Microbial Activity

To begin a review about Phase II composting first we should think about the organism we are trying to grow and why it has such a finicky food source.


The mushroom is a fungus not a green plant because it does not have chlorophyll. Chlorophyll is the green substance in plants that through photosynthesis produces plant food from sunlight. Green plants are the builders of energy however mushroom, as people, are users of this energy and produce CO2. Mushrooms lack the ability to use energy from the sun. Mushrooms extract their carbohydrates and proteins from a rich medium of decaying organic matter vegetation. This rich organic matter first must be prepared into a nutrient rich substrate that our mushroom can consume. When correctly made this food may become available exclusively to the mushroom and should not support the growth of much else. The sequence to produce this specific substrate for the mushroom is called composting or compost substrate preparation and is divided into two stages, Phase I and Phase II. Each stage has distinct goals or objectives. It is the grower's responsibility to provide the necessary ingredients and environmental conditions for these chemical and biological processes required to complete these goals. It is managing these ingredients and conditions that makes composting for growing mushrooms so demanding.

The Microbes

Decaying organic matter, or the raw ingredients have many naturally occurring organisms. Organisms too small to see with the unaided eye and can only be seen with a microscope are called microscopic organism or microbes. Bacteria, fungi and actinomycetes are only a few of the many types of microbes that exist in compost. Although they inhabit a different environment, microscopic organisms need some of the same things people need to live. Food, water, and air (oxygen) are the necessary requirements for these microbes to survive. However these microbes can not adjust to changes in the surrounding temperature where they live. Unlike people they can not go inside an environmentally controlled building or add and discard clothing as the temperature changes. Therefore microbes will only grow and survive at a particular temperature. Most beneficial microbes growing during Phase II are thermophilic, in other words they are heat loving microbes.

Since microbes get their food and water from compost substrate there needs to be adequate supplies of both ingredients to complete the composting process. Microbes, like people, need carbohydrates, nitrogen, elements, vitamins, fats and lipids, etc., as food. During Phase I microbes grow and multiply generating heat as they consume food and water. As long as water, oxygen and food are available they continue developing to a maximum population at the highest temperature they can tolerate. Then the self sustaining chemical reactions take over which continue to release heat, CO2 and water vapor. The mechanical turning and mixing of the compost pile should expose all material to these biological and chemical processes. Fresh water or recycled runoff water is added to replenish the water lost during the process. Water is added to maintain the moisture in the compost substrate for these biological and chemical reactions to take place. Phase I composting continues with the formation of ammonia and carbohydrates that the mushroom will eventually use as food. So why not just stop the process after Phase I and spawn the material? Obviously that does not work. We all realize that the mushroom does not like ammonia, so we continue indoors with Phase II composting.

Some of these organisms can be consider "beneficial microbes" that provide food for the mushroom. Others are "unfavorable microbes" that compete for food or may cause disease. The mushroom grower has the job of caring for the good microbes and eliminating the bad microbes. The chemical characteristics of the raw ingredients are converted by microbes and chemical reactions into the specific substrate the mushroom uses as a food source. Therefore it is important to manage these good microbes in compost substrate to achieve productive crops.

Goals of Phase II

Phase II composting is the second step of compost substrate preparation. Regardless how the Phase I composting is done, Phase II must achieve its own important goals. The first objective is to pasteurize the compost substrate making it more selective to give the mushroom a head start growing through this substrate. The compost substrate is pasteurized to reduce or eliminate the bad microbes like insects, other fungi, and bacteria. This is not the complete sterilization but a selective killing of pests that will compete for food or directly attack the mushroom, yet minimize the loss of good microbes.

The second goal of Phase II is to complete the composting process. Since ammonia is toxic to the mushroom mycelium it must be converted to a food the mushroom can use. The good microbes in Phase II convert toxic ammonia in solution and amines (other readily available nitrogen compounds) substances into protein, the more specific food for the mushroom. Most of this conversion of ammonia and carbohydrates is accomplished by the growth of the microbes in the compost. These microbes are very efficient in using Phase I composting products, like ammonia, as one of their main sources of food. The ammonia is incorporated as mostly protein into their bodies or cells. Eventually these packets of nutrients are used as food by the mushroom.

Phase II objectives seem simple to accomplish, but anyone who has tried managing a Phase II may recognize it is one of the most difficult procedures in growing mushroom. Because of a composting or other cultural problem growers sometimes have adjust Phase II programs. Phase II may be managed more than one way, however when changes have to be made controlling the activity of the good microbes should remain constant.

