Compost Microbiology and the Soil Food Web (2)

Part I: The Composting Process and Associated Microorganisms

Compost Microorganisms

Sources. The microorganisms needed for composting are found throughout the natural environment. They are present in compost feedstock as well as in the water, air, soil, and machinery the feedstock and compost are exposed to during processing.

These sources ensure a high diversity of microorganisms, which helps to maintain an active microbial population during the dynamic chemical and physical processes of composting, such as shifts in pH, temperature, water, organic matter, and nutrient availability. Only on rare occasions will the addition of microorganisms be warranted (see “Inoculating Compost” section).

Microbe Types and Requirements. The microbiological components of compost consist of bacteria and fungi. Because of their unique nature, actinomycetes are discussed here as a third microbiological component, though in actuality actinomycetes are a particular kind of bacteria. The majority of microorganisms responsible for the formation of compost are aerobes in that they require or work best in the presence of oxygen.

Many difficulties associated with composting may be traced to insufficient oxygen levels to support the decomposition of compost feedstock. Compost microbes also require a moist environment because they live in the water films surrounding composting organic matter particles. A 50 to 60 percent moisture content is optimal.

Fungi. Fungi form their individual cells into long filaments called hyphae. Fungal hyphae are larger than actinomycetes and may be more easily seen with the naked eye. They penetrate throughout the composting material, decomposing both chemically and mechanically the more recalcitrant* organic matter fraction such as lignins and cellulose. Fungal hyphae physically stabilize the compost into small aggregates, providing the compost with improved aeration and drainage.

Fungi number between 0.01 and 1 million propagules* per gram of soil. About 70,000 different species of fungi have been described worldwide, but an estimated 1 million additional species remain undiscovered and undescribed. Ecologically, fungi play a vital role in breakdown of dead plant materials.

Bacteria. The most numerous biological component of compost is the bacteria. Although they often can exceed 1 billion microorganisms per gram of soil, bacteria (with the exception of actinomycetes) do not contribute as much to the overall microbiological mass as fungi because of their relatively small size. Although bacteria (with the exception of actinomycetes) exist as individuals and do not form filaments, they also contribute to the stabilization of aggregates through the excretion of organic compounds that bind adjacent organic matter and soil particles together. Bacteria are typically associated with the consumption of easily degraded organic matter. They are the dominant population throughout the entire composting process, whereas the actinomycetes and fungi typically proliferate in the later stages.

Actinomycetes. While actinomycetes are visually similar to fungi in that they have networks of individual cells that form filaments or strands, they are actually a type of bacteria. These filaments allow for a colony* of actinomycetes to spread throughout a compost pile, where they are typically associated with the degradation of the more recalcitrant compounds.

Actinomycetes number between 0.1 and 10 million propagules per gram of soil. Their filaments contribute to the formation of the stable organic aggregates typical of finished compost. Actinomycetes are tolerant of lower moisture conditions than other bacteria and are responsible for the release of geosmin, a chemical associated with the typically musty, earthy smell of compost.

Composting Process

Composting proceeds in predictable stages. During different stages, temperatures and nutrient availabilities vary and affect the kinds and numbers of microorganisms that develop. Initially, the pile is at approximately the ambient temperature. The composting material warms through the mesophilic* temperature range (50°–105°F) as the microorganisms become more active. Soon, microbial activity raises the temperature of the pile to thermophilic* temperatures (106°–170°F). This is considered the most productive stage of composting.

Mesophiles and thermophiles are microbes adapted to mesophilic and thermophilic conditions, respectively. Composting proceeds at a much faster rate under thermophilic conditions. Eventually, readily available substrates within the feedstock are exhausted, temperatures gradually return to the mesophilic range, and curing begins. The following section expands on the microbiology of each stage.

Initial Stage. The process of transporting and manipulating the feedstock for composting exposes the organic matter to additional sources of microorganisms, all of which may contribute toward initiating the composting process. Initially, mesophiles predominate and proceed to decompose the readily degradable sugars, proteins, starches, and fats typically found in undigested feedstocks.

The availability of easily usable organic substances enables the proliferation of the fastest-growing microorganisms, the bacteria. Mesophilic bacteria, therefore, dominate initial decomposition. These bacteria release heat from the breakdown of large amounts of easily degraded organic matter. This heat begins to raise the temperature within the pile due to the high insulating capacity of a properly sized compost pile. Within just hours the temperature of the compost pile can rise above the 106°F thermophilic threshold.

Active Stage. As the compost reaches higher temperatures, thermophiles begin to dominate the bacterial community. The active stage is typically the stage where most of the organic matter is converted into carbon dioxide and humus, and the microorganism population grows. The thermophilic population continues generating more heat by decomposing the remaining organic matter.

Due to limitations with isolation techniques, laboratory studies have only been able to isolate a few genera of bacteria from the thermophilic stage (Bacillus, Clostridium, and Thermus), but many microorganisms remain to be discovered and described. In a properly ventilated composting pile, the temperature will be maintained between approximately 131° and 155 °F. Fortunately, pathogens such as human viruses and infectious bacteria are typically unable to persist in such a hostile environment. The higher temperatures will ensure rapid organic matter processing while simultaneously providing optimal conditions for the destruction of human and plant pathogens as well as weed seeds.

