Jun 26, 2026

OceanOmics Centre: eDNA Sample Collection with the Ocean Diagnostic Ascension Device 

DOI
https://dx.doi.org/10.17504/protocols.io.261ge19djv47/v1
OceanOmics Centre: eDNA Sample Collection with the Ocean Diagnostic Ascension Device
  • 1Minderoo Foundation;
  • 2Minderoo OceanOmics Centre at UWA
Laura Missen
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DOI: https://dx.doi.org/10.17504/protocols.io.261ge19djv47/v1
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 Collection with the Ocean Diagnostic Ascension Device . protocols.io https://dx.doi.org/10.17504/protocols.io.261ge19djv47/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: February 04, 2026
Last Modified: June 26, 2026
Protocol  Integer ID: 242654
Keywords: eDNA, environmental DNA, Automation, Automated sampling, In situ filtration, marine sampling, marine eDNA, OceanOmics, Ocean Diagnostics , Ascension , sample collection with the ocean diagnostic ascension device, use onboard oceanomics research vessel, oceanomics research vessel, ocean diagnostic ascension device, ocean diagnostics ascension device, samples in marine environment, oceanomics centre, marine environment, automated water filtration, precise sampling metadata, monitoring for precise sampling metadata, water filtration, ascension system, mm disc filter, edna, affiliated tender boat, sample, sample collection, sensor
Abstract
This protocol describes the procedure for operating the Ocean Diagnostics Ascension device for in-situ collection of environmental (eDNA) samples in marine environments. The Ascension system enables automated water filtration of seven samples at up to 400m depths, and is integrated with CTD (conductivity, temperature, depth) sensors, and flow monitoring for precise sampling metadata. The protocol specifically, is for operating the instrument in manual mode, and with 47 mm disc filters of 0.45 µM pore size. 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.
  • Use tips with filters to avoid contamination.
  • 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.

For me details on the device and it's operation, see the manufacturer's manual: Download Ascension Instrument Manual.pdfAscension Instrument Manual.pdf6.8MB

Materials
Equipment
  • Ocean Diagnostics Ascension eDNA depth sampling device: https://oceandiagnostics.com/ascension
  • Tether reel (Ocean Diagnostics)
  • Laptop
  • 7x filter cassettes (Ocean Diagnostics)
  • Syringe with filter adaptor (Ocean Diagnostics)
  • White valve tubing (Ocean Diagnostics)
  • Buckets (large enough to fit Ocean Diagnostics Ascension device)
  • Nally bins
  • Dissecting scissors
  • Dissecting forceps
  • Beige peristaltic tubing (Ocean Diagnostics)
  • 500 mL Nalgene bottle
  • 96-well microtube rack
  • 4-way flipper rack
  • Permanent marker

Consumables
  • MCE membrane filter, 0.45 µM pore size, 47 mm diameter (Merck)
  • 2.0 mL DNA LoBind tubes
  • 50 mL conical tubes
  • Nitrile gloves
  • Cryogenic boxes

Reagents
  • 10% bleach
  • Laboratory grade DI water
Buffer ATLQiagenCatalog #19076

Troubleshooting
Problem
Low water flow rate
Solution
The intake could be blocked or there could be a valve malfunction. Check tubing and valves for wear and tear, or kinks. Replace tubing if necessary and restart sampling.
Problem
Low volume collected
Solution
The most likely cause is filter saturation due to high turbidity. To resolve, filter desired volume through multiple filters and then combine after extraction.
Problem
Communication loss
Solution
Most likely due to Bluetooth connection issues. Retry connecting instrument using File > Connect Profiler (Bluetooth). Instrument will typically continue to operate at last setting until reconnected.
Problem
Contamination detected
Solution
Contamination can occur when the filter housing is opened, or the O-rings are damaged. Replace the filter housing components and sterilise with 10% bleach. Check O-rings for damage and discard if necessary. Ensure there is no wobble in the filter housing.
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.

Equipment Hazards:
The Ascension device uses a lithium-ion polymer (LiPo) battery. If overcharged, heated, short-circuited, or damaged, a fire may occur. LiPo fires are extremely hot, produce toxic smoke, and are difficult to distinguish. Use the following controls:
  • Charge only with approved LiPo charger according to the battery specifications.
  • Charge on a non-flammable surface (e.g. concrete or steel), and away from flammable materials.
  • Do not leave charging batteries unattended.
  • Store and transport in a non-flammable container.
  • Regularly check battery condition.

Do not operate the instrument:
  • Exceeding 400 m depths.
  • Outside the temperature range of 0°C to 40°C.
  • In an area with underwater obstructions that could damage or snag the instrument.

