Operations Manual for SITC Recirculating Aquaculture System (RAS)

This user-friendly SITC RAS operations manual was developed by HSWRI staff to make it easy to have a SITC aquaculture system in your classroom. Below you will find an overview of components within the RAS followed by guides for conditioning tanks, maintaining bacteria, water quality, daily responsibilities, and tips for troubleshooting. 

Tank System Conditioning

This guide will take teachers through step-by-step instructions on how to condition their tank system to be ready to receive white seabass.

What is biological filtration and why is it needed?

Biological filtration is the process by which fish waste gets converted into molecules that can be used by other organisms in an aquatic ecosystem. Because our SITC RAS has a high population density compared to conditions in nature, it is essential that the biological filtration system is equipped to handle the amount of fish waste produced. This process begins when the toxic ammonia in the fish’s waste is converted to nitrite by nitrifying bacteria. Other bacteria then convert the nitrite into nitrate, which is less toxic to fish than either nitrite or ammonia. In nature, nitrate is removed from the water column by both aquatic plants and chemosynthetic bacteria. In our SITC RAS, we remove nitrate from the system manually through regular water changes.

Requirements for Efficient Biological Filtration

Biological filters are typically used to control water levels of ammonia and nitrite, in aquaculture and fish and seafood holding systems. Three categories of factors affect biological filters: the biological community, the water chemistry, and the physical design.

Biological Community

Control and conversion of the potentially harmful ammonia that the fish excrete is accomplished by nitrifying bacteria that have become established in the biofilter.  A solution containing nitrifying bacteria can be added to the system to help establish a healthy population of these bacteria in a short period of time, 1-2 weeks. Many factors can inhibit these bacteria from achieving their maximum nitrification ability such as lighting, excessive organic material in the tank, oxygen and water chemistry. A balanced population of bacteria is essential to controlling the different forms of toxic ammonia in the tank.

Water Chemistry

• Ammonia and nitrite are only sources of nitrogen for the bacteria. Other nutrients including carbon, phosphorus, and trace elements are also essential. Carbon must be inorganic and is measured as carbonate alkalinity. Sodium bicarbonate (baking soda, not baking powder) is commonly used to add carbonate alkalinity. Water with more than 150 mg carbonate alkalinity/L (ppm) is normally adequate; lack of carbonate alkalinity (<100 ppm) will stop nitrification.

• The alkalinity also provides pH buffering. The optimal pH for nitrification is near 8.0. Values outside of 7.0-8.5 can be expected to reduce nitrification efficiency. Nitrosomonas, a nitrifying bacteria, produces acid (H+ ions) during its conversion of ammonia into nitrite which will lower pH; the pH must be monitored and adjusted.

• Nitrifying bacteria require adequate oxygen. Water exiting a biological filter should always contain at least 5 mg/l or ppm oxygen but preferably above 80% dissolved oxygen saturation (7.5 mg/l). The optimal temperature for nitrification is about 30°C (86°F); the nitrification rate will be cut in half for every decrease of 10°C (22°F). Thus, a filter working at 30°C (86°F) may remove the same amount of ammonia as one twice as large but operating at 20°C (69°F).  The temperature for the classroom systems should be kept around 18 oC (64.5oC) while fish are in the tank.  The Education Coordinator will provide chiller temperature setpoints for your system; prior to delivery, after delivery, and before release.  The temperature should not be adjusted by more than 1 oC per day.

Physical Design

• The role of a biological filter is to provide a home (attachment material) for the nitrifying bacteria.  More surface area allows for the development of larger bacterial populations as long as water exiting the fish tank comes in contact with all the material covered with nitrifying bacteria in the biofilter.

• Biological filtration results in the growth of bacterial biomass; filters with inadequate surface area block rapidly. A well designed biofilter should be virtually self-cleaning. The nature of the physical substrate can also affect start up time. Slippery surfaces are more difficult for the bacteria to colonize than rough ones.

• Water flow patterns are very important. An adequate flow is essential to assure that the pollution or food reaches the bacteria, which are immobile. They use the nutrients around them, so sufficient water movement is essential for growth and performance. All water should be physically filtered to remove solids before entering the biological filter.  Additionally, solids should be removed (siphoned) from the tank and the system as quickly as possible. Inadequate water flow, combined with solids accumulation, can cause unhealthy water quality. Anoxic zones may develop where there can be a synthesis of ammonia and nitrite even in the biofilter. Nitrite is produced not only as a byproduct of ammonia removal but also from the partial denitrification of nitrate.

