Compost Microorganisms

In sessions for schools on Compost Creatures and Compost Safaris, we concentrate on the larger creatures involved in composting, as well as those others that will find their way into the heap.

Third Level Decomposers

These larger creatures, sometimes known as Macro-organisms, physically break down the organic material by chewing, tearing and, in some cases, sucking it into smaller pieces.  Ants, beetles, centipedes, “composting” worms, flies, millipedes, slugs, snails, spiders, and. woodlice (sow bugs) are all in this group and can be easily seen by the naked eye. These creatures make up the third level of decomposers who work to produce compost.

Second Level Decomposers

The second level decomposers e.g. springtails, nematodes, beetle mites, mold mites and protozoa, eat the organic matter and the organisms that make up the first level decomposers. These tend to be smaller and the use of a hand lens or stereoscopic microscope is useful to observe them in detail.

First Level Decomposers

The first level decomposers are the much smaller Microorganisms and they play the major role in the composting process. They use the organic matter in the compost bin or heap as a source of food resulting in its decomposition to the rich brown material we know as compost. We can speed up the   natural decomposition process by providing optimum conditions for the soil microorganisms to breakdown more quickly than would occur without our intervention. Many of these bacteria, fungi, and actinomycetes break down the organic material chemically, in contrast to the physical action of the macroorganisms. The actual species of composting microorganism in any given heap will vary, depending on the climate, moisture content, pH Compost pH, temperature and the conditions within the particular part of the heap at the time of collecting the samples for identification and counting. These bacteria, actinomycetes and fungi will be present in massive numbers.

 The “On-Farm Composting Handbook” gives examples of the numbers of each group of microorganisms present.

  • Bacteria 1,000,000 – 1 billion present per gram of compost.
  • Actinomycetes 100,000 -100 million in a gram of compost.
  • Fungi 10,000 -1,000,000, fungal cells per gram of compost.

 (On-Farm Composting Handbook {NRAES-54}. ©1992 by NRAES (Natural Resource, Agriculture, and Engineering Service)},

 A further source of information has been the on-line Cornell University Composting resources at

 In addition to the microorganisms involved in the creation of compost, the organic material being composted may be contaminated by a wide range of microorganisms found:

  • In water gaining access to the heap or bin and being used to provide moisture,
  • In the soil,
  • In manure and any other material being composted or added to the bin,
  • On larger creatures gaining access and
  • Contaminants from other sources, such as animal and human faeces.

These will soil, water and contaminate microorganisms will include those that are pathogenic to humans. 

Compost Bacteria

Bacteria are small single celled organisms and are the largest group of microorganism involved in the composting process with between 1,000,000 – 1 billion present per gram of compost. The majority of bacteria are spherical (Cocci) or rod shaped (Bacilli). A data microscope, stereoscopic or general laboratory microscope will enable you to see a number of these.

Bacteria are the dominant population of microorganism during all stages of the composting process and are particularly active in the breaking down of the easily degraded organic material whereas the actinomycetes and fungi typically proliferate in the later stages.

Bacteria require carbon (Browns) and nitrogen (Greens), using carbon as a source of protein and nitrogen as their main source of energy. 


The Actinomycetes are actually bacteria but in most publications are discussed separately as they play a major role in the decomposition the less easily degraded than that favoured by other bacteria. Actinomycetes can also tolerate dryer conditions than other bacteria and produce a chemical (geosmin) responsible for the typical musty, earthy smell of compost. They are normally found in compost 5-7 days after the start of the process. The Mesophilic actinomycetes operate best in medium temperature areas (20º–50ºC) of the compost normally the edges of the heap or bin and at the end of the process. Thermophilic Actinomyces grow at between 30º–60°C. The optimum temperature for thermophilic fungi is 40–50°C which is also the optimum temperature for lignin degradation in compost.

 Like fungi, Actinomycetes form threads, filaments, or strands, which spread throughout a compost heap or soil. After bacteria, Actinomycetes are the second most abundant microorganism in the compost heap. There are typically 100,000 -100 million in a gram of compost.  They do not respond well to acidic conditions (below pH 5.5) or in the presence of a high moisture conditions.



