A Growing Culture


bacteriaA wide array of microorganisms live in a compost pile. Bacteria are especially abundant and are usually divided into several classes based upon the temperatures at which they best thrive. The low temperature bacteria are the psychrophiles, which can grow at temperatures down to -100C, but whose optimum temperature is 150C (590F) or lower. The mesophiles live at medium temperatures, 20-450C (68-1130F), and include human pathogens. Thermophiles thrive above 450C (1130F), and some live at, or even above, the boiling point of water.

Strains of thermophilic bacteria have been identified with optimum temperatures ranging from 550C to an incredible 1050C (above the boiling point of water), and many temperatures in between.20 The strains that survive at extremely high temperatures are called, appropriately enough, extreme thermophiles, or hyper- thermophiles, and have a temperature optimum of 800C (1760F) or higher. Thermophilic bacteria occur naturally in hot springs, tropical soils, compost heaps, in your excrement, in hot water heaters (both domestic and industrial), and in your garbage, to name a few places.   Thermophilic bacteria were first isolated in 1879 by Miquel, who found bacteria capable of developing at 720C (1620F). He found these bacteria in soil, dust, excrement, sewage, and river mud. It wasn’t long afterward that a variety of thermophilic bacteria were discovered in soil — bacteria that readily thrived at high temperatures, but not at room temperature. These bacteria are said to be found in the sands of the Sahara Desert, but not in the soil of cool forests. Composted or manured garden soils may contain 1-10 percent thermophilic types of bacteria, while field soils may have only 0.25% or less. Uncultivated soils may be entirely free of thermophilic bacteria.22

Thermophiles are responsible for the spontaneous heating of hay stacks which can cause them to burst into flame. Compost itself can sometimes spontaneously combust. This occurs in larger piles (usually over 12 feet high) that become too dry (between 25% and 45% moisture) and then overheat.23 Spontaneous fires have started at two American composting plants — Schenectady and Cape May — due to excessively dry compost. According to the EPA, fires can start at surprisingly low temperatures (1940F) in too-dry compost, although this is not a problem for the backyard composter. When growing on bread, thermophiles can raise the temperature of the bread to 740C (1650F). Heat from bacteria also warms germinating seeds, as seeds in a sterile environment are found to remain cool while germinating.24

Both mesophilic and thermophilic microorganisms are found widely distributed in nature and are commonly resident on food material, garbage and manures. This is not surprising for mesophiles because the temperatures they find to be optimum for their reproduction are commonly found in nature. These temperatures include those of warm-blooded animals, which excrete mesophiles in their stools in huge numbers.

A mystery presents itself, on the other hand, when we consider thermophilic microorganisms, since they prefer living at temperatures not commonly found in nature, such as hot springs, water heaters and compost piles. Their preference for hot temperatures has given rise to some speculation about their evolution. One theory suggests that the thermophiles were among the first living things on this planet, developing and evolving during the primordial birthing of the Earth when surface temperatures were quite hot. They have thus been called the “Universal Ancestor.” Estimated at 3.6 billion years old, they are said to be so abundant as to “comprise as much as half of all living things on the planet.” 25 This is a rather profound concept, as it would mean that thermophilic organisms are perhaps more ancient than any other living thing. Their age would make dinosaurs look like new-born babes still wet behind the ears, however extinct. Of course, we humans, in comparison, have just shown up on Earth. Thermophiles could therefore be the common ancestral organism of all life forms on our planet.

Just as extraordinary is the concept that thermophiles, despite their need for a hot environment, are found everywhere. They’re lingering in your garbage and in your stool and have been since we humans first began to crawl on this planet. They have quietly waited since the beginning of time, and we haven’t been aware of them until recently. Researchers insist that thermophiles do not grow at ambient or room temperatures.26 Yet, like a miracle, when we collect our organic refuse in a tidy pile, the thermophiles seem to be sparked out of their dormant slumber to work furiously toward creating the primordial heat they so desire. And they succeed — if we help them by creating compost piles. They reward us for our help by converting our garbage and other organic discards into life-sustaining earth.

