Protein Skimmer Q&A

questions answered by Chris Stowers and Dr. Robert D. Tanner of Vanderbilt University

Proteins can range greatly in size and chemical nature. What kinds of proteins do protein skimmers remove?

Protein skimmers can remove a wide range of proteins depending on their size and type. In general, larger proteins, proteins with hydrophobic appendages, and linear natured proteins (not coiled) will be removed easier. The efficiency of a skimmer will determine the rate and extent that a certain protein will be removed. Most coral and fish waste has potential to be removed by foam fractionation (skimming).

What determines what kinds/sizes of proteins a skimmer will remove?

Bubble contact time- The time which a bubble generated from a skimmer spends in contact with the water and proteins. The longer the time a protein spends in contact with a bubble, the more likely it will be adsorb to the surface of the bubble and removed.

Salinity- Higher salinity can increase bubble production and therefore increase the amount of proteins removed.

Skimmer Size- Larger skimmers generally have longer contact times and process more water leading to more efficient skimming.

Water Chemistry- Certain chemicals such as surfactants have been shown to greatly skew the ability for proteins to be removed from water by foam fractionation. Other chemicals such as tannins have led to similar results. Thus, one should be aware that the presence of a chemical that greatly modifies bubble production will affect protein skimming.

What else (if anything) do protein skimmers remove?

Protein skimmers can remove any substance that is hydrophobic in nature. Most chemicals other than proteins in the reef water column are hydrophilic. However, proteins often complex with nutrients such as Mg allowing them to be removed along with the protein.

Do skimmers remove bacteria and algae too?

Yes, but not efficiently. Although bacteria and algae can be removed by skimming, they are encompassed by a cellular membrane which is hydrophilic on the exterior making them practically immune to skimming.

How do protein skimmers remove phosphates?

Protein skimmers can remove organic phosphate, but will likely not remove vast amounts of inorganic phosphate.

How do protein skimmers remove heavy metals?

Heavy metals can often form chemical complexes with organic content (i.e. proteins) which can in turn be removed by skimming.

Is there any way to tell what my skimmate is or how concentrated it is?

Generally, the darker the skimmate, the more concentrated. It is possible to run a BOD (biological oxygen demand) analysis on your skimmate, but these can be costly and timely.

Does the color/shade of the skimmate mean anything?

See above

My skimmer produces bubbles faster sometimes than others, does that mean that sometimes my tank is "dirtier" and sometimes it's "cleaner?"

Yes. This can mean that your tank water is dirtier. However, it can also mean that either your skimmer needs cleaning or there is a chemical (i.e. a surfactant) in your tank water that has modified bubble formation.

Does the size of the bubbles produced by the skimmer make a  difference? If so, how?

The smaller the bubble, the higher the efficiency of skimming will be. This is due to the increased bubble residence time. This is because smaller bubbles take longer to rise to the surface.

Can we make our skimmers produce smaller/larger bubbles? Which kinds of skimmers produce smaller bubbles?

Some skimmers such as Beckett skimmers and needle wheel skimmers have adjustable air intakes whereas other skimmers do not. Adjusting the skimmer air intake will change bubble size and effect skimming.

Does the column size (the distance the bubbles have to travel up before they are traped by the skimmer cup) make a difference?

Yes. See explanation above.

Is there any way to control our skimmers such that they pull out more of the proteins we don't want and less of the proteins we might want?

Not that I am aware of.

To what extent do protein skimmers oxygenate water? What else is there to know about gas exchange and protein skimming?

Protein skimmers greatly oxygenate the water in a tank. Skimmers can also modify the tank pH by allowing the CO2 in air to reach equilibrium with the CO2 in tank water. In the winter, CO2 concentrations can build up within a home. For this reason, it is often wise to use outside air for the skimmer air intake. Using air high in CO2 content can lead to too low of pH values.

Do protein skimmers remove biologically toxic substances (like the toxic terpenoids leather corals produce)?

It has been widely speculated that skimmers can remove many toxic substances. Some substances such as oils and detergents will certainly be removed by a skimmer. However, other chemicals that may be released from coral would need to be investigated on a case by case basis.

Can I tell if I'm over-skimming my tank?

Not that I am aware of.


Dr. Tanner is one of the few remaining experts in the country studying foam fractionation. Chris Stowers is a graduate student and reef aquarium hobbyist pursuing a PhD in Chemical Engineering.