Mushroom Contamination: How to Spot and What to Do

In the world of mushroom cultivation, contamination is as inevitable as death and taxes.  That’s why a solid understanding and consistent practice of the fundamentals of sterile technique is so important.

Yet even with a flawless workflow, contamination will at some point find its way into your grow bag, grain jar, Petri dish, or monotub. All that’s needed is a nutrified substrate, a weak mycelial culture, and a chance. When that moment arrives, you want to know how to spot mushroom contamination, and just as importantly, what to do about it.

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Mushroom Contamination #1:


Trichoderma is a genus of green mold that preys on other fungal mycelium and is easily distinguished by its vibrant blue-green color during sporulation. Of all the types of contamination you may encounter, trichoderma is one of the easiest to identify—especially after sporulation—and one of the most difficult to contain. Trichoderma harzianum is the most common and is known to produce an aggressive white mycelium that causes a soft decay in mushrooms before it sporulates into a vibrant green.


Trying to identify and eradicate trichoderma when it is in the stage of growth right before sporulation is difficult yet vital to save your crop. At this point in its life cycle, it can appear similar to mycelium. In the photo below, note the thick, fluffy appearance on trichoderma rising from the substrate. Mycelium does not look like this. Instead, mycelium appears more rope-like and stays tight to the substrate.

mushroom contamination

Once trichoderma sporulates, though, it’s practically impossible to misidentify. In the photo below, note the green splotches characteristic of trichoderma.

mushroom contaminaton


Trichoderma is notorious for being practically impossible to contain once it takes hold. If it starts to sporulate, your best bet is to get the trichoderma-contaminated petri dish, grain jar, grow bag, or monotub as far away from your lab and/or fruiting room as quickly as possible. If you don’t, you risk it spreading and your mushroom contamination issue turning into a full fledged crisis as it contaminates neighboring dishes, jars, bags, and tubs.

Nonetheless, if you’re hell bent on trying to save whatever it is that’s contaminated, spreading salt on the affected area is one approach used in Agaricus mushroom production farms when encountering trichoderma. We don’t recommend this approach unless it’s, say, your only tub. We think simply cutting your losses and ditching the trich’ train altogether is a better idea.

After you spot, identify, and rid yourself of trichoderma, it is a good idea to sanitize everything in the affected area as much as possible before beginning another grow. It’s also smart to look back at your processes to attempt at identifying where the mushroom contamination issue likely began (more on that later).

Mushroom Contamination #2:


E.g. Bacillus spp

When it comes to bacterial mushroom contamination, the most common type is Bacillus spp., also known as “wet spot” or “sour rot.” Mushroom cultivators typically soak their grains for 12 to 24 hours before hydrating or sterilizing them.


Because bacterial endospores can be heat resistant, meaning they’ll survive the pressure cooking process. By soaking the grains overnight, we circumvent this issue. In essence, soaking the grains causes any bacterial endospores on the grains to awake and germinate. Then, once the grains reach sterilization temperatures during the pressure cooking process, those pesky heat resistant endospores die off. Without the soak, the endospores could lay dormant and survive the sterilization process, coming to life after you’ve already inoculated your grains and ruining your grow.


In grains, bacterial contamination appears dull gray, slimy, excessively wet, similar in appearance to mucus, and is easy to identify by taking a big ‘ole whiff of your grain jar when you suspect it is present. As the nickname “sour rot” suggests, if your grains smell sour, you’re probably dealing with Bacillus spp.

As seen in the photo to the left, if you have an almost fully colonized grain jar with a slimy, uncolonized patch—oftentimes in the bottom corner of the jar—it’s probably Bacillus spp. contamination.

As for its appearance on petri dishes, bacterial contamination looks like a slimy, wet patch, hence the nickname “wet spot.” In the photo below, bacterial contamination is identified as the wet looking slime stretching out in finger-like formations from the patch of white mycelium.



The best way to avoid bacterial mushroom contamination like Bacillus spp. is to soak your grains for 12 to 24 hours at room temperature before you begin the sterilization process. In this way, the heat resistant endospores, if viable, will germinate and then be susceptible to the standard sterilization process.

