution on network structure, with implication for comparative ecology

  2018cites this paper
• Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples

  2018cites this paper
• Characterising plant pathogen communities and their environmental drivers at a national scale

  2018cites this paper
• El Niño and the structure of mutualistic and antagonistic bat food webs revealed by DNA barcoding

  2018cites this paper