Fungi also form threadlike filaments know as hyphae, which spread through the compost heap or bin. Fungi play an essential role, as they are able to breakdown the more resistant organic material e.g.  cellulose and lignin. Fungal hyphae aid the aeration and drainage of the compost pile by physically aggregating into small particles.  There are between 10,000 -1,000,000, fungal cells per gram of compost.

Many fungal hyphae are relatively easily seen by the naked eye being larger than those of actinomycetes

Most fungi cannot survive  thermophilic stage of  hot composting as they do not grow above  50°C and although there are some  heat tolerant thermophilic fungi, indeed some start to grow at 60°C e.g. Chaetomium thermophile, some Humicola species Thermoascus aurantiacus and have a role in decomposing cellolose and hemicelloloses. Aspergillus fumigatus can also be active at these temperatures and will continue to function when the compost is reoccupied by mesophilic organisms.


Aerobic and Anaerobic Respiration

Microorganisms can be divided into those that respire aerobically, using the oxygen present in the air for energy metabolism, and anaerobic bacteria that do not use oxygen for energy metabolism.

 In home and garden composting, we make use of aerobic bacteria to produce compost from the organic waste this requires the presence of air, moisture and produce heat. Systems such as the Bokashi bin involves Anaerobic decomposition as a  result of sealing the material in a container without air the material  in a Bosashi bins does not produce heat. A similar situation can occur if food waste is stored in a kitchen caddy or bin, for more than a week or so it starts to turn soft, mushy and eventually liquid making it unpleasant to handle.

 Aerobic Bacteria

Aerobic bacteria are the most important to the process of converting organic waste to compost. They are necessary for the conversion of the organic material into the moist, rich compost we are attempting to produce.

These aerobic bacteria require oxygen levels of more than 5% to oxidize carbon to provide them with energy. This oxidation process produces the heat that raises the temperature of the compost heap, or bin, during the early stages of the composting process.  As described, in the section on hot composting, under the right conditions the compost will heat up within a day or two to 60C or higher, due to the aerobic bacteria consuming readily decomposable material. In addition to carbon. Nitrogen is also necessary to the composting process enabling the bacteria to form the protein necessary for them to grow and reproduce. Hence the importance of the C: N ratio.

If the oxygen level falls below five percent bacterial activity will slow down and the decomposition rate can be reduced by as much as 90%

 Anaerobic bacteria

Where there is insufficient oxygen present to support the growth of aerobic microorganisms i.e. under anaerobic conditions, anaerobic bacteria will ferment the organic material. Unfortunately, for the composter, the anaerobic process results in the production of organic acids and amines, producing the easily recognizable smell of ammonia, as well as hydrogen sulfide (rotten eggs smell). The organic material is turned into a wet, smelly black mess. In practice, if this happens it is because we have the C: N ratio wrong. We can try to rectify the situation by adding additional carbon rich (Brown) material and turning the compost to open the mix to create conditions under which aerobic bacteria can function.

The requirement for a moist mix during the composting process, 50% - 60 % moisture content, is because the Compost microorganisms live in the water films surrounding the particles of organic matter.

Examples of Compost Bacteria

There are a wide range of bacteria that occur naturally in the soils and will be present in compost. The table contains brief notes on the habitats in which they are normally found.



Gram stain blue (positive) or Red (negative). Respiration


Alcaligenes faecalis


Aerobic, rod-shaped bacteria.

Aerobic but  some strains of  are capable of anaerobic respiration,;

 Intestinal tracts of vertebrates, decaying materials, dairy products, water, and soil; they can be isolated from human respiratory and gastrointestinal tracts and wounds in hospitalized patients with compromised immune systems. They may cause of opportunistic infections


Gram Negative rods


Brevibacillus  (Bacillus) brevis


 spore forming rod shaped bacteria

Commonly found in soil, air, water, and decaying matter

Bacillus species

B.coagulans,     B.circulans B.licheniformis, B.megaterium

B.pumilus,        B.sphaericus B. subtilis


Bacillus is a genus of Gram-positive, rod-shaped spore forming bacteria  

Bacillus species can be obligate aerobes (oxygen reliant), or facultative anaerobes (having the ability to be aerobic or anaerobic respiration). 


