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Compost Microbiology and the Soil Food Web Introduction Microbe Types and Requirements. The microbiological components of compost consist of Compost is the product of an aerobic* process bacteria and fungi. Because of their unique nature, during which microorganisms* decompose organic actinomycetes are discussed here as a third matter into a stable amendment for improving soil microbiological component, though in actuality quality and fertility. During composting, actinomycetes are a particular kind of bacteria. microorganisms use the organic matter as a food The majority of microorganisms responsible for the source, producing heat, carbon dioxide, water formation of compost are aerobes in that they vapor, and humus* as a result of their furious require or work best in the presence of oxygen. growth and activity. When applied to and mixed into the soil, humus can promote good soil Many difficulties associated with composting may structure, improve water- and nutrient-holding be traced to insufficient oxygen levels to support capacity, and help to control erosion. Humus the decomposition of compost feedstock. Compost makes up approximately 60 percent of finished microbes also require a moist environment compost. because they live in the water films surrounding composting organic matter particles. A 50 to 60 A wide range of organic materials such as yard percent moisture content is optimal. trimmings, manures, and food processing discards go into producing composts. Materials used to Fungi. Fungi form their individual cells into long feed compost microorganisms are referred to as filaments called hyphae. Fungal hyphae are larger compost feedstocks.* than actinomycetes and may be more easily seen with the naked eye. They penetrate throughout the Part I of this fact sheet addresses the composting composting material, decomposing both process and associated microorganisms. Part II chemically and mechanically the more recalcitrant* then addresses how compost contributes to the organic matter fraction such as lignins and soil food web and overall plant health. cellulose. Fungal hyphae physically stabilize the compost into small aggregates, providing the Part I: The Composting Process and compost with improved aeration and drainage. Associated Microorganisms Fungi number between 0.01 and 1 million propagules* per gram of soil. About 70,000 Compost Microorganisms different species of fungi have been described Sources. The microorganisms needed for worldwide, but an estimated 1 million additional composting are found throughout the natural species remain undiscovered and undescribed. environment. They are present in compost Ecologically, fungi play a vital role in breakdown of feedstock as well as in the water, air, soil, and dead plant materials. machinery the feedstock and compost are Bacteria. The most numerous biological component exposed to during processing. of compost is the bacteria. Although they often can These sources ensure a high diversity of exceed 1 billion microorganisms per gram of soil, microorganisms, which helps to maintain an active bacteria (with the exception of actinomycetes) do not microbial population during the dynamic chemical contribute as much to the overall microbiological and physical processes of composting, such as mass as fungi because of their relatively small shifts in pH, temperature, water, organic matter, size. Although bacteria (with the exception of and nutrient availability. Only on rare occasions actinomycetes) exist as individuals and do not will the addition of microorganisms be warranted form filaments, they also contribute to the (see ―Inoculating Compost‖ section). stabilization of aggregates through the excretion of 2 organic compounds that bind adjacent organic mesophiles predominate and proceed to matter and soil particles together. Bacteria are decompose the readily degradable sugars, typically associated with the consumption of easily proteins, starches, and fats typically found in degraded organic matter. They are the dominant undigested feedstocks. population throughout the entire composting The availability of easily usable organic process, whereas the actinomycetes and fungi substances enables the proliferation of the fastest- typically proliferate in the later stages. growing microorganisms, the bacteria. Mesophilic Actinomycetes. While actinomycetes are visually bacteria, therefore, dominate initial decomposition. similar to fungi in that they have networks of These bacteria release heat from the breakdown individual cells that form filaments or strands, they of large amounts of easily degraded organic are actually a type of bacteria. These filaments matter. This heat begins to raise the temperature allow for a colony* of actinomycetes to spread within the pile due to the high insulating capacity throughout a compost pile, where they are of a properly sized compost pile. Within just hours typically associated with the degradation of the the temperature of the compost pile can rise more recalcitrant compounds. above the 106F thermophilic threshold. Actinomycetes number between 0.1 and 10 million Active Stage. As the compost reaches higher propagules per gram of soil. Their filaments temperatures, thermophiles begin to dominate the contribute to the formation of the stable organic bacterial community. The active stage is typically aggregates typical of finished compost. the stage where most of the organic matter is Actinomycetes are tolerant of lower moisture converted into carbon dioxide and humus, and the conditions than other bacteria and are responsible microorganism population grows. The thermophilic for the release of geosmin, a chemical associated population continues generating more heat by with the typically musty, earthy smell of compost. decomposing the remaining organic matter. Due to limitations with isolation techniques, Composting Process laboratory studies have only been able to