Chemical Hazards:
  • Buffer ATL contains 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: Download Buffer ATL SDS.pdfBuffer ATL SDS.pdf170.6KB

Before start
Ensure standard lab set-up as per the guidelines.
Prepare all 2.0 mL tubes required by adding 540 µL Buffer ATL. 2x tubes are required per replicate, per site.
Scissors and forceps must be sterilised before handling filter papers:
  1. Prepare one 50 mL tube with 10% bleach
  2. Prepare one 50 mL tube of ddH20.
  3. Dip scissors and tweezers in bleach for 10 minutes, then rinse in distilled water. Scissors must be open.
  4. Repeat after each use.

Ensure the Ascension device is fully charged at the start of each sampling day:
  1. Plug the yellow end of the instrument charging cable into the charger.
  2. Plug the black AC cable into the charger and into the wall.
  3. Ensure power LED is illuminated red. This will switch to green once fully charged.
  4. Remove dummy port (8-pin) from the top of the device and insert the red charging plug.




Ensure the tether spool is fully charged at the start of each sampling day:
  1. Plug USB cable into USB port on the side of the tether spool.
  2. Plug USB cable into computer or wall charger.
  3. Ensure charge LED is illuminated. This is orange when charging and green when fully charged.


Familiarise yourself with all instrument components and perform all instrument checks. Specific instructions can be found in the manual.



  1. Inspect the instrument frame to ensure there is no visible damage. Ensure all top and bottom frame pins are secured.
  2. Ensure fluidic channel is fully inserted into the flow meter intake.
  3. Ensure all load bearing tether lanyards are attached and intact (4 total).
  4. Ensure pump and flow meter cables are plugged into core and tight (2 total).
  5. Ensure there is no damage or kinks in the tubing between the flow meter and the peristaltic pump. If damage is present, replace the tubing.
  6. Gently open each valve by hand, all valves should open freely (7 total).
  7. Inspect the tether for kinks and damage.
  8. If required, grease tether and charging ports with Molykote 44 Medium.




Filter Housing Preparation and Assembly
Sterilise a bucket with 10% bleach, rinse, then fill with DI water.
Fill another bucket with a 10% bleach solution.
Disassemble the filter housing into 5 separate parts, soak all components in bleach for 15 minutes then place in the DI water bucket to rinse.
Lay the filter housing components out to dry in a clean space (e.g. disinfected bench with a paper towel or laminar flow hood).

Safe stopping point.
Once dry, filter housing components can be stored in clean zip-lock bags until required, or proceed immediately to assembly.
There are five filter housing components:
  1. Top (with white tubing)
  2. Bottom (with metal adapter)
  3. Filter support (x2)
  4. O-ring (x3)
  5. Screw cap (outer ring)

If new tubing is required, cut a new section of the white valve seal tubing (65 mm in length), and install onto the barbed fitting on the intake of the filter housing.
Place a white filter support into the top and bottom halves of the filter housing.


Using sterilised forceps, place the filter paper on top of the filter support of the bottom half of the housing. Ensure the filter paper lies flat with no folds or debris, and the gridlines face up.


Install the top half of the filter housing and then tighten down the outer ring. Do not overtighten.





NOTE: the filter casing with the tubing attached should be firmly in place and not have any wiggle. If there is movement, try loosening and re-tightening these parts or use a different housing part.

Instrument Purge
Power on the Ascension device using the bottom switch (rotate and push up until it clicks in). Ensure blue status LED is flashing.



Power on tether spool by a single press of the side button. Ensure status LED is flashing green.




Connect the tether to the instrument by removing the red dummy plug and inserting the tether port (2-pin), then tighten the red locking sleeve.




Connect tether thimble to instrument using the anchor shackle. Add a cable tie as shown in the image below as a safety.




Ensure any unpopulated ports are sealed with dummy plugs. The 2-pin dummy plug is for the tether port, and the 8-pin dummy plug is for the charging port.

NOTE: all parts are unique, meaning none of the external connectors can be accidentally plugged into the wrong port.
On the tablet/laptop, open the Ascension desktop software.
Connect to instrument: File > Connect Profiler (Bluetooth). Wait for the instrument serial number to appear in the top right corner.


Fill a bucket with freshwater (this water does not have to be DI but must be clean with no particles). Ensure the bucket is large enough to fit the device.
Ensure the safety plug on the bottom of the unit is installed before deployment. This plug is removed for air freight to accommodate pressure changes during transport, so it is critical to be reinstalled before the unit is submerged in water.
Submerge the device in the bucket. Ensure the water level is above the pump exhaust port.


Safety information
Lift device from tether lanyards, do not lift from the electrical ports.





Run a flush routine:
  1. Run > Control > Flush Routine.
  2. Run for ~1 minute to prime the instrument. The purpose of this is to remove any air gaps in the instrument, the prime is finished when no more bubbles are coming out of the device.
  3. Cancel flush routine to end the flush.

