Disease and Biosecurity in Recirculating Systems

How pathogens spread and persist in a recirculating loop, how stock, water and people are screened, how systems are disinfected between batches, and why treatments threaten the biofilter.

Why recirculation changes disease risk

The FAO guide to recirculation aquaculture notes that a recirculating aquaculture system (RAS) uses little water, usually from a borehole, drainage system or spring, so far fewer pathogens arrive from outside than on farms fed by rivers, lakes or the sea; many systems run without disease problems at all. The flip side is that a disease in one tank of a shared loop will almost certainly spread to every other tank. SRAC Publication 452 adds that once a disease is introduced into a recirculating system it is generally hard to control and treatment may disrupt the biofilter. General farm biosecurity and disinfectant chemistry have their own guides; this one covers what is specific to the loop.

How pathogens persist in the loop

SRAC Publication 452 warns that disease spreads quickly when equipment moves freely between tanks or when all the water is mixed in a common sump, particle filter or biofilter. It lists Ich (Ichthyophthirius) and Trichodina among protozoa and columnaris, Aeromonas, Streptococcus and Mycobacterium among bacteria as particularly troublesome in recirculating systems. A 2026 review in Frontiers in Microbiology (Bartkova et al.) describes biofilms in tanks, pipelines and supply systems as reservoirs for Aeromonas, Flavobacterium and Vibrio that sustain recurring infections, notes that suspended organic matter may shield viruses and prolong their persistence, and names internal pathogen build-up through biofilms in biofilters and distribution lines as a RAS-specific risk.

Air is a second route. At two commercial Atlantic salmon (Salmo salar) smolt RAS in the Faroe Islands, Krishna et al. (2025, Scientific Reports) detected several salmon viruses, including infectious pancreatic necrosis virus (IPNV), and Flavobacterium psychrophilum in aerosol samples, with the highest detection rates in the biofilter room. After an IPNV outbreak, viable virus was recovered from aerosols, which the authors describe as the first field evidence of viable airborne IPNV from a RAS and a sign that airborne transmission is possible.

Keeping pathogens out

Water: FAO recommends a disease-free source such as a borehole or well, or sterilising intake water, typically with a sand filter followed by UV or ozone.
Stock: FAO advises stocking eggs or fish from certified disease-free strains, and bringing in eggs rather than fish where possible, since eggs can be disinfected. Pathogens carried inside the egg, such as those causing infectious pancreatic necrosis (IPN), bacterial kidney disease (BKD) and possibly herpesviruses, cannot be removed by egg disinfection.
Quarantine: SRAC Publication 452 advises checking new fish for parasites and diseases, with a few fish examined by a certified fish diagnostician, quarantining them where needed, and never adding hauling water to the system.
Equipment: SRAC advises separate nets and baskets for each tank and sterilising equipment, for example with a chlorine dip, before moving it between tanks. The FAO prevention scheme uses a 1.5 % iodine solution dip or spray left for 20 minutes before rinsing.
People: FAO lists a change of clothing and footwear for staff, hand washing or disinfection, a 2 % iodine footbath for visitors and a no-touch policy inside the facility.

Separating units and disinfecting between batches

FAO recommends running the hatchery, fry unit, grow-out unit and any broodstock as separate closed systems, so a disease can be stamped out in one without the others. Under the all-in all-out principle each unit is emptied completely and disinfected before restocking, which FAO notes is easy for eggs and small fish but hard for large grow-out volumes. Its example scheme disinfects a whole system by filling it with water and raising the pH to 11–12 with sodium hydroxide, roughly 1 kg per m3 of water depending on buffer capacity. Viral diseases such as IPN and viral haemorrhagic septicaemia (VHS) cannot be treated; FAO states that the only way out is to empty the farm, disinfect the system and start again.

Disinfecting a biofilter without losing it is not well understood. In a DTU Aqua study (Qi et al., 2025, Biofilm), biofilm carriers from a freshwater pilot RAS were exposed for 1 hour to peracetic acid at 0–16 mg/L. Nitrite oxidation was the most sensitive process, with activity halved at 1.27 mg/L, followed by ammonia oxidation at 1.59 mg/L. Carriers from a commercial RAS with a history of peracetic acid use were much less sensitive, losing 39 % of nitrite oxidation and 51 % of ammonia oxidation only at 16 mg/L. SRAC Publication 452 states that a new biofilter needs at least one month to become active, and one destroyed by chemicals takes 3–4 weeks to re-activate.

Chemical treatments versus the biofilter

FAO stresses that medication added to a recirculating system reaches the fish and the biofilter alike, and that exact doses cannot be prescribed because the effect depends on water hardness, organic matter, temperature and flow. Concentrations should be raised cautiously from one treatment to the next, and a local veterinarian or fish pathologist must prescribe the medication. SRAC Publication 452 reports that biofilter bacteria are inhibited to some degree by formalin, copper sulfate, potassium permanganate and certain antibiotics, and that even sudden changes in salt concentration lower biofilter efficiency. FAO gives the following figures, which it describes as very approximate.

Salt (sodium chloride), freshwater: free-swimming stages of Ich are killed at 10 ‰ salinity, and newer results suggest bottom stages at 15 ‰; most freshwater fish tolerate about 8 ‰ for several weeks; 3–5 ‰ prevents fungal infection in hatcheries.
Formalin: 15 mg/L for 4–6 hours has worked against Ichthyobodo necator, Trichodina, Gyrodactylus, sessile ciliates and Ich. The biofilter degrades it at about 8 mg per hour per m2 of biofilter surface at 15 °C, but it can lower nitrification rates.
Hydrogen peroxide: 8–15 mg/L for 4–6 hours has shown promise in experiments; biofilter performance can be inhibited for at least 24 hours and returns to normal within a few days.
Copper sulfate and chloramine-T: not recommended in RAS by FAO because the biofilter is likely to suffer severely.
Antibiotics in medicated feed: the concentration reaching the water is low, so the effect on the biofilter is small, but water quality should be watched for changes.

Exposure of the biofilter can be reduced. FAO describes treating a single tank with the inlet closed and aeration running, then reopening the inlet so the chemical is diluted by the rest of the loop, or pumping treated water to a separate compartment instead of recirculating it. SRAC describes isolating the biofilter while tanks are treated and flushed, with the risk that the biofilter reintroduces the pathogen afterwards, and advises being ready to exchange water, watching dissolved oxygen closely and adjusting feeding, since fish usually eat less after treatment.