 There are species of this genus saprophytic in soil, water, and a wide range of other environments. Some e.g. B.cereus,  B .ubtilis and 

B.licheniformis, are associated with infections of wounds and disease. B.stearothermophilus  is a thermophile (heat resistant )

Clostridium thermocelium

 Gram-positive Anaerobic and thermophilic spore producing rod

  Found in plants and animals. In cattle and horses etc digestive system it breaks down the cellulose of grass. 

Escherichia coli

(and other Enterobactericae)

Gram negative rods,

 facultative anaerobe

Normally found in human and animal guts. Some are pathogenic, causing diarrhea or other illness.  Pathogenic  E. coli that can be transmitted through contaminated water,  food and by  through contact (now wash your hands)

Flavobacterium sp.

Gram-negative, rods

Found in soil and water

Pseudomonas sp

Gram-negative rods, aerobic 

Different species are widespread in water, plant seeds and a  wide range of locations

 P.aeruginosa  can be a human pathogen and often causes ear infections in dogs.  P. syringae is a  plant pathogen 

Serratia sp

Gram-negative rods,

facultative anaerobic,

Widespread in the environment,

S.marcescens can be pathogenic.

Streptocuccus (Enterococcus)

Gram positive cocci (spheres)


Thermus sp

  Gram negative rods thermophilic thrives at 70°C (160°F), but can survive at temperatures of 50°C to 80°C (120°F to 175°F)

Found in  soil, faeces, meat, sewage and  thermal springs. 

Vibrio sp







Streptomyces is the source of over two-thirds of the clinically useful antibiotics 



Nitrogen fixing bacteria. About 15% of the world's naturally fixed nitrogen is species of Frankia  and their host plants

other Actinomycetes (at least 14 species have been identified) incl. micromonospora

Facultative anaerobes but some are anaerobic

Decomposers digesting tough plant tissues like the cellulose and lignin in bark, paper and stems and the chitin or hard exoskeletons of insects as part of the composting process.



Examples of Compost Fungi

Compost Fungi

Aspergillus fumigatus

Fungal mould

Found in soil and decaying organic matter, i.e. compost, bird droppings, tobacco, stored foods.Can grow at temperatures up to 50 °C  and  survive at 70 °C  conditions found in hot composting.

Basidiomyces sp


Important in the degradation of lignin

Humicoli grisea, Humicoli insolens, Humicoli lanuginosa

Thermophylic Fungal mould

 Found in soil and plant material. Common in compost

Malbranchea pulchella



Myriococcum thermophilium



Paecilomyctes variotti



Papulaspora thermophilia



Penicillium sp (incl P.dupontii)



Scytalidium thermophilim



Termonmyces sp., 



Tricoderma sp




Bacterial Activity and Temperature

 Composting is a self-heating, aerobic biodegradative process of organic materials. The microbes involved in the composting process will need:


  • adequate ventilation, to provide oxygen for their aerobic respiration,
  • adequate moisture, ideally 40-60%, and
  • nutrients to support their growth.


When the microbes flourish, they will raise the heap temperature as a result of their metabolic heat generation during the conversion of composting materials to energy, carbon dioxide, water and compost.  During different stages, the temperature of the organic material and its nutrient content will vary and will provide a favourable habitat for different types of microorganisms. Microorganisms can be grouped by the temperatures at which they can live.


Different authors have classified the Composting stages based on the temperatures created by predominant bacteria groups at any time, simply as the Initial stage, Active stage, Curing and Maturing stages while others have described the stages on the basis of what is happening to the organic material e.g Degradation, Conversion and Maturation (DCM).


The phases are:


  • The Pyschophilic bacterial stage (A resting stage. Not recognized as the first stage of the process by all).
  • The Initial stage during which Mesophilic organisms predominate, this also forms the start of the Degradation stage
  • The Active or thermophilic phase which continues the Degradation of the material;
  • A possible overheating phase and cooling leading to the return to the Mesophilic.)
  • The Maturation or Cooling and Curing phases.




Psychrophilic stage

During the winter, the compost heap may become frozen and even on warmer days, the temperature may not rise above 13ºC. Psychrophilic microorganisms function at low temperatures from -10º to 18ºC or 20ºC (14 – 68ºF) but below about 13ºC most of the microorganisms in the heap will be semi-dormant and there will be little decomposition of the material.

