ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2019
Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Mitochondrial Genome Reduction and Accelerated Evolution in Planktonic Foraminiferans.MicrobiologyOpen · 2026Article
- Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.The ISME journal · 2025Article
- Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.Journal of microbiology and biotechnology · 2024Review
- Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.PloS one · 2024Article
- Homing in on the rare virosphere reveals the native host of giant viruses.bioRxiv : the preprint server for biology · 2023Article
- The Application of Single-Cell RNA Sequencing in the Inflammatory Tumor Microenvironment.Biomolecules · 2023Review
- One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology.Frontiers in microbiology · 2022Article
- Understanding the pathogenesis of infectious diseases by single-cell RNA sequencing.Microbial cell (Graz, Austria) · 2021Review
- Article
- CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology.Frontiers in microbiology · 2021Review
- Article
- Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle.Frontiers in microbiology · 2020Article
- Single cell ecology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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Abstract
Understanding the diversity and evolution of eukaryotic microorganisms remains one of the major challenges of modern biology. In recent years, we have advanced in the discovery and phylogenetic placement of new eukaryotic species and lineages, which in turn completely transformed our view on the eukaryotic tree of life. But we remain ignorant of the life cycles, physiology and cellular states of most of these microbial eukaryotes, as well as of their interactions with other organisms. Here, we discuss how high-throughput genome-wide gene expression analysis of eukaryotic single cells can shed light on protist biology. First, we review different single-cell transcriptomics methodologies with particular focus on microbial eukaryote applications. Then, we discuss single-cell gene expression analysis of protists in culture and what can be learnt from these approaches. Finally, we envision the application of single-cell transcriptomics to protist communities to interrogate not only community components, but also the gene expression signatures of distinct cellular and physiological states, as well as the transcriptional dynamics of interspecific interactions. Overall, we argue that single-cell transcriptomics can significantly contribute to our understanding of the biology of microbial eukaryotes. This article is part of a discussion meeting issue 'Single cell ecology'.
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