isolate a Composting proceeds in predictable stages. During few genera of bacteria from the thermophilic stage different stages, temperatures and nutrient (Bacillus, Clostridium, and Thermus), but many availabilities vary and affect the kinds and numbers microorganisms remain to be discovered and of microorganisms that develop. Initially, the pile is at described. In a properly ventilated composting approximately the ambient temperature. The pile, the temperature will be maintained between composting material warms through the mesophilic* approximately 131° and 155 F. Fortunately, temperature range (50–105F) as the pathogens such as human viruses and infectious microorganisms become more active. Soon, bacteria are typically unable to persist in such a microbial activity raises the temperature of the pile to hostile environment. The higher temperatures will thermophilic* temperatures (106–170F). This is ensure rapid organic matter processing while considered the most productive stage of composting. simultaneously providing optimal conditions for the destruction of human and plant pathogens as well Mesophiles and thermophiles are microbes adapted as weed seeds. to mesophilic and thermophilic conditions, respectively. Composting proceeds at a much faster Because the composting pile is cooler on its outer rate under thermophilic conditions. Eventually, surface, periodic mixing of the outer layer into the readily available substrates within the feedstock are pile is essential for maximum pathogen and seed exhausted, temperatures gradually return to the kill. Mixing or turning the pile also helps to mesophilic range, and curing begins. The following ventilate it by increasing the size and number of section expands on the microbiology of each stage. air pores. This is important because in an unventilated compost pile, the temperatures can Initial Stage. The process of transporting and exceed 160F, effectively stopping all microbial manipulating the feedstock for composting activity. The air pores also serve as passages for exposes the organic matter to additional sources oxygen to enter the pile. Microbes require oxygen of microorganisms, all of which may contribute to efficiently break down organic matter. toward initiating the composting process. Initially, 3 Overheating. If a pile does overheat, surpassing degradation of these compounds requires the use approximately 170F, most microbes will be of extracellular enzymes.* destroyed and microbial activity will virtually Once the complex organic compounds are broken cease. Surviving microorganisms are typically down into smaller and more soluble forms, they those able to survive as spores.* The spores will can enter the cell and become food and energy for germinate when the composting pile returns to a the microorganism. Microbes able to produce more favorable temperature. These spores are extracellular enzymes suitable for breaking down thick-walled structures that are formed by the recalcitrant materials will have a selective microorganism under stress such as heat, cold, advantage at this point in the composting process. drought, and low nutrient conditions. A novel feature of many of the extracellular After overheating, the composting pile will cool to enzymes common in fungi is that they are capable a mesophilic state, requiring the activity of of breaking down a wide range of compounds that mesophilic microorganisms to return the pile to would otherwise require several specific thermophilic conditions. If the composting pile is enzymes*, a feature not commonly found in a low in readily utilizable organic substrates, the pile single microorganism. Fungi, though they grow may not be able to support the microbial activity and reproduce more slowly than bacteria when needed to return to thermophilic conditions. In food is readily available, are well suited for such a case, it may be necessary to supplement exploiting an environment rich in complex the composting pile with additional feedstock to recalcitrant organic compounds like those found in ensure maximal degradation and pathogen the compost during the curing stage. removal. The curing process can vary in duration; a longer An overheated composting pile may return to curing period provides more assurance that the thermophilic temperatures through the germination compost is free of pathogens and phytotoxins.* If and activity of spore-forming microorganisms, and the compost is incompletely cured (i.e., not through the infiltration of microorganisms from the stable), it maintains a higher microbial activity, outer surface of the composting pile where the leading to increased oxygen consumption. When temperature was less extreme. unstable compost is applied in the field, it can Curing Stage. A properly functioning composting thereby decrease the supply of oxygen available pile will eventually deplete itself of a majority of the to plant roots. easily degradable organic substrates leaving some In addition, immature compost can contain higher cellulose, but mainly lignins and humic materials. levels of soluble organic matter (i.e., organic Bacteria are generally considered less adept at acids), which can lead to toxicity problems for metabolizing these remaining compounds. certain horticultural applications, such as seed Consequently, the bacterial population will decline germination. Detailed information on assessing in numbers as compared to fungi and compost stability and maturity is included in the actinomycetes. Because less heat is generated at California Integrated Waste Management Board this point, the temperature of the composting pile (CIWMB) publication Compost: Matching will slowly fall to mesophilic temperatures. With the Performance Needs with Product Characteristics return of mesophilic conditions, the final curing listed at the end of this document. stage of composting begins. As the curing stage continues, there is a gradual During the curing stage, the fungi and increase in the humus