Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment

Environmental DNA, i.e., DNA extracted directly from environmental samples, has been used to understand microbial communities in the environment and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA...

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Main Authors: Bairoliya, Sakcham, Koh, Jonas Zhi Xiang, Cao, Bin
Other Authors: School of Civil and Environmental Engineering
Format: Article
Language:English
Published: 2022
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Online Access:https://hdl.handle.net/10356/158312
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-1583122022-05-21T20:11:33Z Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment Bairoliya, Sakcham Koh, Jonas Zhi Xiang Cao, Bin School of Civil and Environmental Engineering Singapore Centre for Environmental Life Sciences and Engineering (SCELSE) Engineering::Environmental engineering Science::Biological sciences::Microbiology Engineering::Chemical engineering::Biotechnology Extracellular DNA Environmental DNA Environmental DNA, i.e., DNA extracted directly from environmental samples, has been used to understand microbial communities in the environment and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggested several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods, including qPCR and fluorescent DNA binding dyes; (iii) carefully interpreting the effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses. Ministry of Education (MOE) National Research Foundation (NRF) Submitted/Accepted version This research/project was supported by the National Research Foundation, Singapore, under its NERC-NRF Joint Grant Call (Award SEAP-2020-0004). This research is also supported by the National Research Foundation and MOE Singapore under its Research Centre of Excellence Program, Singapore Centre for Environmental Life Sciences Engineering (SCELSE) (M4330005.C70 to B.C.), Nanyang Technological University, Singapore. 2022-05-18T02:26:49Z 2022-05-18T02:26:49Z 2022 Journal Article Bairoliya, S., Koh, J. Z. X. & Cao, B. (2022). Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment. Applied and Environmental Microbiology, 88(3), e01845-21-. https://dx.doi.org/10.1128/AEM.01845-21 0099-2240 https://hdl.handle.net/10356/158312 10.1128/AEM.01845-21 34818108 3 88 e01845-21 en SEAP-2020-0004 M4330005.C70 Applied and Environmental Microbiology © 2022 American Society for Microbiology. All rights reserved. This paper was published in Applied and Environmental Microbiology and is made available with permission of 2022 American Society for Microbiology. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering::Environmental engineering
Science::Biological sciences::Microbiology
Engineering::Chemical engineering::Biotechnology
Extracellular DNA
Environmental DNA
spellingShingle Engineering::Environmental engineering
Science::Biological sciences::Microbiology
Engineering::Chemical engineering::Biotechnology
Extracellular DNA
Environmental DNA
Bairoliya, Sakcham
Koh, Jonas Zhi Xiang
Cao, Bin
Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment
description Environmental DNA, i.e., DNA extracted directly from environmental samples, has been used to understand microbial communities in the environment and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggested several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods, including qPCR and fluorescent DNA binding dyes; (iii) carefully interpreting the effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.
author2 School of Civil and Environmental Engineering
author_facet School of Civil and Environmental Engineering
Bairoliya, Sakcham
Koh, Jonas Zhi Xiang
Cao, Bin
format Article
author Bairoliya, Sakcham
Koh, Jonas Zhi Xiang
Cao, Bin
author_sort Bairoliya, Sakcham
title Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment
title_short Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment
title_full Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment
title_fullStr Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment
title_full_unstemmed Extracellular DNA in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment
title_sort extracellular dna in environmental samples: occurrence, extraction, quantification, and impact on microbial biodiversity assessment
publishDate 2022
url https://hdl.handle.net/10356/158312
_version_ 1734310189497057280