The Role of Biological Treatment in RAS

There are several essential processes in a Recirculating Aquaculture System (RAS): solids removal, biological treatment, oxygen injection, CO₂ removal, and sterilisation. Among these, biological treatment stands out as the most critical. Without a well-functioning biofilter, a RAS will never succeed, no matter how effective the other components may be.

In RAS, we are effectively farming two types of organisms: fish and bacteria. Neither is more important than the other, and both require optimum conditions. While many system designs aim to meet these needs, they often fall short, particularly when it comes to supporting beneficial bacterial communities.

Types of Biofilters Used in RAS

Fixed-bed biofilters are submerged systems filled with packing material or bio carriers. Water flows either horizontally or vertically through these filters, where nitrification occurs alongside the entrapment of organic solids such as fish faeces and uneaten feed. Since the bio carriers are stationary, they support the build-up of solids, aiding mechanical filtration but potentially compromising biological stability.

Trickling filters utilise a fixed media bed over which water trickles downward. While anaerobic zones are rare, excessive biofilm can accumulate and become problematic. These filters are sometimes paired with submerged fixed-bed filters.

Moving Bed Bioreactors (MBBRs), on the other hand, keep bio carriers in motion using aeration. This movement promotes efficient substrate transfer into the biofilm and maintains high oxygen levels, supporting a more effective nitrification process.

The Early Days and Evolving Needs

When RAS technology emerged in the early 1980s, fixed-bed and trickling filters were the default choice, largely borrowed from municipal wastewater treatment. However, the priorities in aquaculture are distinct: while wastewater treatment focuses on removing organic matter (BOD), aquaculture must target ammonia and nitrite to ensure fish safety and wellbeing.

This distinction means prioritising nitrifying bacteria, which convert toxic ammonia into the less harmful nitrate. Yet these bacteria reproduce much more slowly than heterotrophic bacteria, which consume organic matter. If a system favours the latter by accumulating sludge, nitrifiers are quickly outcompeted. This is precisely the risk in fixed-bed biofilters, which unintentionally foster the growth of heterotrophs at the expense of nitrifiers.

Challenges with Fixed-Bed Biofilters

Originally, combining nitrification, denitrification, and solids entrapment in one unit seemed efficient. However, fixed-bed filters trap fine solids left behind by mechanical filtration. As this sludge builds up, filters require frequent backwashing. In the intervals between cleanings, the accumulating waste can clog filter media, create low-oxygen zones, and lead to undesirable processes such as denitrification.

A key limitation is that fixed-bed filters do not remove sludge from the system but merely relocate it. Water from fish tanks continues circulating through these increasingly clogged filters, making it difficult to monitor or control the biological activity within them.

Some improvements have been made, such as limited aeration to prevent anaerobic conditions without disturbing trapped solids. Adjustments to design, like reducing water depth, have made backwashing easier. Nonetheless, fixed-bed filters require careful and continual management to avoid microbial imbalances and performance issues.

Biological Risks in Poorly Managed Systems

In environments with accumulated organic matter and low oxygen levels, heterotrophic bacteria may initiate a process known as dissimilation, converting harmless nitrate back into toxic nitrite and ammonia. This can occur in oxygen concentrations as high as 2–4 mg/L, levels easily found in sludge pockets within filters that aren’t regularly backwashed.

Other processes, such as fermentation, may produce hydrogen, CO₂, alcohols, acetic acid, and methane—substances that, while not always lethal, can inhibit fish growth. In saltwater systems, sulphate reduction can produce hydrogen sulphide, a highly toxic compound. This process can also occur in freshwater systems, where sulphur-containing amino acids in fish feed contribute to sulphate build-up.

These risks are not merely theoretical. Fish kills linked to hydrogen sulphide have been reported in fixed-bed systems, particularly in saltwater RAS, although poor sludge management outside the biofilter can also contribute to such events.

Declining Performance Over Time

Another issue is that heterotrophic bacteria can gradually dominate the surface area within fixed-bed biofilters. Even immediately after backwashing, their faster growth rate means they quickly recolonise the media, reducing nitrification capacity. This microbial shift can lead to declining performance year over year.

Additionally, sludge-laden filters are prime environments for bacteria that produce geosmins and MIBs, compounds that cause off-flavours in fish. This results in more frequent and expensive purging. In contrast, MBBR-based systems such as Skagen Salmon have operated for two years without requiring purging.

Why MBBRs Have Gained Ground

Over the past decade, MBBRs have become the dominant biofilter choice in RAS, primarily due to their safety and consistency. One of their key advantages is Biofilm Control (BFC). Thanks to constant movement and aeration, biofilm thickness is kept in check, ensuring efficient transfer of oxygen and waste into and out of the biofilm.

Because MBBRs do not trap fine particulate matter, some solids remain in the water, which can lead to a cloudy appearance. Initially, this led some to believe MBBRs were inferior to fixed-bed filters. Today, however, this issue is easily managed through sidestream filtration methods such as ozone skimming, now standard in most MBBR-based systems. The result is water clarity equivalent to that of fixed-bed systems, without the associated risks.

Some systems even incorporate fixed-bed filters on a sidestream basis, using them strictly for solids entrapment and keeping biological activity low. These can be taken offline as needed, offering flexibility without compromising safety.

Separation of Processes for Better Control

Separating biological treatment from solids removal makes practical sense. When each process operates independently, it’s easier to quantify, monitor, and optimise performance. In contrast, the interactions within a fixed-bed filter make it difficult to determine which biological processes are occurring, especially when conditions vary across the filter bed.

In Conclusion

Fixed-bed biofilters can work well but carry inherent risks if not carefully managed. Accumulated sludge, microbial shifts, and potential for toxic by-product formation mean these systems require close oversight. While poorly designed MBBRs can also perform poorly, a properly configured and aerated MBBR offers a safer, more stable solution for modern RAS.

As with any technology, success depends on thoughtful design, thorough understanding, and proactive management.