Jun 01, 2024
Subsampling Ethanol Preservative from Zooplankton Museum Collections for DNA Extractions
- 1University of British Columbia
- Pelagic Ecosystems Lab
- Hakai Genomics
External link: http://hakai.org
Protocol Citation: Andreas Novotny 2024. Subsampling Ethanol Preservative from Zooplankton Museum Collections for DNA Extractions. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlk888wl5r/v1
Manuscript citation:
Andreas Novotny, Caterina Rodrigues, Loïc Jacquemot, Rute B G Clemente-Carvalho, Rebecca S Piercey, Evan Morien, Moira Galbraith, Colleen T E Kellogg, Matthew A Lemay, Brian P V Hunt, DNA metabarcoding captures temporal and vertical dynamics of mesozooplankton communities, ICES Journal of Marine Science, Volume 82, Issue 2, February 2025, fsaf007, https://doi.org/10.1093/icesjms/fsaf007
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
This version of the protocol is published as a supplementary to:
Andreas Novotny, Caterina Rodrigues, Loïc Jacquemot, Rute B G Clemente-Carvalho, Rebecca S Piercey, Evan Morien, Moira Galbraith, Colleen T E Kellogg, Matthew A Lemay, Brian P V Hunt, DNA metabarcoding captures temporal and vertical dynamics of mesozooplankton communities, ICES Journal of Marine Science, Volume 82, Issue 2, February 2025, fsaf007, https://doi.org/10.1093/icesjms/fsaf007
Created: May 31, 2024
Last Modified: June 01, 2024
Protocol Integer ID: 100973
Keywords: ethanol preservative from zooplankton museum collection, dna from archived sample, dna extraction, dna extractions this protocol, subsampling ethanol preservative, actual zooplankton biomass, archived sample, zooplankton museum collection, dna, ethanol, sample
Abstract
This protocol is used to sample DNA from archived samples preserved in ethanol, without having to subsample or split the actual zooplankton biomass.
Guidelines
MIOP: Minimum Information about an Omics Protocol
| MIOP Term | Value | |
| analyses | Nucleic Acid Extraction | |
| audience | scientists | |
| broad-scale environmental context | marine biome ENVO_00000447 | |
| creator | Andreas Novotny | |
| environmental medium | sea water [ENVO:00002149] | |
| geographic location | North Pacific Ocean [GAZ:00002410] | |
| hasVersion | 1 | |
| issued | 2017 | |
| language | en | |
| license | CC BY 4.0 | |
| local environmental context | coastal sea water [ENVO: 00002150] | |
| materials required | Sterile workbench, Fume Hood, Centrifuge, Incubator | |
| maturity level | Mature | |
| methodology category | Sample collection | |
| personnel required | 1 | |
| project | Biomolecular surveys of marine biodiversity in the Northern Salish Sea, BC | |
| publisher | Hakai Institute, Ocean Observing Program | |
| purpose | DNA Extraction | |
| skills required | sterile technique | pipetting skills | |
| target | DNA | |
| time required | 1 day |
AUTHORS
| PREPARED BY All authors known to have contributed to the preparation of this protocol, including those who filled in the template. | AFFILIATION | ORCID (visit https://orcid.org/ to register) | DATE | |
| Andreas Novotny | University of British Columbia | https://orcid.org/0000-0001-8910-6183 | 2024 |
RELATED PROTOCOLS
| PROTOCOL NAME AND LINK | ISSUER / AUTHOR | RELEASE / ACCESS DATE | |
This is a list of other protocols which should be known to users of this protocol. Please include the link to each related protocol.
ACRONYMS AND ABBREVIATIONS
| ACRONYM / ABBREVIATION | DEFINITION | |
GLOSSARY
| SPECIALISED TERM | DEFINITION | |
BACKGROUND
This protocol is used to sample DNA from archived samples preserved in ethanol, without having to subsample or split the actual zooplankton biomass.
Spatial coverage and environments of relevance
As part of the Hakai Institute Ocean Observing Program, biomolecular samples have been collected weekly, from 0 to near bottom (260 m), to genetically characterize plankton communities in the Northern Salish Sea since 2015, developing a climatology from which we can begin uncover the physical, chemical and biological drivers of community and functional change in the dynamic coastal waters of coastal British Columbia.
This protocol has been used as an alternative source of genetic information, when it is not practical to remove biomass from the zooplankton samples.
Personnel Required
1 Technician
Safety
Identify hazards associated with the procedure and specify protective equipment and safety training required to safely execute the procedure!
Training requirements
Sterile technique, pipetting skills. Work-safe laboratory practices.
Time needed to execute the procedure
1 h
Protocol materials
Sterivex Filter (0.2 um)Merck Millipore (EMD Millipore)Catalog #SVGPL10RC
Before start
Read background information, MIOP and BePOP-OBON information under the "Guidelines" tab.
PREPARATIONS
ETHANOL SUBSAMPLING
To re suspend DNA in the zooplankton sample, invert the sample jar three times.
Let settle for 30 minutes
Use a serological pipette to remove 50 ml of the ethanol preservative, and transfer to a 50 mL falcon tube.
Use a syringe to push the ethanol through a Sterivex Filter (0.2 um)Merck Millipore (EMD Millipore)Catalog #SVGPL10RC .
Seal the outflow of the filter with parafilm.
Add 1800 μL sucrose lysis buffer (SLB).
Seal the inflow opening with parafilm.
Label filter units and store them at -80°C for downstream DNA extraction.
DNA EXTRACTION
Follow the same extraction procedures as for Environmental DNA:
Protocol
CREATED BY
Andreas Novotny
Alternative extraction method:
Protocol
CREATED BY
Andreas Novotny