Mushroom Farming: Troubleshooting

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So often, Farmers is facing a lot of obstacles while growing their own mushroom. I have collated here common things that might go wrong and what are the possible ways to manage it. 

“Preventing is better than solving the problems”




Mycelium fails to form.

Improper initiation strategy.

Consult parameter of growth. Alter moisture, temperature, light, carbon dioxide, etc.

Note: If the substrate is too moist, decrease moisture.

Chlorinated or contaminated water.

Use activated charcoal water filters to eliminate chemical contaminants or any other ways of simple or appropriate technology. 

Bad substrate.

Check substrate. Spread the substrate and remix the substrate, package again, make sure all raw materials are good and fresh.

Note: It is necessary to pasteurize immediately after bagging otherwise fermentation gas will slow down the rate of growth of mycelium or stop mycelium growth.

Bad pasteurization.

Check method of pasteurization. Release all air and make sure there is continuous steam before starting pasteurization for a period of 3 hours. 

Substrate in the bag is too hot when inoculation. 

Make sure that the substrate bag is not too hot before inoculation.

Bad strain or spawn.

Obtain younger strain of known vitality & history. 

Spawn contaminated.

Pasteurize and inoculate again with good spawn. 

Forgot to inoculate the bag. 

Make sure to inoculate.

Poor spread of mycelium, bad smell, spots and mites.

Good pasteurization but must decrease the temperature in the pasteurization chamber. Pasteurization was too quick and/or the chamber door was opened too quickly. 

Slowly decrease the temperature in the chamber. Do not open the cover of the chamber too quickly. Check that the cotton plug is tightly closed. 

Inoculation process.

Inoculate in hygiene conditions; clean and with no air movement. 

Too high density in the incubation area, not enough ventilation to decrease accumulated temperature. 

Spread the substrate bag and make more air ventilation in the incubation area. Check temperature and control surroundings to maintain 25-35 degrees Celsius. 

Too high carbon dioxide. 

Not more than 5% carbon dioxide. Check ventilation. 

Hygiene of the incubation house. 

Improve hygiene in the incubation house.

Mycelium develops in patches. Substrate is not evenly prepared and some parts have more nutrients than others 

Mix well the substrate.

Bacteria, other fungi contamination.

Check the process causing contamination. Separate contaminated bags as soon as possible. Remix substrate separately. Remake substrate bags and pasteurize for a longer time. Follow process. 

Mite contamination.

Immediately separate contaminated bags and pasteurize again. Continue the normal process.


*Keep hygiene management; make sure to clean every thing (person, area, tools, equipment, and surroundings during every step.

*Stop using the area to cut the life cycle of all contaminants for a period of at least 1-2 weeks. For serious contamination cases, spray area with chemicals.

*Use black-light with water or sticky-trap to decrease insects.

Mycelium grows but fails to produce mushrooms.

Substrate formula is not suitable.

Adjust the formula; check pH; sawdust; additives; etc.

Mites, mold, virus, bacteria and insects.

Check pasteurization process, inoculation, other processes and mushroom house management for hygiene. 

Inhibited by environmental toxins. 

Remove source of toxins.

Bad strain or spawn

Acquire new strains. 

Mushrooms form, but abort or delay mushrooming.

Premodia and growth condition of fruiting body are not good enough 

Check temperature and humidity. Open or close doors and window to adjust accordingly.

There is contamination such as mold, bacteria, insects, worms and mites.

Check hygiene, adjust environment of light, temperature, humidity and ventilation. In more severe cases, use half a teaspoon of sulfur in 3.5 liters of water. Mist the bags and the surface of mushrooms. Remove contaminated bags from mushroom house and recycle. 

Chemical contamination from solvents, gas, chlorine, etc. 

Remove toxins.

Bad strain.

Acquire a new strain or find a new supplier. 

Mushrooms form, but stems are long; caps underdeveloped.

Inadequate light.

Increase or adjust light to correct wavelength.

Excessive carbon dioxide.

Increase air exchange, open doors or windows and close at correct time. 

Massive numbers of mushrooms form; few develop.

Too long time incubation. 

Shorten the period for the formation of premodia.

Lack of oxygen, inadequate light.

Increase air ventilation and open more windows or doors to receive more light. 

Inadequate substrate nutrition or low quality. 

Reformulate or check raw materials.

Low rate mycelium growth.

Use the high rate spawn or adjust good conditions for rate of growth. 

Poor strain.

Obtain better strain. 

Mushrooms are deformed, decay and die.

Disturbed by germs or competing microorganisms.

Adjust mushroom house to favor mushrooms and not germs and competitors. 

Dirty surface of substrate bags. 

Clean the surface of substrate.

Not enough air ventilation, too high humidity.

Increase air circulation. Reduce humidity to the prescribed levels. Surface water must evaporate from mushrooms several times per day. Check watering; if there is water in bags, pierce bags and drain water. 

Bad strain.

Acquire better strain. 

Use of chemicals during this period.

Never use chemicals during the fruiting stage. 

Mushrooms produced only in the first flush, fail to produce subsequent flushes.

Inadequate substrate nutrition.



Check hygiene, adjust light, temperature, humidity, air and ventilation. 

Poor growing house management. 

Improve management.

Bad strain.

Acquire new strain. 

Mushrooms small sized.

Too many mushrooms coming out at the same time. 

Reduce the size of opening(s).

Lack of nutrients in substrate. 

Review quality of substrate.

Change of weather.

Beware of wide range changes in temperature. 

Spawn unhealthy.

Check origin of spawn. 

Pests and insects.

Natural occurrence, humid climate.

Place lemongrass plants around mushroom house. Spread lime on shelves, on poles and ground in the mushroom house. Clean (and maintain clean) the mushroom house properly. 

Mushroom waste lying around mushroom house. 

Try to use the waste as fertilizer or recycle.


Mix detergent with water and place on their paths. Do not put on mushroom. 

Mushrooms are light in weight. 

Shortage of water.

Check humidity of mushroom.

Mushroom quickly spoil.

Mushrooms too mature when harvested. 

Harvest when younger.

Mushrooms too warm before packaging. 

Chill mushrooms before placing in marketing containers.

Mushrooms too wet when harvested.

Reduce humidity several hours before harvesting. 

Mushrooms stored beyond shelf life. 

Sell mushrooms faster.

Rotting spot on the mushroom fruiting body because of bacteria during flush.

Bacteria (Pseudomonas tolaasii, Pseudomonas fluorescens) on Oyster mushroom.

Control humidity in the mushroom house and maintain 80-85 %.

Give enough time for water to evaporate from mushroom surfaces before further watering.

For sever cases, use 113 grams chlorine mixed in 45 liters of water or 4 ounces of chlorine per gallon of water. 

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