fraction. Humus is a actinomycete populations predominate, while the complex class of chemicals that result from the bacterial population may decline somewhat. Fungi incomplete degradation of organic matter. Humus and actinomycetes proliferate on the remaining is among the most resistant compounds to less degradable organic matter such as chitin, degradation in nature. It is also one of the major cellulose and lignin. These compounds are more mechanisms for the retention of nutrients (e.g., persistent because they are insoluble in water nitrogen, phosphorus) and micronutrients (e.g., and, due to their size and chemical complexity, copper, zinc, iron, manganese, calcium) in the soil. cannot pass into the bacterial cell. Thus, Because humic compounds retain micronutrients 4 and water so well, they are often the site for the Part II: Contributions of Compost to highest biological activity, including microorgan- the Soil Food Web and Plant Health isms, protozoans, invertebrates (e.g., worms, springtails) and plants. Many growers think of compost as primarily a source of nutrients to add to the soil. However, its The Microbiology of Cured Compost contribution of a diverse set of microorganisms combined with its high levels of organic matter Identifying Compost Microbes. Compost may offer even more significant benefits. microbes are tremendously diverse and their ecologies are extremely complex. Methods used Soil consists of many organic and inorganic to identify individual species include analysis components that interact with each other in a based upon metabolic activity and/or fatty acid dynamic, living system. From organisms as small content. as bacteria to larger insects such as earthworms, all of these players help cycle nutrients and However, because of the great diversity, contribute to the overall health of the soil food web identification of individual species in cured and surrounding plant life. compost is rarely done and is generally considered impractical and extraordinarily A quality compost that has been prepared under expensive. Laboratories, instead, are more likely aerobic conditions and adequately cured can to identify and count species by organism group, contribute to the health of plants and the soil food such as actinomycetes, aerobes, anaerobes, web in several ways. Compost introduces a variety fungi, nitrogen-fixing bacteria, or pseudomonads. of microorganisms that may assist in the cycling of nutrients and in the control of pathogens. Compost Guidelines for desirable levels of each of these also contributes organic matter to the soil that may microbe groups are listed in the Compost Quality serve as a source of food for the various microbes, Standards document referenced at the end of this among other functions. fact sheet. A commercial laboratory that specializes in compost analysis developed these Compost Introduces Beneficial levels, which are based on numerous samples and Microorganisms observations in various applications. When incorporated into soil, compost introduces a New techniques of DNA analysis are providing wealth of beneficial microorganisms. As discussed researchers with additional tools to identify in Part I, plant and human pathogens are compost and soil microbes. However, this method destroyed during the composting process. The of identification is in its infancy and is not remaining beneficial microbes assist with a commonly available in commercial soil labs. number of functions that assist in soil and plant Inoculating Compost. Many researchers and health. companies suggest they can determine the Nutrient cycling. To be available to plants, ―health‖ of a compost product and recommend nitrogen must be in an inorganic form, such as inoculants to improve its quality or performance. - + nitrate (NO3 ) or ammonium (NH4 ). Plants are not However, there is no conclusive evidence that the capable of converting organic nitrogen to these addition of any specific microorganism to cured inorganic forms. Fortunately, microorganisms compost will improve any characteristic of commonly found in soil and compost convert compost. Native microorganisms may quickly organic nitrogen into inorganic nitrogen, a process dominate introduced microorganisms. The called mineralization. Plants may then take up the introduced microorganisms may provide possibly nutrients released by these. nothing more than additional nutrients to organisms already in the compost. Inoculants, if Soils that have been exposed to harsh agricultural desired, can be added just prior to application of pesticides, such as methyl bromide, may have the compost. reduced populations of these beneficial microorganisms. Compost may help to re- inoculate these soils with nutrient-cycling microbes. It is important to note that inadequately 5 cured, unstable compost may immobilize nitrogen organic pollutants in contaminated soils and water. in soil. Detailed information on assessing compost Compost bioremediation has proven effective in stability and maturity is included in the CIWMB degrading or altering many types of contaminants, publication Compost: Matching Performance including chlorinated and nonchlorinated Needs with Product Characteristics listed at the hydrocarbons, solvents, pesticides, and petroleum end of this document. products. The microorganisms in the compost break down the contaminants into components Disease suppression. Composts contain an that pose less of an environmental hazard. The astonishing variety of microbes, many of which United States Environmental Protection Agency may be beneficial in controlling pathogens. (U.S. EPA) publication Innovative Uses of Beneficial microbes help to control plant Compost: Bioremediation and Pollution Prevention pathogens through either specific or general discusses bioremediation in detail. It is available suppression. on the U.S. EPA’s Web site listed at the end of this General suppression occurs when a beneficial document. microbe fills an ecological niche