The concentrated nature of aquaculture often leads to higher than normal levels of fish waste in the water. Fish waste is organic and composed of nutrients necessary in all components of aquatic food webs. In some instances such as nearshore, high-intensity operations, increased waste can adversely affect the environment by decreasing dissolved oxygen levels in the water column. Onshore recirculating aquaculture systems, facilities using polyculture techniques, and properly-sited facilities (e.g. offshore or areas with strong currents) are examples of ways to reduce or eliminate the negative environmental effects of fish waste.
Aquaculture can be more environmentally damaging than exploiting wild fisheries. Some heavily-farmed species of fish, such as salmon, are maintained in net-contained environments. Unused feed and waste products can contaminate the sea floor and cultured fish can escape from these pens. Escapees can out compete wild fish for food and spread disease, as well as dilute wild genetic stocks through interbreeding. Farming carnivorous fish like salmon may actually increase the pressure on wild fish, as for farming one kilo of farmed fish up to six kilo of wild fish are used for feeding.[ However considerable research and commercial feed improvements during the 1990s & 2000s has lessened many of these environmental impacts
Certain forms of aquaculture such as the culture of seaweeds and filter feeding bivalve mollusks such as oysters, clams, mussels and scallops are relatively benign environmentally.
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