To start a biological filter:

Add ~50 mL of Dr. Tim’s Nitrifying Bacteria.

Maintaining Bacteria When Fish are NOT Present

Nitrifying bacteria (Nitrosomonas, Nitrobacter, and others) grow on the filter media in the sump of the SITC tank system utilizing ammonia released by the fish, excess food, and feces in the system. When there are no fish in the tank, there is no source of food (ammonia and nitrite) for these bacteria, and they may go dormant or die. To re-establish or maintain the established bacterial population, ammonia will need to be added to the system.

Ammonium chloride is a source of ammonia to feed the nitrifying bacteria. However, before adding ammonium chloride to the system, the alkalinity level will need to be at or above 120 mg/L and closer to or above 150 mg/l. Use the alkalinity adjustment calculator provided to help determine the amount of sodium carbonate or bicarbonate (baking soda) to add to the system. Check the alkalinity the following day, and if it is not above 150 mg/L, then repeat the process. Once the alkalinity is above 150 mg/L, add 1 to 2 grams (about 1 tsp) of ammonium chloride to the seawater system. The ammonium chloride should be added to the sump where the media for your biological filtration is located. Nitrifying bacteria will increase in density to accommodate the ammonia dose. 

Establish a healthy biofilter requires oxygen as well as warm water temperatures and no UV light exposure (turn off UV light on the system). The optimal temperature for nitrification is 30°C (86°F). It will be best to turn off the chiller when no fish are in the tank and let the system operate at ambient conditions. Most likely, the water temperature will not reach 30°C, but it will be warmer than the normal operating temperature (18°C) when fish are in the tank. If possible, test the ammonia levels in the system the next day. The ammonia concentration (TAN) should be elevated the next day and then start to decline as the bacteria convert the ammonia. The rate of TAN decline will depend on the health of the biofilter. If after a week the TAN levels are still high, then the nitrifying bacteria are still getting established in the system. Once the bacteria have metabolized the ammonia and the TAN levels have dropped (<0.25 mg/L), add another dosage and repeat the process. Depending on the nitrifying bacterial load in the system, weekly dosages may be needed to maintain their healthy population levels.

Adding excess ammonium chloride should increase the nitrifying bacteria community over time, but doing so may potentially result in the die-off of excess bacteria after fish are re-introduced into the system. This may happen because the fish, feces, and food waste may not provide a similar level of ammonia for the bacterial population that has become established in the system. Not to worry as you’ll most likely not observe the decrease in the nitrifying bacteria population in the system. Although, keep in mind that as the nitrifying bacteria begin to flourish and fix inorganic carbon, the alkalinity and pH in the system will begin to drop. Begin checking alkalinity after the first week of dosing and add sodium carbonate as needed to adjust alkalinity and keep it above 150mg/L.

Water Quality Parameters and Measurement

When measuring the water quality parameters in your system, it is important to get accurate results to prevent the unnecessary addition of chemicals or water changes by you and your students. Please familiarize yourself with how your test kit works and make sure that the chemicals or test strips have not expired or have been handled improperly (e.g. accidentally getting drops of water into your test strip bottle). Below are the different parameters and the levels you and your students should strive to maintain.

Water Temperature: 17-19°C. However, we will provide target temperatures when you're getting ready to receive fish or release fish to avoid temperature shock and undue stress.

Salinity: 33-35 ppt to mimic ocean salinity.

Dissolved oxygen (DO): 90-100% saturation or 8-9 mg/L (temperature dependent). Excessive DO in the tank (supersaturation; >102%) for prolonged periods (days) can cause air bubbles in the eyes of white seabass. On the other hand, low levels of DO will also stress the fish and limit the ability of the nitrifying bacteria to convert potentially toxic compounds (ammonia and nitrite) to non-toxic forms.

Total Ammonia Nitrogen (TAN) and Unionized Ammonia: <1.0 mg/L TAN; <0.04mg/L NH3.  Most seawater test kits/strips mention that they are testing ammonia when in reality they are testing TAN. TAN is composed of ionized ammonia (NH4+) and unionized ammonia (NH3). The difference between these two forms is important to understand because unionized ammonia is 100 times more toxic to fish than ionized ammonia. Both seawater temperature and pH will affect which form of ammonia is predominant in the tank. Levels of NH3 should remain below 0.04 mg/L so as to reduce stress and damage to gills and other tissues in white seabass. To quantify the amount of NH3 in your system, please see the accompanying pdf on Ammonia in Aquatic Systems.