The knowledge of living creatures incomprehensibly ancient, so small as to be entirely invisible, thriving at temperatures hotter than those normally found in nature, and yet found alive everywhere, is remarkable enough. The fact that they are so willing to work for our benefit, however, is rather humbling.

By some estimates, humanure contains up to a trillion (1,000,000,000,000) bacteria per gram.27 These are, of course, mixed species, and not by any means all thermophiles. A trillion bacteria is equivalent to the entire human population of the Earth multiplied by 166, and all squeezed into a gram of organic material. These microbiological concepts of size and number are difficult for us humans to grasp. Ten people crammed into an elevator we can understand. A trillion living organisms in a teaspoonful of crap is a bit mind-boggling.

Has anyone identified the species of microorganism that heats up compost? Actually, a large variety of species, a biodiversity, is critical to the success of compost. However, the thermophilic stage of the process is dominated by thermophilic bacteria. One examination of compost microorganisms at two compost plants showed that most of the bacteria (87%) were of the genus Bacillus, which are bacteria that form spores,28 while another researcher found that above 650C, the organisms in the compost were almost purely Bacillus stearothermophilus.29


There is a huge difference between a backyard humanure composter and a municipal composter. Municipal composters handle large batches of organic materials all at once, while backyard com- posters continuously produce a small amount of organic material every day. Municipal composters, therefore, are “batch” composters, while backyard composters tend to be “continuous” composters. When organic material is composted in a batch, four distinct stages of the composting process are apparent. Although the same phases occur during continuous composting, they are not as apparent as they are in a batch, and in fact they may be occurring concurrently rather than sequentially.

The four phases include: 1) the mesophilic phase; 2) the thermophilic phase; 3) the cooling phase; and 4) the curing phase.

Compost bacteria combine carbon with oxygen to produce carbon dioxide and energy. Some of the energy is used by the microorganisms for reproduction and growth; the rest is given off as When a pile of organic refuse begins to undergo the composting process, mesophilic bacteria proliferate, raising the temperature of the composting mass up to 440C (1110F). This is the first stage of the composting process. These mesophilic bacteria can include E. coli and other bacteria from the human intestinal tract, but these soon become increasingly inhibited by the temperature, as the thermophilic bacteria take over in the transition range of 440C-520C (1110F-125.60F).

This begins the second stage of the process, when thermophilic microorganisms are very active and produce a lot of heat. This stage can then continue to about 700C (1580F),30 although such high temperatures are neither common nor desirable in backyard compost. This heating stage takes place rather quickly and may last only a few days, weeks or months. It tends to remain localized in the upper portion of a backyard compost bin where the fresh material is being added; whereas in batch compost, the entire composting mass may be thermophilic all at once.

After the thermophilic heating period, the humanure will appear to have been digested, but the coarser organic material will not. This is when the third stage of composting, the cooling phase, takes place. During this phase, the microorganisms that were chased away by the thermophiles migrate back into the compost and get to work digesting the more resistant organic materials. Fungi and macroorganisms such as earthworms and sowbugs also break the coarser elements down into humus.

After the thermophilic stage has been completed, only the readily available nutrients in the organic material have been digested. There’s still a lot of food in the pile, and a lot of work to be done by the creatures in the compost. It takes many months to break down some of the more resistant organic materials in compost such as “lignin,” which comes from wood materials. Like humans, trees have evolved with a skin that is resistant to bacterial attack, and in a com- post pile these lignins resist breakdown by thermophiles. However, other organisms, such as fungi, can break down lignin, given enough time; since many fungi don’t like the heat of thermophilic compost, they simply wait for things to cool down before beginning their job.