At 13º- 21ºC, the psyochophiles become more active. They produce only a small amount of heat compared with other bacteria and can be active during the winter without significantly raising the temperature of the compost in cold weather. As the weather becomes warmer, the heat they produce can be sufficient to increase the temperature of the heap of bin.  As the temperature rises, the psychophiles are denatured and a group of organism that function at over 25ºC, the Mesophiles, become important to the process. Using the  Degradation, Conversion and Maturation (DCM) Classification the Degradation  phase  commences at about 12ºC. 

Mesophilic or Initial Stage

Many workers consider the Mespohilic phase to be the first phase of real composting. This is a continuation of the Degradation phase under the DCM classification.

 Mesophiles are  found in water and soil. Under favourable conditions, mesophiles can double their numbers in 20-30 minutes; they are responsible for most of the bacterial diseases of humans.

When a heap of pile is first made, the material is exposed to an addition source of microorganisms and the microbes receive a fresh source of foodstuffs. The temperature and the presence of easily decomposed organic material favours the mesophiles and they commence the decomposition of the easily digested materials in earnest, quickly utilizing soluble sugars and starch, until the heat produced by their activity causes the temperature of the heap to rise


This moderate temperature mesophile stage ranges between 20ºC- 40ºC or 45ºC, although many mesophile species thrive best  between 21º and 32ºC. The initial mesophilic stage  normally lasts for two or three days. During this period the mesophilic organisms break down the soluble, more easily degraded organic compounds producing, in addition to heat, acids and carbon dioxide. As the temperature rises Thermophilic organism begin to dominate.

 In a cold composting “add as you go” systems,  where organic material is added regularly  in small amounts e.g. when using a small compost bin or heap,  the compost may never reach a higher temperature as the heat produced by bacterial activity is lost to the environment not  allowing the thermophiles to become dominant and requiring the mesophiles to do most of the work.

 During the Mesophilic and Thermophilic stages of the composting process, actinomycetes and fungi are confined to the outer 2 to 6 inches of the heap of bin. Some molds also grow in this outer zone of the composting galaxy. Unless the compost is aerated by turning frequently fungi and actinomycetes, hyphae can give grayish white appearance to this outer zone. Frequent aeration where the cooler material in the outer areas is turned into the centre of the heap prevents the formation of sufficient hyphae to produce a colour change of be visible to the naked eye.  

Thermophilic or “Active” stage

The activity of the Mespohiles results in the production of heat and a significant increase in the temperature of the heap to that which favours thermophilic organisms (40°C to 70°C). These are the most efficient decomposing bacteria in a hot composting pile and continue the Degradation Phase under the DGM classification.  These organisms start to dominate the heap at temperatures of about 40ºC in batch composting. Composting proceeds at a much faster rate under thermophilic conditions.  It is during this stage that most of the organic matter is converted into carbon dioxide and humus. There is also a growth in the number of microorganisms present.

These high temperatures accelerate the breakdown of cellulose, hemicellulose and other complex carbohydrates, proteins and fats. The thermophilic population continues generating more heat by decomposing the remaining organic matter. As  this food source is used, the activity of the thermophilic microbes declines, unless the heap is regularly fed new material and turned to aerate it and move materials from the cool sides to the centre, and the compost temperature falls after three to twelve days (depending on the compost technique used). This allows the return of  Mesophilic organisms once again become the dominate group of bacteria in the   compost heap. During this period, the Conversion phase beings. In a compost bin or heap this conversion will occur at the bottom  as the organic material starts to take on the appearance of compost.

As mentioned above the period of thermophilic activity can be extended turning/mixing the heap and aeration.

The stages are easily monitored in batch composting as the temperature changes can be made to apply to the whole heap provided it is turned regularly. If the material is not turned the area at which the  high temperature occurs may only only to within 4 to 8 inches of the surface.  

In hot composting using a heap, the temperature can be monitored and the heap turned, outside to the centre, as it starts to cool so as to hold the material at a sufficiently high temperature (see the page on Compost Temperatures). Where a tumbler bin is being used this mixing and  aeration occurs  daily when the tumbler is turned.  Hot composting  at temperatures 55°-60° C and over  will destroy the majority of  plant and  human pathogens and weed seeds present. 

