How to Prevent Contamination in Mycology

A Complete Guide to Clean Mushroom Cultivation

Contamination in cultivation is one of the most common and frustrating challenges faced by mushroom growers at every experience level. Whether you’re working with agar plates, spore syringes, liquid culture, grain spawn, or ready-to-use grow bags, understanding how to prevent contamination in mycology is essential for consistent results and healthy mycelium.

Contamination in mushroom spores and contamination in mushroom substrate can appear at any stage of the process. Early identification is critical. If you’re asking what does contamination look like or what can I do about contamination, this guide provides clear answers, practical prevention strategies, and proven workflows used by experienced cultivators and laboratories.

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What Is Contamination in Mycology?

In mycology, contamination refers to unwanted organisms growing alongside—or instead of—your intended fungal culture. These organisms compete for nutrients, release inhibitory compounds, and can completely stall or destroy mycelial growth.

Common contaminants include:

• Moulds (such as Trichoderma)

• Bacteria

• Yeasts

• Wild airborne spores

Because fungal spores are microscopic and constantly present in the environment, contamination can never be eliminated entirely. Prevention is about reducing exposure, strengthening sterile technique, and ensuring healthy, fast-growing mycelium that can outcompete invaders.

Why Contamination Happens in Mushroom Cultivation

Most contamination events can be traced back to one or more of the following causes:

• Poor or rushed sterile technique

• Inadequate cleaning or sanitation

• Improper sterilisation or pasteurisation

• Dirty air or uncontrolled airflow

• Overly wet substrates or stressed mycelium

Healthy mycelium grown under clean conditions is surprisingly resilient. In the majority of cases, contamination is the result of process errors rather than chance.

The Most Common Types of Contamination in Mycology

1. Green Mould (Trichoderma)

Trichoderma is one of the most aggressive and destructive contaminants in mushroom cultivation. It often begins as white mycelium before turning green as it sporulates.

Common sources include:

• Poorly sterilised grain

• Contaminated agar transfers

• Dirty grow spaces or tools

Once established, Trichoderma spreads rapidly and should be isolated or discarded immediately.

2. Black Mould

Black mould is usually a sign of severe contamination and poor environmental hygiene. It is commonly associated with:

• Damp, stagnant grow areas

• Old or improperly stored substrates

Black mould contamination typically requires full disposal of affected materials.

3. Bacterial Contamination

Bacterial contamination often presents as:

• Slimy or wet patches

• Sour, sweet, or fermented odours

• Stalled or patchy mycelial growth

It is commonly caused by:

• Overhydrated grain

• Dirty syringes or spore sources

• Poor gas exchange during incubation

4. Yeast Contamination

Yeasts grow quickly and are most often seen in liquid culture, appearing cloudy or creamy rather than fibrous.

They are usually introduced through:

• Non-sterile inoculation

• Inadequately cleaned containers

Core Principles of Contamination Prevention in Mycology

Every successful cultivation workflow follows these four core rules:

1. Clean everything

2. Never heat or wipe new needles

3. Sterilise what needs sterilising

4. Control airflow

5. Work slowly and deliberately

Mastering these principles will dramatically reduce contamination across all stages of cultivation.

Sterile Technique: The Foundation of Clean Mycology

Sterile technique is not optional. It is the foundation of contamination prevention.

Essential Sterile Technique Practices

• Wash hands thoroughly before every session

• Wear gloves and disinfect them frequently

• Use 70% isopropyl alcohol (not 99%)

• Flame-sterilise tools between every transfer

• Avoid unnecessary movement while working

Rushing or skipping steps almost always leads to contamination.

Working in a Still Air Box (SAB) or Laminar Flow Hood

Still Air Box (Beginner-Friendly)

A still air box reduces airborne contamination by eliminating airflow. When used correctly, it is one of the most effective and affordable tools for clean mycology.

Best practices include:

• Thoroughly cleaning the interior before use

• Allowing air to settle for 10–15 minutes

• Moving slowly and deliberately during work

Laminar Flow Hood (Advanced)

Laminar flow hoods provide HEPA-filtered air and are ideal for frequent agar work and culture expansion. While more expensive, they significantly reduce contamination when used correctly.

