Common Contaminants

green mold in grain bags

Whether you’re a hobbyist or commercial mushroom grower, the leading cause of crop failure is contamination. Contamination, or ‘contam’ in grower slang, is anything unwanted in your substrate or mycelium that negatively impacts your grow, and can include bacteria, molds, and animal pests. In this article we’ll review the common sources of contamination in mushroom growing, highlight five common contaminants, and offer tips for reducing contamination in future cultivation activities.


Basic Signs of Contamination

Before we get into it, here is a list of the basic signs of contamination in mushroom cultivation:

  • Discoloration: Changes in color, such as yellow or brown spots or streaks on the surface of the mushrooms or growing medium.
  • Off-odors: A strong, foul odor emanating from the growing containers or growing medium.
  • Abnormal growth: Mushrooms that grow abnormally, such as those that are misshapen or stunted.
  • Presence of molds: The appearance of molds, such as white or blue-green growths on the surface of the mushrooms or growing medium.
  • Presence of insects: The presence of insects, such as flies or mites on the substrate or fruiting bodies.

If you notice any of these signs, it is important to take action immediately to prevent further contamination. This may involve ditching your tub or jars, disinfecting the growing area, or adjusting growing conditions to improve the overall health of your grow.


Sterile Technique and Common Sources of Contamination

As we have discussed in previous articles, proper sterile technique is the most important step in preventing contamination. As a reminder, sterile technique, or ‘tek’ refers to the process of maintaining a sterilized environment during the full length of the cultivation process in order to prevent contamination by unwanted microorganisms, such as bacteria and fungi. It involves using sterilized equipment, growing mushroom spawn on sterilized substrates, and maintaining a clean and controlled environment for which to conduct mycology work.

A laminar flow hood filters 99% of particles from the air

Airbourne Contamination

Fungi reproduce with the help of spores, which are released from the fungal fruit-body and often dispersed through the air. They are hardy and can remain viable for long periods of time, in some cases indefinitely without constant moisture. The best way to reduce undesired spores in your workspace is through the use of a laminar flow hood, which is a workbench that includes a filter pad, fan and a HEPA (High Efficiency Particulates Air) filter built into it. The system is costly but worth the investment especially for medium to large-scale agar work and inoculations. If a flow hood is financially not feasible, the next best option is a still air box, or SAB which serves well for small scale operations.

Contamination from Substrates

Mushroom substrates are the perfect breeding ground for unwanted microbes, and if not properly treated through pasteurization or sterilization, can lead to wasted crops as the desired fungi are outcompeted. As a reminder, pasteurization simply reduces microscopic competition in a substrate while sterilization eliminates it entirely. Different species prefer different treatments, but some options include pasteurization using our tek for growing mushrooms in buckets and containers, and sterilization using a pressure sterilizer such as the All American.

Human-borne Contamination

The human body may be the greatest source of contamination in mushroom cultivation. Human hands and clothes contain vast amounts of bacteria and spores that can ruin a crop, so a shower and liberal use of hand sanitizer is recommended. Clean clothes, including a lab coat or scrubs can be helpful along with a face mask or mouth covering and laboratory gloves. Not talking or even opening your mouth when working can aid in limiting contamination especially when near open containers such as plates, jars or substrate blocks.


Contam vs. Mycelium

Mycelium is the vegetative part of fungus consisting of a network of thin, branching filaments called ‘hyphae’ and in nature, it’s the part of the mushroom we never see (as it lives underground). In home cultivation it’s the white-ish (or sometimes colored) growth we see in and on plates, jars or substrate blocks. Mycelium has many forms and textures, and can appear transparent or opaque, bumpy, fluffy, crystalline, webby, hairy, wispy, filamentous or clumpy. As mycelium grows and colonizes a substrate it will often excrete an odorless, yellow liquid called mushroom exudate, alternatively called mushroom urea or mushroom pee, which is a natural part of growth and metabolism but at times can be a sign that the mushroom is under attack or working overtime to thwart a microbial rival for its food supply. Spend time getting to know what your mycelium is supposed to look like so you can better identify unhealthy or contaminated patches.

Contamination generally takes the form of green, blue, gray, or black patches or discolorations on the surface of your substrate. Keep in mind that blue stains on certain kinds of mycelium may just be natural bruising and not contamination, especially if the substrate is pressing the mycelium against glass or plastic. One simple trick for determining whether your discoloration is contamination or not is to gently wipe a Q-tip over it, as contamination will transfer to the swab while bruising will not. Aside from discoloration, contamination can take the form of slimy patches on your substrate and can be the result of excess moisture which can foster unwanted bacterial growth.

mycelium on grain

Five Common Contaminants

There are trillions of microbes present in the air, soil, and water of our planet. Most are harmless and go about their lives cohabitating and even supporting our own. Unfortunately, there are some that actively compete with us for the food we eat, and even prey upon the mushrooms we grow. Here are five of the most common contaminants seen in mushroom cultivation along with some helpful tips to limit their spread.

1. Trichoderma

White mycelium turns green with age and sporulation
Trichoderma, a common contaminant of mushroom growers

Trichoderma is a group of green mold fungi that is present in all soils, with several species having the ability to form symbiotic relationships with plants and plant roots. One species in particular, Trichoderma harzianumis one of the most common forms of contamination seen in mushroom cultivation. This mold produces white mycelium that will rapidly cover substrates before producing emerald-green spore-bearing structures. In its mycelial stage it can be difficult to detect as it appears similar to mushroom mycelium. Unlike mushroom mycelium, which appears more rope-like and remains tight on the substrate, Trichoderma has a fluffy appearance that rises from the substrate.