that would otherwise be exploited by a pathogen. For Compost Provides a Source of Organic example, a beneficial organism may out-compete Material a pathogen for energy, nutrients, or ―living space,‖ Soil organic matter can come from a variety of thereby decreasing the survival of the pathogen. sources, including crop or plant residues, cover Specific suppression occurs when a beneficial crops, and compost. Compost consists primarily of organism secretes chemicals toxic to a pathogen organic matter, which serves a variety of vital or when it preys upon the pathogen for food. Many functions in the soil: plant pathogens contain cellulose (the principal Provides food for microorganisms. Bacteria component of paper) or chitin (commonly found in and fungi that release nutrients from soil use insects, and fungi), and all contain sugar-polymers organic matter as their food or source of (commonly found in all life). Certain compost energy. Thus, compost provides a source of microorganisms, such as Gliocladium, both microorganisms and their fuel. Compost Pseudomonas, Trichoderma, and Streptomycetes, also provides an excellent habitat for produce enzymes capable of breaking these microorganisms. compounds down, killing the pathogens in the process. Holds nutrients and water. In addition to providing a source of nutrients, organic Exposure to heat during the thermophilic stage of material can hold onto many nutrients through composting is often responsible for killing plant its cation exchange capacity.* Because and human pathogenic microorganisms. This heat compost molecules are negatively charged, also kills those beneficial microorganisms that they attract and hold onto positively charged cannot tolerate the high temperature. Thus for ions, such as calcium, potassium, ammonium, compost to serve as a means for minimizing plant and magnesium. pathogens in the field, it must be re-colonized by beneficial microorganisms. Forms aggregates and increases porosity. Organic matter increases the aggregation of Commercial compost producers in California do soil that results in a crumb-like structure. not routinely inoculate their compost. Analysis, Changes in porosity can alter water retention when performed, commonly shows that this re- properties and the water infiltration rate. inoculation occurs naturally. However, some Consequently, consistent compost use may studies suggest that controlled inoculation of improve irrigation efficiency. compost with known biocontrol agents (fungi and bacteria) is necessary for consistent levels of Glossary pathogen suppression in the field after application. Aerobic––Requiring oxygen for metabolic Degradation of pollutants. Mature compost has processes. been shown to be an effective tool for reducing 6 Cation exchange capacity—The ability of Additional Resources negatively charged particles to hold positively Compost: Matching Performance Needs with charged ions (cations) through an electrical Product Characteristics, CIWMB Publication attraction. #443-00-005. Available from the CIWMB at Colony––A microbial population originating from (916) 341-6300 and also at www.ciwmb.ca.gov/ the same cell. Publications/Organics/44300005.doc. Extracellular enzyme—Complex protein Composting Reduces Growers’ Concerns About structures that degrade organic compounds Pathogens, CIWMB Publication outside the cell of the microorganism. #442-00-014. Available from the CIWMB at Enzyme—Commonly a protein that speeds up a (916) 341-6300 and also at www.ciwmb.ca.gov/ chemical reaction or reactions. Lactose Publications/Organics/44200014.doc. intolerant people lack the enzyme lactase, which Persistence and Activity of Pesticides in is used in the chemical reaction of breaking Composting, CIWMB Publication down lactose (a sugar). #442-00-015. Available from the CIWMB at Feedstock—Starting materials to be composted. (916) 341-6300 and also at ww w.ciwmb.ca.gov/ Publications/Organics/44200015.doc. Humus—Recalcitrant, highly stable byproducts of organic matter decomposition. Compost Quality Standards, Organic Ag Advisors and BBC Laboratories, Inc. Available Mesophilic—Temperature range of 50–105F. from the CIWMB at (916) 341-6300. Microorganism—Bacterium (including California Integrated Waste Management Board: actinomycetes) or fungus. www.ciwmb.ca.gov/Organics/ Phytotoxin—Chemicals harmful to plant health. Soil Quality Institute’s Soil Biology Primer, Propagule—Any part of a microorganism that www.statlab.iastate.edu/survey/SQI/SoilBiology can grow and reproduce. Primer/ Recalcitrant—Relatively resistant to biological, U.S. EPA’s Bioremediation Fact Sheet, chemical, and/or photodegradation. www.epa.gov/epaoswer/non-hw/compost/ bioremed.pdf Spore—A dormant and highly resilient microbial state induced by unfavorable environmental BBC Laboratories, Inc., www.bbclabs.com, conditions. (480) 967-5931. Thermophilic—Temperature range over 105F. Soil Foodweb, Inc., www.soilfoodweb.com/, (541) 752-5066. The energy challenge facing California is real. Every Californian needs to take immediate action to reduce energy consumption. For a list of simple ways you can reduce demand and cut your energy costs, see our Web site at www.ciwmb.ca.gov. Publication #442-00-013 Revised June 2001 The California Integrated Waste Management Board does not discriminate on the basis of disability in access to its programs. IWMB publications are available in accessible formats upon request by calling the Public Affairs Office at (916) 341-6300. Persons with hearing impairments can reach the IWMB through the California Relay Service, 1-800-735-2929. Note: This fact sheet is intended to provide general information and point out issues to consider regarding composting. Reference does not imply endorsement by the California Integrated Waste Management Board. Prepared as one of three publications as part of contract number IWM-C8034 (total contract amount: $49,747.50, includes other services).
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