New Research Suggests We Don’t Know—And Should Be Worried
A new study from Chile’s salmon industry offers a troubling snapshot of what may already be occurring beneath Tasmania’s fish farms – the widespread use of an antibiotic is fundamentally altering the marine ecosystem on the ocean floor.
The research, published in October 2025 in the journal Antibiotics, examined the health of ocean sediments beneath salmon farms in southern Chile.
Scientists found that when fish farms treated their stock with florfenicol—an antibiotic used routinely to prevent disease—the bacterial communities in the seabed underwent dramatic changes.
Healthy, diverse microbial populations collapsed. Resistant, stress-tolerant bacteria proliferated. The ecosystem shifted toward conditions more like a dead zone.
The problem – Tasmania’s salmon farms use similar, if not identical practices. And the poignant question is anyone checking if the same thing is happening here.
The Chilean Warning
Chile is the world’s second-largest salmon producer. It uses florfenicol intensively—so much so that the antibiotic now accounts for 97 per cent of all antibiotics given to farmed salmon in Chile’s marine operations. In 2020 alone, the country imported over 493 tonnes of florfenicol destined for fish farms.
When researchers sampled sediments beneath two treated Chilean farms and compared them to an untreated control site, the differences were unmistakable.
The treated sites had lost microbial diversity. The bacterial communities had shifted dramatically toward species adapted to degraded, oxygen-poor conditions. The seabed ecosystem was, in short, changing in ways that could compromise its ability to function.
“Florfenicol treatment significantly altered the microbial community structure, leading to a reduction in taxonomic diversity,” the researchers reported.
What matters is that Chile and Tasmania operate in similar southern ocean environments.
Both now rely on the same antibiotic. Both face the same regulatory approval structure. If this is what florfenicol does in Chile, then it is almost certainly going to happen in Tasmania.
The seabed beneath salmon farms is not empty ocean floor—it is a living ecosystem that filters water, cycles nutrients, breaks down waste and maintains the basic chemistry of the surrounding waters. When that ecosystem changes, everything downstream changes with it.
The Chilean research shows that approved doses of florfenicol—doses considered safe by regulators—trigger these changes. This is not about overdosing or misuse. This is about the inherent ecological cost of using this antibiotic, even when used exactly as directed.
There is another concern – florfenicol does not simply vanish.
Between 45 and 60 per cent of the antibiotic administered to fish is not absorbed and instead enters the marine environment through fish waste. It persists in sediments and it breaks down into multiple byproducts that may be as toxic as the original drug.
Tasmania’s salmon farming industry has operated for more than 25 years with minimal public scrutiny of what happens on the ocean floor beneath the farms. Regulators focus on monitoring fish health and antibiotic residues in the harvested product.
Are our regulators monitoring whether Tasmania’s seabed ecosystems are undergoing the same degradation documented in Chile?
This is not a question of whether the industry is breaking rules. It is a question of whether the rules are adequate. The current regulatory framework does not require—or even permit—monitoring of sediment ecology at aquaculture sites.
“To ensure the long-term sustainability of salmon aquaculture, it is essential to implement management strategies that reduce antimicrobial use and its environmental footprint,”
the Chilean researchers concluded.
The Chilean study amounts to a credible warning from an identical industry in a comparable environment.
It suggests that Tasmania’s salmon farms may be causing ecological damage that goes unmeasured and therefore unacknowledged.
Several questions now demand answers from Tasmania’s regulators and the salmon farming industry:
Is anyone monitoring sediment health beneath Tasmanian salmon farms? If not, why not?
What will be the cumulative ecological cost of florfenicol use in Tasmania’s waters?
Until these questions are answered, Tasmanians have no way of knowing whether the expansion of aquaculture in our southern waters comes at an environmental cost that simply goes unnoticed.
APA Format: Lynch, S., Thomson, P., Santibañez, R., & Avendaño-Herrera, R. (2025). Influence of florfenicol treatments on marine-sediment microbiomes: A metagenomic study of bacterial communities in proximity to salmon aquaculture in southern Chile. Antibiotics, 14(10), 1016. https://doi.org/10.3390/antibiotics14101016
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