There are mixed veiws on the number of times the heap should be turned.  A single through turning may be sufficient eliminate the pathogens and parasites but for this to be effective  all the outside  material most be  completely turned to the inside, most hot composters will turn material at least twice with many opting for   three or five turnsto be on the" safe side". Alternatively the turning can be undertaken in conjunction with measure the temperature of the heap and continuing turning the material until there is no marked change in temperature following the aeration.

The killing of pathogens is an advantage offered by the hot composting techniques but it is not necessary unless there is a specific concern about killing disease organisms and seeds.

 An alternative to killing pathogens is not to add diseased materials that will survive cold composting to the bin in the first place.

Many “good bacteria” i.e.  decomposers are inactivated or killed when temperatures of the heap rises above 60ºC (140ºF). If the heap temperature exceeds 72ºC (160ºF), it can be cooled turning/aerating. If a pile does overheat, exceeding 72-76ºC most of the bacteria will be destroyed and the composting process will almost come to a stop. It has been  found that during  the thermophillic stage in some bins  87%   of the organism present  were Bacillus species, which are spore forming, with one species Bacillus stearothermophilus predominant at temperatures of over 65°C.  Bacterial spores are formed by bacteria of the species Bacillus and Clostridium as a survival mechanism when the organism is under stress such as heat. Bacterial spores will  survive to germinate when the heap cools to a suitable temperature  although most Bacillus species are unable to grow unable to grow above 70oC.    Thermus species, originally  found in  geothermal sites, which while growing at 40-80oC have an  optimum temperature of between 65oC and 75oC. are active in compost at these higher  temperatures  

 Other of thermpphiles that  play a role in composting. Fungi such as Rhizomucor pusillus, are active as the temperature rises but is inactivated at peak heating  while   a second group of thermophilic fungi now play a role in the decomposition of cellulose and hemicelluloses, including: 

Chaetomium thermophile,  Humicola  insolens,  Humicola  lanuginosus,  Thermoascus aurantiacus and   Aspergillus fumigatus. 

Eventually insufficient nutrients will be available to maintain the higher temperatures and the heap will return to the cooler levels of the mesophilic stage, even when turned i.e mixing by turning and turning the compost fails to lead to any increase in the temperature of the compost.

In cold composting, while temperatures that  favour  thermophiles may be reached in  particular parts of the heap after  new material is added  most of the heap will not exceed  40ºC and it is it is mesophiles,  not thermophiles,  that will do most of the work.

Curing or Maturation phase

At this stage of the composting process, the easily degradable organic materials will have been utilized leaving material that is insoluble in water and cannot be absorbed into the bacterial cell due to their chemical complexity size. The fungi and actinomycetes now come into the picture as these can degradation of these compounds using extracellular enzymes allowing them to be absorbed. The materials include chitin, lignins, humic materials, some remaining cellulose, starches and proteins. As they reduce materials, they liberate carbon, nitrogen, and ammonia, making nutrients available for higher plants. They are especially important in the formation of humus - organic matter that has reached the final state of decomposition. They are responsible for the earthy smell associated with compost and appear five to seven days after the start of the composting process. Actinomycetes develop into large clusters and become most evident during the later stages of decomposition

Actinomycetes assume a major role during the final stages of decomposition, and may produce antibiotics that inhibit bacterial growth. They work on tough-to-break-down organic materials such as avocado, seeds and glossy leaves.  In order to avoid breaking up the hyphae of actinobacteria (and fungi) I would recommend that tumbler composters are not turned  during the curing phase and that the compost in conventional heaps, piles or bins are not mixed or aerated.

Fungi also play a significant role during the final stages of composting. Fungi are primitive plants that can be either single celled or many celled and filamentous. Fungi are present in smaller in numbers in the compost than actinomycetes or bacteria, but larger in body mass. Their main contribution to a compost pile is to break down cellulose and lignin. They prefer cooler temperatures 22C-24C and easily digested food sources.

 During this curing and maturation stage of composting the cooler temperatures encourages the entry of worms, insects mites and the other Macroorganisms we find on when undertaking a  Compost Safari.

The time of the curing process will vary but a longer process is desirable as it reduces the likelihood of pathogens and phytotoxins being present as well as organic acids, which may limit its use in seed compost. The levels of Humus in the compost increase with the length of the curing process

Compost Microorganisms Pathogenic to Humans

There are a considerable number of disease causing microorganisms that may be found as contaminants of compost and could present a risk of infection to the composter. WRAP published a booklet in 2003 “The Occurrence and Survival of Pathogens of Animals and Humans in Green Compost”    which contains information on potentially pathogenic microorganisms which may contaminate green compost in the UK.

