Jun 26, 2026
OceanOmics Centre: eDNA Sample Filtration with MasterFlex®
- Marcelle Ayad1,
- Laura Missen2,
- OceanOmics UWA2
- 1Minderoo Foundation;
- 2Minderoo OceanOmics Centre at UWA
External link: https://www.uwa.edu.au/oceans-institute/partnerships/minderoo-oceanomics-centre-at-uwa
Protocol Citation: Marcelle Ayad, Laura Missen, OceanOmics UWA 2026. OceanOmics Centre: eDNA Sample Filtration with MasterFlex®. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6obdklqe/v1
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: June 26, 2026
Last Modified: June 26, 2026
Protocol Integer ID: 319872
Keywords: filtration, eDNA, masterflex, environmental eDNA, marine eDNA, oceanomics, filter paper, sampling, marine sampling, samples for the oceanomics centre, use onboard oceanomics research vessel, oceanomics research vessel, oceanomics centre, filtering seawater sample, sample filtration, environmental dna, edna, sample
Abstract
This protocol describes the procedure for filtering seawater samples with a MasterFlex® peristaltic pump to obtain Environmental DNA (eDNA) samples for the OceanOmics Centre. This method is intended for use onboard OceanOmics research vessels and their affiliated tender boats. Adjustments to procedure or equipment may be made as needed to accommodate other users and laboratories.
Guidelines
Standard lab set-up:
- Ensure competency and training requirements are met.
- Wear gloves and a lab coat during filtration.
- Use tips with filters to avoid contamination.
- Wipe workspace with 10% bleach, leave to decontaminate for 10 minutes before wiping with ddH20.
- Sterilise all equipment with 10% bleach, leave to decontaminate for 10 minutes before wiping with ddH20.
- UV pipettes, racks and tubes (lids open) for 15 minutes before use if possible.
- All filter housing components must be decontaminated by soaking in 10% bleach for 15 minutes followed by rinsing with ddH20. Once decontaminated, leave and dry and stored in clean zip-lock bags.
- All waste must be disposed of following institutional biosafety regulations.
Materials
Equipment
- Niskin bottle
- 2L Nalgene wide-mouth straight-sided PPCO jars with closure
- Esky filled with ice
- Nally bins and buckets
- MasterFlex® Pump (Cat# 07557-04, John Morris)
- MasterFlex® Motor (Cat# 07557-02, John Morris)
- MasterFlex® Tubing Cat# 96410-14, John Morris)
- Dissecting forceps
- Dissecting scissors
- 96-well microtube rack
- 4-way flipper rack
- Permanent marker
Consumables
- Nitrile gloves
- 2.0 mL DNA LoBind tubes
- 50 mL conical tubes
- Cryogenic boxes
Reagents
Buffer ATLQiagenCatalog #19076
- 10% bleach
- Lab grade DI water
Safety warnings
Field sampling conducted on boats or near open water presents inherent risks including slips, falls, exposure to weather and incorrect handling of equipment. All personnel must comply with institutional fieldwork safety requirements and have appropriate training. This protocol also involves the use of potentially hazardous biological materials, chemicals, and electrical laboratory equipment. Always wear appropriate personal protective equipment (PPE), including a lab coat, gloves, and eye protection. Be familiar with the relevant Safety Data Sheets (SDS) and laboratory risk assessments before commencing work. Follow institutional safety guidelines and dispose of waste in accordance with local regulations. Exercise caution when handling sharp instruments, or heavy equipment.
Chemical Hazards:
- Buffer ATL and AL contain Guanidine Hydrochloride. This is harmful if swallowed, inhaled, or in contact with skin.
- Avoid mixing guanidine hydrochloride with bleach or strong oxidiser as toxic gas will form.
Link to SDS: 
Buffer ATL SDS.pdf170.6KB
Buffer ATL SDS.pdf170.6KB Before start
Ensure standard lab set-up as per the guidelines.
Load vessel/vehicle with all equipment.
Sample Collection
Ensure sample collection has been carried out as per the protocol OceanOmics Centre: eDNA Sample Collection with a Niskin bottle. After sample collection, proceed to filtration as quickly as possible.
Filter Housing
Prepare the filter housing by removing the screw parts to open the cartridge. Place the filter paper marked side up (gridlines visible) onto the beige mesh part of the housing.
Place the red O-ring on top of the filter paper.
Close the filter cartridge and ensure all three screws are screwed on tight.
NOTE: filter cartridges can be prepared the day/night before filtering and placed into a clean Ziplock
bag until needed.
Filter Preparation
Wipe all surfaces with 10% bleach. Leave to decontaminate for 10 minutes before wiping with
DI water.
Ensure filter housings are set-up as per Section 1.
