title: Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA.
abstract: Preserving biodiversity is a global challenge requiring data on species' distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species' distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource-intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species' eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false-negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.
authors.affiliation: Center for Ocean Solutions, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Jesse A
authors.initials: JA
authors.lastname: Port
authors.affiliation: School of Marine and Environmental Affairs, University of Washington, Seattle, WA, 98105, USA.
authors.forename: James L
authors.initials: JL
authors.lastname: O'Donnell
authors.affiliation: Center for Ocean Solutions, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Ofelia C
authors.initials: OC
authors.lastname: Romero-Maraccini
authors.affiliation: Hopkins Marine Station, Stanford University, Pacific Grove, CA, 93950, USA.
authors.forename: Paul R
authors.initials: PR
authors.lastname: Leary
authors.affiliation: Hopkins Marine Station, Stanford University, Pacific Grove, CA, 93950, USA.
authors.forename: Steven Y
authors.initials: SY
authors.lastname: Litvin
authors.affiliation: Hopkins Marine Station, Stanford University, Pacific Grove, CA, 93950, USA.
authors.forename: Kerry J
authors.initials: KJ
authors.lastname: Nickols
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA.
authors.forename: Kevan M
authors.initials: KM
authors.lastname: Yamahara
authors.affiliation: School of Marine and Environmental Affairs, University of Washington, Seattle, WA, 98105, USA.
authors.forename: Ryan P
authors.initials: RP
authors.lastname: Kelly
mesh_terms: D000818:Animals; D044822:Biodiversity; D002140:California; D058893:DNA Barcoding, Taxonomic; D017753:Ecosystem; D004784:Environmental Monitoring / Q000379:methods; D005399:Fishes / Q000145:classification / Q000235:genetics; D044423:Kelp; D008322:Mammals / Q000145:classification / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D014714:Vertebrates / Q000145:classification* / Q000235:genetics
chemical_list: D012335:RNA, Ribosomal; C075526:RNA, ribosomal, 12S
keywords: biodiversity; eDNA; fish; metabarcoding; monitoring; next generation sequencing