Is My Mushroom Substrate Contaminated?

Whether you’re a hobbyist or a commercial mushroom grower, contamination is the leading cause of crop failure. Contamination, or "contam" in grower slang, refers to anything in your substrate or mycelium that negatively impacts your grow. This can include bacteria, molds, and even animal pests. In this article, we’ll dive into the common sources of contamination in mushroom growing, highlight five common contaminants, and offer tips for reducing contamination in future cultivation activities. By the end, you’ll know if your mushrooms are contaminated, how it may have happened, and how to prevent it from happening again using sterile techniques and equipment like a still air box.

What Are the Basic Signs of Contamination?

Before we get into the nitty-gritty, let’s review 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’s important to take action immediately to prevent further contamination. This might involve ditching your tubs 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

Sterile technique, or "tek," refers to maintaining a clean environment throughout the cultivation process. This involves using sterilized equipment, growing mushroom spawn only on sterilized substrates, and maintaining a clean and controlled environment at all times.

Airborne Contamination

Fungi reproduce through spores, which are microscopic cells released from the mushroom and often dispersed through the air. They can remain viable for long periods, sometimes indefinitely. The best way to reduce undesired spores and other airborne contamination in your workspace is by using a laminar flow hood. This workbench includes a filter pad, fan, and a HEPA (High-Efficiency Particulate Air) filter. While costly, it's worth the investment for medium to large-scale culture plate work and liquid culture inoculations. If a flow hood is not in your budget, a still air box like the NocBox Still Air Box is an excellent alternative for small-scale projects and is a popular choice among home cultivators.

Contamination from Substrates

Mushroom substrates are perfect breeding grounds for unwanted microbes. Contamination can lead to wasted crops if not properly treated through pasteurization or sterilization. Pasteurization reduces microscopic competition in a substrate, while sterilization eliminates it entirely. Purchasing or making your own sterile substrate is crucial for your operation. Different species prefer different treatments, but some options include pasteurization using the 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 is the greatest source of contamination in mushroom cultivation. Human hands and clothes carry lots of bacteria and spores that can ruin a crop. Before you start working, take a shower and use hand sanitizer. Clean clothes, including a lab coat or scrubs, are helpful, along with a face mask or mouth covering and laboratory gloves. Avoid talking when working to limit contamination, especially near open containers such as plates, jars, or substrate blocks.

Contam vs. Mycelium

Mycelium, the vegetative part of fungi, consists of a network of thin, branching filaments called hyphae. In nature, mycelium is unseen as it exists below ground or inside decaying wood. In home cultivation, it’s the white-ish growth seen on substrate blocks, plates, and jars. Mycelium can appear transparent or opaque, bumpy, fluffy, crystalline, webby, hairy, wispy, filamentous, or clumpy and often excretes an odorless, yellow liquid called exudate. Also known as mushroom urea or mushroom pee, its presence is natural but can indicate that the mycelium is under attack or working hard to compete for its food supply. To better identify unhealthy or contaminated patches, spend time getting to know what your mycelium should look like.

While mycelium is typically white and filamentous, contamination generally appears as green, blue, gray, or black patches or discolorations in your substrate. Note that blue stains on certain kinds of mycelium may just be natural bruising, not contamination, especially if the substrate is pressing the mycelium against glass or plastic. One simple trick to determine whether discoloration is contamination or not is to gently wipe a Q-tip over it—contamination will transfer to the swab while bruising will not. Contamination can also appear as slimy patches on your substrate, often due to excess moisture fostering unwanted bacterial growth.

Five Common Contaminants

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

1. Trichoderma

Trichoderma is a group of green mold fungi present in all soils. One species, Trichoderma harzianum, is one of the most common forms of contamination in mushroom cultivation. This mold produces white mycelium that rapidly covers substrates before producing emerald-green spore-bearing structures. It can be difficult to detect in its mycelial stage as it appears similar to mushroom mycelium. Unlike mushroom mycelium, which is 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. If Trichoderma contamination is detected, isolation is key. Remove and dispose of contaminated substrate 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 can wipe out an entire crop.

To prevent Trichoderma infestation, increase air circulation and ventilation, maintain a clean and sanitized growing environment, and regularly monitor for signs of contamination. Always practice proper sterile technique and fully sterilize substrates before 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, also known as red bread mold or pink mold, is another common and fast-growing fungal contaminant. While used in genomics research, this 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. These patches produce round, lumpy formations if allowed to grow, but it’s best to catch the fungus before this stage. Once found, contain the source by sealing it in a plastic bag and disposing of it immediately. Be 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.

3. Bacillus spp. (Bacterial Contamination)

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, called endospores, are heat-resistant, meaning they survive the sterilization process. To prevent it, soak grains for 12 to 24 hours at room temperature before sterilization, allowing the endospores within the grain to germinate and be eliminated during sterilization. If contamination is encountered, it can be separated from the rest of the myceliated grains (if the patch is small and confined to one area) by scooping out the patch using an alcohol-sanitized or flame-sterilized spoon. This can also be done 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 harmful fungi species 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, resembling mycelium, but its growth pattern is more three-dimensional, appearing to hover above the substrate in wispy, white tufts. This mold often forms in the last days of incubation, when substrates are fully colonized just before 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 cause pinning mushrooms to abort their growth and mature mushrooms to become rotten.

To prevent cobweb mold, lower the humidity in your grow chambers and monotubs by carefully managing substrate hydration and improving Fresh Air Exchange (FAE). 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 can help control future cobweb contamination and trichoderma and bacterial contamination.

5. Black Bread Mold

Also known as pinhead mold, black bread mold (Rhizopus stolonifer) is a common mushroom contaminant found in soil and air and is one of the first molds to appear on stale bread. This fast-growing fungus has a dense mycelium that starts white, turns gray, and eventually becomes black. 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 like fungus gnats and fruit flies carry this mold’s spores. While hydrogen peroxide spray can help contain the early spread of most molds, including this one, once the mold advances to a recognizable stage, it may be too late for the grow. At this point, the best course of action is to abandon the grow and start over.

Final Thoughts

Mushroom growers will inevitably encounter contamination at some point, so it’s crucial to learn to identify common contaminants and how to handle them. Develop a rigorous sterile technique and keep your grow room airtight to prevent pests that may spread mold spores. Build redundancies into your cultivation so that your entire grow isn’t compromised if one system fails. Mushrooms are delicate and finicky crops that require specific conditions to thrive, and practice makes perfect. Treat each failure as an opportunity to learn, and you’ll be successful in no time.

By following these guidelines and maintaining a clean, controlled environment, you can minimize contamination risks and enjoy a bountiful mushroom harvest. Happy growing!