title: Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA.
abstract: Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing. The main portions of this protocol consists of 1) filtration of water samples (water volumes ≤4 L or >4 L); (2) extraction of DNA on the filter using a roller shaker placed in a preheated incubator; and (3) purification of DNA using a commercial kit. With the use of this and previously-used protocols, we perform metabarcoding analysis of eDNA taken from a huge aquarium tank (7,500 m3) with known species composition, and show the number of detected species per library from the two protocols as the representative results. This protocol has been developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.
authors.affiliation: Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba; miya@chiba-muse.or.jp.
authors.forename: Masaki
authors.initials: M
authors.lastname: Miya
authors.affiliation: Graduate School of Human Development and Environment, Kobe University.
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Minamoto
authors.affiliation: Faculty of Science and Technology, Ryukoku University.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Yamanaka
authors.affiliation: Okinawa Churashima Research Center.
authors.forename: Shin-Ichiro
authors.initials: SI
authors.lastname: Oka
authors.affiliation: Okinawa Churashima Research Center.
authors.forename: Keiichi
authors.initials: K
authors.lastname: Sato
authors.affiliation: Graduate School of Human Development and Environment, Kobe University.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Yamamoto
authors.affiliation: Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sado
authors.affiliation: Graduate School of Simulation Studies, University of Hyogo.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Doi
mesh_terms: D000818:Animals; D004247:DNA; D004777:Environment; D005374:Filtration; D005399:Fishes; D014867:Water
chemical_list: D014867:Water; D004247:DNA