NOTE: after the flush routine, the device must be carried upright and not be tilted onto its side.
Filter Housing Prime and Loading
Draw ~20 mL of DI water through the purging syringe. Holding the cartridge upright, connect the metal clip of the syringe into the metal clip of the filter cassette.




Push water through the cassette until water comes out the side.
Insert the cassette by opening the two valve control handles, hold open while sliding the tube attached to the filter housing up through the valve opening. Push the metal clip down until it clicks.
Close the valve by releasing the valve control handles.




Repeat for all 7 cassettes.
Ascension Manual Deployment and Filtration
Set-up deployment in the software:
  1. Open the instrument controller: Control > Real-Time Controller.
  2. Open Home Position using the Sample Channel Selector.
  3. Start a deployment by selecting File > New Manual Deployment.
  4. Fill out Station and User information.
  5. Home the device.
  6. Click Launch Deployment.
Deploy the device by lowering it vertically using the tether line. Ensure the instrument remains upright at all times.


Safety information
Deployment should be performed using a two-person procedure for safety. Operator one should guide and support the device during lowering, while operator two manages the tether spool and releases cable in a controlled manner. Maintain clear communication throughout to prevent sudden drops, tangles, or uncontrolled tension on the line.

Once instrument is fully submerged, use the software to monitor instrument depth during descent. Once the target depth is reached, secure the tether line by tying off the cable to a stable point like a cleat. Ensure the tether is tensioned smoothly without sharp bends, kinks, or abrasion points.

NOTE: depth reads within the first ~5m are less reliable and may underestimate true depth. The Ascension device is more appropriate for depths >5m.
Open the desired filter channel using the Sample Channel Selector.

NOTE: only run the pump when device is fully submerged in water, never run the pump when dry.
Set pump throttle using the Pump Throttle Controller. The pump is most efficient at 30%.

NOTE: the ideal flow rate is 0.2, if the rate is significantly below this, there may be issues with the tubing, or the cassettes were not primed properly. Stop the deployment and check the device. Flow rate may be slightly reduced in turbid environments.
Once target volume (2L) has been collected, set pump throttle to 0%, move to the next channel and Open Valve.

NOTE: you can move between channels at any time.
Once all desired samples are collected, close all channels by selecting Close All Valves and click End Deployment.
Retrieve the instrument by using a two-person procedure: operator one should steadily pull up the tether line, while operator two manages the tether spool, ensuring smooth cable movement and preventing snags. Avoid contact with the hull/jetty.


Safety information
Coil the tether line as it is retrieved, keep your feet clear of the spool/cable at all times.

Lift out of the water and place upright on a flat surface.
Using sterile gloves, remove filter housings from the device and proceed immediately to sample retrieval.
Sample Retrieval
Transport filter housings to a protected area (i.e. away from wind or water splash).
With a new pair of gloves, gently open the filter housing by unscrewing the outer ring.
Place the metal clip inside a well of a microtube rack to keep it upright.
Using sterilised forceps and scissors, roll the filter paper into a cylinder, fold in half, and then cut the filter paper in half.



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 in another pre-prepared 2.0 mL DNA LoBind tube containing 540 µL buffer ATL.




Label the tubes clearly with site name and replicate number. Label one half 'A', and the other half 'B'.
Vortex for 5 seconds (or invert to mix if a vortex is not available).
Safe stopping point.
Store samples at in a Cryogenic box at -20°C or -80°C until further processing.
Instrument Flush Routine and Storage
Disconnect fluidic channel fitting from flowmeter intake then invert the device to drain seawater from the fluidic system. Reconnect after seawater has been drained.
Rinse the exterior of the device with freshwater (does not have to be DI water).
Sterilise a bucket with 10% bleach then fill with DI water. Fill another bucket with 10% bleach.
Connect tether to the device and launch Ascension desktop software to connect the instrument.
Fully submerge the Ascension device into the bucket filled with 10% bleach. Ensure the water level is above the pump exhaust port.
Click Control > Flush Routine > Start Flush Routine. Allow to run for the full duration.
Transfer the device into the bucket of DI water, ensure fully submerged.
Repeat

Remove device from the bucket and invert to drain all the water from the fluidic system.
Power-off the device using the bottom switch, and power-off the tether. Ensure no LED lights are on.
Disconnect the tether thimble from the instrument anchor shackle by removing the red locking sleeve.
Rinse the tether spool with freshwater. Do not submerge in water, it is rinse-safe only.
Install dummy plug on tether port and tighten locking sleeve.
Leave all components to dry fully before storing into Pelican case.
Download device log files. The data should be saved to the C: drive of the computer.
Protocol references
All diagrams are sourced from the Ascension instrument manual.