Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method

Electronic versions

Documents

  • Kristy Deiner
    University of Zurich
  • Jacqueline Lopez
    Univesity of Notre Dame
  • Steve Bourne
    University of Southampton
  • Luke E. Holman
    University of Southampton
  • Mathew Seymour
  • Erin K. Grey
    Governors State University, IL, USA
  • Anais Lacoursiere-Roussel
    Universite Laval
  • Yiyuan Li
    Univesity of Notre Dame
  • Mark A. Renshaw
    Univesity of Notre Dame
  • Michael E. Pfrender
    Univesity of Notre Dame
  • Marc Rius
    University of Southampton
  • Louis Bernatchez
    Universite Laval
  • David M. Lodge
    Univesity of Notre Dame
The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 μm, 0.7 μm and 1.2 μm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styela clava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples
Original languageEnglish
JournalMetabarcoding and Metagenomics
Early online date2 Nov 2018
StateE-pub ahead of print - 2 Nov 2018
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