Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.

Desalination technology based on Reverse Osmosis (RO) membrane filtration has been resorted to provide high-quality drinking water. RO produced drinking water is characterized by a low bacterial cell concentration. Monitoring microbial quality and ensuring membrane-treated water safety has taken adv...

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Autores principales:	Ratna E Putri, Lan Hee Kim, Nadia Farhat, Mashael Felemban, Pascal E Saikaly, Johannes S Vrouwenvelder
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fe6dade229264bdd88083f46c6df9add
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spelling	oai:doaj.org-article:fe6dade229264bdd88083f46c6df9add2021-12-02T20:10:06ZEvaluation of DNA extraction yield from a chlorinated drinking water distribution system.1932-620310.1371/journal.pone.0253799https://doaj.org/article/fe6dade229264bdd88083f46c6df9add2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253799https://doaj.org/toc/1932-6203Desalination technology based on Reverse Osmosis (RO) membrane filtration has been resorted to provide high-quality drinking water. RO produced drinking water is characterized by a low bacterial cell concentration. Monitoring microbial quality and ensuring membrane-treated water safety has taken advantage of the rapid development of DNA-based techniques. However, the DNA extraction process from RO-based drinking water samples needs to be evaluated regarding the biomass amount (filtration volume) and residual disinfectant such as chlorine, as it can affect the DNA yield. We assessed the DNA recovery applied in drinking water microbiome studies as a function of (i) different filtration volumes, (ii) presence and absence of residual chlorine, and (iii) the addition of a known Escherichia coli concentration into the (sterile and non-sterile, chlorinated and dechlorinated) tap water prior filtration, and directly onto the (0.2 μm pore size, 47 mm diameter) mixed ester cellulose membrane filters without and after tap water filtration. Our findings demonstrated that the co-occurrence of residual chlorine and low biomass/cell density water samples (RO-treated water with a total cell concentration ranging between 2.47 × 102-1.5 × 103 cells/mL) failed to provide sufficient DNA quantity (below the threshold concentration required for sequencing-based procedures) irrespective of filtration volumes used (4, 20, 40, 60 L) and even after performing dechlorination. After exposure to tap water containing residual chlorine (0.2 mg/L), we observed a significant reduction of E. coli cell concentration and the degradation of its DNA (DNA yield was below detection limit) at a lower disinfectant level compared to what was previously reported, indicating that free-living bacteria and their DNA present in the drinking water are subject to the same conditions. The membrane spiking experiment confirmed no significant impact from any potential inhibitors (e.g. organic/inorganic components) present in the drinking water matrix on DNA extraction yield. We found that very low DNA content is likely to be the norm in chlorinated drinking water that gives hindsight to its limitation in providing robust results for any downstream molecular analyses for microbiome surveys. We advise that measurement of DNA yield is a necessary first step in chlorinated drinking water distribution systems (DWDSs) before conducting any downstream omics analyses such as amplicon sequencing to avoid inaccurate interpretations of results based on very low DNA content. This study expands a substantial source of bias in using DNA-based methods for low biomass samples typical in chlorinated DWDSs. Suggestions are provided for DNA-based research in drinking water with residual disinfectant.Ratna E PutriLan Hee KimNadia FarhatMashael FelembanPascal E SaikalyJohannes S VrouwenvelderPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 6, p e0253799 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ratna E Putri Lan Hee Kim Nadia Farhat Mashael Felemban Pascal E Saikaly Johannes S Vrouwenvelder Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.
description	Desalination technology based on Reverse Osmosis (RO) membrane filtration has been resorted to provide high-quality drinking water. RO produced drinking water is characterized by a low bacterial cell concentration. Monitoring microbial quality and ensuring membrane-treated water safety has taken advantage of the rapid development of DNA-based techniques. However, the DNA extraction process from RO-based drinking water samples needs to be evaluated regarding the biomass amount (filtration volume) and residual disinfectant such as chlorine, as it can affect the DNA yield. We assessed the DNA recovery applied in drinking water microbiome studies as a function of (i) different filtration volumes, (ii) presence and absence of residual chlorine, and (iii) the addition of a known Escherichia coli concentration into the (sterile and non-sterile, chlorinated and dechlorinated) tap water prior filtration, and directly onto the (0.2 μm pore size, 47 mm diameter) mixed ester cellulose membrane filters without and after tap water filtration. Our findings demonstrated that the co-occurrence of residual chlorine and low biomass/cell density water samples (RO-treated water with a total cell concentration ranging between 2.47 × 102-1.5 × 103 cells/mL) failed to provide sufficient DNA quantity (below the threshold concentration required for sequencing-based procedures) irrespective of filtration volumes used (4, 20, 40, 60 L) and even after performing dechlorination. After exposure to tap water containing residual chlorine (0.2 mg/L), we observed a significant reduction of E. coli cell concentration and the degradation of its DNA (DNA yield was below detection limit) at a lower disinfectant level compared to what was previously reported, indicating that free-living bacteria and their DNA present in the drinking water are subject to the same conditions. The membrane spiking experiment confirmed no significant impact from any potential inhibitors (e.g. organic/inorganic components) present in the drinking water matrix on DNA extraction yield. We found that very low DNA content is likely to be the norm in chlorinated drinking water that gives hindsight to its limitation in providing robust results for any downstream molecular analyses for microbiome surveys. We advise that measurement of DNA yield is a necessary first step in chlorinated drinking water distribution systems (DWDSs) before conducting any downstream omics analyses such as amplicon sequencing to avoid inaccurate interpretations of results based on very low DNA content. This study expands a substantial source of bias in using DNA-based methods for low biomass samples typical in chlorinated DWDSs. Suggestions are provided for DNA-based research in drinking water with residual disinfectant.
format	article
author	Ratna E Putri Lan Hee Kim Nadia Farhat Mashael Felemban Pascal E Saikaly Johannes S Vrouwenvelder
author_facet	Ratna E Putri Lan Hee Kim Nadia Farhat Mashael Felemban Pascal E Saikaly Johannes S Vrouwenvelder
author_sort	Ratna E Putri
title	Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.
title_short	Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.
title_full	Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.
title_fullStr	Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.
title_full_unstemmed	Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.
title_sort	evaluation of dna extraction yield from a chlorinated drinking water distribution system.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/fe6dade229264bdd88083f46c6df9add
work_keys_str_mv	AT ratnaeputri evaluationofdnaextractionyieldfromachlorinateddrinkingwaterdistributionsystem AT lanheekim evaluationofdnaextractionyieldfromachlorinateddrinkingwaterdistributionsystem AT nadiafarhat evaluationofdnaextractionyieldfromachlorinateddrinkingwaterdistributionsystem AT mashaelfelemban evaluationofdnaextractionyieldfromachlorinateddrinkingwaterdistributionsystem AT pascalesaikaly evaluationofdnaextractionyieldfromachlorinateddrinkingwaterdistributionsystem AT johannessvrouwenvelder evaluationofdnaextractionyieldfromachlorinateddrinkingwaterdistributionsystem
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Evaluation of DNA extraction yield from a chlorinated drinking water distribution system.

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