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Article

Testing Different Membrane Filters for 16S rRNA Gene-Based Metabarcoding in Karstic Springs

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Emil Racovitza Institute of Speleology, Cluj Department, Clinicilor 5, 400006 Cluj-Napoca, Romania
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Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, 400000 Cluj-Napoca, Romania
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Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 400000 Cluj-Napoca, Romania
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National Institute of Research and Development for Biological Sciences, Institute of Biological Research, 400015 Cluj-Napoca, Romania
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National Institute for Research and Development of Optoelectronics Bucharest INOE 2000, Research Institute for Analytical Instrumentation Subsidiary, 400293 Cluj-Napoca, Romania
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Emil Racovitza Institute of Speleology, Calea 13 Septembrie 13, 050711 București, Romania
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Authors to whom correspondence should be addressed.
Water 2020, 12(12), 3400; https://doi.org/10.3390/w12123400
Received: 8 October 2020 / Revised: 13 November 2020 / Accepted: 29 November 2020 / Published: 3 December 2020
(This article belongs to the Special Issue Research on Karst Eco-Hydrology and Sediment)
Introduction: Karstic springs are used worldwide by rural communities as sources of fresh water for humans and livestock. In Romania, one-third of the population has no direct access to a public water supply. The present study is part of a country-wide project to develop simple, quick and cheap methods for seasonal environmental and microbiological monitoring of karstic springs used as drinking water by rural populations. Critical steps for monitoring workflow consist of evaluating water quality and selecting suitable membrane filters to efficiently capture environmental DNA for further microbial diversity estimation using 16S rRNA gene-based metabarcoding. Methods: Several commercial membrane filters of different compositions and pore sizes were tested on the water sampled from three karstic springs in Romania, followed by water chemistry and whole community 16S rRNA gene-based metabarcoding analysis. Results: We found that different types of applied membrane filters provide varying recovery in diversity and abundance of both overall and pathogenic bacteria. Conclusions: The result of the experiment with different filters shows that mixed cellulose ester, cellulose acetate, and nitrate membranes of 0.20 and 0.22 µm are the best for amplicon-based metabarcoding monitoring of karst springs. View Full-Text
Keywords: spring water; karst; 16S rRNA gene; membrane filters; metabarcoding; pathogenic bacteria spring water; karst; 16S rRNA gene; membrane filters; metabarcoding; pathogenic bacteria
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MDPI and ACS Style

Moldovan, O.T.; Baricz, A.; Szekeres, E.; Kenesz, M.; Hoaghia, M.A.; Levei, E.A.; Mirea, I.C.; Năstase-Bucur, R.; Brad, T.; Chiciudean, I.; Banciu, H.L. Testing Different Membrane Filters for 16S rRNA Gene-Based Metabarcoding in Karstic Springs. Water 2020, 12, 3400. https://doi.org/10.3390/w12123400

AMA Style

Moldovan OT, Baricz A, Szekeres E, Kenesz M, Hoaghia MA, Levei EA, Mirea IC, Năstase-Bucur R, Brad T, Chiciudean I, Banciu HL. Testing Different Membrane Filters for 16S rRNA Gene-Based Metabarcoding in Karstic Springs. Water. 2020; 12(12):3400. https://doi.org/10.3390/w12123400

Chicago/Turabian Style

Moldovan, Oana T.; Baricz, Andreea; Szekeres, Edina; Kenesz, Marius; Hoaghia, Marial A.; Levei, Erika A.; Mirea, Ionuț C.; Năstase-Bucur, Ruxandra; Brad, Traian; Chiciudean, Iulia; Banciu, Horia L. 2020. "Testing Different Membrane Filters for 16S rRNA Gene-Based Metabarcoding in Karstic Springs" Water 12, no. 12: 3400. https://doi.org/10.3390/w12123400

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