Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels
By A. Djurhuus, Jesse A. Port, Collin J. Closek, K. Yamahara, Ofelia C Romero-Maraccini, K. Walz, Dawn B. Goldsmith, R. Michisaki, Mya Breitbart, A. Boehm and 1 more. Frontiers in Marine Science, 2017
184 citations recorded by the source corpus.
Metabarcoding of marine environmental DNA (eDNA), the DNA suspended in seawater originating from tissue, cells, or extracellular DNA, offers the opportunity to survey the biological composition of communities across multiple trophic levels from a non-invasive seawater sample. Here we compare results of eDNA metabarcoding of multiple trophic levels from the same seawater samples collected from a kelp forest in Monterey Bay, California in order to establish methods for future cross-trophic level eDNA analysis. Triplicate 1 L water samples were filtered using five different 47 mm diameter membrane filters (PVDF, PES, GFF, PCTE, and NC) and DNA was extracted from triplicates of each filter-type using three widely-used extraction methods (the DNeasy Blood and Tissue kit, the MoBio PowerWater DNA Isolation kit, and standard phenol/chloroform methods) resulting in 45 individual eDNA samples prepared with 15 workflow combinations. Each DNA extract was amplified using PCR primers for the 16S rRNA gene (microorganisms; Bacteria and Archaea), 18S rRNA gene (phytoplankton), and the 12S rRNA gene (vertebrates) genes, and PCR products were sequenced on an Illumina MiSeq platform. The richness and community composition of microbial, phytoplankton, and vertebrate OTUs were not significantly different between any of the 0.2 μm pore-size filter types extracted with the DNeasy or MoBio kits. However, phenol/chloroform extraction resulted in significantly different community structures. This study provides insight into multiple choices for extraction and filtration methods to use eDNA metabarcoding for biodiversity assessment of multiple trophic levels from a single sample. We recommend any combination of either DNeasy or MoBio with PES, PCTE, PVDF, or NC filters for a cross trophic level comparison.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/4cc1665e5cc7237bea830b88d1aa3dc06231f837
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In Ecology
- Henrique M. Pereira
- Yunne-Jai Shin
- J. Emmett Duffy
- Raphael M. Kudela
- Neil J. Gemmell
- Woody Turner
- Mark John Costello
- Xavier Pochon
In Molecular Biology
Citations in the corpus
- Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance (2021, methodology): “Comparable estimates of biodiversity have been described from these two kits; however, representation should be investigated prior to committing to a strategy [29,82].”
- Advancing Marine Biological Observations and Data Requirements of the Complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) Frameworks (2018, background): “…capitalize on the genetic material that is derived from whole microbial cells or shed from multicellular organisms via metabolic waste, damaged tissue, or sloughed skin cells, all of which are ubiquitous in the environment (Thomsen et al., 2012; Andruszkiewicz et al., 2017; Djurhuus et al., 2017).”