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Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums

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Abstract

Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (β) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.

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All the raw data of qPCR can be found in the Supplemental information.

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Acknowledgements

I thank Dr. Hiroki Yamanaka (Ryukoku University) for partially providing financial support for the study. I also thank an editor and anonymous reviewers whose comments significantly improved the manuscript and Alaina Eckert for proofreading the manuscript. The proofreading of the manuscript was also supported by Grammarly (https://app.grammarly.com).

Funding

This work was supported by the Grant-in-Aid for JSPS Research Fellows (Grant Numbers JP22J00439 and JP22KJ3043).

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Authors and Affiliations

  1. Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan

    Toshiaki S. Jo

  2. Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan

    Toshiaki S. Jo

  3. Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan

    Toshiaki S. Jo

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  1. Toshiaki S. Jo
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T.J.S. conceived the study, performed molecular and statistical analyses, and wrote and edited the manuscript.

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Correspondence to Toshiaki S. Jo.

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Communicated by: Matjaž Gregorič

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Jo, T.S. Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums. Sci Nat 111, 18 (2024). https://doi.org/10.1007/s00114-024-01904-w

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