title: Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding.
abstract: Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206-L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina-sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Nathan T
authors.initials: NT
authors.lastname: Evans
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Brett P
authors.initials: BP
authors.lastname: Olds
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Renshaw
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Cameron R
authors.initials: CR
authors.lastname: Turner
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Yiyuan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Jerde
authors.affiliation: Department of Biology and Institute for Great Lakes Research, Central Michigan University, 190 Brooks Hall, Mount Pleasant, MI, 48859, USA.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Mahon
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Pfrender
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: Gary A
authors.initials: GA
authors.lastname: Lamberti
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Lodge
mesh_terms: D000663:Amphibians / Q000145:classification / Q000235:genetics*; D000818:Animals; D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D004784:Environmental Monitoring; D005399:Fishes / Q000145:classification / Q000235:genetics*
keywords: community ecology; environmental DNA; mesocosm; metabarcoding; species diversity