If you encounter bacteria on a petri dish, it can be a fun experiment to let it sit for a few days to see how your mycelium culture responds. Perhaps it will consume the bacteria. If it does, voila, you have a wicked strong culture capable of fighting off bacteria. Bacterium do sporulate but not to the degree of trichoderma 

the risk of it spreading to other plates isn’t as high. Nonetheless, it’s always a good idea to separate your clean cultures from the contaminated ones.

If bacterial mushroom contamination is encountered on grain, it is possible to separate the bacterially contaminated grains from the rest of the healthy myceliated grains. However, this usually only works if the bacterial patch is small and contained to one area. To accomplish this separation, scoop out the bacterial patch using an alcohol sanitized or flame sterilized spoon. This can also be done in a monotub with an isolated patch of bacteria, which often can be identified by a yellowing of the substrate, seen in the photo above. Note that in the photo, the bacteria isn’t yellow. Instead, the yellowing represents the mycelium’s reaction to the bacteria as the mycelium secretes metabolites/enzymes to protect itself.

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Mushroom Contamination #3:


e.g. Hypomyces spp.

Cobweb mold is not one species of mold but rather a closely related group of mold species that tend to cause soft rot in mushrooms. Usually, one encounters cobweb mold in grain spawn and monotubs.


Cobweb mold can be difficult to spot because it appears grey, white, and fluffy, similar to mycelium. Typically, it grows three-dimensionally, levitating above the substrate in wispy, white tufts. Cobweb mold spreads fast, causes your baby mushrooms to abort their growth, and in some cases can prevent your mushrooms from growing at all. When cobweb mold contacts a mushroom, the mold soon envelopes the mushroom with its soft, mildewy mycelium and causes a soft rot in the mushroom. Cobweb is also a parasite of wild mushrooms.

To identify cobweb mold, you must learn how to distinguish it from mycelium. Cobweb mold is usually greyer and more wispy than typical mycelium. It possesses very fine strands when compared to the rope-like hyphal growth of mycelium, and has the smell of mildew. If you open your tub to the sight of wispy gray tufts growing three-dimensionally and the scent of a damp basement meets your nostrils, you’ve likely just encountered cobweb mold. In the photo below, note the clouds of wispy grey growing upward from the substrate. This is cobweb mold. The more vibrant but smaller white patches located near the sides of the container are mycelium.

mushroom contamination

Another way to identify cobweb mold is by the sheer speed of its growth. A small patch the size of a penny can grow to cover an entire jar or tub in 24 to 48 hours. In the photo below, cobweb mold on grain is distinguished by its light wispy appearance when compared to the more vibrant white patches of mycelium.


If spotted early, you can control cobweb mold and salvage your grow using hydrogen peroxide. Hydrogen peroxide (H2O2) spray is a great weapon in the battle against mold because it will not harm your mycelium but will kill any mold and/or spores trying to take over your monotub. So spray, spray, spray away.

To limit the chances of encountering cobweb mold, make sure your grains/substrate aren’t overhydrated since cobweb mold prefers high humidity (i.e. an overhydrated substrate) and stagnant air. By lowering the humidity and providing more air circulation, you can help limit the potential for and spread of cobweb mold mushroom contamination. After a H2O2 spray down, soaking a paper towel in H202 and laying it where the contamination once was is another strategy and can be used for trichoderma and bacterial contamination, too.

Where You Went Wrong

The most common cause of mushroom contamination is incorrect sterilization. If you create a nutrified substrate that’s not completely sterilized, you’re basically placing a fat plate of food in front of a table of hungry hippos. One of those hippos, or maybe a few of them, are going to eat. Your mycelium culture will then go hungry, weaken, and lose out. Poor sterile workflow is another common cause, as is working with weak mycelial cultures or trying to cut corners with your preparation.

As for where exactly the contamination is coming from, you don’t have to look far. In fact, go take a look in the mirror. You, you dirty human, are one heck of a vector for mushroom contamination. There are billions of microorganisms on you right now. Yuck! Take a shower before you do any sterile lab work to limit the chance of those little guys jumping into your grow.

If you practice good sterile technique, make sure you properly prepare and sterilize your substrates, and ensure you’re as clean as you can be before working with sterile substrates, you’ll definitely increase your chance at success. And if you find yourself overjoyed with the process and ever thirsty for more, you may have just found your calling at the perfect time.

