From The Shroomery Wiki
Jump to navigation Jump to search

Most specialty mushrooms are grown on sterilized substrates, and once a contaminant gets a foothold, it flourishes in the absence of competition from other contaminants. In nature, complex interactions among hundreds of other fungi, bacteria, nematodes, etc. maintain an ecological equilibrium. In a sterilized medium, the grower provides ideal conditions for the contaminant to prosper. In sawdust bags, contamination usually involves another fungus living off the waste products or on the remains of the cultivated fungus, or sometimes on the living mycelium or fruiting body of the cultivated fungus. The only competition for these contaminants is the cultivated fungus itself.

Signs of Contamination[edit | edit source]


When two different fungal species are growing in the same substrate they tend to form distinct borders between the two mycelia. Often a line of metabolites may be seen where the two fungi meet. Hourglass shaped mold sectors in PF jars are almost always the result of a compromised dry vermiculite layer whereas circular mold colonies are usually the result of a mold growing from one of the inoculation points.


Sporophores are the spore producing structures of a fungus. In some cases they're large enough to see individually without magnification. When the spores mature most change color making it obvious they're present. However, with a good eye they can be identified before that occurs. The appearance of the larger sporophores before maturation typically resembles a small whisker with a white dot on the end.


Odor can be extremely helpful in detecting a contaminant when it's not visible. It can also be helpful in telling mushroom mycelium from molds that resemble mushroom mycelium. It is sometimes possible to catch a hidden mold in a spawn jar simply by smelling the spawn before use. Odors are easiest to detect immediately after breaking apart the grains.


A common sign of bacteria and yeasts is a slimy appearance of mycelium or grains. In areas where substrate presses against glass and condensation is present brown-yellow slimy rings may be present around the grains. Oils and starches from burst grains may appear similar and but will already be present at the end of sterilization whereas contaminants will appear later.

Dusty Texture

As already mentioned sporophores are usually too small to see individually. However they can often be seen collectively as a powdery layer covering the substrate or mycelium. Looking for this texture is very helpful in distinguishing them from bruising or other discolorations the mushroom mycelium may develop.


These are the most obvious signs. Molds often change colors once they've started to produce spores as the spores mature. Some also change the color of the substrate through the production of metabolites. Bruising does not normally occur in still colonizing spawn or PF jars.


Bright white mycelium that colonizes over a colonized substrate, casing layer or the vermiculite fruiting PF cakes have been rolled in is often the first sign of Trichoderma. Watch for the formation of green spores if these appear. Some cultures of Psilocybe Natalensis will overlay heavily without any contamination present.

Soft Patches

Contaminated substrate may become squishy or soft and crumble apart easily. The bright white patches Trichoderma can produce has the consistency of a squishy skin. PF cakes may crumble apart easily when contaminated.

Pinning In Partially Colonized Spawn or PF jars

In a properly prepared PF or spawn jar this is contamination related. Unfortunately since the short half-pints have become difficult to find the tall jars are often used in the PF tek in which case that alone can cause pinning before full colonization. It's even common when pints are used for it so consider that first if no other signs are present.

Spongy Mycelium

Molds, especially pins molds, can create a very dense mycelium in jars that seems to press against the glass and fill up the empty volume of the jar. The mycelium has a smooth texture compared to mushroom mycelium.

Not Signs of Contamination[edit | edit source]

Bruising Bruising occurs when cell walls in mycelia/mushroom tissue are damaged. Most often this is result of touching, particularly while harvesting the mushroom, and can also occur from dehydration. Dehydration bruising is often widespread in the mycelium and occurs mostly around the base of pins and mushroom on that substrate. Bruising may be green or blue and very heavy bruising may appear black. Extreme bruising is normally found on the stumps of harvested mushrooms.


Spores produced by Cubensis are a dark violet with the exception of certain mutant/novelty strains. Spores often first appear on the torn veil but if left to sporulate mushrooms will drop large amounts of spores on the substrate and other mushrooms. Air currents may carry spores and deposit them on the tops of the caps.

"Mutant" Blobs

Blobs usually appear when pinning first begin with less blobs being produced later. Mutant blobs are the result of genetic abnormalities and are particularly common in degenerated cultures and certain varieties such as Penis Envy. Environmental conditions also seem to play a role in blob development. On PF cakes they are mostly seen in when cakes are fruited immediately after full colonization.


Rhizomorphs are large threads of mycelium that carry nutrients to pins hence they occur when pinning has begun. Very large rhizomorphs may occur when nutrients are being transferred to a pin growing on a non-nutritious surface such as a glass jar or the sides of a plastic tub. Aerial rhizomorphs are usually seen when a casing layer is used. They appear as cottony strands poking out of the casing layer many of which eventually knot and grow into pins.


Although a large amount of metabolites often indicates contamination, small amounts are common on fully colonized substrates and spawn/PF jars. Metabolites are normally yellow but red metabolites sometimes occur in spawn jars. Metabolites may also appear as a yelllow discoloration of the mycelium.


Pins that stop growing, develop a black cap, but are not slimy or show other signs of disease do not seem to be caused by pathogens.

Invitro Pinning

Tan growths pressing against the glass, usually developing a dark circle in the center and eventually forming into obvious pins.

Causes of Contamination[edit | edit source]

Contaminated inoculant

Causes: Mold or bacteria in PF jars

        Mold or bacteria in grain spawn

        Mold or bacteria during or after spawn run (uncommon)

When a spore syringe is contaminated most or all jars inoculated with that syringe usually show the same contaminants. They are common problem for new cultivators. Obtain syringes from a reputable vendor and use peer reviewed techniques for making your own.