The final stage of the composting process is called the curing, aging or maturing stage, and it is a long and important one. Commercial composting professionals often want to make their com- post as quickly as possible, usually sacrificing the compost’s curing time. One municipal compost operator remarked that if he could shorten his compost time to four months, he could make three batches of compost a year instead of only the two he was then making, thereby increasing his output by 50%. Municipal composters see truckloads of compost coming in to their facilities daily, and they want to make sure they don’t get inundated with organic material waiting to be composted. Therefore, they feel a need to move their material through the composting process as quickly as possible to make room for the new stuff. Household composters don’t have that problem, although there seem to be plenty of backyard composters who are obsessed with making compost as quickly as possible. However, the curing of the compost is a critically important stage of the compost-making process.

A long curing period, such as a year after the thermophilic stage, adds a safety net for pathogen destruction. Many human pathogens have only a limited period of viability in the soil, and the longer they are subjected to the microbiological competition of the compost pile, the more likely they will die a swift death.

Immature or uncured compost can produce substances called phytotoxins that are toxic to plants. It can also rob the soil of oxygen and nitrogen and can contain high levels of organic acids. So relax, sit back, put your feet up, and let your compost reach full maturity before you even think about using it.


Compost is normally populated by three general categories of microorganisms: bacteria, actinomycetes and fungi (see Figure 3.3 and Table 3.6). It is primarily the bacteria, and specifically the thermophilic bacteria, that create the heat of the compost pile.

Although considered bacteria, actinomycetes are effectively intermediates between bacteria and fungi because they look similar to fungi and have similar nutritional preferences and growth habits. They tend to be more commonly found in the later stages of compost, and are generally thought to follow the thermophilic bacteria in succession. They, in turn, are followed predominantly by fungi during the last stages of the composting process.

There are at least 100,000 known species of fungi, the over- whelming majority of them being microscopic.31 Most fungi cannot grow at 500C because it’s too hot, although thermophilic fungi are heat tolerant. Fungi tend to be absent in compost above 600C and actinomycetes tend to be absent above 700C. Above 820C biological activity effectively stops (extreme thermophiles are not found in compost).32

To get an idea of the microbial diversity normally found in nature, consider this: a teaspoon of native grassland soil contains 600- 800 million bacteria comprising 10,000 species, plus perhaps 5,000 species of fungi, the mycelia of which could be stretched out for several miles. In the same teaspoon, there may be 10,000 individual protozoa of perhaps 1,000 species, plus 20-30 different nematodes from as many as 100 species. Sounds crowded to me. Obviously, good compost will reinoculate depleted, sanitized, chemicalized soils with a wide variety of beneficial microorganisms (see Figures 3.4 and 3.5).33

Figure 3.3


A frequent question is, “How do you know that all parts of your compost pile have been subjected to high enough temperatures to kill all potential pathogens?” The answer should be obvious: you don’t. You never will. Unless, of course, you examine every cubic centimeter of your compost for pathogens in a laboratory. This would probably cost many thousands of dollars, which would make your compost the most expensive in history.

It’s not only the heat of the compost that causes the destruction of human, animal and plant pathogens, it’s a combination of factors, including:

• competition for food from compost microorganisms;
• inhibition and antagonism by compost microorganisms;
• consumption by compost organisms;
• biological heat generated by compost microorganisms; and
• antibiotics produced by compost microorganisms.

For example, when bacteria were grown in an incubator with- out compost at 500C and separately in compost at 500C, they died in the compost after only seven days, but lived in the incubator for seventeen days. This indicated that it is more than just temperature that determines the fate of pathogenic bacteria. The other factors listed above undoubtedly affect the viability of non-indigenous microorganisms, such as human pathogens, in a compost pile. Those factors require as large and diverse a microbial population as possible, which is best achieved by temperatures below 600C (1400F). One researcher states that, “Significant reductions in pathogen numbers have been observed in compost piles which have not exceeded 400C [1040F].” 34

There is no doubt that the heat produced by thermophilic bacteria kills pathogenic microorganisms, viruses, bacteria, protozoa, worms and eggs that may inhabit humanure. A temperature of 500C (1220 F), if maintained for twenty-four hours, is sufficient to kill all of the pathogens, according to some sources (this issue is covered in Chapter Seven). A lower temperature will take longer to kill pathogens. A temperature of 460C (1150F) may take nearly a week to kill pathogens completely; a higher temperature may take only minutes. What we have yet to determine is how low those temperatures can be and still achieve satisfactory pathogen elimination. Some researchers insist that all pathogens will die at ambient temperatures (normal air temperature) given enough time.

