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Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. / Deiner, Kristy ; Lopez, Jacqueline; Bourne, Steve et al.
In: Metabarcoding and Metagenomics, Vol. 2, e28963, 02.11.2018.

Research output: Contribution to journalArticlepeer-review

HarvardHarvard

Deiner, K, Lopez, J, Bourne, S, Holman, LE, Seymour, M, Grey, EK, Lacoursiere-Roussel, A, Li, Y, Renshaw, MA, Pfrender, ME, Rius, M, Bernatchez, L & Lodge, DM 2018, 'Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method', Metabarcoding and Metagenomics, vol. 2, e28963. https://doi.org/10.3897/mbmg.2.28963

APA

Deiner, K., Lopez, J., Bourne, S., Holman, L. E., Seymour, M., Grey, E. K., Lacoursiere-Roussel, A., Li, Y., Renshaw, M. A., Pfrender, M. E., Rius, M., Bernatchez, L., & Lodge, D. M. (2018). Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics, 2, Article e28963. https://doi.org/10.3897/mbmg.2.28963

CBE

Deiner K, Lopez J, Bourne S, Holman LE, Seymour M, Grey EK, Lacoursiere-Roussel A, Li Y, Renshaw MA, Pfrender ME, et al. 2018. Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics. 2:Article e28963. https://doi.org/10.3897/mbmg.2.28963

MLA

VancouverVancouver

Deiner K, Lopez J, Bourne S, Holman LE, Seymour M, Grey EK et al. Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics. 2018 Nov 2;2:e28963. doi: 10.3897/mbmg.2.28963

Author

Deiner, Kristy ; Lopez, Jacqueline ; Bourne, Steve et al. / Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. In: Metabarcoding and Metagenomics. 2018 ; Vol. 2.

RIS

TY - JOUR

T1 - Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method

AU - Deiner, Kristy

AU - Lopez, Jacqueline

AU - Bourne, Steve

AU - Holman, Luke E.

AU - Seymour, Mathew

AU - Grey, Erin K.

AU - Lacoursiere-Roussel, Anais

AU - Li, Yiyuan

AU - Renshaw, Mark A.

AU - Pfrender, Michael E.

AU - Rius, Marc

AU - Bernatchez, Louis

AU - Lodge, David M.

PY - 2018/11/2

Y1 - 2018/11/2

N2 - The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 μm, 0.7 μm and 1.2 μm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styela clava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples

AB - The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 μm, 0.7 μm and 1.2 μm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styela clava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples

KW - eDNA

KW - 18SS ribsomal

KW - Seawater

KW - High-throughout sequencing

KW - Metazoaneukaryotes

KW - Non-indigenous species

U2 - 10.3897/mbmg.2.28963

DO - 10.3897/mbmg.2.28963

M3 - Article

VL - 2

JO - Metabarcoding and Metagenomics

JF - Metabarcoding and Metagenomics

SN - 2534-9708

M1 - e28963

ER -