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The Korean Society of Phycology (한국조류학회(藻類))
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Optimal filter materials for protist quantification via droplet digital PCR

  • Juhee Min (Department of Oceanography, College of Natural Sciences, Chonnam National University) ;
  • Kwang Young Kim (Department of Oceanography, College of Natural Sciences, Chonnam National University)
  • Received : 2024.01.06
  • Accepted : 2024.03.05
  • Published : 2024.03.21
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Abstract

The use of droplet digital polymerase chain reaction (ddPCR) has greatly improved the quantification of harmful protists, outperforming traditional methods like quantitative PCR. Notably, ddPCR provides enhanced consistency and reproducibility at it resists PCR inhibitors commonly found in environmental DNA samples. This study aimed to determine the most effective filter material for ddPCR protocols by assessing the reproducibility of species-specific gene copy numbers and filtration time across six filter types: cellulose acetate (CA), mixed cellulose ester (MCE), nylon (NY), polycarbonate (PC), polyethersulfone (PES), and polyvinylidene fluoride (PVDF). The study used two species of Chattonella marina complexes as a case study. Filtration rates were slower for NY, PC, and PVDF filters. Moreover, MCE, NY, PES, and PVDF yielded lower DNA amounts than other filters. Importantly, the CA filter exhibited the lowest variance (38-39%) and the highest determination coefficients (R2 = 0.92-0.96), indicating superior performance. These findings suggest that the CA filter is the most suitable for ddPCR quantification of marine protists, offering quick filtration and reliable reproducibility.

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Acknowledgement

This research was supported by a National Research Foundation (NRF) grant funded by the Korean government (MSIT) (NRF-2016R1A6A1A03012647, NRF-2020- R1A2C3005053, NRF-2022M3I6A1085991) to KYK.

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