title: Spatial distribution of environmental DNA in a nearshore marine habitat.
abstract: In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.
authors.affiliation: School of Marine and Environmental Affairs, University of Washington , Seattle , WA , United States of America.
authors.forename: James L
authors.initials: JL
authors.lastname: O'Donnell
authors.affiliation: School of Marine and Environmental Affairs, University of Washington , Seattle , WA , United States of America.
authors.forename: Ryan P
authors.initials: RP
authors.lastname: Kelly
authors.affiliation: Earth Resource Technology, Inc., Under Contract to the Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration , Seattle , WA , United States of America.
authors.forename: Andrew Olaf
authors.initials: AO
authors.lastname: Shelton
authors.affiliation: Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration , Seattle , WA , United States of America.
authors.forename: Jameal F
authors.initials: JF
authors.lastname: Samhouri
authors.affiliation: School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America; School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America.
authors.forename: Natalie C
authors.initials: NC
authors.lastname: Lowell
authors.affiliation: Pacific States Marine Fisheries Commission, Under Contract to the Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration , Seattle , WA , United States of America.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Williams
keywords: Environmental monitoring; Estuarine; Marine; Metabarcoding; Metagenomics; Molecular ecology