Science and Engineering

Compost Microorganisms

by Nancy Trautmann and Elaina Olynciw

The Phases of Composting

In the process of composting, microorganisms break down organic matter and produce carbon dioxide, water, heat, and humus, the relatively stable organic end product. Under optimal conditions, composting proceeds through three phases: 1) the mesophilic, or moderate-temperature phase, which lasts for a couple of days, 2) the thermophilic, or high-temperature phase, which can last from a few days to several months, and finally, 3) a several-month cooling and maturation phase.

Different communities of microorganisms predominate during the various composting phases. Initial decomposition is carried out by mesophilic microorganisms, which rapidly break down the soluble, readily degradable compounds. The heat they produce causes the compost temperature to rapidly rise.

As the temperature rises above about 40°C, the mesophilic microorganisms become less competitive and are replaced by others that are thermophilic, or heat-loving. At temperatures of 55°C and above, many microorganisms that are human or plant pathogens are destroyed. Because temperatures over about 65°C kill many forms of microbes and limit the rate of decomposition, compost managers use aeration and mixing to keep the temperature below this point.

During the thermophilic phase, high temperatures accelerate the breakdown of proteins, fats, and complex carboydrates like cellulose and hemicellulose, the major structural molecules in plants. As the supply of these high-energy compounds becomes exhausted, the compost temperature gradually decreases and mesophilic microorganisms once again take over for the final phase of "curing" or maturation of the remaining organic matter.


Bacteria are the smallest living organisms and the most numerous in compost; they make up 80 to 90% of the billions of microorganisms typically found in a gram of compost. Bacteria are responsible for most of the decomposition and heat generation in compost. They are the most nutritionally diverse group of compost organisms, using a broad range of enzymes to chemically break down a variety of organic materials.

Bacteria are single-celled and structured as either rod-shaped bacilli, sphere-shaped cocci or spiral-shaped spirilla. Many are motile, meaning that they have the ability to move under their own power. At the beginning of the composting process (0-40°C), mesophilic bacteria predominate. Most of these are forms that can also be found in topsoil.

As the compost heats up above 40°C, thermophilic bacteria take over. The microbial populations during this phase are dominated by members of the genus Bacillus. The diversity of bacilli species is fairly high at temperatures from 50-55°C but decreases dramatically at 60°C or above. When conditions become unfavorable, bacilli survive by forming endospores, thick-walled spores that are highly resistant to heat, cold, dryness, or lack of food. They are ubiquitous in nature and become active whenever environmental conditions are favorable.

At the highest compost temperatures, bacteria of the genus Thermus have been isolated. Composters sometimes wonder how microorganisms evolved in nature that can withstand the high temperatures found in active compost. Thermus bacteria were first found in hot springs in Yellowstone National Park and may have evolved there. Other places where thermophilic conditions exist in nature include deep sea thermal vents, manure droppings, and accumulations of decomposing vegetation that have the right conditions to heat up just as they would in a compost pile.

Once the compost cools down, mesophilic bacteria again predominate. The numbers and types of mesophilic microbes that recolonize compost as it matures depend on what spores and organisms are present in the compost as well as in the immediate environment. In general, the longer the curing or maturation phase, the more diverse the microbial community it supports.


The characteristic earthy smell of soil is caused by actinomycetes, organisms that resemble fungi but actually are filamentous bacteria. Like other bacteria, they lack nuclei, but they grow multicellular filaments like fungi. In composting they play an important role in degrading complex organics such as cellulose, lignin, chitin, and proteins. Their enzymes enable them to chemically break down tough debris such as woody stems, bark, or newspaper. Some species appear during the thermophilic phase, and others become important during the cooler curing phase, when only the most resistant compounds remain in the last stages of the formation of humus.

Actinomycetes form long, thread-like branched filaments that look like gray spider webs stretching through compost. These filaments are most commonly seen toward the end of the composting process, in the outer 10 to 15 centimeters of the pile. Sometimes they appear as circular colonies that gradually expand in diameter.


Fungi include molds and yeasts, and collectively they are responsible for the decomposition of many complex plant polymers in soil and compost. In compost, fungi are important because they break down tough debris, enabling bacteria to continue the decomposition process once most of the cellulose has been exhausted. They spread and grow vigorously by producing many cells and filaments, and they can attack organic residues that are too dry, acidic, or low in nitrogen for bacterial decomposition.

Most fungi are classified as saprophytes because they live on dead or dying material and obtain energy by breaking down organic matter in dead plants and animals. Fungal species are numerous during both mesophilic and thermophilic phases of composting. Most fungi live in the outer layer of compost when temperatures are high. Compost molds are strict aerobes that grow both as unseen filaments and as gray or white fuzzy colonies on the compost surface.


Protozoa are one-celled microscopic animals. They are found in water droplets in compost but play a relatively minor role in decomposition. Protozoa obtain their food from organic matter in the same way as bacteria do but also act as secondary consumers ingesting bacteria and fungi.


Rotifers are microscopic multicellular organisms also found in films of water in the compost. They feed on organic matter and also ingest bacteria and fungi.

Techniques for Observing Compost Microorganisms


The illustrations and photographs were produced by Elaina Olynciw, biology teacher at A.Philip Randolf High School, New York City, while she was working in the laboratory of Dr. Eric Nelson at Cornell University as part of the Teacher Institute of Environmental Sciences.

Thanks to Fred Michel (Michigan State University, NSF Center for Microbial Ecology) and Tom Richard for their helpful reviews of and contributions to this document.


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Cornell Waste Management Institute ©1996
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