Let us consider both Phase II objectives together since the requirements for one goal may affect the conditions for achieving the other goal. Even through pasteurization occurs over a relatively short time, when and how we conduct the pasteurization affects the growth of the good microbes who condition or convert the food. The mushroom grower manages the temperature and ventilation in the room and compost substrate to achieve Phase II goals.

Ventilating for the Microbes

The function of ventilation is to regulate temperatures, provide uniform air movement, both vertically across the beds and horizontally through the beds. Figure 1 shows how ventilation also supplies the microbes with oxygen and removes CO2, heat and water vapor from the environment.

Figure 1: Phase II

Volume and quality of the compost substrate and the quality of air influence microbial activity that will determine ventilation requirements in a Phase II room. The air movement within the compost substrate depends on the amount of microbial activity. The heat produced by the microbes in the compost substrate causes the cool air around it to be drawn towards the heat. This movement of air ensures that adequate oxygen in the compost substrate for the microbes to grow. As long as there is good air movement within the compost substrate there should be adequate oxygen for the microbes.

Temperature and ventilation decisions will change according to the Phase II goal. Let us examine the change of microbial activity that affect our decisions during Phase II.

Microbial activity in compost substrate depends on the availability of their growth requirements, physical and chemical characteristics of the compost, and the stage of Phase II. The availability of food, water, oxygen and temperature largely depends on the compost substrate physical (length, texture and moisture) and chemical characteristics (degree of composting, aerobic or anaerobic, quantity and quality of food).

Using too much fresh air in a Phase II during the cold weather may cause more steam to be used to maintain temperature in the room. Excessive steam can condense on the surface of the straw. Free moisture on the straw will make the environment for the microbes too wet or anaerobic. Wet and dense compost substrate without proper ventilation and aeration after filling may result in anaerobic conditions. A lack of oxygen will favor microbes which directly or indirectly changes compost substrate and this change decreases the stability of compost substrate for mushroom growth. For example, after filling compost temperatures above the conditioning range and anaerobic conditions may result in readily available carbohydrates and a lower pH in the compost substrate. This combination may favor the growth of fungi like Trichoderma green mold.

Six Stages of Phase II

A conventional Phase II program for beds or trays can be divided into six stages; (1) Heat up; (2) Pre pasteurization; (3) Pasteurization (4) Post pasteurization; (5) Conditioning and (6) Cooling down. Since I am most familiar with a six stage Phase II program I will use it as an example for discussion. The "natural" cookout or other programs and Phase II composting in bulk have the similar goals that are achieved different ways. It is not to say that the six stage temperature program is better, but I have found it is one program growers are most often able to follow successfully.

1. Heat up

After a high temperature and aerobic Phase I composting, the first important step in Phase II is filling compost substrate into the beds, trays or tunnels. Compost substrate with uniform moisture, maturity and structure will make the filling job much easier. The depth and compaction in the beds, tunnels or trays are critical details to achieve proper ventilation and temperature control for the microbes. Extra attention in tightly packing compost substrate into the sides of the beds or trays will create more even temperatures across the bed. Cold sideboard compost temperatures are difficult to condition properly and often are the areas that do not have a thorough pasteurization. Attention to all filling details will ensure uniform heating and air movement in the compost substrate. The time it takes to get the compost substrate into the a temperature range that the microbes begin to grow rapidly depends on the thermogenic capacity of the compost.

2. Pre-pasteurization

The goal of the pre-pasteurization stage is to maintain the temperature in a range that the favorable microbes will multiply and reach their maximum populations. Amount of compost substrate dry weight, volume of air, compost substrate physical and chemical characteristics all influence when the maximum population of good microbes is reached after filling. During pre-pasteurization the compost substrate should appear to have moderate firefang and sometimes an abundance of surface moisture molds.

Pasteurization (peak heat, boost) should be completed toward the start of Phase II. A good rule of thumb is to pasteurize perhaps the second to fourth day after filling. Pasteurizing three or four days after filling is not a problem and will not shorten the time needed to complete the conversion of ammonia. As long as the beneficial microbes have the proper temperature and oxygen they will continue converting ammonia to protein before pasteurization.

The advantage of delaying the pasteurization until two to four days after filling is to reach this maximum population of microbes in the compost substrate before pasteurization. The characteristic reduction in air to compost substrate differential indicates that the biological activity is diminishing and compost substrate is ready for pasteurization. Another indication is that the ammonia smell in the compost substrate or room itself is much less than the day of or day after filling. At this time the microbes have reached peak populations and their food supply is dwindling. A missing growth requirement will result in fewer microbes which may delay the start of the pasteurization. Let's consider a theoretical situation to illustrate this concept, Figure 2.