When Westerberg and Wiley composted sewage sludge which had been inoculated with polio virus, Salmonella, roundworm eggs, and Candida albicans, they found that a compost temperature of 47- 550C (116-1300F) maintained for three days killed all of these pathogens.35 This phenomenon has been confirmed by many other researchers, including Gotaas, who indicates that pathogenic organ- isms are unable to survive compost temperatures of 55-600C (131- 1400F) for more than thirty minutes to one hour.36 The first goal in composting humanure, therefore, should be to create a compost pile that will heat sufficiently to kill potential human pathogens that may be found in the manure.

Nevertheless, the heat of the compost pile is a highly lauded characteristic of compost that can be a bit overblown at times. People may believe that it’s only the heat of the compost pile that destroys pathogens, so they want their compost to become as hot as possible. This is a mistake. In fact, compost can become too hot, and when it does, it destroys the biodiversity of the microbial community. As one scientist states, “Research has indicated that temperature is not the only mechanism involved in pathogen suppression, and that the employment of higher than necessary temperatures may actually constitute a barrier to effective sanitization under certain circumstances.” 37

Perhaps only one species (e.g., Bacillus stearothermophilus) may dominate the compost pile during periods of excessive heat, thereby driving out or outright killing the other inhabitants of the compost, which include fungi and actinomycetes as well as the bigger organisms that you can actually see. A compost pile that is too hot can destroy its own biological community and leave a mass of organic material that must be repopulated in order to continue the necessary conversion of organic matter to humus. Such sterilized compost is more likely to be colonized by unwanted microorganisms, such as Salmonella. Researchers have shown that the biodiversity of compost acts as a barrier to colonization by such unwanted microorganisms as Salmonella. In the absence of a biodiverse “indigenous flora,” such as caused by sterilization due to excess heat, Salmonella were able to regrow.38

The microbial biodiversity of compost is also important because it aids in the breakdown of the organic material. For example, in high-temperature compost (800C), only about 10% of sewage sludge solids could be decomposed in three weeks, whereas at 50- 600C, 40% of the sludge solids were decomposed in only seven days. The lower temperatures apparently allowed for a richer diversity of living things which in turn had a greater effect on the degradation of the organic matter. One researcher indicates that optimal decomposition rates occur in the 55-590C (131-1390F) temperature range, and optimal thermophilic activity occurs at 550C (1310F), which are both adequate temperatures for pathogen destruction.39 A study conducted in 1955 at Michigan State University, however, indicated that optimal decomposition occurs at an even lower temperature of 450C (1130F).40 Another researcher asserts that maximum biodegradation occurs at 45-550C (113-1310F), while maximum microbial diversity requires a temperature range of 35-450C (95-1130F).41 Apparently, there is still some degree of flexibility in these estimates, as the science of “compost microhusbandry” is not an utterly precise one at this time. Control of excessive heat, however, is probably not a concern for the backyard composter.

Some thermophilic actinomycetes, as well as mesophilic bacteria, produce antibiotics that display considerable potency toward other bacteria and yet exhibit low toxicity when tested on mice. Up to one half of thermophilic strains can produce antimicrobial com- pounds, some of which have been shown to be effective against E. coli and Salmonella. One thermophilic strain with an optimum growth temperature of 500C produces a substance that “significantly aided the healing of infected surface wounds in clinical tests on human subjects. The product(s) also stimulated growth of a variety of cell types, including various animal and plant tissue cultures and unicellular algae.” 42 The production of antibiotics by compost microorganisms theoretically assists in the destruction of human pathogens that may have existed in the organic material before composting.