Prepare 2 x 2.0 mL DNA LoBind tubes per filter housing.
Add 540 µL Buffer ATL to all 2.0 mL DNA LoBind tubes required.
NOTE: other preservation buffers may be used but this may affect downstream analysis.
Prepare 50 mL conical tubes for decontamination of equipment:
- Fill as many tubes as required with 10% bleach- soak scissors and forceps for 15 minutes before use.
- Fill as many tubes as required with DI water- rinse scissors and forceps for 10 minutes before use.
NOTE: maximum of 6 utensils per tube.
Prepare a bucket with 10% bleach to decontaminate filter housing after filtration. This bleach should be changed every sampling day.
Fill a clean, sterilised 1L Nalgene bottle with DI water to be used as the filtration control.
Place all required equipment on the clean bench as per the image below:
Filtration directly from Niskin Bottles
Load clean tubing into the MasterFlex® pump head and lock into place using the lever. Ensure there is enough length in the tubing to reach both the Niskin bottle and somewhere appropriate to drain.
Place a loaded filter housing onto one end of the tubing, ensuring the housing inlet side is facing the right way (screws up).
Tie a cable around the hose inlet of the filter housing to avoid it popping off with increased pressure during filtration.
Connect the other end of the tubing directly to the spigot of the Niskin bottle and pull the spigot slightly out to open. Below is an image of how the filtration set-up should look like:
Set the pump speed to 80 and ensure it is flowing in the correct direction.
Turn on the MasterFlex® controller. Check that the water is flowing appropriately and adjust the tubing to remove air bubbles if required. Opening and closing the lever on the pump head can resolve the trapped air.
When all the sample water has passed through the filter, disconnect the filter housing from the tubing and place onto a rack (insert outlet into tube tack, screws face up).
Filtration from Collection Bottles
Load clean tubing into the MasterFlex® pump head and lock into place using the lever. Ensure there is enough length in the tubing to reach the bottom of a sampling bottle and to drain into a sink/bucket.
Place a loaded filter housing onto one end of the tubing, ensuring the inlet side is the right way.
Tie a cable around the hose inlet of the filter housing to avoid it popping off with increased pressure during filtration.
Remove the sample bottles from the esky and invert them three times to mix the sample water.
Wipe the outer surface of the sample bottles with 70% ethanol before placing bottle next to the allocated filtration station.
Insert the other end of the tubing (the side without the filter housing) into the sampling bottle.
Below is an image of how the filtration set-up should look like:
Set the pump speed to 80 and ensure it is flowing in the correct direction.
Turn on the MasterFlex® controller. Check the water is flowing appropriately and adjust the tubing to remove air bubbles if required. Opening and closing the lever on the pump head can resolve the trapped air.
When all the sample water has passed through the filter, disconnect the filter housing and place onto a rack.
Follow the same procedure using 1L of DI water. This is the Water Control (WC).
(Optional) Follow the same procedure as the WC with 1L of the bleach that was used to sterilise the equipment. This sample is the Bleach Control (BC). The use of this control is user/research group dependent, it is not a requirement.
Sample Preservation
Open the cartridge and remove the O-ring.
Using decontaminated forceps and scissors, roll the filter paper into a cylinder (illustrated in the figure below as steps 1-4), fold the cylinder in half (illustrated in the figure below as step 5), and cut the filter paper in half (illustrated in the figure below as step 6).
Place one half of the filter paper into a pre-prepared 2.0 mL DNA LoBind tube containing 540 µL Buffer ATL. Place the other half into another pre-prepared 2.0 mL DNA LoBind tube containing 540 µL Buffer ATL. The filter papers should be submerged in buffer.
Label each of the DNA LoBind tubes with half the filter paper clearly with the site name and replicate number. Label one tube as 'A' and the other tube as 'B'.
Label the water control with site name and WC.
Vortex for 5 seconds (or invert to mix if a vortex is not available).
Safe stopping point.
Store samples at -20°C or -80°C until further processing.
Clean-Up
Following completion of filtration for all site replicates and controls, remove all tubing and filter housing.
Soak the filter housing in 10% bleach for 15 minutes. Rinse with DI water, then leave to dry
fully on a clean, decontaminated surface.
Clean the tubing:
In a 2L bucket, prepare a 5% bleach solution using liquid bleach (100 mL) and regular tap water (2L).
Set-up used tubing onto a filter pump head with both ends of the tubing in the bleach
bucket.
Secure all tubing with a cable tie if needed.
Set the MasterFlex‱ pump to 150 and run for 15 minutes.
Swap the bleach bucket for a 2L bucket filled with DI water. Repeat this run for another
15 minutes.
Wipe the outside of the tubing with 10% bleach, followed by 70% ethanol.
Store tubing in a clean, decontaminated bucket for the next sampling event.