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Section: Ecology
Topic: Ecology, Genetics/Genomics

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Turba, Rachel1  ; Thai, Glory H.1; Jacobs, David K.1 
1 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095 USA

10.24072/pcjournal.256 - Peer Community Journal, Volume 3 (2023), article no. e33.

Get full text PDF Peer reviewed and recommended by PCI

Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had different effects on community composition for each primer, especially for the 16S, when using a filter of larger pore size (3 μm). Nevertheless, pre-freezing water samples can still be a viable alternative for storage and processing of turbid water samples when focusing on fish communities (12S). The use of sediment samples as an alternative to processing water samples should be done with caution, and at minimum the number of biological replicates and/or volume sampled should be increased.

Published online:
DOI: 10.24072/pcjournal.256
Type: Research article
Keywords: metabarcoding; turbidity; method comparison; fish
Keywords: metabarcoding, turbidity, method comparison, fish
Turba, Rachel 1; Thai, Glory H. 1; Jacobs, David K. 1

1 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095 USA
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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     author = {Turba, Rachel and Thai, Glory H. and Jacobs, David K.},
     title = {Different approaches to processing environmental {DNA} samples in turbid waters have distinct effects for fish, bacterial and archaea communities},
     journal = {Peer Community Journal},
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     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
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     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.256/}
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Turba, Rachel; Thai, Glory H.; Jacobs, David K. Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities. Peer Community Journal, Volume 3 (2023), article  no. e33. doi : 10.24072/pcjournal.256. https://peercommunityjournal.org/articles/10.24072/pcjournal.256/

Peer reviewed and recommended by PCI : 10.24072/pci.ecology.100427

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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