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Microbes of Phase II.

Many naturally occurring organisms are found in the raw materials that are used in substrate preparation. Organisms too small to see with the unaided eye and can only be seen with a microscope are called microscopic organisms 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 survive. Food, water and air (oxygen) are the necessary requirements for these microbes.


However, many organisms cannot readily adjust to changes in the surrounding temperature where they live; microbes will only grow and survive within a particular temperature range. Most beneficial microbes that survive pasteurization and grow during Phase 11 composting are thermophilic; in other words, they are heat-loving microbes growing at temperatures roughly between 115[degrees] and 145[degrees]F (46-63[degrees]C).


The actinomycetes grow in higher temperature ranges (~130[degrees]-145[degrees]F) but convert compounds only in a defined surface area around their colony. The thermophilic fungi grow better in the lower temperature ranges (~ 115[degrees]-130[degrees]F), and their growth is more like spawn, filamentous and able to grow into tight, dense compost. Some of these organisms can be considered "beneficial microbes" that provide food for the mushroom. These microbes use up leftover Phase I residual carbohydrates and convert ammonia and other nitrogenous compounds into protein for the mushroom. This conditioning of the compost makes it selective for the mushroom and not for its competitors. The dead bodies of these microbes also contain nutritious fats and oils that the mushroom requires. 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.

Phase II objectives, pasteurization and conditioning seem simple to accomplish regardless of the system; whether it's in beds, trays or bulk tunnels. However, anyone who has tried managing a Phase II may recognize it is one of the most difficult procedures in growing mushrooms. Because of weather variations, compost or other cultural problems, growers sometimes have to change their Phase II programs. For example, with shorter, dense compost it is very important to favor the growth of the thermophilic fungi for a longer time so they can penetrate the tight dense areas of compost. Phase II maybe managed more than one way, however when changes have to be made, the objectives in managing the activity of the good microbes should remain constant.

Being vigilant to the four basic needs (food, water, oxygen and temperature) of the microbes during Phase II will most often solve any conditioning problems and minimize the growth of competitor or weed molds. When the basic requirements are not managed properly, such as not ensuring enough oxygen during Phase II or not obtaining adequate pasteurization temperatures, problems will arise.

Some of the beneficial microbes growing during Phase II use other types of food besides ammonia. If this non-ammonia food is not completely used during Phase II, competitor molds or weed molds may use these readily available compounds to grow and develop. Not only may these undesirable molds be a visual concern, it also means there is less food available for the mushroom. A common sign or symptom of inadequate conversion is the appearance of "black spots" during the spawn run (Figures 1 and 2). These spots often suggest that compost in that "lump" was either not in a conditioning temperature range long enough, was too wet, (therefore oxygen deprived) or too much nitrogen was available to be fully converted by the microbes in the time allowed during the Phase II.



We are interested in trying to isolate microbes from these black spots, so if you have any, please send us a confidential email (; so we can arrange to collect a sample. A better understanding of how these microbes grow and work in compost substrate should make the management of Phase II a little easier.

David M. Beyer, Ph. D.

Professor - Mushroom Extension SWpecialist Department of Plant pathology Penn State

John A. Pecchia, Ph. D.

Manager, Mushroom Researh Facilities Penn State
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Title Annotation:the penn state lines
Author:Beyer, David M.; Pecchia, John A.
Publication:Mushroom News
Date:Apr 1, 2010
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