Even if every speck of the composting material is not subject-ed to the high internal temperatures of the compost pile, the process of thermophilic composting nevertheless contributes immensely toward the creation of a sanitary organic material. Or, in the words of one group of composting professionals, “The high temperatures achieved during composting, assisted by the competition and antagonism among the microorganisms [i.e., biodiversity], considerably reduce the number of plant and animal pathogens. While some resistant pathogenic organ- isms may survive and others may persist in cooler sections of the pile, the dis- ease risk is, nevertheless, greatly reduced.” 43

If a backyard composter has any doubt or concern about the existence of pathogenic organisms in his or her humanure compost, s/he can use the compost for horticultural purposes rather than for food purposes. Humanure compost can grow an amazing batch of berries, flowers, bushes, or trees. Furthermore, lingering pathogens continue to die after the compost has been applied to the soil, which is not surprising since human pathogens prefer the warm and moist environment of the human body. As the World Bank researchers put it, “even pathogens remaining in compost seem to disappear rapidly in the soil.” [Night Soil Composting, 1981] Finally, compost can be tested for pathogens by compost testing labs.

“Another point most folks don’t realize is that no compost and no soil are completely pathogen free. You really don’t want it to be completely pathogen free, because you always want the defense mechanism to have something to practice on. So a small number of disease-causing organisms is desirable. But that’s it.” 44 Pathogens are said to have “minimum infective doses,” which vary widely from one type of pathogen to another, meaning that a number of pathogens are necessary in order to initiate an infection. The idea, therefore, that compost must be sterile is incorrect. It must be sanitary, which means it must have a greatly weakened, reduced or destroyed pathogen population.

In reality, the average backyard composter usually knows whether his or her family is healthy or not. Healthy families have little to be concerned about and can feel confident that their thermophilic compost can be safely returned to the soil, provided the simple instructions in this book are followed regarding compost temperatures and retention times, as discussed in Chapter Seven. On the other hand, there will always be those people who are fecophobic, and who will never be convinced that humanure compost is safe. These people are not likely to compost their humanure anyway, so who cares?


  • Comment by Derek — November 4, 2012 @ 4:41 am

    Great article, but I believe your temperatures must be wrong. Should there be a decimal point in these figures? For instance, in the transition between the first and second stage of composting you mention the heat rising to over 440 degrees Celsius. This is reaching the boiling point of sulfur, so I think you mean to say 44.0 degrees Celsius. Other than these decimal issues, well done!

  • Comment by Mojtaba — January 2, 2013 @ 12:37 am

    Thanks for technical points in your site

  • Comment by Phil — March 17, 2013 @ 9:26 am

    To Derek, that’s a degree symbol. I was confused as well but it supposed to represent degrees Celsius.

  • Comment by S del Cano — April 13, 2013 @ 3:55 pm

    important word(s) missing to complete the meaning of the sentence:

    The four phases include: 1) the mesophilic phase; 2) the thermophilic phase; 3) the cooling phase; and 4) the curing phase.

    Compost bacteria combine carbon with oxygen to produce carbon dioxide and energy. Some of the energy is used by the microorganisms for reproduction and growth; the rest is given off as […]

    When a pile of organic refuse begins to undergo the composting process, mesophilic bacteria proliferate, raising the temperature of the composting mass up to 440C (1110F). This is the first stage of the composting process. These mesophilic bacteria can include E. coli and other bacteria from the human intestinal tract, but these soon become increasingly inhibited by the temperature, as the thermophilic bacteria take over in the transition range of 440C-520C (1110F-125.60F).

  • Comment by Asher — April 30, 2013 @ 10:55 pm

    THanks S del Cano for finding this!


  • Comment by Habtamu Mengistu — October 15, 2015 @ 3:58 am

    this article helped me as prominent source for my study (MSc in organic horticulture). thank you for producing it.

  • Comment by ali — January 16, 2016 @ 8:11 am

    very nice thank you

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