10.1371/journal.pone.0157505 Nicole A. Fahner Nicole A. Fahner Shadi Shokralla Shadi Shokralla Donald J. Baird Donald J. Baird Mehrdad Hajibabaei Mehrdad Hajibabaei Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers Public Library of Science 2016 soil samples 35 soil samples DNA barcode database trn L P 6 loop Environmental DNA Metabarcoding length DNA barcode regions DNA markers plant diversity DNA metabarcoding soil plant eDNA analysis DNA barcoding markers rbc L rbc L plant community composition 2016-06-16 06:00:55 Dataset https://plos.figshare.com/articles/dataset/Large-Scale_Monitoring_of_Plants_through_Environmental_DNA_Metabarcoding_of_Soil_Recovery_Resolution_and_Annotation_of_Four_DNA_Markers/3449741 <div><p>In a rapidly changing world we need methods to efficiently assess biodiversity in order to monitor ecosystem trends. Ecological monitoring often uses plant community composition to infer quality of sites but conventional aboveground surveys only capture a snapshot of the actively growing plant diversity. Environmental DNA (eDNA) extracted from soil samples, however, can include taxa represented by both active and dormant tissues, seeds, pollen, and detritus. Analysis of this eDNA through DNA metabarcoding provides a more comprehensive view of plant diversity at a site from a single assessment but it is not clear which DNA markers are best used to capture this diversity. Sequence recovery, annotation, and sequence resolution among taxa were evaluated for four established DNA markers (<i>mat</i>K, <i>rbc</i>L, ITS2, and the <i>trn</i>L P6 loop) <i>in silico</i> using database sequences and <i>in situ</i> using high throughput sequencing of 35 soil samples from a remote boreal wetland. Overall, ITS2 and <i>rbc</i>L are recommended for DNA metabarcoding of vascular plants from eDNA when not using customized or geographically restricted reference databases. We describe a new framework for evaluating DNA metabarcodes and, contrary to existing assumptions, we found that full length DNA barcode regions could outperform shorter markers for surveying plant diversity from soil samples. By using current DNA barcoding markers <i>rbc</i>L and ITS2 for plant metabarcoding, we can take advantage of existing resources such as the growing DNA barcode database. Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding.</p></div>