A1 Refereed original research article in a scientific journal
Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate
Authors: Jeevannavar, Aditya; Florenza, Javier; Divne, Anna-Maria; Tamminen, Manu; Bertilsson, Stefan
Publisher: Springer Nature
Publication year: 2025
Journal: ISME Journal
Journal name in source: The ISME Journal
Article number: wraf046
Volume: 19
Issue: 1
ISSN: 1751-7362
eISSN: 1751-7370
DOI: https://doi.org/10.1093/ismejo/wraf046(external)
Web address : https://doi.org/10.1093/ismejo/wraf046(external)
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/491615414(external)
Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.
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Funding information in the publication:
None declared.
