Animal Care Resources


Biological Filtration

In a closed, recirculating aquatic life support system, the most important organisms are not the animals living in the system; they are the unseen nitrifying bacteria living on the wet surfaces of the system. Some genera of bacteria are able to process the toxic nitrogenous waste produced by aquatic animals as Total Ammonia Nitrogen (TAN) and oxidize this compound into nitrite (NO2.) Other genera are able to oxidize nitrite, which is also toxic, into nitrate (NO3,) which is much less harmful to aquatic animal health. Please note that TAN and NO2 can negatively affect animal health at concentrations as low as .25ppm. Higher concentrations result in more acute and longer-lasting health effects capable of affecting project data.

Ammonia (TAN) à Nitrite (NO2) à Nitrate (NO3)

TAN = NH3 or NH4, depending on system temperature and pH. NH4 is much less toxic to aquatic animals but an unexpected uptick in either value in a cycled life support system should be investigated as soon as practical.

When we begin to see measurable levels of nitrate in an aquatic life support system, we refer to the system as “cycled,” as the biological filtration is established, and the system is safe to add animals with much less concern about ammonia or nitrite toxicity. The length of time it takes to begin seeing measurable levels of nitrate in a closed system is largely dependent on the temperature of the water in the system. In a tropical marine or freshwater system, for example, it takes around 30 days for the biological filtration to become established.

There are a wide range of different biomedia to choose from when choosing an appropriate substrate for nitrifying bacteria for your system. Some are expensive and require a designated vessel to hold them, while others are inexpensive and can simply be placed in a mesh bag in the sump. Many of the more expensive options have a large amount of surface area in a small amount of space for your biofilter to colonize. Whichever type of biomedia you choose, it is highly recommended to oversize the surface area available so that your biofilter can easily scale to the bioload on the system.

The aquatic animal health specialists in the Aquatic Animal Health Program strongly recommend daily water quality testing and documentation when cycling a new system and weekly water quality testing after a system is cycled. Testing and tracking this data routinely allows researchers and students to gain insights into system and animal health. This data is also invaluable for diagnosing health problems and proactively preventing them.

If you have questions about biological filtration, which biomedia might be best for your research project, recommendations for cycling a new life support system, expected cycling timelines for a system’s fitness to hold animals safely, or any other aspect of aquatic animal health, please reach out to the AAHP Aquatic Husbandry Lab Manager.


Mechanical Filtration

Mechanical filtration should be the first step in the process of water filtration on any aquatic life support system. There are several different ways to achieve mechanical filtration on a system, and some may be more suitable and beneficial for a lab’s life support system than others, but they all trap large particles of waste, uneaten food and other detritus that can decompose and negatively impact water quality. Some examples of mechanical filtration include:

Filter Socks: This type of filter usually has a draw string, fabric strap, rigid plastic collar or other means of helping it remain in place as water passes through it. It is typically available in different porosities ranging from 10 microns to 200 microns.

Advantages: It is easy to monitor, most are easy to clean, and inexpensive.

Disadvantages: Socks with rigid plastic collars are difficult to clean properly.

Filter Floss: This type of filter often comes in a larger roll of material that labs can cut to size for their system. It is available as coarse, fine, or a combination where the coarse layer is bonded to a fine layer

Advantages: Fairly inexpensive, easy to work with, traps detritus over a wider area of the filter.

Disadvantages: After multiple cleanings, the coarse floss begins to break down, is less effective at removing waste and needs to be discarded.

Canister Filters: Canister filters typically have pleated sleeves inside a plastic vessel that water is forced through by pressure. The sleeves are available in a few different porosities, depending on the type of life support system.

Advantages: They can do a very effective job removing solids from the system.

Disadvantages: The pleated sleeves are difficult to clean properly, expensive to replace, and are impossible to monitor properly without opening the filter vessel. Good canister filters typically have a pressure gauge on the lid to inform when the sleeve needs to be cleaned but they become less reliable over time. Worst of all, canister filters are often easily overlooked for routine maintenance.

Sand Filters: Sand filters operate by forcing water under pressure through various grades of gravel and sand, which trap waste. Typically, water is pumped through the finest layer at the top of the filter and the ever-larger grades of sand and gravel support the upper layer(s.) Sand filters usually also have a pressure gauge on the lid, to help monitor when the filter needs maintenance via backwashing, which reverses the flow of water in the vessel and the trapped waste is flushed out of the filter and system.

Advantages: When set up and maintained properly, sand filters can do a very effective job of mechanical filtration.

Disadvantages: This type of mechanical filtration is more expensive, has a large footprint, requires an oversized pump to work properly, and over time, the filtration media become channelized by debris and bacteria and needs to be replaced.

Sponge Filters: A very simple, old-school method of mechanical filtration. An airstone is suspended inside a perforated plastic tube in the middle of a foam cylinder. As the air bubbles rise, they induce a current, drawing detritus into the foam cylinder. They are available in many different sizes and are best for small, simple systems, as the foam can also act as a substrate for nitrifying bacteria.

