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Active Microbiome Management

Updated: Apr 26, 2022

Tom Scrope, Nova Q Ltd.

How Recirculating Aquaculture System (RAS) managers can get the most out of their biofilter microbiome.

Active Microbiome Management (regularly adding functional bacteria) should be part of every RAS farmer's toolkit.

Why RAS?

Recirculating Aquaculture Systems (RAS) can help make aquaculture more sustainable – whether in the much-hyped full-grow out systems or for hatchery, smolt, and now post-smolt production of Atlantic Salmon.

Not only do RAS have a low direct environmental impact (especially if renewable power sources are available), but they provide optimal growing conditions. They can reduce mortality and improve feed conversion ratios, reducing the overall emissions per kilo produced. Improvements that can make RAS more efficient and reliable will play a key role in making the aquaculture industry more environmentally sustainable.

The Challenge

RAS aquaculture, though, is not just about farming fish, but the bacteria of the biofilter too. RAS managers recognize that bacteria are crucial to operating a RAS. But as long as adequate nitrification kicks in following “seeding”, most producers are inclined to leave the biofilter “well alone” for fear of disturbing the delicate balance.

While other aspects of RAS are being continuously improved – from genetics to system engineering – the functionality of the bacteria in RAS has not been optimized in the same way. To do things better, by definition, we need to do them differently.

This lack of innovation has led to problems currently facing RAS sites:

  • Inefficient nitrification, including nitrite spikes.

  • Slow and unpredictable restarts – particularly problematic for sites with short timescales before the introduction of fish to the system (e.g. research sites).

  • Hydrogen sulphide (H₂S) spikes caused by sulphate reducing bacteria being able to establish themselves in the system.

  • Off-flavour compounds (OFCs) in grow-out RAS reducing the value of stock and requiring expensive and inefficient “purging” to remove.

Advances in the last few years in sequencing technology (especially 16S rRNA sequencing) need to be combined with innovative tools to positively influence the microbiome and solve the problems identified above. Some of these tools will involve a more considered use of inputs (e.g. feed) that impact the microbiome.

Table. 1 Fast-growing potentially pathogenic r-strategists (“A”) outgrow many slow-growing, beneficial K-strategist species (“B”).
A vital part of the toolkit for any RAS farmer should be Active Microbiome Management

Regularly adding large quantities of functional bacteria removes their slow reproduction rates as a limiting factor. (It’s worth noting that developing the composition and stabilization of an appropriate consortium of functional bacteria is an area that has been at the core of the R&D work Nova Q and our partners have undertaken over the last 40 years. Simply introducing single-species products or poorly balanced consortia can lead to an unstable microbiome in the medium term). This approach allows the efficient nitrification of high quantities of ammonia – much higher than would ever be ordinarily produced in a RAS.

What is Active Microbiome Management?

Active Microbiome Management, an advanced form of bio-augmentation, involves directly influencing the biofilter microbiome through constant additions of beneficial bacteria. This approach is already common in wastewater treatment (WWT) to avoid the system becoming dominated by “undesirable” bacteria.

The critical insight here is that many beneficial species are slow to reproduce K-strategists (we refer to them as functional species). By contrast, potentially pathogenic r-strategists (opportunists) can multiply much faster (Table 1).

How does Active Microbiome Management work in RAS?

There are key challenges to harnessing the power of bacteria in RAS:

  • While the overall nutrient load in RAS is lower than in WWT, so is the hydraulic retention time – RAS bacteria don’t have much time to perform their functions (Fig. 2).

  • Disinfection systems in RAS loops, including ozone and UV, can damage the populations of beneficial bacteria in the biofilter.

  • RAS often require rapid restarts to meet stocking deadlines.

Figure 2. The quality of water coming out of the biofilter (Eeff) is dependent on the incoming water quality (Einf), the volume of bacteria (Xc ), the efficiency of the bacteria (Ks ), and the length of time the bacteria have to perform their functions (fh ). In RAS fh is relatively low, so Xc and Ks need to be increased to make up for this.