 These include the food poisoning bacteria that are often featured in the press following a disease outbreak e.g.  Salmonella, Campylobacter, Clostridia perfringens, Clostridia tetani, E. coli, Staphylococcus aureus, as well as other pathogens such as  Coxiella burnettii (the cause of Q fever), Pasteurella, Listeria, Erysipelothrix, Leptospira, Serpulina hyodysenteriae and  mycobacterium.

 However, Home Composting material from your own kitchen or garden is less likely to be contaminated with animal and faecal waste than materials collected by kerb-side collection or from other sources. (It is not unknown for garden waste bins left for collection to contain disposable nappies!). Luckily most of the pathogenic bacteria will not be present in large enough numbers to cause disease in humans and in the majority of cases; the composting process will kill them if hot composting techniques are used.

Microorganism that occur naturally in soils and water Pathogenic to Humans

 Bioaerosols (airborne microorganisms including bacteria and fungi spores) are frequently implicated in cases of infection from compost.  The number of bioaerosols will be dependent on the degree of contamination of the initial organic material, the growth of the organisms while waiting composting and during the composting process. 


In recent years there have been a number of cases of reported in the press of Legionella species causing disease in people exposed to compost.  Legionella are Gram-negative bacteria that are common in many environments, including soil and aquatic systems, with at least 50 species

S. L. Currie, T. K. Beattie, C. W. Knapp and D. S. J. Lindsay examined 24 composts for the presence of Legionella species. More than half of the samples tested positive for Legionella, twelve different species. The most commonly isolated Legionella species was Legionella sainthelensi.

(Legionella species in UK Composts – a potential public health issue?  In Clinical Microbiology and Infection )

 Of the Legionella species two most important pathogens are:

 Legionella pneumonophila causes Legionaires disease a form of pneumonia normally associated with air conditioning systems and aerosols from showers etc. is also a risk in “standing” water sources between 20C-45C were aerosols are formed.

Legionella longbeachae, which  occurs naturally in soil and compost, can also produce respiratory disease (Pontiac fever) It must be stressed that the majority of people who breathe the bacterial aerosols show no ill-effects  Where illness occurs it is most likely to involve older people, smokers and those with weakened immune systems. In addition to inhalation of the organisms ingestion as a result of poor hygiene practices, including lack of hand washing has been implicated in cases of infestation by L. longbeachae


Tetanus, Staphylococcus and Streptococcus


The Tetanus bacteria (Clostridium tetani) is common in compost, soil and manure and it is likely that any gardener will be in contact with it quite frequently. Vaccination is recommended.


Staphlococcus and Streptococcus can cause Paranychia, an infection that develops in the skin round the fingernails, when working in compost with bare hands which allows entry of the bacteria through small cuts and abrasions. Large numbers of Staph and Strep species are present in compost

Aspergillus fumigatus

The fungus Aspergillus fumigates, which causes a group of diseases known as ‘Aspergilloses’, is commonly present in crop plants, decomposing material,  and decaying vegetation, including compost heaps with the risk that fungal spores will be inhaled when turning the compost. Not only does it produce numerous spores it is able to survive thermophilic temperatures, which presents an occupational hazards to those working in industrial composting facilities.

Aspergillus fumigatus aerosols have been detected during the physical disturbance e.g. aeration or harvesting of compost, in all Home Compost bins, and a statistically significant reduction in airborne emissions where worms had been added to the  home compost bin, in one study

Risk Control when composting

The risks associated with infection when working with compost are  small and a few simple precautions will reduce that risk to a very low level.

  • Wear gloves either gardening gloves or nitrile/latex for more delicate tasks
  • Wash hands and/ or use hand sanitizer if washing facilities are not available

 Handling compost

  • Moisten compost before aeration and consider wearing a dust mask (particularly if the compost smells musty).
  • Do not hold your head immediately over the compost bin when aerating the compost to avoid directing aerosols or spores into the face.
  • Do not store compost in the greenhouse where it will warm up during the summer allowing microorganisms to multiply.
  • Shred woody material in a well ventilated area