ArticleThe ISME journal2011
Capturing diversity of marine heterotrophic protists: one cell at a time.
Article in The ISME journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- A contamination-reduced genome of Plasmodiophora brassicae with comprehensive functional annotation.BMC microbiology · 2026Article
- Environmental diversity ofmSystems · 2025Article
- The first single-cell sequencing ofFrontiers in microbiology · 2025Article
- Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean.MicrobiologyOpen · 2024Article
- Loop-Mediated Isothermal Amplification for the Fast Detection ofPathogens (Basel, Switzerland) · 2024Article
- Cercozoan diversity of spring barley grown in the field is strongly plant compartment specific.Frontiers in microbiomes · 2024Article
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- Can Aggregate-Associated Organisms Influence the Fouling in a SWRO Desalination Plant?Microorganisms · 2022Article
- Niche Partitioning of Labyrinthulomycete Protists Across Sharp Coastal Gradients and Their Putative Relationships With Bacteria and Fungi.Frontiers in microbiology · 2022Article
- Niche adaptation promoted the evolutionary diversification of tiny ocean predators.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set ofFrontiers in fungal biology · 2021Article
- Single Cell Genomics Reveals Viruses Consumed by Marine Protists.Frontiers in microbiology · 2020Article
- Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.Scientific reports · 2019Article
- Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.Nature communications · 2018Article
- Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis.Scientific reports · 2017Article
- Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells.Scientific reports · 2017Article
- Survey of the green picoalga Bathycoccus genomes in the global ocean.Scientific reports · 2016Article
- Ecological and evolutionary significance of novel protist lineages.European journal of protistology · 2016Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent applications of culture-independent, molecular methods have revealed unexpectedly high diversity in a variety of functional and phylogenetic groups of microorganisms in the ocean. However, none of the existing research tools are free from significant limitations, such as PCR and cloning biases, low phylogenetic resolution and others. Here, we employed novel, single-cell sequencing techniques to assess the composition of small (<10 μm diameter), heterotrophic protists from the Gulf of Maine. Single cells were isolated by flow cytometry, their genomes amplified, and 18S rRNA marker genes were amplified and sequenced. We compared the results to traditional environmental PCR cloning of sorted cells. The diversity of heterotrophic protists was significantly higher in the library of single amplified genomes (SAGs) than in environmental PCR clone libraries of the 18S rRNA gene, obtained from the same coastal sample. Libraries of SAGs, but not clones contained several recently discovered, uncultured groups, including picobiliphytes and novel marine stramenopiles. Clone, but not SAG, libraries contained several large clusters of identical and nearly identical sequences of Dinophyceae, Cercozoa and Stramenopiles. Similar results were obtained using two alternative primer sets, suggesting that PCR biases may not be the only explanation for the observed patterns. Instead, differences in the number of 18S rRNA gene copies among the various protist taxa probably had a significant role in determining the PCR clone composition. These results show that single-cell sequencing has the potential to more accurately assess protistan community composition than previously established methods. In addition, the creation of SAG libraries opens opportunities for the analysis of multiple genes or entire genomes of the uncultured protist groups.
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