Trichoderma can grow at any stage of the cultivation process and causes numerous problems as it feeds on the desired species under cultivation. If Trichoderma contamination is detected, isolation is key. Removal and disposal of contaminated substrate must happen immediately before it spreads to other substrates including grow bags, jars and monotubs. Wash affected tools with a bleach solution or alcohol to kill off any spores. If left untreated, Trichoderma is difficult to control and can wipe out an entire crop.

Several measures can be implemented to prevent Trichoderma infestation before it appears, including increased air circulation and ventilation, maintaining a clean and sanitized growing environment, and regularly monitoring your operation for signs of contamination. Always practice proper sterile technique and fully sterilize substrates prior to inoculation. Unfortunately the best method for control once Trichoderma is detected is to ditch your operation, deep clean, and start anew.

2. Orange Bread Mold

Orange bread mold, Red bread mold, or Pink mold are alternative names for Neurospora crassa, another common and extremely fast-growing fungal contaminant. While used for decades in genomics research this bright neon orange mold can wreak havoc on your operation in as little as 8-12 hours. It first appears as an orange-white wisp but quickly develops into a bright orange powdery patch. If allowed to grow, these patches produce round lumpy formations, but it is best to catch the fungus prior to this stage. Once found, contain the source by sealing it in a plastic bag and disposing of it immediately, being careful not to disturb the mold as it will release a fine cloud of orange spores into the air which can quickly spread. After disposal, sanitize the affected area and inspect your workspace for the source, which could include discarded coffee grounds, compost, or damp, untreated wood.

Orange Bread Mold in a monotub

3. Bacillus spp. (Bacterial contamination)

Bacterial contamination often appears excessively wet, or slimy

The most common form of bacterial contamination in mushroom cultivation is known as “wet spot” or “sour rot”. It is characterized by a dull gray slime with a sour-smelling odor that appears excessively wet or mucus-like and often forms in uncolonized patches along the bottom of grain jars. Their reproductive structures are called endospores, which are heat resistant, meaning they will survive the sterilization process. To prevent it, grains can be soaked for 12 to 24 hours at room temperature prior to sterilization, allowing the endospores within the grain to germinate and be eliminated during sterilization. If the contamination is encountered, it is possible to separate it from the rest of the myceliated grains (so long as the patch is small and confined to one area) by physically scooping out the patch using an alcohol sanitized or flame sterilized spoon. This can also take place in a monotub with an isolated patch of contamination where mushroom exudate has turned the affected area yellow, indicating an attempt by the mushroom to fight off the rival bacteria.  

4. Cobweb Mold

Cobweb Mold (Hypomyces rosellus) is another species of harmful fungi that can be encountered in mushroom cultivation, especially in environments with still air, very little oxygen, and high humidity such as grain jars and monotubs. It can be difficult to detect due to its gray, white, and fluffy appearance which resembles mycelium but its growth pattern is more three-dimensional, appearing to hover above substrate in wispy, white tufts. Additionally, this mold often forms in the last days of incubation, when substrates are fully colonized just prior to fruiting. Cobweb mold spreads fast: a small patch the size of a penny can grow to cover an entire jar or monotub in 24 to 48 hours. All fungi in the Hypomyces group live as parasites on other fungi, so if left untreated the infection can result in pinning mushrooms aborting their growth and mature mushrooms to become rotten.

Growers can prevent cobweb mold by lowering the humidity in their grow chambers and monotubs, which can be accomplished through careful attention to substrate hydration and improving Fresh Air Exchange (FAE) or by physically fanning your grow chamber or monotub several times a day if already in the fruiting stage. If spotted early, cobweb mold can be controlled with a 3% hydrogen peroxide solution sprayed on the infected area. Following direct application, soaking a paper towel in hydrogen peroxide and placing it on the affected area is helpful at controlling future cobweb contamination, in addition to trichoderma and bacterial contamination.

Cobweb mold parasitizing a mushroom

5. Black Bread Mold

Black bread mold with its characteristic black spore-bearing structures

Also known as Pinhead mold, Black bread mold (Rhizopus stolonifer) is a common mushroom contaminant that is common in soil and air and is one of the first molds to appear on stale bread. This fast growing fungi has a dense mycelium that is white at first and becomes gray then takes on a black appearance. Similar to Cobweb mold, Black bread mold is wispy but develops tiny black dots at the ends of its mycelium where its spores are produced. Animal pests such as fungus gnats and fruit flies are the carriers of this mold’s spores. Hydrogen peroxide spray can help contain the early spread of most molds, including this one, but once the mold advances to the stage that it is easily identifiable, it may be too late for the grow. At this point, the best way to deal with it is to abandon it and start over.


Final Thoughts

All mushroom growers are going to run into contamination sooner or later, so learn to identify common contaminants and how to handle them. Develop a rigorous sterile technique. Keep your grow room airtight to prevent pests that may spread mold spores. Build redundancies into your cultivation so that if one system fails, your whole grow isn’t compromised. Mushrooms are a delicate and finicky crop that require certain conditions to thrive, and practice makes perfect. Treat each failure as an opportunity to learn and you’ll be successful in no time.