Advantages: Very inexpensive, easy to use, easy to clean and effective when maintained properly. Great for small, temporary systems, such as quarantine tanks. Easy to keep in a designated biofarm for on-demand biological and mechanical filtration.

Disadvantages: Not good for removing finer particles from the water.

If you have questions about mechanical filtration, such as which type of mechanical filtration is recommended for your research life support system or how to modify the filtration on an existing system, the aquatic animal health specialists in the Aquatic Animal Health Program can be a resource. Reach out to the AAHP’s Aquatic Husbandry Lab Manager.


Chemical Filtration

Chemical filtration on aquatic life support systems is accomplished in many different ways and which types of filtration are best for your research system largely depends on the specifics of your research project. Some types of chemical filtration are good are removing dissolved organic compounds from a system, others are effective at adsorbing pollutants and medication from a system, others are highly effective in freshwater systems but much less so in marine systems, and another type is good for pathogen control. In professionally designed and constructed life support systems, chemical filtration usually occurs after mechanical filtration and before the designated location for biological filtration.

Here are some of the most common types of chemical filtration in aquatic life support systems:

Protein Skimmers: Also called foam fractionators, protein skimmers remove dissolved organic compounds via the process of adsorption and are used almost exclusively in marine systems. Animal waste and other types of impurities in the water, as well as medication and other compounds are adsorbed to the surface of microbubbles in the fractionation chamber. If this life support component is tuned properly, the bubbles rise to the top of the chamber and form a dry bubble crown, which is then pushed into a collection cup.

Advantages: Very effective at pulling impurities out of system water, DIY skimmers can work as well as commercially available skimmers at a much lower cost. Most are easy to clean and tune properly.

Disadvantages: Can also pull desirable compounds such as medication, small foods and supplements for corals and other invertebrates out of solution. Can remove water from a closed system if not tuned properly. Many commercially available skimmers are difficult to clean properly, which affects their performance.

UV Sterilizers: UV sterilizers use ultraviolet light in specific wavelengths to irradiate and disrupt the genetic material of pathogens, algae, and other undesirable organisms as the water passes through the sterilizer vessel. When properly installed, they will be plumbed into a system with multiple valves so that the contact time of the water in the vessel can be controlled.

Advantages: Effective at pathogen control in a life support system, also helps control nuisance algae.

Disadvantages: UV lamps should be replaced every six months, need to be unplugged during system maintenance or can overheat and ruin the vessel, UV lamps are not inexpensive.

Activated Carbon: This type of chemical filtration removes impurities from system water via the process of adsorption. Each granule has an extraordinary amount of surface area for its size and it is commonly used to remove medication, discoloration, and other substances from the water.

Advantages: Very easy and inexpensive to use, can be placed in a mesh bag in an area with high water circulation on a system and will be very effective, can be safely discarded when its adsorptive properties are spent.

Disadvantages: Will remove medication, additives, fertilizers and other beneficial additives from system water unless removed beforehand, just as other types of chemical filtration can.

Specialized Chemical Filtration: There are many different types of specialized chemical filtration available for aquatic life support systems. Many are formulated to target and remove specific compounds from system water. Examples include granular ferrous oxide to remove phosphates, zeolite for unionized ammonia control in freshwater systems, and others.

If you have questions about chemical filtration and which type(s) might be best for your lab’s aquatic research system, the aquatic animal health specialists in the Aquatic Animal Health Program are a very good resource. Contact the AAHP Aquatic Husbandry Lab Manager for more information.



There are many different aspects to consider when implementing aquatic research animal quarantine protocols in a lab. In an aquatic research lab, quarantine means a wide range of measures implemented to prevent the introduction of pathogens into a lab and/or aquatic research system, containment to prevent the transfer of pathogenic organisms within a lab from one animal holding system to another, and the mindset of lab personnel so that they don’t inadvertently introduce pathogens from a quarantine system to a research system. Some of the most practical quarantine protocols include:

Finding Animals from Reliable Sources: One of the most important aspects of quarantine is sourcing animals from purveyors that have their own stringent quarantine protocols. While this adds time and often also adds additional costs, it can be a good investment, as reliable sources of aquatic research animals have a vested interest in making sure that their animals are routinely screened for internal and external pathogens capable of affecting research data.

  • Please also be mindful that when working with aquatic research animals that are not collected from Oregon waters, all effluent from quarantine and other aquatic research system must be treated with a disinfectant for at least 20 minutes. The effluent must then neutralized with sodium thiosulfate or another neutralizing compound before it can be released into floor trenches that lead to Yaquina Bay. This is to prevent non-native animals and microorganisms from being released into Oregon waters.
  • If the effluent is directed toward a drain connected to the municipal sewer system, no disinfection is required but be aware that there are restrictions on how much saltwater can be added to the sewer system in a given period of time.

Aquatic Quarantine Systems: Under ideal conditions, an aquatic quarantine system should be a purpose-built aquatic life support system located in an area separate from the main research animals and systems or separated by distance, curtains, or other physical barriers. It should have most or all of the features of an aquatic research system, have a fully cycled and functioning biofilter, be easily accessible for routine system checks and maintenance, and have its own daily log sheets and water quality records.