When spores transferred from a particular area of a spore print are contaminated the result is usually a single contaminated jar or plate. Any syringes made from that transfer will usually be contaminated. Limit transfers to small amounts of spores only to help avoid this. Avoid taking spores from outer edges of the printed area.

Liquid cultures are easily contaminated as all contaminants in the inoculant used to create them will be directly exposed to the medium (the broth). Contaminated liquid culture jars usually appear normal even when contaminated although heavy bacterial contamination can give it a cloudy appearance or create blob-like formations.

Agar cultures can be contaminated without showing signs. The contaminant could be something that landed on a colonized area or something growing beneath the mycelium. To avoid this isolate mycelium from spore or tissue inoculated plates by transferring a small piece of mycelium from the outer edge of the colony with an inoculation loop. Fully colonized plates should be avoided as the hyphae can grow up and out the sides of the plate. It may be helpful to smell the inoculation after a transfer if you suspect a contaminant may be present.

Botched inoculation

Causes: Mold or bacteria in grain spawn

        Mold or bacteria in PF jars

        Mold during or after spawn run

        Bacteria or stalling during spawn run

When steps have been taken to prevent cross-contamination this will result in a single contaminated jar, and at some or all inoculation points in PF jars. Things that can contaminate an inoculation include: touching a needle, scalpel, or inoculation with something that isn't not sterile, touching the sterile inside part of a jar with your gloves, exposure of sterile items to airborne contaminants, moving unsterile item over sterile areas, or moving unsterile items between the filter and sterile while using a flow hood.

Botched grain to grain transfer

Causes: Mold in spawn jars     

        Slow recolonization or stalling in spawn jars

        Slow colonization during spawn run

        Bacteria or stalling during spawn run

        Mold during or after spawn run (most common)


Similar causes to botched inoculations. The contaminant typically does not show up until the jar has been spawned. Contaminated g2gs often lead to a large number of jars becoming contaminated. G2Gs should always be done in a still air box or in front of a flow hood. Jars should be checked for odors before spawning. It's particularly important that jars and lids be disinfected as the vibrations created during the transfer can easily shake loose contaminants into the receiving jars.

Insufficient sterilization

Causes: Bacteria and stalling in spawn jars (most common)

        Bacteria and stalling in PF jars     

When sterilization temperature/times are not adequate bacterial contamination may occur. The bacteria is usually widespread in the substrate appearing days to weeks after the sterilization. It's important that steam fills the entire pressure cooker/pot before you start timing the procedure.

Larger substrates require longer times for the heat penetrate to the center, i.e. a gallon jar requires longer than 4 quart jars even though it's same amount of substrate.

Whole grain jars contain a lot of empty space between the grains which slow down heat penetration and require either a pressure cooker or very long sterilization times.

Compromised dry vermiculite layer

Causes: Mold or bacteria in PF jars (most common)

        Mold on dry vermiculite layer of PF jars

        Mold on PF cakes after birthing

When doing the PF the dry vermiculite layer on top acts as a filter. If it fails before the jar is fully colonized contaminants may start to grow in the uncolonized areas. This a common cause of contamination that first appears away from the inoculation points.

If the layer is shifted while moving the jar it creates an opportunity for the contaminated vermiculite on the surface to reach the sterile substrate. For that reason it's a good idea to have the layer fill the entire of the jar so the lid will help hold it in place. Coarse vermiculite in less effective so fine vermiculite should be used. If the layer becomes damp it will not prevent contaminants from reach the substrate.

Filter failure

Causes: Mold in spawn jars

        Bacteria or stalling in spawn jars       

When a filter becomes damaged, wet, or leaves any kind of open gap around the air holes

Improper pasteurization

Causes: Mold in later flushes (most common)

        Mold during spawn run or early flushes

Pasteurization temperatures range from 130-170F. The lower end of that range is not always sufficient in preventing survival of heat resistant molds.

In contrast, when temperatures are too high or sustained for too long it destroys more of the beneficial bacteria which would normally survive. Manure and compost substrates are most vulnerable to this. A common result from excessive pasteurization temperatures is incomplete colonization of the bulk substrate (early pinning) followed by visible Trichoderma infection.

Cross contamination after pasteurization

Causes: Mold during or after spawn run

When spawning it's important to limit exposure of the spawn grains and pasteurized substrate to contaminants. Hands, clothes, and hair are major vector for recontamination of pasteurized substrate. Cooling substrate should be protected from dust as much as possible.

Casing material is also vulnerable and contaminated casing material may lead to diseases like cobweb or verticillium. If using unpasteurized casing material it should be used straight from freshly opened or sealed bags.

Insufficient gas exchange during spawn run

Causes: Bacteria or stalling during spawn run

        Mold during spawn run

        Fermentation odor during spawn run

A lack a gas exchange while bulk substrates are colonizing creates anaerobic conditions which can stall the recovery and colonization of the mushroom mycelium and promote the growth of anaerobic bacteria. A fermentation odor may develop. In serious cases the mushroom mycelium does not recover allowing mold to colonize the grains.

Insufficient cooling of bulk substrate

Causes: Bacteria or stalling during spawn run

        Mold during spawn run

Mushroom mycelium is easily killed by high temperatures. All of the bulk substrate must be cooled to room temperature before spawning.