The following guide is unfinished. Feel free to offer information, high quality pictures or to correct any misinformation. Plenty of guides like this have been posted in the past. The difference here is this one will focus on Cubensis in particular although most of the information could apply to any mushroom species being grown.
Signs of Contamination
Sectoring - 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.
When the contaminant is bacterial the contaminated area appears uncolonized and are often rectangular shaped. When the mycelium encounters the infected area the edge loses it's thread-like appearance and metabolites are often present.
Sporophores - 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 - 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 spawning. Odors are easiest to detect immediately after shaking.
Odor can also be helpful when it comes to agar work. While not all molds produce an odor I haven't found a P. Cubensis culture that didn't smell like mushrooms.
Slime - A common sign of bacteria is a slimy appearance of mycelium or grains. In areas where substrate presses against glass and condensation is present brown-yellow slimy rings are often present around the grains. On the other grains it may be noticed as a sort of gel or a crust on the grain's surface. Oils and starches from burst grains may appear similar and but will already be present at the end of sterilization whereas bacteria 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.
Discolorations - 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 occur in still colonizing spawn or PF jars with exception of after a g2g when using a master jar that has been allowed reach the pinning stage (regardless of whether or not any hyphal knots have actually formed).
There are also discolorations not caused by contamination, see "Not Signs of Contamination" below.
Overlay - 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 on this area.
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.
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 all 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
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 - 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 - 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.
Metabolites - 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.
Aborts - 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.
In vitro pinning - Tan growths pressing against the glass, usually developing a dark circle in the center and eventually forming into obvious pins.
Identifying Contaminants
PenicilliumOdors: Musty, Dirt
Sources: Soil, Food, Compost, Air
The most common mold found in indoor air, Penicillium species produce tiny spores which are easily dispersed and stay airborne for relatively long periods of time. Early growth is white and nearly indistinguishable from mushroom mycelium. Colonies are usually circular with a white edge. Most species sporulate very soon after first appearance producing green, yellow, or most commonly blue-green spores. This contaminant is common on agar and in spawn jars where it's ability to spread quickly allows it to overwhelm any mushroom mycelium that may be growing. Contamination after spawning is uncommon and is usually limited to uncolonized grains with little effect on yield. Wood trays can harbor this mold and should never be used in home cultivation.
Known contaminant species include:
P.
expansumP.
chrysogenumAspergillusOdors: Musty, Oily
Sources: Soil, Wood, Dust, Air
Also very common indoor air, like Penicillium, Aspergillus species produce tiny spores which can travel relatively large distances before settling. Many species which are common contaminants of mushroom substrates. Mycelium is usually light grey with linear threadlike growth and may be mistaken for mushroom mycelium. Some colonies may appear ringlike with denser mycelium near the edges. Aspergillus produces it's spores on large sporophores which change color as they mature. Color and size of sporophores varies by species and substrate with yellow, black, green, blue and grey all being common, making it easy to mistake with other mold species. Aspergillus is a common contaminant of grain spawn and can be recognized by it's very grainy appearance as spore production begins.
Known contaminant species include:
A.
flavus, a yellow to green mold, can produce large amounts of toxins
A.
niger, dark brown pins on a white-yellow mycelium
A.
fumigatus, blue/grey to green/grey, highly pathogenic to people with suppressed immune systems
A.
versicolor, produces a wide a variety of colors
TrichodermaSources: Soil, Dust, Clothing
Odors: Coconut, Musty
Although the spores are far less common indoors than the previous molds Trichoderma's aggressive nature makes it one of the most common contaminants in mushroom cultivation. It's mycelium is a tranparent to light grey color and can be very difficult to see depending on the substrate. The first visible sign is often a thick bright white aerial mycelium that grows over the surface of the substrate. Spore are produced on this mycelium turning it a yellow to green color often with a noticeable bright white 'apron' still surrounding the colony. The wet spores it produces are too heavy to become airborne on their own but are able adhere to airborne dust particles and become airborne that way. The sticky nature of the spores make them a common contaminant in still air box work as they easily stick to gloves and jars. Sporulation occurs from various triggers including light, nutrients in the substrate, full colonization, and damage to colonies. Often times sporulation will not be triggered until after spawning, leaving unsuspecting cultivators unaware their healthy appearing spawn is actually contaminated. Smell testing jars before use is essential for catching this mold before spawning although not all species produce a distinct odor.
Contamination is also common after spawning, Freshly spawned grains are quite vulnerable when Trichoderma spores are present in large amounts and cross contamination can occur after handling sources of the spores such as dust and soil. The spores are killed very easily by pasteurization however sterilizing many bulk substrate will actually leave them more vulnerable. Generally Trichoderma does not grow aggressively until it has reached the grain spawn so contamination related to improper pasteurization tends to occur in later flushes.