To learn more check out our YouTube video on "How to Spot Contamination in your Agar, Grains and Liquid Culture"

about the author

Sam is a writer, award-winning journalist and professional mycologist from the United States who arrived at the Fungi Academy one midsummer’s day in 2019 and left six weeks later with lifelong friends and a passion for mushroom cultivation.

In the past year three years, he’s built a laboratory and fruiting room in his home, cultivated and foraged over 20 species of gourmet and medicinal mushrooms, started a medicinal mushroom tincture business and returned to the Fungi Academy to teach his techniques to students.


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  1. I really enjoyed that, very informative thank you! And Just like So Many Before me that also felt very confident and quiet educated, to now JUST learning about about contam on my cakes! 🥴 I was aware and prepared for the innoculations and sterile sterile sterile, unfortunately that was as far as I got On that, I was led to believe once the mycelium covered the substrate we were home free baby!! 🥳 and yeah, not the case I only knew to look up info about contaminated cakes after it was already to late. What a bummer Cuz I looked All over you tube for a COMPLETE start to finish everything happens could happen, best ways, best spores, things I’d need And what bullshit to stay away from rip offs expensive Martha tents ECT ECT so yeah, I would have loved to known that’s all I’m saying, damn 🤫🤗✌️

    1. Contamination, like s#it, happens. It happens to everyone. Identifying where you went wrong and tightening up your sterile technique is all you can do. Reading this article I learned something new. I have always been told to cook, not soak, my grains. Now I have sour mold in my some of my grain jars for the first time. So even though I am grower going into my 3rd year, I am still learning new things all the time.

  2. I have a monotub that is displaying gray and white mycelium I’m concerned it’s contaminated. I don’t smell sour or gym sock just kind of musky

    1. Some of the DNAs produce very suspicious stuff on the top – especially if you are using casing layer (I do vermiculite for some of my spawns) – but just let it sit for a day or two and typically it ends all fine – all the contam failures typically hitted me during innoculation and early mycelium growth, I never experienced contam in my cakes – just follow the 101 for best practices and dont overcomplicate your stuff.

  3. The surface of my growkit mycelium is turning slightly yellow and brown in 1 corner. I first noticed it today: It’s in the stage where the first mushroom heads have started popping up above the surface 3 days ago. The discoloration is faint, but it’s definitely yellowing/browning somewhat.
    What could this be and what can I do to prevent it’s spread?

    1. So if it showed up, black stuff on the mushroom caps…seemingly over night, it’s most likely spores that the mushrooms released, I like to harvest them right before the veil under the cap breaks. Cuz all those black spores just aren’t too pretty. However they are harmless.

  4. I have a contaminated bag of rye spawn that I inoculated with spores. It looks wet and green now. I bought the spawn bag pre-made.

    I realize it’s done for.

    But I’m curious- instead of simply chucking it in the trash- what about opening the bag and pouring the contents somewhere to see what happens? I live in a rural area where I can dump it outside at the base of a tree in shade. It’s very hot these days so I’m not sure how that’ll go. But what do you think?

    Could nature surprise us?

    1. I can tell you for a fact 4 times over from dumping tubs in my flower beds and one in the woods, it can and probably will fruit. I dumped 4 over the summer due to contam. I live in Texas. The weather was very hot and dry (over 100 degrees Fahrenheit ). Obviously nothing happened for a while, but about 6 weeks later, we got a good rain and poof…there they were…4 different spots…fruiting like crazy.

    1. That’s from harvesting a touch late- spores dropped onto the mycelium. That’s if it has already produced a flush.

  5. Hi, my B+ started to develop a big white elongated head on the top. Not one but all of them. Currently, I am growing 2 monotub and only one tub has this. It seems like there is no contamination but I am worried.
    I wish I could put on a picture to show. Do you know what this is?

  6. My B+ has started to develop a white elongated thing on the top. Not one but all of them. I have two monotub and the only one tub has this thing. My impression is not contamination but I am worried. Any idea?

  7. I have something in one corner of my substrate that looks similar to the cobweb mold but it is coral colored and looks almost like dust in some parts. Has anyone else experienced this. The tub does not smell moldy so I am confused.

