Mushroom Contamination: Signs, Causes and Clean Technique

Mushroom contamination is another organism, usually mold or bacteria, growing in your substrate or spawn instead of, or alongside, your mushroom mycelium. UF/IFAS says blue, green, black or yellow spots are the sign, and that heavily contaminated bags are best discarded. Our sources manage it with clean technique and discarding, not cures. This guide covers the signs, why it happens, and the technique extension sources describe. It belongs to our wider guide to growing mushrooms.

Signs of contamination

UF says to look closely at bags for blue, green, black or yellow spots. Trichoderma, one of the common contaminants, shows as rapid greenish growth.

UF’s advice is that contaminated bags, especially highly contaminated ones, are best removed and discarded. Our sources give no way to rescue a contaminated bag and no way to tell a harmless patch from a harmful one by sight, so we offer neither. If you are unsure what you are seeing, treat our list as a prompt to check against the instructions that came with your kit or spawn.

Why contamination happens

Our sources give a few causes, and we state only those.

• Airborne contamination. UF says transfers are ideally done inside a still-air transfer chamber or a laminar flow hood to avoid airborne contamination.
• Skipping substrate treatment. Every protocol in our sources heat-treats or otherwise cleans substrate before inoculating, which is a step you cannot skip. See mushroom substrate.
• Waiting too long on logs. Cornell says the longer you wait to inoculate a log, the more likely it is to be infested with competitive fungi or dry out.
• Open holes. Wisconsin and Cornell both say to seal inoculation holes with wax to prevent contamination and drying out.
• Outdoor straw. Cornell says straw inoculated outdoors involves little contamination concern, but outdoor straw gets insect larvae.

Our sources do not rank these causes, so we cannot say which is most common.

Clean technique

UF’s protocol for oyster spawn and agar work is the main source here. It is a home-scale protocol, but it still assumes lab-style equipment.

Clean the work surface

UF uses 70% ethanol to clean the working table before inoculating. Wear gloves, and work in a transfer hood or chamber.

Sterilize your tools by flame

UF says the metal transfer tool needs to be sterilized immediately before each transfer, with its tip heated red-hot in a flame from an alcohol lamp or burner.

Use a still-air box or hood

UF says to do transfers ideally inside a still-air transfer chamber or a laminar flow hood to avoid airborne contamination. It also mentions working within a still-air transfer box. The idea of both is to give you a space with little moving air, so that spores floating in the room do not land on your work. Our sources give no build plans or flow-hood procedure beyond that description, so we do not give any.

Sterilize in a pressure cooker

UF sterilizes seeds inside containers by heat and vapor pressure in a pressure cooker. In general, 30 minutes at 15 psi is suggested. Let the cooker cool, and do not open it while there is positive pressure inside, or the media may boil over.

The two schedules are for different containers and scales, so do not mix them.

Agar basics

Agar is a gel medium on which mycelium grows in a dish. UF makes spawn by inoculating grain with mycelium from pure cultures, and agar is how those cultures are kept. UF’s potato dextrose agar (PDA) recipe:

Boil for about 5 minutes, sterilize, and let the sterilized media cool to about 50°C (122°F) before pouring into plates or suitable containers. Stored mother cultures are kept at 4°C (39°F) and subcultured every 6 to 12 months (UF). See mushroom spawn for how cultures become spawn.

Contamination risk by stage

Home scale and commercial scale

Illinois Extension and Cornell write for growers running many blocks or logs, and their schedules and tolerances are not the same as a hobbyist’s. UF’s oyster protocols are home-scale in the sense that a person with a pressure cooker and a transfer chamber can follow them. Where a sourced step needs equipment you do not have, the sources do not offer a lower-tech substitute, so we do not invent one.

A short routine

1. Clean the surface with 70% ethanol and put on gloves.
2. Work inside a still-air chamber or hood, if you have one.
3. Flame the transfer tool until red-hot just before each transfer.
4. Seal what you inoculate: wax on log holes, closed containers elsewhere.
5. Check the bags or jars for spots. Remove and discard any that are heavily contaminated.

When a batch is contaminated

UF’s guidance is short: remove and discard heavily contaminated bags. Our sources do not say how to dispose of them, whether lightly contaminated bags can recover, or whether mushrooms from a bag with a few spots are safe to eat, so we make no claims on any of these. Start the next batch with fresh substrate and the same clean routine, and change one thing at a time if the problem repeats.

Contamination in kits and logs

If you grow from a kit, your main job is to watch for the spots UF describes and discard a heavily contaminated bag. If you grow on logs, the clean steps are timing and wax: inoculate soon after cutting and seal every hole. Making your own spawn and working with agar is where the full routine above applies.

What our sources do not cover

Our sources do not give instructions for building a still-air box, for operating a flow hood, or for treating a contaminated batch. They also do not tell home growers whether a kit or log needs these steps at all. Logs are inoculated outdoors with wax, and kits arrive colonized, so most of this guide matters most for growers making their own spawn. See grow kits and logs for the simpler routes.