Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization

作者: Gert‐Jan Jeunen , Michael Knapp , Hamish G. Spencer , Helen R. Taylor , Miles D. Lamare

DOI: 10.1002/ECE3.4843

关键词: StandardizationProtocol (science)Biodiversity assessmentDNA extractionEnvironmental DNAComputational biologyBiodiversitySpecies levelBiologySpecies richness

摘要: … employed four metabarcoding assays. We assessed OTU and species richness per replicate and the overall detected biodiversity within both treatments for each metabarcoding assay. …

参考文章(39)
Tony Dejean, Alice Valentini, Christian Miquel, Pierre Taberlet, Eva Bellemain, Claude Miaud, Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus Journal of Applied Ecology. ,vol. 49, pp. 953- 959 ,(2012) , 10.1111/J.1365-2664.2012.02171.X
Kimiko Uchii, Hideyuki Doi, Toshifumi Minamoto, A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes Molecular Ecology Resources. ,vol. 16, pp. 415- 422 ,(2016) , 10.1111/1755-0998.12460
David Keith, H. Resit Akçakaya, Stuart H.M. Butchart, Ben Collen, Nicholas K. Dulvy, Elizabeth E. Holmes, Jeffrey A. Hutchings, Doug Keinath, Michael K. Schwartz, Andrew O. Shelton, Robin S. Waples, Temporal correlations in population trends: Conservation implications from time-series analysis of diverse animal taxa Biological Conservation. ,vol. 192, pp. 247- 257 ,(2015) , 10.1016/J.BIOCON.2015.09.021
Andrew Ogram, Gary S. Sayler, Tamar Barkay, The extraction and purification of microbial DNA from sediments Journal of Microbiological Methods. ,vol. 7, pp. 57- 66 ,(1987) , 10.1016/0167-7012(87)90025-X
Mashal Alawi, Beate Schneider, Jens Kallmeyer, A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample. Journal of Microbiological Methods. ,vol. 104, pp. 36- 42 ,(2014) , 10.1016/J.MIMET.2014.06.009
Kristy Deiner, Jean-Claude Walser, Elvira Mächler, Florian Altermatt, Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA Biological Conservation. ,vol. 183, pp. 53- 63 ,(2015) , 10.1016/J.BIOCON.2014.11.018
Caren S. Goldberg, Katherine M. Strickler, David S. Pilliod, Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms Biological Conservation. ,vol. 183, pp. 1- 3 ,(2015) , 10.1016/J.BIOCON.2014.11.040
Cameron R. Turner, Derryl J. Miller, Kathryn J. Coyne, Joel Corush, Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.) PLoS ONE. ,vol. 9, pp. e114329- ,(2014) , 10.1371/JOURNAL.PONE.0114329
Xavier Pochon, Nathan J. Bott, Kirsty F. Smith, Susanna A. Wood, Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLOS ONE. ,vol. 8, pp. 1- 12 ,(2013) , 10.1371/JOURNAL.PONE.0073935
David A W Soergel, Neelendu Dey, Rob Knight, Steven E Brenner, Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences The ISME Journal. ,vol. 6, pp. 1440- 1444 ,(2012) , 10.1038/ISMEJ.2011.208