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Suggested Sampling Supplies and Procedures

Recommended procedures for collecting and storing water samples for total alkalinity and total carbon analyses are available in Dickson et al. (2007) Guide to best practices for ocean CO2 measurements.

Sampling supplies

  • 300 or 500 milliliter Biological Oxygen Demand (BOD) bottles with ground glass stoppers
  • Silicon sample transfer tubing
  • Apiezon® stopper grease
  • Saturated mercuric chloride (HgCl2) in deoinized water
  • 100 microliter pipette
  • Taper clips/stopper clamp/rubberband, or black tape to secure stoppers
  • Permanent marker

Preparation for sampling and sampling procedure (modified from Dickson et al. 2007).

Sample bottles should be precombusted in a muffle furnace to remove organic carbon. If bottles are acid washed, all acid must be rinsed. Label sample bottles in at least two locations by writing directly on the bottle (label tape frequently falls off during sample transport). Record sample information on the sample sheet provided.

From Niskin Bottles or Flow-Through Sampling Systems

  • When sampling from Niskin bottles, sample as quickly as possible after the Niskin bottle reaches the surface to prevent contamination of the sample with atmospheric carbon.
  • Attach silicon tubing to the stopcock of the Niskin bottle or to the sample port of a flow-through sampling system, vent the Niskin bottle at the top. 
  • Place the tubing at the bottom of the bottle, open the stopcock or sampling port and begin filling the bottle. Gently squeeze the tubing to remove bubbles if necessary.  Fill the bottle from the bottom (while leaving the tube at the bottom) to avoid bubbles and minimize turbulence at the sample surface. Allow the water to overflow at least one full volume.
Photo of a Niskin bottle with the sample tube inserted and the stopper sitting beside it
Place sample tube at bottom of bottle and fill from the bottom.
  • Once full, stop the water flow by closing the stopcock on the Niskin bottle or closing the sampling port of the flow-through system. With the tube touching the bottom of the bottle, slowly withdraw the silicon tube. Once the tube is removed, there should be a small head-space (approximately 1% of the sample volume) in the top of the bottle to allow for sample expansion.
  • Wearing gloves, carefully add 100 microliters (for a 500 milliliter sample) of saturated HgCl2 solution using a 100 microliter pipette. The recommended minimum amount is 0.02% by volume.
Close-up of a Niskin bottle with a 100 microliter pipette held at the mouth
Add 100 microliters of saturated HgCl2 solution per 500 milliliters of sample.
  • Apply a very small amount of Apiezon® stopper grease (3 to 4 thin lines) approximately 1/2 of the distance up from the bottom (tapered end) of the ground glass stopper and extending toward the top of the stopper. Insert the stopper into the neck of the bottle and twist while applying downward pressure to spread the grease evenly around the stopper and bottle neck to form a gas-tight seal. Continue twisting the stopper while applying downward pressure until resistance is met. Visually inspect the seal to ensure that the grease is distributed evenly and continuously around the stopper and bottle neck!
Photo of the stopper held between thumb and fingers with tiny dabs of stopper grease in 2 dabs
A very small amount of Apiezon ® stopper grease is applied to the ground glass of the stopper to form a gas-tight seal.
  • Secure the stopper by using a rubber band and taper clip, or other positive pressure method, then invert bottle several times to mix the HgCl2 solution.
Photo of a Niskin bottle with rubber band and taper clip attached to the stopper
The stopper is secured with positive pressure, using a rubber band and a taper clip.
Close-up of a full Niskin bottle with black tape stretched across the stopper and secured
Black tape is stretched across the stopper of the Niskin bottle and secured to form a positive pressure seal.
  • Store samples in a cool, dark location until analysis, DO NOT FREEZE!

Filtering samples

When sampling in locations where high concentrations of particulates are found (for example in estuaries, reef environments, or other coastal environments), samples should be filtered to remove particulates.

  • Samples should only be pressure filtered, NEVER vacuum filtered! This can be accomplished by using either the flow pressure in a flow-through sampling system, or by connecting a peristaltic pump to the sampling port of a Niskin bottle or flow-through system. In either case, care must be taken to avoid introduction of bubbles. Lines should be carefully checked and cleared of bubbles before filling sample container.
  • Place clean 0.45 micron filter (we typically use either polycarbonate or glass fiber) in filter holder. Attach filter holder to outflow port of flow-through system or peristaltic pump using silicon tubing. Attach silicon sample transfer tube to outflow of filter holder.
  • Allow several volumes of water to flow into filter holder and through filter to wet filter and remove bubbles. Check very carefully for bubbles inside of the filter holder and the sampling tube. Either vent filter holder (if a vent is present), or invert filter holder, rotate and tap gently to help remove bubbles.
  • Proceed with sampling as previously described.


Dickson, A.G., Sabine, C.L., and Christian, J.R. (eds). 2007. Guide to best practices for ocean CO2 measurements. PICES special publication 3, 191 pp.