A new approach for measuring the impact of fish farm waste on rocky marine bottoms

Marine aquaculture is a growing industry vital for global food security. However, its growth involves the release of significant amounts of fish feces and uneaten feed into the marine environment. This waste can generate organic enrichment on the seabed, altering biodiversity and ecosystem functions.

Traditionally, monitoring these impacts has focused on soft, easily sampled sediments. However, many modern fish farms are located on rocky or mixed bottoms, where conventional sampling methods with grabs are ineffective, hindering proper environmental management.

A recent study, published in Marine Pollution Bulletin, presents an innovative dual approach that combines microbial environmental DNA (eDNA) analysis and structured visual assessment to quantify the influence of this waste on hard-bottom habitats, opening new doors for more effective monitoring and more sustainable aquaculture.

The challenge of monitoring on hard bottoms

Seabeds act as particle sinks and reflect recent environmental stressors. While soft sediments cover approximately 85% of the world’s coastlines, the remaining 15% corresponds to hard or mixed substrates, prevalent in areas with steep coastlines such as fjords, which in turn are ideal for aquaculture. In Norway, the world’s largest salmon producer, a significant proportion of fish farms are located on these challenging bottoms.

The Norwegian standard method (NS 9410:2016) for benthic monitoring (MOM system) depends on the successful collection of sediment samples. When grabs fail on hard bottoms (between 30-39% of cases in some Norwegian production areas), the assessment often defaults to a classification of “good” or “very good condition,” even if waste discharge is high or moderate. This situation highlights a significant limitation for effective environmental management.

A new methodology: combining visual and molecular approaches

To address this issue, researchers from the Institute of Marine Research, the Cawthron Institute, and the Norwegian University of Life Sciences developed and tested an alternative and quantitative approach at seven salmon farms in Norway: six on hard or mixed bottoms and one on a soft bottom for reference. According to the study, the methodology integrates two main components:

• Substrate-Independent Benthic Sampling (SIBS) and microbial eDNA analysis: Scientists used a device called the Substrate-Independent Benthic Sampler (SIBS) to collect the surface layer of organic material and fine sediment that covers any type of seabed. This material contains the benthic microbial assemblage. From these samples, they extracted DNA and analyzed the V3-V4 region of the 16S rRNA gene, a common genetic marker for studying bacterial communities. With this information, they calculated a bacterial Metabarcoding Biotic Index (bMBI). The bMBI is based on the proportion of bacterial sequences that match a database of 440 bacterial bioindicators, whose abundance changes according to the organic enrichment gradient. The index ranges from 1 (pristine conditions) to 7 (excessively enriched and anoxic).
• Structured quantitative visual assessment: Simultaneously, they took images and videos of the seabed at each sampling station using a GoPro camera mounted on the SIBS. These images were analyzed to estimate the coverage of visual indicators of organic enrichment, such as:
  • Anaerobic white bacteria.
  • Aggregations of opportunistic polychaetes (OPAs).
  • Salmon feces and uneaten feed.
  • Accumulated organic matter. Two indices were created from this data: Visual Organic Loading (VOL) and Visual Ecological Effects (VEE).

Key findings of the study

The study showed that the traditional approach, when applied to hard substrates, is essentially qualitative and can lead to inappropriate conclusions about the environmental status. The new dual methodology offered much more robust and quantitative results:

• SIBS sampling efficacy: The SIBS device proved effective for collecting superficial flocculent material from hard and mixed bottoms, allowing for microbial eDNA analysis. The quality of the eDNA sample (measured by ASV and bioindicator richness) was not significantly affected by the proximity of the sampling head to the bottom or the visual content of the sample, although high particle resuspension did tend to decrease ASV richness.
• Sensitivity of indicators:
  • Visual indicators (VOL and VEE) were useful for quantifying and classifying effects directly beneath fish farm cages. However, their utility decreased considerably with greater distance, being rarely evident beyond 100-250 meters from the farms.
  • The bMBI index derived from microbial eDNA proved to be highly quantitative and sensitive both in the immediate vicinity of the farms and in more distant areas. This index could detect the influence of the farms at distances of 500 and even 1000-2300 meters in some cases, showing a wider dispersion of waste than could be inferred from visual methods alone.
• Validation of the bMBI index: The bMBI values obtained from SIBS samples showed a strong correlation (R² = 0.87 – 0.90) with established and widely accepted macrofaunal indices (AMBI and NSI) derived from grab samples in soft sediments, which validates its reliability as an indicator of organic enrichment.
• Variability between farms: Significant differences were observed in impact levels (according to VOL, VEE, and bMBI) among the different farms studied, even directly beneath the cages. This suggests that factors such as site hydrodynamics, and the level and stage of fish production influence the magnitude and dispersion of waste.

Implications for aquaculture

This new approach has significant implications for the environmental management of aquaculture:

• Improved monitoring on hard bottoms: It provides a solid basis for developing a quantitative monitoring system in hard-bottom habitats, allowing for a more accurate assessment of the impact of fish farms. This is crucial to prevent farms with unacceptable enrichment levels from going unnoticed, as can happen with current methods.
• Informed decision-making: Quantitative data on the extent and magnitude of organic enrichment can help producers and regulators make more informed decisions about farm location, ecosystem carrying capacity, and necessary mitigation measures.
• Understanding waste dispersion: The use of bMBI allows mapping the actual “footprint” of farm waste regardless of substrate type, which can improve particle dispersion models and the understanding of spatial variability of impacts.
• Early detection and proactive management: The combination of VOL (potential effects from recent organic matter accumulation) and VEE (visible ecological effects) directly under the cages, along with bMBI to assess wider dispersion, offers a powerful tool. For example, a very high VOL could indicate feed spills and trigger a management response. Elevated levels of VEE or bMBI far from the cages could signal compliance issues. The study also points to the need to standardize sampling methods and genetic analysis, simplify tools for use by non-scientists, and establish a framework for adopting new technologies as they emerge.

Conclusion

The research presents a significant advancement in how to quantify and monitor the impact of fish farm waste on hard-bottom habitats. The combination of structured visual assessment with microbial eDNA analysis using the bMBI index offers a tool that is much more sensitive, quantitative, and spatially comprehensive than traditional methods. The new dual approach not only allows for a better assessment of the environmental status under the farms but also helps delineate the true extent of the waste’s influence.

Adopting and standardizing these new techniques could lead to more effective environmental management and promote the long-term sustainability of the aquaculture industry, especially in complex and sensitive coastal ecosystems. Furthermore, the eDNA methodology with SIBS has broader potential for ecological research and monitoring of other stressors in various marine environments.

The Norwegian Research Council funded the study under the projects: ‘SUSTAINable AQUAculture in the North: identifying thresholds, indicators and tools for future growth,’ and AQUAed: ‘On-site monitoring of aquaculture impact on the environment by open-source nanopore eDNA analyses.’ The project also received from the Institute of Marine Research.

Nigel Keeley
Institute of Marine Research
PO Box 6606, Langnes, 9296 Tromsø, Norway.
Email: [email protected]

Reference (open access)
Keeley, N., Dunlop, K., Laroche, O., Hansen, P. K., Angell, I. L., & Rudi, K. (2025). An approach for quantifying the influence of fish farm waste on hard-bottom habitats. Marine Pollution Bulletin, 217, 118039. https://doi.org/10.1016/j.marpolbul.2025.118039