Hit them with H2O2 (peroxide) get some from the hydro store and mix it at a rate of 5 ml 3% peroxide to 1 liter water, so you need 12 ml for each bucket. do this every 4 days till gone.
You problems come from a number of sources, light getting into your res or buckets, water is warm to name a couple.
One of the most common and costly diseases associated with hydroponics; root rot is caused by Pythium spp. These pathogens produce oospores and zoospores which contaminate by contact or move freely throughout water allowing easy access to your plant's delicate root zone. Pythium spp can affect all stages of crops until finishing and primarily attack plant roots but can cause stem rots, cuttings rot, and foliar blight under the right conditions. Temperatures which are ideal for Pythium disease differ for each species and plant affected. Poorly aerated nutrient solution or waterlogged crops can easily create a perfect atmosphere for Pythium spp to thrive, causing severe damage to roots in the process. Once roots are infected with root rot organisms they tend to absorb less water and nutrients. This can in turn lead to foliar wilting and/or nutrient deficiencies. Healthy white roots will begin to turn brown followed by a developing coat of slime(adhesive glycoproteins). Left untreated, the roots will literally rot and detach from the base of the plant. Pythium spp root rot in its worst case will cause crops to die.
Several simple steps can be taken to prevent root rot in your hydroponic garden:
1- Use new or sterilized pots and grow media.
2- Avoid over-watering / over-fertilizing.
3- Adequately aerate your nutrient solution.
4- Ensure proper drainage of your grow media.
5- Keep a clean environment for storage of tools, measuring cups/spoons, and nutrient stock.
Biological control is also available:
1- Hygrozyme*- An enzyme-based product made from all natural, bacteria free ingredients. It breaks down the old root mass to allow for and stimulate new growth. I use this product at 10mL per gallon every solution change followed by a maintenance dose of 25mL per gallon half way through the solution change-out period and can attest to its effectiveness. Used from veg throughout flowering. MAY BE used with H2O2.
2- Serenade*- This product uses Bacillus subtilis as the active ingredient and is approved for organic gardening by the EPA, USDA, and OMRI. I use this product at 1mL per gallon directly in my reservoir every other water change throughout all stages of growth. NEVER combine with H2O2.
3- Florashield*- This product uses Chitosan as the active ingredient and is considered safe to use on and around actively growing plants at all stages of growth. I've used this product before with success but prefer a combination of the two products listed above. DO NOT use this product with Serenade* mixed together in your reservoir; adverse reaction to one another negates their effectiveness. However, Serenade* may still be used separately as a foliar spray to protect against fungi while using Florashield* in your reservoir to protect against root rot. NEVER combine with H2O2. A mix of Chitosan and peroxide will induce oxidative degradation.
Chemical control is also available:
1- H2O2- Hydrogen peroxide is the only effective yet "garden safe" chemical control I feel comfortable recommending. It may be used while growing consumables which isn't always the case with other chemical controls. I used a concentration of approximately 70ppm (test strips aren't 100% accurate) in my nutrient solution with success. I used no other chemical or biological control at the time, but did experience one drawback. The concentration level would dissipate down to 0ppm in two or three hours. If left unattended for one full day algae would start to appear.
References: Chase A. R., 1999, Pythuim Root Rot on Ornamentals, pp 1-2, Western Farm Services; Bagnall R., 2007, Control of Pythium wilt and root rot of hydroponically grown lettuce by means of chemical treatment of the nutrient solution, M.Sc. thesis, University of Pretoria; Owen-Going T. N., 2002, Etiology and epidemiology of Pythium root rot in bell pepper (Capsicum annuum L.) in commercial-scale and small-scale hydroponic systems, M.Sc. thesis, University of Guelph; Owen-Going T. N., Sutton J. C., & Grodzinski B., 2003, Relationships of Pythium isolates and sweet pepper plants in single-plant hydroponic units, Canadian Journal of Plant Pathology 25: pp 155–167; Murinov K. Yu., Romanko T. V., Kuramshina A. R., Kabal'nova N. N., Murinov Yu. I., 2006, Oxidative Degradation of Chitosan under the Action of Hydrogen Peroxide, pp 159-160, Institute of Organic Chemistry, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Bashkortostan, Russia.
*(Hygrozyme is a trademark of Sipco Industries Ltd; Serenade is a registered trademark of AgraQuest Inc; Florashield is a registered trademark of General Hydroponics Inc)