Nitrate: <15 mg/L. This is the end product of the nitrogen cycle, and for the most part, is considered harmless to fish. However, because your SITC tank is a closed system, nitrate (NO3-) will accumulate. As levels approach this threshold, a 10-15% exchange of seawater will help to reduce the level. After the water change, retest the following day, and if the level is still elevated, then exchange another 10-15%. Continue this process until nitrate levels are significantly lower.

Nitrite: < 0.2 mg/L.  It is important to note that this compound is also toxic to fish.

Alkalinity: 120-160 mg/L. This parameter is important because it prevents dramatic changes to the pH of the seawater in the system. Dramatic changes to the pH can be deleterious to the fish. Maintaining alkalinity is also very important to the health of your biological filtration. The alkalinity will continually decline as the nitrifying bacteria in the biological filtration use carbon. If alkalinity and pH dip below the acceptable level, the addition of sodium bicarbonate or carbonate will be needed (see equations for adjusting alkalinity).

pH: 7.8-8.2.  The pH of water in an aquatic system is another one of the most important water quality parameters because it influences a myriad of chemical, physical, and biological processes. For the SITC tank, the pH should be kept in the range of 7.8 to 8.2.

Tank Cleanliness: It is important to note that overfeeding and not removing excess food settled on the bottom of the tank will lead to increased ammonia levels. Be sure to observe the feeding behavior of the fish as they are not likely to eat during periods of stress or illness. If the fish are not eating, do not continue to feed them. Again, excess food in the tank is the major contributor to high ammonia concentrations. Tank cleanliness is of the utmost importance to maintaining a healthy biological filter and safe water quality parameters.

Daily Responsibilities When Fish are Present

Tank Cleanliness and Water Changes

• Check water temperature and water flow daily. Ideal water temperature will be given at the time of fish drop-off, dependent on ambient ocean temperatures, but usually, in the range of 17-19° C. Set the grey temperature control box to a +/- 1 degree C of drift. 

• Siphon the bottom of the tank to remove solid debris daily. Excess debris will cause unwanted bacterial growth leading to poor water quality such as ammonia in the system. Siphoning should be done slowly as to not startle the fish, this may lead to fish accidentally jumping out of the tank. 

• Siphon and replace approximately 10% of seawater from the fish tank weekly or as needed based on water quality

Fish Feeding and Behavior

• Use this daily log to record fish feeding and observations

• Weigh out the appropriate amount of pellets (recommended daily guideline is 3% of total tank biomass) and disperse a portion of the pellets to the seabass several times throughout the day so that by the end of the day all the pellets are fed to the fish.

• Feed only a few pellets at a time and do not feed more pellets until all previous pellets are eaten.

• Stop feeding when fish no longer attempt to eat the pellets dropping down the water column or off the bottom.

• If fish are eating all the pellets then provide more pellets until they stop eating.  Their feeding behavior will change daily and they’ll feed more aggressively on Mondays as they may have not been fed for several days.

• Watch fish carefully during feeding to identify any signs of health concerns early – e.g. lethargic fish; note general condition of the fish in the daily log.

Water Quality Chemistry Testing

• Record tank temperature.

• Measure critical water quality parameters weekly – i.e. pH, ammonia, nitrite, nitrate, alkalinity, and salinity. Suggested analytical devices are linked.

Record Keeping

• Record all results and observations on classroom worksheet and transfer to Google Drive worksheet.

Troubleshooting Guide

What do I do if a fish dies?

Don’t panic. Collect the fish from the tank, put it in a Ziploc bag, and put it in the freezer. Send the Aquaculture Education Coordinator an email about it and he/she will collect it the next time they visit the school. If it’s just one fish, there’s not much to worry about. If it ends up being two or three fish over a week or more over several weeks, contact the Aquaculture Education Coordinator immediately and he/she will help you further.

What should I do if my chiller stops working?

First, try to unplug it and then plug it back in as a way to reset it. If that doesn’t work, try checking your filter - sometimes a dirty filter sock will reduce the flow of water, and since the chiller will only work when there is water flowing through it, a clogged sock will cause it to shut down. Another option is to unplug the chiller from its current location and plug it into a different outlet.  If the chiller works after this approach, then there is most likely a low flow to the chiller due to a dirty filter.  The filter needs to be cleaned and the chiller plugged back into its original location.  Otherwise, if the chiller continues to operate under low flow conditions it could cause expensive or irreparable damage to the chiller.  If that doesn’t work, let the Aquaculture Education Coordinator know and they will help you further.