How problem child El Niño threatens Chilean fish farming

This year’s El Niño has already had an impact on fish farming globally by forcing Peruvian authorities to suspend anchovy fishing and pushing up the price of fishmeal and fish oil used in aquafeed, but that’s far from the only problem it could bring in Chile, the world’s second-largest producer of salmon.

El Niño, Spanish for “the Child”, is the climate pattern marked by the warming of surface waters in the central and eastern tropical Pacific Ocean. Among other things, it reduces nutrient-rich upwellings, forcing anchovy to dive deeper or migrate, and leading to plummeting biomass and a cancelled fishing season that cut world fishmeal supply dramatically.

But for salmon and trout farmers in Chile, rising feed prices aren’t the only difficulty El Niño can cause. Potential effects of the climate pattern include increased instances of harmful algal blooms, hypoxia, salmonid rickettsial setpticaemia (SRS), and lice infestations, according to a new paper by Austral University of Chile, San Sebastián University, Canadian company AquaBC Consulting, and CIBA (Centre for Applied Biological Research), which has laboratories in Puerto Montt and Puerto Aysén.

While the arrival of a strong El Niño event is usually associated with a rise in sea temperatures, one of its most significant effects for salmonid farmers could originate outside the sea: a reduction in rainfall and the flow of water that feeds southern Chile’s fjords and channels, weakening the surface layer of freshwater, altering salinity, vertical mixing, nutrient transport, and the environmental conditions faced by the fish.

The contribution of the rivers

The fjord and channel systems of southern Chile typically operate under an estuarine regime. Rainfall and river runoff create a surface layer of lower salinity above denser, more saline ocean waters. This density difference maintains a relatively stable separation between surface and deep waters. The freshwater layer then acts as a barrier that limits vertical mixing within the water column.

When rainfall decreases and rivers lose flow, this structure can weaken. The surface layer becomes more saline and less stable, facilitating the intrusion of deep waters to levels closer to the surface, potentially altering variables fundamental to aquaculture production, such as temperature, salinity, oxygen availability, and nutrient transport. Therefore, an atmospheric drought is not only a land problem but can also transform into an oceanographic disturbance within aquaculture areas.

Lessons from 2016

During the southern hemipshere’s summer of 2016, western Patagonia experienced a confluence of an intense El Niño event and an extreme positive phase of the Southern Annular Mode, which favoured a persistent atmospheric blocking pattern off the Chilean coast, diverting frontal systems. This blocking pattern weakened westerly winds and caused precipitation deficits exceeding 50% between 40° and 47° south latitude. The reduced cloud cover also increased the amount of solar radiation reaching the sea surface by approximately 30%.

This led, for example, to a decrease in the flow of the Puelo River - one of the main sources of freshwater for the inland sea of Chiloé - from a historical average of 360 cubic metres per second to 175 m³/s, less than half its historical average. This reduction weakened the stability of the first few metres of the water column: surface salinity exceeded 30 practical salinity units, facilitating the intrusion and upwelling of denser, saline, and nutrient-rich waters near the surface.

Effect on fish

Rising surface temperatures increase the metabolic demands of fish. Furthermore, warmer water has a reduced capacity to hold dissolved oxygen, limiting the available oxygen levels to respond to handling, feeding, or other stressful events. These changes in salinity, mixing, and oxygen levels can also affect gill condition, the primary interface between the fish and its environment, as gills are involved in respiration, osmoregulation, acid-base regulation, and nitrogenous waste elimination.

Consequently, sustained changes in water quality can lead to acute or chronic responses, such as increased mucus production, circulatory disturbances, thickening, lamellar fusion, and loss of gill tissue. These injuries can reduce respiratory capacity and increase susceptibility to health challenges.

The document also warns that these changes may coincide with increased pressure from SRS and lice infestations (caligidosis). In the case of the Chilean sea louse Caligus rogercresseyi, the temperature increase may accelerate the development of its larval stages and lead to faster or more intense infestations.

Physical alterations to fjords and their waters can also influence phytoplankton communities. However, the probability and magnitude of harmful algal blooms will depend on the interaction between temperature, salinity, nutrients, stratification, and the ecological characteristics of each species.

Monitoring is critical

Given this scenario, specialists recommend strengthening continuous monitoring of temperature, oxygen, salinity, chlorophyll, and phytoplankton, ideally per culture unit and integrated into early warning systems. This environmental monitoring should be complemented by systematic assessments of fish welfare and health, incorporating gill scoring, necropsies, histopathology, and other laboratory tools capable of detecting alterations before they manifest as mortalities.

In farms historically exposed to environmental events, consideration is also given to reviewing densities, feeding strategies, oxygenation capacity, early harvests, and logistical availability to move or remove biomass when conditions require it and with sufficient advance notice.

Understanding El Niño’s connection between watersheds, the water column, and fish health will be key to anticipating the risks of the upcoming season and mitigating expected impacts based on lessons learned from past events and newly acquired knowledge, say the authors.