Casing layers are also vulnerable to Trichoderma. Casing material should always be pasteurized. Although very few species can actually grow on living mushrooms, the enzymes produced can degrade the quality of the mushrooms causing brown spotting and aborts. In case where mold is present on a mushroom will be obvious dark brown damage to the mushroom. In the case of Cubensis it will generally be on old aborted mushrooms. Trichoderma is generally harmless aside allergic reaction to airborne spores so no need to get overly worried about if a mushroom may have hidden mold in it or anything like that. If the mushroom looks healthy keep it. It should be noted however that Trichoderma infected mushrooms may produce the appearance of mold after harvest if not promptly dried and is most likely the case when Trich appears on any harvested mushroom.
Known contaminant species include:
T.
viride, more common in bulk substrates, produces a coconut-like odor
T.
harzianum, more common on casing layer and as a pathogen of fruit bodies, produces a more typical musty mold odor
T.
koningi, no odor, fast spore germination
MucorSources: Soil, Plants, Air
Often referred to as pin mold for the grey to black sporophores which look like tiny pinheads. It's appearance is very similar to Rhizopus.
Commonly a contaminant of spawn and less common in bulk substrates. It typically won't colonize coir/vermiculite substrate but the sporophore may grow to the surface directly from the contaminated spawn below.
RhizopusSources: Soil, Air
Odors: Alcohol, Sour
The fastest growing of the common contaminants. It's appearance is very similar to that of Mucor. It is also capable to parasitizing damaged or aborted mushrooms. It often produces large volumes of aerial mycelium.
Known contaminant species include:
R.
stolonifer, grows very rapidly
R.
oryzaeFusariumSources: Soil, Plants, Unsterilized Grain, Humidifiers
This mold has a white mycelium very similar to mushroom mycelium and produces bright colors commonly purple, pink, orange, and yellow. Color change commonly occurs after 3 weeks of growth and may not be seen on short-lived agar cultures. Fusarium may inhibit mushroom growth causing mushrooms to remain small with tiny caps and a brown discoloration inside the stem. This can occur even when the mold itself is not visible.
Fusarium contamination is most commonly seen in PF jars as a result of contaminated syringes. The mold looks like mushroom mycelium and grows at a similar speed. After a couple weeks, the jar being about 1/2 - 3/4 colonized the purplish color develops. The spores are generally not airborne but can stick to airborne dust and water droplets.
CladosporiumOdors: Musty
A relatively common contaminant mold of spawn. Cladosporium's most distinguishing feature is dark-green spores which turn grey or black with age.
AlternariaOdors: Musty
Usually black or dark grey. Common on agar and spawn and spreads though airborne spores.
ChaetomiumA green mold which can be recognized by the appearance of numerous small green to tan bur like structure spread across the substrate during the spawn run. In many cases mushroom mycelium may colonize into these areas eventually. Chaetomium spore are very heat resistant (for a fungus) and can survive short pasteurization times and/or low pasteurization temperatures. For the most part you'll run into this this in straw or compost as a result of it's preparation and pasteurization.
MoniliaA powdery white, grey, or pink mold.
One form (Neurospora) produces a rapidly growing aerial mycelium which eventually turns bright red or orange.
Neurospora on casing layer
ScopulariopsisForms patches of white mold with a powdery appearance. Color may turn slightly pink after a week. It occurs in substrates with a high pH or high ammonia content. Yield is reduce significantly and in worst cases no mushrooms develop at all.
CoprinusOdors: Various
Coprinus are the most common mushroom producing contaminant. They're appearance indicates there is excess ammonia in the substrate, usually manure, which doesn't support the growth of normal mushroom mycelium. They typically appear during the spawn run and will continue to appear until the ammonia is used up at which point the substrate will become habitable to the normal mushroom mycelium. There are many species so the appearance will vary but they're fairly easy to recognize.
Effect on yield is usually minor. Coprinus fruit bodies should be removed when spotted however since they grow poorly if it all in properly prepared substrate they pose little risk to other substrates.
SchizophyllumSchizophyllum commune is a mushroom producing contaminant. Indoor occurrences are usually the result of contaminated inoculant.
DiehliomycesOdors: Chlorine
A pathogen that infects the mushroom mycelium. Mycelium is initially white. Brown lumpy fruit bodies 3-44mm in size appear on the substrate which eventually appear wrinkled and then crumble into powder. It can be prevented with proper pasteurization. Mushroom mycelium may eventually disappear from the substrate.
BacillusOdors: Feet, Rotten Apple
Bacillus, the most common contaminant species being Bacillus subtilis, is a bacteria and a common contaminant of spawn producing a foul smell and brownish slime or crust on the grains. Appearance of the bacteria may indicate your sterilization was insufficient and it's occurance is more likely when spawn is incubated at temperatures above room temperature.
It can also be introduced in a contaminated culture or spores. If the spawn hasn't been shaken since inoculation this is indicated by it's appearance starting on the upper grains and spreading downward. The most common contaminant species are non-motile and generally do not spread quickly in spawn unless shaken but may originate on multiple grains when sterilization related.