Figure 2: Phase II

The population of microbes before a pasteurization will determine the number of microbes left after the peak heat. Assuming (because we do not know) that a normal pasteurization will eliminate 70% of the beneficial microbes. Therefore if we have 1 million microbes before pasteurization there will be about 300,000 left afterwards. If the pasteurization starts with only 500,000 microbes only about 150,000 will survive. Fewer microbes will take a longer to multiply and reach the maximum population delaying the conversion of ammonia to mushroom food after pasteurization.

3. Pasteurization

An effective pasteurization will eradicate harmful bacteria, nematodes, insects and fungi. In general a compost substrate temperature of 140° F for 4 hours is adequate for a complete pasteurization. To insure a complete pasteurization it is suggested to have a minimum of 2 hour crossover time, where both the air and compost substrate at 140° F together. Growers may make several compromises to this recommendation. Unless all the compost substrate surfaces and areas are exposed to this temperature range some destructive organisms may survive causing problems later in the crop.

If the compost substrate never rises much above 140° F there is minimum effect on the good microbes that convert ammonia. However on most commercial farms the compost substrate temperature reaches 140° F before the air temperature will. When this happens the compost substrate temperatures will continue to rise as the air temperature reaches and is held at 140° F. Usually the compost substrate temperature continues to climb into the high 140° F, or sometimes to 160° F and this maximum temperature is sometimes referred to as the "override." High override temperatures may kill or inactivate the good microbes. Sometimes it is necessary to have a high override because the cross over time is lengthen to insure inconsistent compost substrate is properly pasteurized. The compromise with a high override temperature is that it will take longer to convert ammonia to protein after the pasteurization, because more good microbes are killed or inactivated. To illustrate this concept we will consider the earlier example however we start pasteurization with the same number of microbes, e.g., 1 million. If we have a high override (160° F) about 90% of the good microbes are killed and we will have only 100,00 left, Figure 3.

Figure 3: Phase II

If we have a lower override only 50% of the good microbes may be killed, so 500,000 will survive. Therefore it takes less time for the population to reach the maximum growth phase and the conversion of ammonia and carbohydrates continue at a faster rate. This is not to suggest to use a shorter crossover time to lower the override and reducing the kill during pasteurization to speed up conditioning. The idea is to be prepared to handle the post-pasteurization more carefully after a higher override.

4. Post-pasteurization

After pasteurization many microbes have been killed or inactivated and they need to recover. A longer recovery time for the microbial activity causes compost substrate to have less heating ability immediately after pasteurization. It is at this stage that the compost substrate may want to drop faster or go to low. Therefore extra care should be taken after pasteurization to stop and level out the compost substrate temperatures above 133° - 135° F. Since fewer microbes are growing less oxygen is required and very little ventilation or fresh air is needed at this stage. Maintaining a flame in a Phase II room indicates there is enough oxygen in the room air. A slight tendency for the compost substrate temperature to rise indicates that the microbes are recovering and more activity is anticipated. More oxygen may be needed and a little more ventilation will be required. Since less food is available at this stage than before pasteurization less ventilation is required for the remaining part of Phase II.

5. Conditioning

The good microbes grow best at temperatures from 115° to 140° F. The longer the microbes in the compost substrate remain in this range with all the critical growth requirements available the faster the ammonia will be converted. The process of going through this temperature range will produce the most protein or the maximum amount of food for the mushroom. A good rule of thumb is not to drop the compost substrate temperature more than 5° F per 24 hours, which maintains the compost substrate in the desired range for about 4 or more days. Of course reality is different. There are many situations that arise where growers have to compromise Phase II management. Compromises are usually made when over or under composted material, wet or dry compost, or any combination of these conditions occur. Dry compost substrate will be difficult to control and there may not be enough moisture for the microbes at the end of the Phase II. Wet or over composted material may have trouble because there is a lack of air or carbohydrates for the microbes to grow. Short compost substrate or too many compost substrate fines or balls are difficult areas to condition properly. Some of the beneficial microbes growing during Phase II use other types of food besides ammonia. If this non-ammonia type food is left over competitor molds or weed molds may use these readily available compounds to grow and develop. Not only may these undesirable molds be a concern it also means there is less food available for the mushroom.

6. Cooling down

Near the completion of the phase II check for ammonia in the compost. The nose is usually the best tool, however there are ammonia testing kits and strips are available to supplement the nose test. The cooler areas of the room should be checked before they are lowered below 115° F. Once the next medium temperature compost substrate is near the lowest conditioning range, check that compost substrate before cooling any further. The warmest areas of the room may clear last and it is important to make sure those areas spend time in the lower temperature range.

