Learning Center
Plans & pricing Sign in
Sign Out

Compost Microbiology and the Soil Food Web - DOC


									             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

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 106F 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–105F) 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–170F). 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 160F, 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,

Overheating. If a pile does overheat, surpassing               degradation of these compounds requires the use
approximately 170F, 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.
                                                               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

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

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
                                                           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
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
pathogen suppression in the field after application.
                                                           Aerobic––Requiring oxygen for metabolic
Degradation of pollutants. Mature compost has
been shown to be an effective tool for reducing

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
                                                                       #443-00-005. Available from the CIWMB at
Colony––A microbial population originating from                        (916) 341-6300 and also at
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
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
Humus—Recalcitrant, highly stable byproducts
of organic matter decomposition.                                       Compost Quality Standards, Organic Ag
                                                                       Advisors and BBC Laboratories, Inc. Available
Mesophilic—Temperature range of 50–105F.                              from the CIWMB at (916) 341-6300.
Microorganism—Bacterium (including                                     California Integrated Waste Management Board:
actinomycetes) or fungus.                                    
Phytotoxin—Chemicals harmful to plant health.                          Soil Quality Institute’s Soil Biology Primer,
Propagule—Any part of a microorganism that                   
can grow and reproduce.                                                Primer/

Recalcitrant—Relatively resistant to biological,                       U.S. EPA’s Bioremediation Fact Sheet,
chemical, and/or photodegradation.                           
Spore—A dormant and highly resilient microbial
state induced by unfavorable environmental                             BBC Laboratories, Inc.,,
conditions.                                                            (480) 967-5931.

Thermophilic—Temperature range over 105F.                             Soil Foodweb, Inc.,,
                                                                       (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

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).

To top