Known contaminant species include:
B.
subtilis, the most heat resistant species
B.
cereusYeastsOdors: Various
There are many yeasts you might tun into in spawn or on agar. Although many people assume their appearance will resemble baker's yeast (which is dehydrated), colonies actually appear very similar to bacteria. Some yeasts are easily recognized by tiny spots, usually white or yellow, appearing through the grain jar. Other yeasts are indistinguishable from bacteria. Their presence slows the mycelium's colonization or stops it completely. They are not contaminants of bulk substrates nevertheless when present in the spawn they are capable of stalling growth after spawning.
PseudomonasOdors: Rot, Fruity
Sources: Lime, Peat moss
Pseudomonas contains many bacteria which are harmless or even beneficial to the fruit bodies and small amounts are naturally present on the mushroom surface. Problems arise when water is in contact with the fruit body for prolonged periods of time, usually from condensation, misting, or soaking. Large amounts of the bacteria can produce enough enzymes to degrade the cell walls of the mushroom. Symptoms are often superficial with minor brown spotting that do not affect the taste, texture, or odor of the mushroom. If the wet conditions persist they can progress to larger brown slimy patches and grooves and can even lead to degradation of large parts of the cap.
Since the bacteria is naturally present, prevention depends on providing adequate air exchange to allow moisture droplets to evaporate quickly. Slimy pins should be removed, especially before misting since the splash can spread large amounts of the bacteria which accelerates the process on the other fruit bodies.
Known contaminant species include:
P.
tolaasii, primary agent of bacterial blotching
CladobotryumSources: Soil, Plants
Odors: Rot, Dirt
This is a parasitic fungus that grows on mushrooms and over casing layers. There are many species and symptoms vary depending on species of the mold and the mushroom. It causes what is known as cobweb disease which is characterized by a cobweb mycelium covering the mushroom leading to decay of the fruit body and heavy spore production. Spotting is particularly common when spores are present in the air. Growth on the casing layer and heavy infection usually occurs in later flushes. In all cases no signs of the mold appears before pinning has initiated. The mold is strictly a casing layer and fruit body contaminant, and does not prevent colonization of spawn or bulk substrate nor are they sources of the infection.
Known contaminant species include:
C.
dendroides, AKA Dactylium dendroides
C.
mycophylum, produces a dirt-like odor
VerticilliumSources: Soil, Plants, Flies
A parasitic mold occurring on all mushroom species the effects of which can vary greatly in severity and form. The most common symptom is brown spotting on the caps and stems. Unlike bacterial blotch the spotting is dry, usually indented, and in very high humidy a light grey fuzz forms in the center. The fungus often infects a single side of a mushroom causing that area to stop growing. As the healthy tissue continues to grow it can cause peeling of stem and lesions and cracking in the cap which may tilt to one side. When primordia become infected the result is small "bubbles" of infected mushroom tissue. Infected tissue on both the bubbles and on growing mushrooms is brown to grey with a dry leathery appearance. Yields are reduced mainly from degradation in mushroom quality and the total weight of the mushrooms grown is not greatly affected.
The cause of this disease is exposure of the developing fruit bodies to verticillium spores. Symptoms appear 7-14 days after the exposure. Unlike competitor molds the spores do not grow significantly on the substrate and effects are generally only noticed on the mushrooms themselves. Spores must come in direct contact with part of a fruit body and will then cause symptoms in that area. Spawn in not normally a vector of the contamination and the bulk substrate is only a possible vector when a casing layer is not used. Pasteurization will destroy any verticillium spores in a substrate or casing material but good hygiene is needed to prevent recontamination.
The primary source of the spores is soil. Spores are sticky and do not become airborne easily from simple air movement. They can be spread indoors though airborne dust, insects, on hands and clothes, and most importantly by the aerosols created by the water splash while misting. A single spray of water hitting a contaminated mushroom or surface can launch spores up to two feet away.
Known contaminant species include:
V.
fungicolaV.
psalliotae MycogoneOdors: Rot
Mycogone is a parasitic fungus which infect primordia and small pins causing monstrous deformations. Once infected the primordia develop into a blob-like mass of mushroom tissue, very large in some cases. When pins are infected they develop swollen stripes and deformed small caps. The mold mycelium appears as a white mat colonizing the outside of the mushroom. As the disease progresses brown discolorations form, colored metabolites may ooze from the mushroom, and eventually an unpleasant odor is produced. The mold spreads quickly often infecting most or all fruit bodies present.
Mycogone is most commonly seen when using a casing layer. It may also occur when pinning begins before full colonization and improve after colonization has finished. This is presumably due to the vulnerability of primordia when forming beneath a surface.
Known contaminant species include:
M.
perniciosaM.
rosea
Cause of Contamination
Contaminated inoculantCauses: 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 inoculationCauses: 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 transferCauses: 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 sterilizationCauses: 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 layerCauses: 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 failureCauses: 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 pasteurizationCauses: 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 pasteurizationCauses: 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 runCauses: 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 substrateCauses: 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.
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