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Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities.use asterix (*) to get italics
Rachel Turba, Glory H. Thai, and David K JacobsPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
<p style="text-align: justify;">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 no effects on community composition for either primer, even when using a filter of larger pore size (3 μ m), and therefore it is a viable approach in this system for comparison of water borne fish, bacteria and archaea. However, the 16S primer showed significantly different community composition in sediments compared to water samples, although still recovering eDNA of organisms from the water column. Sediment sample replicates were heterogeneous, and therefore increasing the number of replicates would be recommended for similar habitats.</p> should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https:// should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https:// should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://
metabarcoding; turbidity; method comparison; fish; bacteria; archaea
NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).
Biodiversity, Community genetics, Conservation biology, Freshwater ecology, Marine ecology, Molecular ecology
Kristy Deiner (, Lynsey R. Harper (, Girish Kumar (, Heather L. A. Robson (, Jianlong Li ( No need for them to be recommenders of PCIEcology. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
e.g. John Doe []
2022-06-20 20:31:51
Claudia Piccini
David Murray-Stoker