Microbial Growth Patterns

The two main types of microbes found in compost substrate during Phase II are thermophilic fungi and actinomycetes. Their names are not as important as the way they grow. The actinomycetes generally prefer the higher temperature ranges. Their colonies of millions of individual cells or fragments appear as the white specs that some growers refer to as "firefang" or "flecking." If you look closely at these specks there are distinct or have well-defined edges, Figure 4. They do not spread out and usually only grow where they are first originate with suitable food, water and temperature.

Figure 4: Phase II

The thermophilic fungi are more thread-like. They have mycelium that looks similar to mushroom spawn growth so they are able to grow in a direction of the food or towards more favorable growing conditions. They are able to penetrate the dense parts of the compost, such as fines or balls found in compost substrate that is excessively decomposed or too short. Some thermophilic fungi grow in the lower temperature ranges of 115-125° F.

Area of Conversion

The plant-soil system can be used to explain the importance of growing different microbes during Phase II. When a plant root grows through soil the root is able to absorb food or nutrients from a distance away from the root surface. Roots obtain these nutrients by absorbing water and the nutrients dissolved in that water. This water is called the soil solution. As the water and nutrients are adsorbed by the root a gradient is created which draws more water and food towards the root. Compost substrate is a complex material that microbes and the mushroom obtain their food and water. The soil is much more simple system than the rich decaying matter the mushroom extracts its food. Unlike the relatively simple plant-soil system, how the mushroom obtains its food and water from compost substrate is an unknown, yet probably similar, process. How much of the root or mycelium is absorbing the nutrient is depends on a number of other factors. However, for this illustration we can assume most of the surface area of the microbe is able to absorb nutrients. Let's consider the region a microbe may adsorb food may be called "area of conversion."

Thermophilic fungi have a larger area of conversion because of the way they can grow through the dense compost substrate as a fine thread of mycelium. The actinomycetes are able to grow in well defined areas and their area of conversion is more confined and overall much smaller. Figure 5 shows the different areas of conversion that the two types of microbes have in a tightly packed or a dense ball of compost. In the higher temperature ranges the actinomycetes can grow and convert food the thermophilic fungi cannot. Actinomycetes are important during and right after the pasteurization. They are able to survive a little better at the high temperatures and they would be the first organism to recover and provide some heating capacity to the compost substrate after the pasteurization.

Figure 5: Phase II

It is just as important to spend time in the lower temperature ranges so the thermophilic fungi can grow and convert compounds into food for the mushroom. Thermophilic fungi are important microbes when the structure of the compost substrate is not structurally typical. These fungi penetrate the dense and tight areas of compost substrate or into these balls of compost, Figure 5. Some of these dense areas where the higher temperature ranges were not reached the actinomycetes did not grow. As the warmer compost substrate is lowered down through the temperature conditioning range, thermophilic fungi grow into the dense areas and finish the conversion of ammonia. In the summer when it takes longer to cool the compost substrate for spawning, the compost substrate naturally remains in this temperature range longer. However, in the winter when the compost substrate can be cooled faster, it is important to manage the Phase II temperatures so that these thermophilic fungi grow.


Managing microbial activity in compost substrate will achieve the goals of Phase II composting. By giving the microbes their necessary growing requirements and conditions will make this management much easier. It is important to grow as many beneficial microbes as possible in the compost substrate before pasteurization to ensure that afterwards there are more good microbes surviving. A better survival rate will make managing the compost substrate easier and the conversion of ammonia will start sooner and finish earlier. Understanding how the microbial population is affected by pasteurization should make managing decisions easier afterwards. Microbes have different temperature ranges, food sources and growth patterns. The actinomycetes are needed for the higher temperature ranges and the thermophilic fungi in the lower ranges. In different types of compost substrate we may want to favor the grow the thermophilic fungi for a longer time so they can penetrate the tight dense areas of compost. Understanding how these microbes grow and work in compost substrate should make the management of Phase II a little easier.

References and Other Literature

Barber, B. 1980. Phase II. Mushroom News 29(6): 8-12.

Carapiet, G. 1981. Phase II or Cookout. Mushroom Science 11: 311-317.

Schisler, L.C. 1985. Management of Phase II. Presented at Ontario Horticultural Crop Conference. Toronto Canada.

Tschierpe, H.J. 1973. Environmental Factors and Mushroom Growing. Mushroom Journal, 1:30-48; 2:77-95.

Wuest, P.J. 1970. The use of Steam for Phase II. Mushroom News 18(9):6-15.

David M. Beyer, Department of Plant Pathology

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Microbial Activity

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David Meigs Beyer
  • Professor Plant Pathology
Phone: 814-863-7059