ArticleProceedings of the National Academy of Sciences of the United States of America2022
The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 60 citations in OpenAlex.
- Environmental drivers and key taxa shaping diatom-dinoflagellate ratios in eutrophic coastal waters.Marine life science & technology · 2026Article
- Balancing photosynthesis and respiration in North Pacific protist communities.The ISME journal · 2026Article
- Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.Nature communications · 2025Article
- Seasonal Transition in the Dominance of Photoautotrophic and Heterotrophic Protists in the Photic Layer of a Subtropical Marine Ecosystem.Environmental microbiology reports · 2025Article
- Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.Applied and environmental microbiology · 2025Review
- Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes.Science advances · 2025Article
- Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes.Microbiome · 2025Article
- Do trophic strategies shape biogeography and environmental niches? Marine dinoflagellates as a case study.ISME communications · 2025Article
- Latitude- and depth-driven divergence in protist trophic strategies revealed by a machine learning model.Frontiers in microbiology · 2025Article
- Deciphering the key stressors shaping the relative success of core mixoplankton across spatiotemporal scales.ISME communications · 2025Article
- Missing microbial eukaryotes and misleading meta-omic conclusions.Nature communications · 2024Article
- Latitudinal patterns in ocean C:N:P reflect phytoplankton acclimation and macromolecular composition.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations.Scientific data · 2024Article
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- Article
- Prevalence and Preferred Niche of Small Eukaryotes with Mixotrophic Potentials in the Global Ocean.Microorganisms · 2024Article
- Transcriptomics reveal a unique phago-mixotrophic response to low nutrient concentrations in the prasinophyteISME communications · 2024Article
- High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click chemistry.ISME communications · 2024Article
- MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes.Scientific data · 2023Article
- PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intricate networks of single-celled eukaryotes (protists) dominate carbon flow in the ocean. Their growth, demise, and interactions with other microorganisms drive the fluxes of biogeochemical elements through marine ecosystems. Mixotrophic protists are capable of both photosynthesis and ingestion of prey and are dominant components of open-ocean planktonic communities. Yet the role of mixotrophs in elemental cycling is obscured by their capacity to act as primary producers or heterotrophic consumers depending on factors that remain largely uncharacterized. Here, we develop and apply a machine learning model that predicts the in situ trophic mode of aquatic protists based on their patterns of gene expression. This approach leverages a public collection of protist transcriptomes as a training set to identify a subset of gene families whose transcriptional profiles predict trophic mode. We applied our model to nearly 100 metatranscriptomes obtained during two oceanographic cruises in the North Pacific and found community-level and population-specific evidence that abundant open-ocean mixotrophic populations shift their predominant mode of nutrient and carbon acquisition in response to natural gradients in nutrient supply and sea surface temperature. Metatranscriptomic data from ship-board incubation experiments revealed that abundant mixotrophic prymnesiophytes from the oligotrophic North Pacific subtropical gyre rapidly remodeled their transcriptome to enhance photosynthesis when supplied with limiting nutrients. Coupling this approach with experiments designed to reveal the mechanisms driving mixotroph physiology provides an avenue toward understanding the ecology of mixotrophy in the natural environment.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.