  8. I have a white film around the lower perimeter of my tub. The spawn otherwise looks super healthy and I’m pretty much ready to move to fruiting. I scraped of a bit of the film which is looks similar to rolling paper but thicker. The film itself smells strongly of mushroom, earthy. Not nasty, sour etc. Should I be worried?

  9. I need help I’m pretty sure I have contamination my friend bought these in a bag kit and they look horrible he spent a lot of money on them so I wanted to try and save them but now after reading this I’m not so sure ;( is it worth trying if so how would I considering they are in a bag with dirt and all ?? Please help

    1. Could be either contaminated spores or contaminated grain that wasn’t properly prepped. Try working with some agar Petri dishes to too if the spores are contaminated to rule that part out at least.

  10. I have blue mold growing on the surface of my grow bag of Lion’s Mane in the kitchen.

    What is it and what did I do wrong?

  11. Thanks alot for the helpful info, I am waiting for my mycelium to start and I think this will help ,but any more tips, would be greatly appreciated. I have a mini boomer mushroom kit ,by monster mushroom

  12. Help. I’m getting stunted mushrooms and I have no idea what’s going on. I’ve been successful prior and no changes… airflow, moisture all good. But mushrooms are capping at 0.5cm. What am I doing wrong?

  13. So my Mycelium did well in the all in one bags and even better once I transferred to the mono tub. When I looked last night after work their is a light tan coloring going on. Any ideas as to what it is other than the light tint the tub looks completely colonized with a light moisture layer. These are blue angels or flying saucers. Don’t know if that matters.

  14. Hi there academy folks,
    Thank you for this excellent article. I’d love to send you a photo. I was under the impression that I had cobweb mold and almost abandoned my grow bags. I put them in my fruiting chamber and there is successful growth. I’m still curious if some of it is cobweb or that’s all mycelium.

  15. We have been encountering mold contamination on our last 3 batches of growing. We were injecting a grain bag, letting the mycelium grow, then transferring it to a grow box. We thought it was our transfer process (box not sterilized, foreign contaminants, etc). On our most recent grow we tried a all-in-1 grow bag. We injected and left it to cultivate. In 1 of the 5 grow bags, we once again had mold take over. We sterilized the needled, and it really was not subjected to any foreign contamination that we can think of. Could it be where we are leaving the bags to sit and grow? Could it be a humidity/temp issue? Could it be mold in the air getting inside the bag and contaminating? I suspect I have a mold issue in my house due to some leaking faucets in the past. Could that be a cause? Could it be a quality issue from the supplier? Any insight is appreciated. I also have pictures of the infected grow bag: thanks in advance!!

  16. For the Hydrogen peroxide application, is the standard, drugstore concentration of 3 percent okay or should it be further diluted with tap or DI water?

  17. So I have them ” fruiting” in a magic bag. There was light orange liquid, and I read about the metabolite response. I poured out 2/3 of the liquid into a jar. No foul smell. I left some so it could do its protective work. I can see good thongs happening, but its been slow. My apt temp is usually like 66 or 67. I had them in the closet for like 6 weeks, then I’ve had them in the light by my bedroom window with no direct light. I’m worried as time goes it will turn sour. I’m a first timer.

  18. Is it true that the owner of Cultural Mushrooms a fraud? I heard his grow bags are bogus and instead of a syringe of a mycelium to inject in the bag to grow happy mushroom is in fact just water.

  19. If I have “Mushroom Contamination #2: Bacteria, e.g. Bacillus spp.” and am using an all-in-one bag that will be ready for fruiting, will it be safe to harvest after fruiting? Should this bacteria not be eaten?

  20. Any experience with a pink colour on mycelium already fruiting? Started as light pink then darker pink spots? Salvaged the mushroom outside of the affected areas and dried them. Do you think they are safe to eat?

  21. Well I’ve been unsuccessful mostly in any large yields, Trichoderma seems to be my nemesis. I should note I and now working in a hand box and sterilizing everything and anything that goes near that box. I am using a inkbird for humidycontrol, is distilled h20 a must, or not at all? The ink bird is a great practical tool but I feel like it opens up a whole new area or entrance point for contamination. Would you recommend this product? I’m getting my grain spawn and any bulk from professional sources claiming all ingredients are fully sterilized. I almost hate to bother you with such a beginners question but I just can’t get around this one fungus. Just one more question I promise, is H2O2 a real solution? Thanks for any input

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