How do I identify and prevent Root Rot?

Contributed by: snoofer

Thanks to: budmonster, highgrade, Baudelaire

introduction . background . Id & Damage . Management Strategies . Emergency Treatment . Prevention . Environmental Control . Additives



"Root rot" is a common waterborne disease that can seriously affect indoor and outdoor crops year round. "Pythium" is a generic term for several different root rot and stem rot fungus species (including Pythium, Verticillium, and Phytophthora, and Fusarium). Root rot is also known as "damping-off" in seeds, seedlings and clones.

Pythium can rapidly infect crops in vegetative and flowering stages. Damage includes strain infection, reduced yields, and crop failure. Pythium is particularly damaging in high-density dwc / hydroponic / aeroponic systems, as these recirculating systems provide ideal conditions for rapid growth and spread of pythium spores. One infected plant can quickly spread rot to all plants if the system has an interconected irrigation system.

This FAQ focuses on indoor prevention and treatment options.



Pythium typically thrives in oxygen-poor (anaerobic), warm (75-85 F), and poorly circulated nutrient solutions. Heavy clay soils with poor drainage are high-risk soil planting sites.

Sources of infection:
  • Unsterilized tools and equipment
  • Unfiltered water
  • Dead roots from previous crops
  • Infected plant material (i.e. clones taken from infected moms)

    Dissolved oxygen, temperature and pythium

The amount of dissolved oxygen (DO) in a nutrient solution depends on the water temperature. Cold water can 'hold' more dissolved oxygen. A fully aerated solution at 20C/68 F is 9 - 10ppm; at 30C/86F it's 7ppm.

Root oxygen requirement doubles for each 10C rise in root system temperature (max 30C/86F). The dilemma for the grower is that with a 10C rise in temperature, root system oxygen requirements will double, while the oxygen carrying capacity of the solution will drop by over 25%!

The nutrient DO is unable to supply the root's oxygen demands, leading to prolonged oxygen starvation. Oxygen starvation will result in slow growth, mineral deficiencies, root die-back and reduced yields. Oxygen starvation will stress the plant, leading to an eventual attack by opportunistic pathogens, such as ever-present pythium.

Identification, Symptoms and Damage:

Healthy roots:(budmonster) Infected roots:anon


  • Yellowed, droopy and wilting leaves (possibly exhibiting mineral deficiencies). Leaf curl over - ram's horns' - roots are unable to uptake nutrients at that strength because they are infected.
  • pH becomes more acidic (pH should rise slowly in a healthy system)
  • 'Burnt' root tips (browning tips may also be a result of light exposure, or over fertilization)
  • Reduced water consumption and rising nutrient strength
  • Brown colored roots. (Note: GH "Micro" will stain roots brown as well; stain darkens @ ppm's. Healthy root should be white or slightly tan)
  • Brown and slimy roots with a slight to strong rotting odor. Plant may appear healthy.
  • Reddish and swollen root collar, becoming blackened over time. Eventually the plant will fall over as all connecting tissue will have been 'eaten away'.
Note: Root damage is permanent; new root hairs can form, but damaged roots will not regenerate. Lightly infected roots may turn white again if treated promptly.

Dead roots serve as energy sources for pythium; snip off dead roots and remove flating root piece by changing the tank frequently.

Physical test of advanced root rot:
"Brown tissue on the outer portion of the root easily pulls off, leaving a thin strand of hair-like vascular tissue exposed."

Management Strategies


Keeping the crop healthy, vigorous and stress-free is the best "cure" against pythium. Pythium is almost impossible to 100% eradicate from an infected system; this involves starting completely over (with new mothers, containers, equipment, etc). An infected crop can be nursed along, and subsequent crops can still yield, provided the grower takes care to minimize the growth and spread of pythium in the system.

Starting with a pythium-free system is the best strategy:

Startup with a new crop:
  • disinfect the system. Manual scrubbing and bleach might be necessary.
  • add tap water
  • disinfect the water with strong h2o2. It takes 100ppm to kill pythium outright, however this can also kill small plants. Wait 24 hours for h2o2 to dissipate to a safe level - do not add tap water to system! Add only h2o2-treated water.
  • add nutrients and beneficial enzymes. The aerobic-loving enzymes will colonize the sterilized medium and system, hopefully displacing any anaerobic bacteria.
Soil tips:
Improved soil is the first step to keeping root rot out of your garden. Adding amendments to improve drainage and aeration will decrease the chances of root rot. Use only sterilized soil/soilless mixes or heat-treated soil before use.
Removing the diseased plants and several inches of affected soil will slow or stop the spread of pythium. Avoid over watering, as saturated soil promotes anaerobic conditions. Remove and destroy roots and surrounding soil near infected plants. Use sterilized soil for transplants. Provide good drainage and avoid overcrowding plants.

