Mushroom Cultivation Contamination Guide

Identifying Contamination

Contamination is one of the most common challenges in mushroom cultivation. The key to managing it is early detection. Healthy mycelium should appear bright white, fluffy, and rope-like. Any deviation from this — unusual colours, slimy textures, or foul odours — warrants immediate investigation.

Visual inspection should happen daily during colonisation. Look through the substrate container for any patches that differ in colour or texture from the surrounding mycelium. Contamination often starts at the edges of jars or in areas where substrate was damaged during preparation. A single contaminated spot can spread to destroy an entire batch within 24–48 hours if left unaddressed.

Pay special attention to the smell. Healthy mycelium has a mild, earthy, mushroom-like scent. Sour, sweet, or putrid odours indicate bacterial contamination. A musty or chemical smell may indicate mould. Trust your nose — it is often the first indicator of a problem even before visual signs appear.

Common Contaminants

Trichoderma (Green Mould): The most feared cultivator contaminant, Trichoderma appears as bright green or blue-green patches. It grows rapidly and produces spores that spread easily through the air. Once established, it is nearly impossible to eliminate without destroying the entire substrate batch.

Cobweb Mould: This appears as thin, grey, wispy strands — distinctly different from the thicker, rope-like mycelium. Despite looking alarming, cobweb mould is relatively easy to manage. Lightly misting the affected area often encourages healthy mycelium to outcompete it. Increase airflow to prevent recurrence.

Bacterial Contamination: Wet rot and bacterial blotch appear as wet, slimy patches, often yellow, brown, or black. The substrate may become soggy and emit a sour odour. Bacterial contamination typically results from excess moisture, insufficient sterilisation, or poor technique during inoculation.

Pin Mould (Mucorale): This appears as fine white or grey filaments with small black heads. While it resembles healthy mycelium at first glance, pin mould lacks the organised rope-like structure and grows in diffuse, chaotic patterns.

Prevention Strategies

Prevention is always preferable to remediation. The most effective prevention strategies target the points at which contaminants typically enter the growing environment.

Sterilisation and pasteurisation are non-negotiable. Substrates must reach sufficient temperatures for adequate time to eliminate competing organisms. For PF Tek jars, 90 minutes at 15 PSI in a pressure cooker is standard. Bulk substrates like straw can be pasteurised at lower temperatures, while grain spawn requires full sterilisation.

Work in still air or use a flow hood during inoculation. The still air box (SAB) is a low-cost option for beginners — a clear plastic tote into which you insert your arms through holes cut in the side. Spray isopropyl alcohol inside before beginning work to settle airborne particles. Wear gloves and a face mask, and flame-sterilise inoculation tools between uses.

Maintain appropriate moisture levels. Substrate that is too wet creates ideal conditions for bacterial growth, while overly dry substrate stresses mycelium and makes it vulnerable. When squeezing a handful of prepared substrate, only a few drops of water should come out.

When to Discard

Isolating a contaminated jar or bag from your grow space is the first step. If Trichoderma or bacterial contamination is confirmed, discard immediately — seal the container in a plastic bag first to prevent spore spread during removal. For minor cobweb mould, you may attempt a targeted mist-and-increase-airflow response, but monitor closely over the next 48 hours.

Never try to pick out contamination or cut away affected substrate. This agitates spores and spreads contamination further. When in doubt, discard. A single lost jar is far preferable to a contaminated grow room that infects all future batches.

After discarding contaminated material, thoroughly clean and sanitise your grow space. Wipe down all surfaces with 70% isopropyl alcohol. Consider using a HEPA air purifier to reduce airborne spores. Review your technique to identify where the contamination likely entered — whether during inoculation, substrate preparation, or fruiting — to prevent recurrence.

Frequently Asked Questions

What does Trichoderma contamination look like?

Trichoderma appears as bright green or teal patches on substrate or mycelium. It often starts small and spreads rapidly. If you see any green coloration in your grow, assume it is Trichoderma and isolate or discard immediately.

Can cobweb mould be treated without discarding the batch?

Yes, cobweb mould is one of the more manageable contaminants. Lightly mist the affected area with clean water and increase fresh air exchange. Healthy mycelium typically outcompetes cobweb mould when given adequate airflow. Monitor daily for 48 hours after treatment.

Why is my substrate turning yellow?

Yellowing can indicate several issues: metabolite excretion from stressed mycelium (often harmless), early bacterial contamination, or bruising. If it is accompanied by slimy texture or bad odour, suspect bacteria. If the mycelium looks healthy and the yellowing is localised, it may be normal metabolite excretion.

How long does sterilisation need to last in a pressure cooker?

For grain spawn in quart jars, 90 minutes at 15 PSI is the standard recommendation. For larger volumes or denser substrates, extend to 2–2.5 hours. Allow the pressure cooker to depressurise naturally, then let jars cool completely before inoculating — hot jars can kill your culture.

What is the most common cause of contamination for beginners?

Inadequate sterilisation and poor inoculation technique are the most common causes for beginners. This includes not pressure-cooking long enough, inoculating while jars are still warm, not flame-sterilising needles, and working in an environment with too much air movement.

Can I reuse contaminated substrate?

No. Contaminated substrate should be discarded, not reused. Even after composting, some contaminants can persist. Double-bag contaminated substrate and dispose of it away from your growing area to prevent reinfection.

How do I sterilise a still air box?

Spray the interior of your still air box liberally with 70% isopropyl alcohol. Let it sit for a few minutes to allow airborne particles to settle. Then wipe down surfaces, re-spray lightly, and allow to air dry before beginning work inside it.

Is green on the outside of a jar always contamination?

If the green is on the inside of the jar on the substrate or mycelium, it is almost certainly Trichoderma. If it is an algae-like growth on the exterior of a glass jar in a humid environment, it may be harmless algae on the glass surface. Inspect the interior substrate carefully before making a decision.

What humidity level prevents bacterial contamination?

During colonisation, substrate should have field capacity moisture — not dripping wet. The fruiting chamber should maintain 80–95% relative humidity for fruiting, but substrate itself should not be waterlogged. Good airflow is critical to prevent stagnant, wet conditions that favour bacteria.

How can I tell the difference between mycelium and cobweb mould?

Healthy mycelium is dense, rope-like, and bright white with a structured appearance. Cobweb mould is thin, wispy, and grey — more like a spider web than cotton. Cobweb mould also tends to grow in diffuse patches rather than colonising in organised fronts like healthy mycelium.