Because the composting pile is cooler on its outer surface, periodic mixing of the outer layer into the pile is essential for maximum pathogen and seed kill. Mixing or turning the pile also helps to ventilate it by increasing the size and number of air pores. This is important because in an unventilated compost pile, the temperatures can exceed 160°F, effectively stopping all microbial activity. The air pores also serve as passages for oxygen to enter the pile. Microbes require oxygen to efficiently break down organic matter.

Overheating. If a pile does overheat, surpassing approximately 170°F, most microbes will be destroyed and microbial activity will virtually cease. Surviving microorganisms are typically those able to survive as spores.* The spores will germinate when the composting pile returns to a more favorable temperature. These spores are thick-walled structures that are formed by the microorganism under stress such as heat, cold, drought, and low nutrient conditions.

After overheating, the composting pile will cool to a mesophilic state, requiring the activity of mesophilic microorganisms to return the pile to thermophilic conditions. If the composting pile is low in readily utilizable organic substrates, the pile may not be able to support the microbial activity needed to return to thermophilic conditions. In such a case, it may be necessary to supplement the composting pile with additional feedstock to ensure maximal degradation and pathogen removal.

An overheated composting pile may return to thermophilic temperatures through the germination and activity of spore-forming microorganisms, and through the infiltration of microorganisms from the outer surface of the composting pile where the temperature was less extreme.

Curing Stage. A properly functioning composting pile will eventually deplete itself of a majority of the easily degradable organic substrates leaving some cellulose, but mainly lignins and humic materials. Bacteria are generally considered less adept at metabolizing these remaining compounds. Consequently, the bacterial population will decline in numbers as compared to fungi and actinomycetes. Because less heat is generated at this point, the temperature of the composting pile will slowly fall to mesophilic temperatures. With the return of mesophilic conditions, the final curing stage of composting begins.

During the curing stage, the fungi and actinomycete populations predominate, while the bacterial population may decline somewhat. Fungi and actinomycetes proliferate on the remaining less degradable organic matter such as chitin, cellulose and lignin. These compounds are more persistent because they are insoluble in water and, due to their size and chemical complexity, cannot pass into the bacterial cell. Thus, degradation of these compounds requires the use of extracellular enzymes.*

Once the complex organic compounds are broken down into smaller and more soluble forms, they can enter the cell and become food and energy for the microorganism. Microbes able to produce extracellular enzymes suitable for breaking down recalcitrant materials will have a selective advantage at this point in the composting process.

A novel feature of many of the extracellular enzymes common in fungi is that they are capable of breaking down a wide range of compounds that would otherwise require several specific enzymes*, a feature not commonly found in a single microorganism. Fungi, though they grow and reproduce more slowly than bacteria when food is readily available, are well suited for exploiting an environment rich in complex recalcitrant organic compounds like those found in the compost during the curing stage.

The curing process can vary in duration; a longer curing period provides more assurance that the compost is free of pathogens and phytotoxins.* If the compost is incompletely cured (i.e., not stable), it maintains a higher microbial activity, leading to increased oxygen consumption. When unstable compost is applied in the field, it can thereby decrease the supply of oxygen available to plant roots.

In addition, immature compost can contain higher levels of soluble organic matter (i.e., organic acids), which can lead to toxicity problems for certain horticultural applications, such as seed germination. Detailed information on assessing compost stability and maturity is included in the California Integrated Waste Management Board (CIWMB) publication Compost: Matching Performance Needs with Product Characteristics listed at the end of this document.

As the curing stage continues, there is a gradual increase in the humus fraction. Humus is a complex class of chemicals that result from the incomplete degradation of organic matter. Humus is among the most resistant compounds to degradation in nature. It is also one of the major mechanisms for the retention of nutrients (e.g., nitrogen, phosphorus) and micronutrients (e.g., copper, zinc, iron, manganese, calcium) in the soil. Because humic compounds retain micronutrients and water so well, they are often the site for the highest biological activity, including microorgan-isms, protozoans, invertebrates (e.g., worms, springtails) and plants.

The Microbiology of Cured Compost

Identifying Compost Microbes. Compost microbes are tremendously diverse and their ecologies are extremely complex. Methods used to identify individual species include analysis based upon metabolic activity and/or fatty acid content.

However, because of the great diversity, identification of individual species in cured compost is rarely done and is generally considered impractical and extraordinarily expensive. Laboratories, instead, are more likely to identify and count species by organism group, such as actinomycetes, aerobes, anaerobes, fungi, nitrogen-fixing bacteria, or pseudomonads.

Guidelines for desirable levels of each of these microbe groups are listed in the Compost Quality Standards document referenced at the end of this fact sheet. A commercial laboratory that specializes in compost analysis developed these levels, which are based on numerous samples and observations in various applications.

New techniques of DNA analysis are providing researchers with additional tools to identify compost and soil microbes. However, this method of identification is in its infancy and is not commonly available in commercial soil labs.

Inoculating Compost. Many researchers and companies suggest they can determine the “health” of a compost product and recommend inoculants to improve its quality or performance. However, there is no conclusive evidence that the addition of any specific microorganism to cured compost will improve any characteristic of compost. Native microorganisms may quickly dominate introduced microorganisms. The introduced microorganisms may provide possibly nothing more than additional nutrients to organisms already in the compost. Inoculants, if desired, can be added just prior to application of the compost.