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In an aquaponic system, water from an aquaculture system is fed to a hydroponic system where the by-products are broken down by nitrifying bacteria initially into nitrites and subsequently into nitrates, which are utilized by the plants as nutrients, and the water is then recirculated back to the aquaculture system.As existing hydroponic and aquaculture farming techniques form the basis for all aquaponics systems, the size, complexity, and types of foods grown in an aquaponics system can vary as much as any system found in either distinct farming discipline.There are many species of warmwater and coldwater fish that adapt well to aquaculture systems.In practice, tilapia are the most popular fish for home and commercial projects that are intended to raise edible fish because it is a warmwater fish species that can tolerate crowding and changing water conditions.Aquatic effluents, resulting from uneaten feed or raising animals like fish, accumulate in water due to the closed-system recirculation of most aquaculture systems.The effluent-rich water becomes toxic to the aquatic animal in high concentrations but this contains nutrients essential for plant growth.

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For temperate climates when there isn't ability or desire to maintain water temperature, bluegill and catfish are suitable fish species for home systems.

Koi and goldfish may also be used, if the fish in the system need not be edible.

These factors influence the concentration of nutrients from the fish effluent, and how much of those nutrients are made available to the plant roots via bacteria.

Green leaf vegetables with low to medium nutrient requirements are well adapted to aquaponic systems, including chinese cabbage, lettuce, basil, spinach, chives, herbs, and watercress.