  • Please note that quarantine protocols also apply to newly arrived animals in open flowthrough systems. If a lab is working with research animals collected in Oregon waters, they also need to be quarantined in a designated quarantine system for at least 30 days before being added to other systems in the lab.

Length of Quarantine: The Associate Attending Veterinarian for Aquatics may prescribe a specific quarantine period for recent additions to a quarantine system and/or lab for various reasons. However, researchers and their teams can expect a quarantine period of no less than 30 days each time new animals arrive to the lab. Any animals added to the quarantine system during this period will result in complete reset of the quarantine period.

Close Observation of Animals in Quarantine: Given the many different stressors aquatic animals endure prior to and after arrival in a research lab, the likelihood of a disease or pathogen outbreak during quarantine is high. This is why it is very important to conduct multiple animal checks each day looking for moribund animals, mortalities, and other indications of a developing or established health problem. Speak with the Associate Attending Veterinarian for Aquatics on how they would prefer you to handle moribund animals and mortalities.

Common Signs of Health Problems for Aquatic Animals in Quarantine: Symptoms of pathogen outbreaks present in quarantine animals in many different ways but some of the more common signs to look for include rapid or irregular respiration rates, breathing at the water surface, loss of equilibrium, clamped fins, atypical position in the water column, anorexia, excessive mucus production, a “dusted” appearance on body and fins, ragged fin tissue, and many others. If you are concerned about the condition of one or more research animals in quarantine, alert the AAHP Aquatic Husbandry Lab Manager as soon as possible.

Stress Reduction in Quarantine: The first week in quarantine is usually the most stressful for aquatic research animals but researchers and students can implement a few simple but effective measures to reduce stress. These measures include:

  • Covers on the top and sides of tanks to reduce the amount of light and the startling motion of researchers working in the lab.
  • If the animals are placed in a closed, recirculating system, making sure that the biological filtration on the system is fully cycled and able to provide healthy water chemistry parameters from the beginning of the quarantine period.
  • Reduced photoperiods when circumstances allow to provide a dark, quiet place for animals to adjust to new surroundings.
  • Simple kinds of habitat and/or “hides,” such as fake plants, pieces of PVC pipe and fittings, and other easy-to-clean and -sanitize items to provide cover.
  • Restricting access. Although it’s natural for lab personnel to be curious about new animals in quarantine, access to the system and animals should be limited to no more than 1 or 2 members of the team. This is also an important biosecurity consideration.
  • Adding a water conditioner and artificial slime coat such as PolyAqua, Stresscoat, or similar product. This provides an extra layer of protection for animals in quarantine and may alleviate osmoregulatory stress.

Quarantine Systems and Medical Treatments: One of the more important and practical aspects of holding animals in quarantine is that if/when a health problem occurs, the entire research animal collection is not at risk and the attending veterinarian and lab personnel have more treatment options available to them. These options might include different kinds of medication, water chemistry adjustments, enhanced husbandry protocols, and other measures that could disrupt the continuity of projects in the main research system(s.)

Dedicated Quarantine System Maintenance Tools: An aquatic quarantine system should have dedicated and clearly labeled maintenance tools to prevent them from being used on other systems and potentially introduce pathogens.

Feeding Animals in Quarantine: Aquatic animals are occasionally fasted before shipping to promote good water quality during transportation and may appear to be ready for food shortly after they arrive in quarantine, but it’s best to hold off feeding them for at least 24 hours after arrival. Feeding newly acclimated animals can actually be stressful for them. Feed new arrivals sparingly after the first 24 hours, gradually increasing over the following days. Slowly scaling up feeding also helps the biological filtration adjust to a higher bioload on the system.

Water Quality Testing and Documentation: Following up on the previous point, newly arrived quarantine animals will likely cause a modest increase in Total Ammonia Nitrogen (TAN) and nitrite in quarantine system water. The AAHP recommends water quality testing and documentation of test results on a daily basis for at least the first week and once a week thereafter to ensure the system water chemistry remains healthy for the animals.

Water Quality Acclimation to Destination System: If a research project involves the manipulation of water chemistry parameters in the main research system(s,) making small, incremental changes in water chemistry while the newly arrived animals are in quarantine allows them to become acclimated and facilitates the eventual transfer with reduced animals stress.

Critical Control Points: In addition to the curtains, designated system tools and other biosecurity measures previously mentioned, lab personnel should consider other critical control points to monitor and/or enhance in the lab to contain and reduce the risk of cross contamination. Common control points to consider include food prep areas, sanitation stations, water quality testing stations, the handles on freezers and refrigerators, and other areas where personnel and water from different systems are likely to occur and cross contaminate.

Signage: Ideally, a designated quarantine system in a lab should have signage indicating this, along with start and finish dates for the animals under quarantine. This helps remind lab personnel about the restricted area, the importance of biosecurity in and around that area of the lab and promotes the top-of-mind awareness critically important for pathogen containment.

If you have questions about designing or building a quarantine system for your lab, ways to improve the biosecurity around an existing quarantine system, or any other aspect of quarantine and biosecurity, reach out to the Aquatic Animal Health Program’s animal health specialists.