Rapid isothermal amplification of diatom rbcL from eDNA and eRNA reveals their abundance and photosynthetic physiology
- 1Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, Heraklion, Crete, Greece
Abstract
Diatoms are major contributors to marine primary production, yet current approaches for monitoring their abundance and function rely on coarse satellite chlorophyll estimates or sparse cell counts and bulk carbon fixation measurements. Molecular markers are a promising approach for high-resolution measurement of both abundance and metabolic activity through analysis of environmental DNA (eDNA) and RNA (eRNA). We present an isothermal quantitative recombinase polymerase amplification (qRPA) assay targeting rbcL gene copies and transcripts of marine diatoms, operating at low temperature and producing results in less than 15 min. We demonstrate specificity and calibration across diverse diatom taxa, then apply the assay to eDNA and eRNA samples from the Long-Term Ecological Research Mare Chiara site in the Gulf of Naples, Italy, alongside microscopy, chlorophyll, physicochemical, and carbon-fixation data. Diatom rbcL DNA tracked abundance across five orders of magnitude despite seasonal shifts in community composition. Combining molecular and optical data revealed increased cellular rbcL copies and chlorophyll in low-light winter populations, suggesting enhanced photosynthetic capacity despite lower abundance. Furthermore, rbcL RNA reflected total carbon fixation rates and identified populations with differing carbon fixation activity. These results support rapid, RPA-based rbcL quantification as a robust approach for biomolecular ocean observing.
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BibTeX
@misc{verret2026rapid,
title = {{Rapid isothermal amplification of diatom rbcL from eDNA and eRNA reveals their abundance and photosynthetic physiology}},
author = {F. G. Verret and K. Hartle-Mougiou and C. Chantzaras and A. Peltekis and F. Margiotta and D. Sarno and U. Cardini and M. Alba and V. Pizziol and I. Markopoulos and I. Papadopoulou and I. Percopo and F. Tramontano and M. Maselli and A. Novellino and S. Psarra and M. Montresor and M. C. Mowlem and E. Gizeli and M. Valiadi},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.30.748096},
url = {https://www.biorxiv.org/content/10.64898/2026.08.30.748096v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Rapid isothermal amplification of diatom rbcL from eDNA and eRNA reveals their abundance and photosynthetic physiology
AU - F. G. Verret
AU - K. Hartle-Mougiou
AU - C. Chantzaras
AU - A. Peltekis
AU - F. Margiotta
AU - D. Sarno
AU - U. Cardini
AU - M. Alba
AU - V. Pizziol
AU - I. Markopoulos
AU - I. Papadopoulou
AU - I. Percopo
AU - F. Tramontano
AU - M. Maselli
AU - A. Novellino
AU - S. Psarra
AU - M. Montresor
AU - M. C. Mowlem
AU - E. Gizeli
AU - M. Valiadi
PY - 2026
DA - 2026/08/30
PB - bioRxiv
DO - 10.64898/2026.08.30.748096
UR - https://www.biorxiv.org/content/10.64898/2026.08.30.748096v1
AB - Diatoms are major contributors to marine primary production, yet current approaches for monitoring their abundance and function rely on coarse satellite chlorophyll estimates or sparse cell counts and bulk carbon fixation measurements. Molecular markers are a promising approach for high-resolution measurement of both abundance and metabolic activity through analysis of environmental DNA (eDNA) and RNA (eRNA). We present an isothermal quantitative recombinase polymerase amplification (qRPA) assay targeting rbcL gene copies and transcripts of marine diatoms, operating at low temperature and producing results in less than 15 min. We demonstrate specificity and calibration across diverse diatom taxa, then apply the assay to eDNA and eRNA samples from the Long-Term Ecological Research Mare Chiara site in the Gulf of Naples, Italy, alongside microscopy, chlorophyll, physicochemical, and carbon-fixation data. Diatom rbcL DNA tracked abundance across five orders of magnitude despite seasonal shifts in community composition. Combining molecular and optical data revealed increased cellular rbcL copies and chlorophyll in low-light winter populations, suggesting enhanced photosynthetic capacity despite lower abundance. Furthermore, rbcL RNA reflected total carbon fixation rates and identified populations with differing carbon fixation activity. These results support rapid, RPA-based rbcL quantification as a robust approach for biomolecular ocean observing.
ER -