New research suggests dissolved organic substances, the waste from fish farms, are altering the ecosystems in Chilean rivers.

After previous studies showed dirty, sediment filled waters were harming Chilean rivers, regulators forced aquaculture operations to do a better job of filtering and cleaning their waste water.

Most fish farms draw water from clean Chilean rivers and return the waste water downstream. New rules have ensured that wastewater is now much less turbid, but new research shows many chemicals -- the remnants of fish and food waste, as well as antibiotics and disinfectants -- still bypass the installed filters.

Previous analysis showed for every 50 tons of farmed salmon, a total of 40 tons of dissolved organic substances -- or dissolved organic matter, DOM -- are deposited into in the river. But what compounds make up the dissolved organic substances include? New research offers clues.

Scientists used fluorescence markers and high-resolution mass spectrometry, as well as nuclear magnetic resonance spectroscopy, to image and analyze the chemical composition of the dissolved waste.

"We were able to determine exactly what DOM molecules were present in the water and in what concentration," Norbert Kamjunke, a biologist at the Helmholtz Centre for Environmental Research, explained in a news release.

Analysis, detailed in the journal Scientific Reports, showed aquaculture wastewater significantly increases the concentrations of carbohydrates and proteins -- as well as their more basic chemical building blocks -- into the river.

Scientists found the uptick in organic compounds and nutrients altered the ecosystem downstream of fish farms. Upstream, clean, low-nutrient waters are rich in algae biofilms. These microorganisms attach to rocks and serve as the main food source for aquatic insects, forming the base of the freshwater ecosystem. The algae also produces oxygen.

Downstream, dissolved organic matter encourages higher concentrations of bacteria, which diminish the presence of algae and depress oxygen levels.

"This changes the entire ecosystem," explained Kamjunke.

The bacteria works to clean the water, but it alters the food chain and ecosystem as it does so. Researchers recommend limiting the amounts of dissolved organic substances allowed to be emptied into rivers in Chile.

"Rivers should not be misused as natural sewage treatment plants," concluded Kamjunke.

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