May 14, 2026
Version 2
Vacuum Filtration and DNA Extraction from Environmental Water Samples V.2
- Grace Semabia Kpeli1,
- Prince Agyirey-Kwakye2,
- Counseller Nutifafa Livingstone1,
- Lillian Teye Cudjoe1,
- Emmanuel Edem Dotse1,
- Ebenezer Nyarko1,
- Ebenezer Zar1,
- Obed Nyarko-Otu1,
- Hubert Kwame Agbogli1,
- Godwin Glilekpeh1,
- Solomon Korankye1,
- Priscilla Essandoh1,
- Daniel Elorm Kabotso3
- 1Department of Biomedical Science, University of Health and Allied Sciences, Sokode Lokoe, Ho, Ghana;
- 2AttoDiagnostics Limited, Norwich, UK;
- 3Department of Basic Science, University of Health and Allied Sciences, Sokode Lokoe, Ho, Ghana
- GSK's workspace
Protocol Citation: Grace Semabia Kpeli, Prince Agyirey-Kwakye, Counseller Nutifafa Livingstone, Lillian Teye Cudjoe, Emmanuel Edem Dotse, Ebenezer Nyarko, Ebenezer Zar, Obed Nyarko-Otu, Hubert Kwame Agbogli, Godwin Glilekpeh, Solomon Korankye, Priscilla Essandoh, Daniel Elorm Kabotso 2026. Vacuum Filtration and DNA Extraction from Environmental Water Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.kqdg3mmkpl25/v2Version created by Grace Kpeli
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
We use this protocol and it's working
Created: May 14, 2026
Last Modified: May 14, 2026
Protocol Integer ID: 317105
Keywords: DNA extraction, vacuum filtration, environmental water, 16S rRNA, QIAamp, NanoDrop, Qubit, dna extraction from environmental water sample, vacuum filtration of environmental water sample, environmental water sample, dna extraction, water sample, vacuum filtration, microbial cell capture, qiaamp dna mini kit, dna quantification, using nanodrop spectrophotometry, nanodrop spectrophotometry, communities in ghana
Disclaimer
Creative Commons Attribution License (CC BY 4.0)
Abstract
This protocol describes vacuum filtration of environmental water samples for microbial cell capture, followed by DNA extraction using the QIAamp DNA Mini Kit. It includes cell resuspension in PBS, DNA quantification using NanoDrop spectrophotometry and Qubit fluorometry, and storage conditions. The protocol was applied to water samples collected from flood-affected communities in Ghana.
Materials
Equipment
- Vacuum filtration apparatus
- NanoDrop™ Spectrophotometer (Thermo Fisher Scientific)
- Qubit™ Fluorometer (Thermo Fisher Scientific)
- -20°C freezer
- Microcentrifuge
- Pipettes and sterile filtered tips
Reagents and Consumables
- Whatman 0.45 µm filter paper (Cytiva, UK)
- 1X Phosphate-Buffered Saline (PBS)
- QIAamp® DNA Mini Kit (Qiagen N.V., Germany) — includes buffers AL, AW1, AW2, AE, and QIAamp spin columns
- Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific)
- Sterile microcentrifuge tubes (1.5 mL and 2 mL)
- 70% ethanol
Part A — Vacuum Filtration
Assemble vacuum filtration apparatus in a clean workspace. Ensure all components are sterile before use.
Place a Whatman 0.45 µm filter paper onto the filtration membrane support using sterile forceps.
Pour the 1.5 L water sample into the filtration funnel. Apply vacuum and filter the entire volume. Replace filter paper if it becomes clogged.
Using sterile forceps, remove the filter paper. Fold inward (cell-side in) and place into a sterile 2 mL microcentrifuge tube.
Part B — Cell Resuspension
Add an appropriate volume of 1X PBS to the tube containing the folded filter paper.
Vortex for 30–60 seconds to resuspend microbial cells from the filter paper into the PBS solution.
Part C — DNA Extraction (QIAamp® DNA Mini Kit)
Proceed with DNA extraction according to the QIAamp® DNA Mini Kit manufacturer's instructions, using the resuspended PBS as the starting material.
Elute the purified DNA in Buffer AE into a clean 1.5 mL microcentrifuge tube.
Part D — DNA Quantification
NanoDrop quantification: Assess DNA concentration and purity. Record A260/280 and A260/230 ratios. Acceptable purity: A260/280 ≈ 1.8–2.0; A260/230 ≈ 2.0–2.2.
Qubit quantification: Confirm DNA concentration using the Qubit™ dsDNA HS Assay Kit following manufacturer's instructions.
Part E — Storage
Store extracted DNA at -20°C until use.
Quality Control and Troubleshooting
Samples with low DNA quality should be flagged and excluded from downstream sequencing if they do not meet minimum quality thresholds.
Five samples from the parent study were excluded from downstream analysis due to low DNA quality.
Process samples promptly after collection; prolonged storage before extraction may degrade DNA.
Protocol references
QIAamp® DNA Mini Kit Handbook — Qiagen N.V., Germany.
Qubit™ dsDNA HS Assay Kit — Thermo Fisher Scientific.