The way around these is to deploy large quantities of the bacteria and optimize the bacteria to system conditions so that they are functional (e.g. nitrifying) straight away.

Although good results can be achieved by experienced operators simply applying stabilized bacteria from a bottle, much more powerful impacts are possible using a bio-reactor grow tank to multiply and activate the bacteria before applying them to the system.

Latest bio-reactor grow tank technology

The two critical necessities for a successful bio-reactor are heat and aeration. It is possible to create a “grow tank” from a spare container, a heater, and an air pump (and some of our customers follow this approach). However, for complete control and ease of application, an automated and purpose-built bio-reactor is a much better solution.

Our Canadian partners have developed the BrewTus range of bio-reactors for this very purpose, following a long process of R&D over the last five years (Fig. 3). BrewTus units are currently used in a wide range of sectors, from agriculture to lake remediation. The technology is being adapted by Nova Q for RAS, with the installation of the first units expected in autumn 2021.

Figure 3. BrewTus bio-reactors. With an advanced control panel, and in-built heating and aeration, these units offer the ability to regularly produce large quantities of functional bacteria for easy Active Microbiome Management.


Active Microbiome Management is a proven approach:

Enhanced nitrification

The SALMSON project at Ireland’s Marine Institute utilizes Active Microbiome Management, with impressive nitrification results (Fig. 4).

Rapid restart

A parr hatchery owned by one of the global salmon producers was under pressure to restart the system in a matter of days (rather than the usual weeks) before the stocking of the system. Bacteria were added directly from a prepared bioreactor to the MBBR on day 1, with fish introduced from day 3 and feed on day 5 (Fig. 5).

  • Nitrification started immediately - nitrate production occurred from the moment feed was added

  • Stable nitrification was maintained even as feed levels increased

  • Nitrite peak at a similar level and quicker recovery than historically normal.

Figure 4. ENHANCED NITRIFICATION: Optimized nitrification throughout the study. Ammonia and nitrite never move above 0.2 ppm. Data courtesy of the Marine Institute. The SALMSON project is funded by BIM Knowledge Gateway – 17/KGS/009.

Off-flavour compound (OFC) control

Regularly “swamping” the systems with large numbers of beneficial bacteria denies opportunistic species - including sulphate-reducing bacteria (H₂S) and cyanobacteria (OFCs) - the chance to gain a “foothold”. (It’s worth noting that Active Microbiome Management does not supersede other forms of good RAS husbandry - e.g. regular cleaning avoids the creation of anoxic zones often responsible for H₂S spikes). There is even evidence that introducing Active Microbiome Management can break down high pre-existing OFC levels.

One study produced by a Nova Q partner showed that only two weeks of dosing with beneficial bacteria at the end of a production cycle reduced high levels of geosmin and MIB (Table 2). Geosmin reduction was comparable to a two-week depuration purge (4.8% weight loss). By contrast, fish with the Active Microbiome Management regime continued to be fed (2.3% weight gain).

Figure 5. RAPID START: The site was under pressure to restart the system in a matter of days following a deep clean of all the fish tanks and the moving bed bioreactor (MBBR).

Table 2. OFF-FLAVOUR COMPOUND (OFC) CONTROL: Geosmin reductions comparable to a purge achieved while still feeding the fish, by using Active Microbiome Management.

Nova Q is currently conducting trials with producer partners to assess the results of longer-term Active Microbiome Management on levels of off-flavour compounds in Atlantic salmon RAS - results expected in Autumn 2021.


Active Microbiome Management (regularly adding functional bacteria) will improve RAS water quality:

  • Enhanced nitrification, reducing the chances of ammonia or nitrite spikes (and accompanying mortalities).

  • Fast restarts, with rapid nitrification.

  • “Crowding out” undesirable species, reducing the risk of potentially lethal H₂S spikes or high OFC levels requiring expensive and inefficient “purging”.

  • Improve the ability to control the system, increasing predictability and allowing more efficient planning of production cycles.

Improving RAS efficiency and profitability will facilitate the expansion of this low-impact technology, driving sustainable aquaculture growth.


Original Publication

HatcheryFeed 0621 PR
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