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Fungus gnats are a slender black fly, about the size of fruit flies. Their larvae feed on fungus, algae and plant roots.
They tunnel through the roots into stems and can wreak havoc with the health and vitality of hydroponic gardens.
The best way to control fungus gnats is via prevention, an ounce of prevention is worth a pound of cure. The adults feed on and lay eggs in moist decaying organic material, this should be eliminated - Remove any dead plant matter from the vicinity of your hydroponic garden. Do this on a regular basis since the fungus gnats feed and lay eggs in wet, decaying leaves and clippings. They have also been known to deposit eggs in moist grow media such as coco coir and spaghum moss.
Allowing the surface of the hydroponic substrate / media to dry out completely between irrigation's will help prevent infestations. Adequate drainage of grow beds or ebb and flow systems is also a good idea. Avoid over watering and allow top 2 inches of the root zone to dry out between waterings.
Screening of doors, windows and vents will help eliminate access by the adults and yellow sticky traps will help keep their populations under control.
Algae is the biggest issue, fungus gnats are attracted to it like flies to shit. The algae needs to be eradicated. In addition to feeding and attracting fungus gnats, algae also depletes Nutrients intended for the crop. As it regenerates and decomposes it also depletes dissolved oxygen from the hydroponic system.
Depleting oxygen from the system creates the biological oxygen demand and subsequently causes roots to suffocate resulting in crop loss. Algae on plant roots which eventually suffocates them, makes them more prone to attack by other opportunist pathogens.
One good organic control for algae in hydroponic systems is Grapefruit Seed Extract. It kills off algae , and there is no evidence that it harms the plants.
If you are certain that you have an infestation, you've seen the larvae in your solution, then it is advisable that you flush out your reservoir, that's where the larvae are growing and feeding on fungi and plant roots.
After draining you'll need to conduct a thorough cleaning of the reservoir itself, the grow media - be it rockwool, Clay balls or whatever, the channels, conduits and tubing - basically the whole nine yards. Use hydrogen peroxide [H202]. A dilution ratio of 60% water is best, although I've seen suggestions ranging from 30% on up. Hydrogen Peroxide will not harm the plants when it is diluted and will only cause minor damage if not diluted. Be certain to use pure H202 with no chemical additives.
After cleaning the reservoir, media, conduits and so forth give them all a thorough boiling Hot water rinse before refilling the system. The HOT water will help to eliminate any surviving eggs the h202 may have missed as well as fungi spores ready to reactivate and reproduce.
Depending on the media/substrate you are using you may want to boil it or get new sterile media. Of course you are expected to use good judgement and common sense - don't subject the plants to hot water, don't submerse any voltage carrying components and allow all media and system parts to cool before going operational again.
If flushing and thoroughly cleaning your system completely is not feasible or you're simply too lazy there are other slower and less labor intensive methods to control fungus gnats.
Neem oil based products work great on outdoor gardens and there are several on the market designated for hydroponic use. They do not work as well as, nor are they as cost effective as Bacillus thuringiensis israelensis.
Bacillus thuringiensis israelensis [Bti] is a naturally occurring beneficial bacteria which produces a toxin proven effective in killing larvae of black flies, fungus gnats, mosquitoes and etcetra. It has no effect on plants. It is sold commercially under several trade names gnatrol, gnatnix, GoGnats and a few others.
Once the larvae have ingested Bti, they become paralyzed, cease feeding and die shortly thereafter. Be certain that what ever product you use it is labeled for use in a hydroponic system. If it is not designated for hydroponic use organic compounds from the products have been known to accumulate near the plant bases and create a moist, damp, organically rich environment that fungus gnats thrive on.
It is advisable that you maintain a regimen of the Bti after the fungus gnats have been visibly eliminated in order to prevent a reinfestation , which is not uncommon. Some growers use diflubenzuron, which is an insect growth regulator but is also a carcinogen.
Methoprene is another insect growth inhibitor sold under the trade names Precor and permethrin.
Shore Flies are another parasitic fly that sometimes finds its way into hydroponic systems. Shore flies more closely resemble common house flies, they are not as damaging to hydroponic systems as their distant cousins the fungus gnat.