dc.contributor.author | Djurhuus, Anni | |
dc.contributor.author | Port, Jesse | |
dc.contributor.author | Closek, Collin J. | |
dc.contributor.author | Yamahara, Kevan M. | |
dc.contributor.author | Romero-Maraccini, Ofelia | |
dc.contributor.author | Walz, Kristine R. | |
dc.contributor.author | Goldsmith, Dawn B. | |
dc.contributor.author | Michisaki, Reiko | |
dc.contributor.author | Breitbart, Mya | |
dc.contributor.author | Boehm, Alexandria B. | |
dc.contributor.author | Chavez, Francisco P. | |
dc.date.accessioned | 2019-01-31T21:27:21Z | |
dc.date.available | 2019-01-31T21:27:21Z | |
dc.date.issued | 2017 | |
dc.identifier.citation | Djurhuus, A. ; Port, J.; Closek, C.J.;
Yamahara, K.M.; Romero-Maraccini, O.;
Walz, K.R.; Goldsmith, D.B.; Michisak,i R.;
Breitbart, M.; Boehm, A.B. and
Chavez, F.P. (2017) Evaluation of
Filtration and DNA Extraction Methods
for Environmental DNA Biodiversity
Assessments across Multiple Trophic
Levels. Frontiers in Marine Science, 4:314, 11pp. DOI: 10.3389/fmars.2017.00314 | en_US |
dc.identifier.uri | http://hdl.handle.net/11329/836 | |
dc.identifier.uri | http://dx.doi.org/10.25607/OBP-387 | |
dc.description.abstract | Metabarcoding of marine environmental DNA (eDNA), originating from tissue, cells,
or extracellular DNA, offers the opportunity to survey the biological composition of
communities across multiple trophic levels from a non-invasive seawater sample. Here
we compare results of eDNA metabarcoding of multiple trophic levels from individual
seawater samples collected from a kelp forest in Monterey Bay, California in order to
establish methods for future cross-trophic level eDNA analysis. Triplicate 1 L water
samples were filtered using five different 47mm diameter membrane filters (PVDF, PES,
GFF, PCTE, and NC) and DNA was extracted from triplicates of each filter-type using
three widely-used extraction methods (the DNeasy Blood and Tissue kit, the MoBio
PowerWater DNA Isolation kit, and standard phenol/chloroform methods) resulting in 45
individual eDNA samples prepared with 15 workflow combinations. Each DNA extract
was amplified using PCR primers for the 16S rRNA gene (microorganisms; Bacteria
and Archaea), 18S rRNA gene (phytoplankton), and the 12S rRNA gene (vertebrates),
and PCR products were sequenced on an Illumina MiSeq platform. The richness and
community composition of microbial, phytoplankton, and vertebrate OTUs were not
significantly different between any of the 0.2 μm pore-size filter types extracted with the
DNeasy or MoBio kits. However, phenol/chloroform extraction resulted in significantly
different community structures. This study provides insight into multiple choices for extraction and filtrationmethods to use eDNAmetabarcoding for biodiversity assessment
of multiple trophic levels from a single sample. We recommend any combination of
either DNeasy or MoBio with PES, PCTE, PVDF, or NC filters for a cross trophic level
comparison. | en_US |
dc.language.iso | en | en_US |
dc.rights | Attribution 4.0 | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.subject.other | Environmental DNA | en_US |
dc.subject.other | Microorganisms | en_US |
dc.subject.other | Phytoplankton | en_US |
dc.subject.other | Trophic levels | en_US |
dc.subject.other | Marine ecosystems | en_US |
dc.subject.other | Biodiversity | en_US |
dc.title | Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels. | en_US |
dc.type | Journal Contribution | en_US |
dc.description.notes | Open Access | |
dc.description.refereed | Refereed | en_US |
dc.format.pagerange | 11pp. | en_US |
dc.identifier.doi | 10.3389/fmars.2017.00314 | |
dc.subject.parameterDiscipline | Parameter Discipline::Biological oceanography | en_US |
dc.bibliographicCitation.title | Frontiers in Marine Science | en_US |
dc.bibliographicCitation.volume | 4 | en_US |
dc.bibliographicCitation.issue | Article 314 | en_US |
dc.description.bptype | Guide | en_US |
dc.description.frontiers | 2017-07-23 | |
obps.contact.contactemail | anni.djurhuus@gmail.com | |
obps.resourceurl.publisher | https://www.frontiersin.org/articles/10.3389/fmars.2017.00314/full | en_US |