Jun 25, 2026
Version 1
OceanOmics Centre: eDNA Sample Collection with a Niskin Bottle V.1
- 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 Collection with a Niskin Bottle. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlk1nq5g5r/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 01, 2026
Last Modified: June 25, 2026
Protocol Integer ID: 242401
Keywords: eDNA, environmental DNA, marine eDNA, marine sampling, sampling, niskin, oceanomics, filter paper, samples for the oceanomics centre, oceanomics research vessel, use onboard oceanomics research vessel, oceanomics centre, collecting seawater sample, seawater sample, environmental dna, using niskin bottle, niskin bottle, edna, sample, sample collection, laboratory
Abstract
This protocol describes the procedure for collecting seawater samples using Niskin bottles 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.
- Sterilise all equipment with 10% bleach, leave to decontaminate for 10 minutes before wiping with ddH20.
- 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, 5L (Standard B, Model 110B, Imbros)
- Brass messenger (1000MG, General Oceanics)
- Nylon rope
- Dive weights
- WiSens TD logger and WiSens Wi-Fi dongle
- Mobile phone with Fulcrum App and WiSens webpage
- 2L Nalgene wide-mouth straight-sided PPCO jars with closure (6 required per site)
- Esky filled with ice
- Nally bins and buckets
- In-line PP filter holder, 47 mm (004304700, Merck)
- Cable ties
- Permanent marker
Consumables
- Nitrile gloves
Reagents
- 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.
Before start
Ensure standard set-up as per the guidelines.
Fill esky with ice.
Ensure that you have at least two pieces of nylon rope (for the Niskin bottle set-up).
Fill 6 clean Nalgene bottles (per site) with a small volume of 10% bleach. For each site, label Nalgene bottles sequentially from 1-5, and label one Nalgene bottle as a control.
Mark the nylon rope to measure 1m intervals (e.g. knots or tape)
Load vessel/vehicle with all equipment.
Niskin Deployment
Attach Niskin bottle to the end of the nylon rope by clamping the rope and tightening the finger nuts, leaving enough length of rope to then attach 3-5 kg of dive weights. Prepare the Niskin bottle by attaching nylon rope, then attach the dive weights and brass messenger to the rope. Ensure the WiSens TD logger is secured to the Niskin bottle using cable ties.
Manually pull back the upper stopper to open it.
Simultaneously, while pressing down on the release mechanism cap until the top of the metal pin is exposed, place the wire loop over the exposed pin and release the push rod to capture the wire.
For the first sample at each site:
With one side of the Niskin opened, rinse with freshwater then pour in the bleach solution from all the Nalgene bottles. Close the Niskin and shake to clean. This avoids contamination between sites.
Manually pull back the bottom stopper to open it (and release the bleach solution). Attach the brass clip over the upper stopper's wire loop.
Ensure the white cap on the upper water release valve is screwed in tight and that the lower release valve is closed.
Deploy the Niskin (ensure correct orientation) and move it around in the surface to rinse with surface water before slowly lowering it to the desired depth. Depth is measured using markers on the rope.
Release the brass messenger down the nylon rope. Place a hand on the rope to feel the vibrations as the Niskin bottle fires shut.
Once shut, retrieve the Niskin bottle from the water by pulling up the nylon rope.
Uncap the sample collection bottle; hold the cap in one hand and the bottle in the other. Avoid placing them in a precarious position with exposure to contamination.
Unscrew the white cap of the Niskin bottle. Do not touch the inside.
Rinse sample bottle 3x with ~ 200 mL of sampled water from the Niskin bottle, then fill the sample collection bottle.
Immediately place the sample bottle into an esky with ice.
Empty the remaining seawater from the Niskin bottle then repeat steps 2-14 for all remaining sites.
Proceed to sample filtration as soon as possible following the protocol OceanOmics Centre: eDNA Sample Filtration with MasterFlex®.