Preventing Contamination When Working With Agar

Agar work is where clean cultures are established and contamination is most easily identified.

Best practices:

• Use properly sterilised agar plates

• Open plates minimally and at an angle

• Flame-sterilise scalpels before every transfer

• Transfer only from strong, clean mycelium

• Reduce condensation by cooling plates correctly

Agar allows contamination to be isolated early, making it one of the most powerful tools in contamination control.

Preventing Contamination in Grain Spawn

Grain spawn is a high-risk stage due to its nutrient density.

Key prevention tips:

• Hydrate grain properly (never overly wet)

• Sterilise at the correct pressure and duration

• Allow jars or bags to cool fully before inoculation

• Shake grain only after mycelium has established

Any grain that smells sour, sweet, or fermented should be discarded immediately.

Clean Spore Handling: Prints, Syringes, and Swabs

Spores are not sterile by nature. Proper handling is essential.

Best practices:

• Always assume spores carry contaminants

• Use agar to clean spores before expansion

• Store spore prints in dry, sealed conditions

• Avoid touching prints directly

• Flame-sterilise needles where applicable

Clean spores combined with agar work result in significantly cleaner cultures.

Spore Syringe Contamination: Needle Handling Explained

To heat or not to heat the needle?

Never wipe or heat the needles supplied with our spore syringes.

The needles provided are British medical-grade quality and are gamma-irradiated and sealed individually. They are sterile as supplied. Simply remove the black syringe tip and attach the needle when ready to use. Only remove the needle protector immediately before inoculation.

Heating or wiping sterile needles can compromise sterility rather than improve it.

Spore syringes for Microscopy

Environmental Cleanliness and Grow Space Hygiene

Your cultivation environment plays a major role in contamination prevention.

Maintain a clean grow space by:

• Regularly disinfecting surfaces

• Avoiding carpets and fabrics

• Managing humidity without standing moisture

• Keeping pets and plants out of grow areas

Dust, excess moisture, and neglect are prime contributors to contamination.

Sterilisation vs Pasteurisation

Understanding the difference is critical:

• Sterilisation (pressure cooking): destroys all organisms

• Pasteurisation: reduces harmful organisms while preserving beneficial microbes

Grain and agar must be sterilised. Bulk substrates are typically pasteurised. Using the wrong method increases contamination risk.

What Does Contamination Look Like?

Contamination can appear as:

• Any colour other than white mycelium

• Fuzzy or hairy patches in green, blue, black, yellow, or red

• Unpleasant or sour odours

• Slimy or wet textures

Bruising may appear blue, and spores themselves are often dark purple or black. When in doubt, isolate or discard.

What Can I Do About Contamination?

If contamination is detected:

• Isolate the affected material immediately

• Do not open contaminated containers indoors

• Dispose of contaminated substrate safely

• Review your sterile technique and workflow

Trying to salvage contaminated grows usually results in further spread.

Common Mistakes That Cause Contamination

Avoid these frequent errors:

• Working too quickly

• Skipping alcohol sanitation

• Reusing dirty tools

• Overhydrating substrates

• Opening containers unnecessarily

• Ignoring early warning signs

Clean mycology rewards patience and consistency.

Long-Term Contamination Prevention Habits

Successful cultivators develop habits that reduce contamination over time:

• Consistent workflows

• Proper storage of equipment and cultures

• Routine cleaning schedules

• Learning from failed attempts

Contamination is part of the learning process—but it should become increasingly rare.

Are there Contamination free grow kits sold in the UK??

There are several grow kits with reduced contamination risk. The Inject & Forget kits as well as the All in one kits sold in our store are designed to stay sealed until you want to harvest the grow kit. This type of grow kit reduces the risk of airborne contamination to 0% giving you the best chances of success even on your first time. 

Final Thoughts: Clean Technique Equals Consistent Success

Learning how to prevent contamination in mycology is a skill refined through practice. Each clean transfer, healthy culture, and successful grow reinforces good habits.

By controlling your environment, applying disciplined sterile technique, and respecting fungal biology, you greatly increase your chances of success.

Clean work is not complicated—it is careful, calm, and consistent.