Preventive gardening:


  • Monitor plants and roots frequently. Inspect roots for browning. Stressed plants are attacked first, so it is important to inspect crop and remove unhealthy plants.
  • Maximize aeration. Use venturis, powerheads, bubble walls/ air curtains, air stones, and daily h2o2 usage to increase dissolved oxygen. Allow nutrients to fall back into the reservoir to create 'waterfall aeration'.
  • Use only healthy clones taken from healthy moms (pythium is systemic and diseased moms will pass on root rot!)
  • Keep ph stable, between 5.5 and 6.0
  • Keep air moving, circulate nutrients continuously
  • Keep reservoir / root zone temps low: 62-65F.(Note: submerged pumps will increase water temperature)
  • Maintain a clean system. Change tank weekly to reduce spore loads. Add only h2o2-sterilized water
  • Use tank additives

    Other tips:
    • Isolate plants. Keep water culture plants isolated in their own containers if possible.
    • "Run-to-waste" systems: nutrients are not re-circulated - reduced spore loads
    • Use separate reservoirs/pumps to isolate systems.
    • Sterilize equipment shared (ie. pH meters) between tanks
    • Make sure cloning mediums (especially rockwool) do not remain saturated for too long. Drain fully after watering.

    Special tips for bubblers:
    (highgrade) "Have an empty, sterile bucket to place the bubbling bucket into when changing nutes. The extra bucket method allows me to run a gallon of water through the pot and flush the grorocs and root mass of any salt build up. Wash the bucket prior to refilling with solution."

    (Baudelaire) ". maintain a humid air gap extending from the root crown down at least 4 inches. This provides the space for aerial roots to form, and keeps water away from the root collar, where root rot typically takes hold."
  • Emergency Treatment:


    1. Hydrogen Peroxide root dunk
    -Remove each plant from system, snip off diseased roots.
    -Dip/swish each plant and container into a strong H2O2 solution, until diseased roots have been removed. Repeat as required.

    2. Sterilize equipment
    All equipment should be disinfected (including hoses and pots, etc) with bleach solution or 10% h2o2 solution before plants are reintroduced into the system. Rinse well.

    3. Add root rot medication. Add anti-pythium additives, Vitamin B1, and fresh nutrients to a sterilized reservoir at a lower strength, at cooler temps. Reduce light levels. After a week or so, after new roots appear, add some root boost additives.

    Environmental control:

    • Maximize reservoir circulation, aeration and cooling
    • Reverse Osmosis (RO) to remove pathogens from source water
    • UV sterilizers. UV kills pathogens as nutrients are passed through unit
    • Ozone. Maintain a 300-400mV level
    • Blow cool air through the root zone
    • Minimize light leaks and cover reservoir (but don't seal) to limit algae growth. Algae will grow, reproduce and die, adding organic material for pythium to feed on. Algae and other slimes may coat the roots, stressing plants even further.

      *Take care using UV and Ozone, as nutrients can precipitate out of solution. Iron is especially susceptible.
  • Chemical/Biological additives:


    Note: H2o2 may kill enzymes used in some biological additives. Additives should be considered preventive only; not all additives may be effective.

    Beneficial bacteria colonize the root system, out-reproducing root disease organisms. Some additives may "feed" on decayed roots. Additives may be added during every tank change, except for H2o2 and Ridomil.
  • .H2O2 (See H2O2 FAQ) .Ridomil (1 app, systemic, toxic, 5 drops/gal).
    .FloraShield (by GH) .Bio Bugs
    Guardian angel (2.5-5 ml/gal) Bio Bran (, 11 enzymes)
    Root Shield ( Sm-90 (citrus extracts @ 2.5 ml/gal)
    Hydro Shield ( Pro-Silica (silicon, basic, up to 5 ml/gal)
    Microkill (kills mold/fungus/mildew/algae) Pro-TeKt (silicon)
    Canna-zyme (Canna,, 15 different enzymes) Power Active
    ATAZYM (Atami) BN-ZYM (bio nova)
    Zyme (Green Planet, 6-8ml/gal)
    Others: Ascend/Fongarid/Consan 20)/Fosetyl-A1 (sold as Aliette)

    For seeds, seedlings and clones:

  • Use 1 drop bleach/gal when sprouting seeds using towel method
  • No-damp (spray cloning domes at 5-10ml/L)
  • Cloning gel/powder with a fungicide


  • UV Sterilizers. UV can kill waterborne organisms, with a slow exposure to UV light. Research suggests iron can precipitate out of solution. Pythium already attached to surfaces in the rootzone will not flow through the sterilizer and not be killed. Aquarium stores sell them.
  • Continuous drip H2o2. According to Maximum Yield, 100ppm is required to kill pythium in solution. This level also adversely affects small plants. Of course, organics and beneficial bacteria in additives will also be destroyed.

    H2o2 should be added to a seperate volume of water and allowed to sit for 20 minutes before adding to the reservoir. The majority of the O2 will be chemically released by the H2o2 by that point. (In high enough concentration, h2o2 will burn off the epeidermis of the roots, exposing it to attack by pathogens and damging fine root hairs).
  • Slow sand filtration. According to interet literature, SSF can remove up to 99.7% of all bacteria. Aquarium stores sell sand filters.
  • Dissolved Oxygen machines. Artifically injecting water with oxygen may inhibit or kill pytium and other anerobic organisms.

    These Documents contain information gathered from many Online Communities and all possible references have been given to the authors of each individual article. For any discrepancies in this please contact "" enjoy