title: In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River.
abstract: Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semi-aquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.
authors.affiliation: Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Ave., Cleveland OH 44195, USA.
authors.forename: M V
authors.initials: MV
authors.lastname: Cannon
authors.affiliation: Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Ave., Cleveland OH 44195, USA.
authors.forename: J
authors.initials: J
authors.lastname: Hester
authors.affiliation: Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Ave., Cleveland OH 44195, USA.
authors.forename: A
authors.initials: A
authors.lastname: Shalkhauser
authors.affiliation: Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Ave., Cleveland OH 44195, USA.
authors.forename: E R
authors.initials: ER
authors.lastname: Chan
authors.affiliation: Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Ave., Cleveland OH 44195, USA.
authors.forename: K
authors.initials: K
authors.lastname: Logue
authors.affiliation: Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Ave., Cleveland OH 44195, USA.|Department of Global Health and Diseases, Case Western Reserve University, 10900 Euclid Ave., Cleveland OH 44106, USA.
authors.forename: S T
authors.initials: ST
authors.lastname: Small
authors.affiliation: Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Ave., Cleveland OH 44195, USA.
authors.forename: D
authors.initials: D
authors.lastname: Serre
mesh_terms: D000663:Amphibians / Q000145:classification / Q000235:genetics; D000818:Animals; D044822:Biodiversity; D001717:Birds / Q000145:classification / Q000235:genetics; D002347:Carps / Q000145:classification / Q000235:genetics; D002965:Classification; D003198:Computer Simulation; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D017753:Ecosystem; D004784:Environmental Monitoring; D059014:High-Throughput Nucleotide Sequencing; D008322:Mammals / Q000145:classification / Q000235:genetics; D056186:Metagenomics; D010944:Plants / Q000145:classification; D045483:Rivers; D013045:Species Specificity
chemical_list: D004247:DNA