• Terry Clayton

5 Minute Biology/Chemistry of Compost

Updated: Dec 1, 2020

With a family of 5 trying to eat healthy, we buy a lot of fruits and vegetables. We also have fruit trees, gardens, and berry producing bushes on our land. Not everything is eaten and a lot of rotten kitchen scraps end up in the trash. Rather than stress our local waste hauler with all this, I decided to begin composting in a corner of our yard. I'm surprised to see we generate 2 - 3 buckets of organic waste each week!

To begin composting, I built a 2 bin system. You can see a short video on how I built it using free materials I found around town here.

It is mid-November (2020) now and the temperature outside is about -1°C (that's about 31°F). Over the last few months, I have notices the piles settling and getting smaller, but is it breaking down? What is the composting process and would it continue now that the cold weather is upon us?

I was pleasantly surprised this morning to see the compost piles are still "cooking" nicely at a balmy 49.3°C (120.7°F). Since I am not adding meat, dairy or animal waste to the piles, there are no offending odors and the local wildlife seem to be leaving it alone; with respect to animals at least. That is not to say the microorganisms are ignoring it. Quite the opposite!

If I dig into the pile with my hands I can feel heat radiating and see steam rising! It's really pretty cool! What is going on in this simple pile or organic waste? Lets break it down (no pun intended). As microorganisms move in I thought I would put together an article on what's happening inside it from a chemistry perspective....As many readers will not have university or journal access, I will include as many "free" links to references as I can.


To start with my compost is made up of the following materials:

  1. Kitchen scraps (egg shells, stale bread, fruits, vegetables, etc..)

  2. mulched leaves

  3. Some grass clippings

  4. Weeds and brush from yard and gardens

  5. Ash from the wood stove

I do not put the following in the compost piles:

  1. meat

  2. dairy

  3. dog poop

  4. other trash...

The compost pile is essentially a mixture of carbohydrates, proteins, lignins, fats, and minerals. My compost piles are random layers over soil with no barrier film as I do want earthworms and other life forms to naturally migrate in the compost promoting vermicomposting.


My piles are essentially cold composting and will take several months to decompose. The process can be broken down into 3 stages:

Mesophilic stage - moderate temperature microorganism thriving

Thermophilic stage- high temperature microorgansims going to work

Maturation stage - cooling down as food (fuel) source is exhausted with mesophilic microorganisms returning and complete conversion of organic waste to rich compost.

Mesophilic Stage

Although there are products on the market to "activate" your compost pile, I decided to let nature decide how it would tackle it. In the early (mesophilic) stage of activation, yeasts and other mesophilic bacteria will go to work. Literally billions and billions of them. If you activate your compost with manure from a cows or other grazing livestock, bacteria similar to what's in a mammals intestinal tract will be present. These can proliferate tolerating temperatures up to 44°C (119°F).

Thermophilic Stage

Once the temperature reaches about 45°C, some microorganisms will die off as the temperature becomes too hot for them. Thermophilic microorganisms temperatures can approach 65°F (150°F). Reaching hotter temperatures is ideal as it can kill plant and animal pathogens as well as weed seeds. As your compost piles exhausts its supply of proteins, fats, and carbohydrates the temperature will lessen.

Maturation Stage

As the compost decreases in temperature, mesophilic microorganisms will finish off the compost into rich humus looking material and temperature will decrease. When temperatures are low enough, earthworms will likely migrate in to introduce vermicomposting. At that point you will have some awesome compost!


Think about what happens in your fire place as you are burning a seasoned oak log in the winter: Cellulose in the log is rapidly reacting with oxygen generating carbon dioxide, water, and a lot of heat! From a chemistry perspective we look at it like this:

This is also what is happening in the cytoplasm of all the bacteria in my compost pile. Burning wood releases a lot of light and heat. However, in living cells, the process is controlled and some of energy is captured and some is released as heat. That captured energy is stored as adenosine triphosphate (ATP) and used to to drive life processes. Things like growing, moving, keeping warm, cell replication, and moving chemicals in and out of the cell.

Earlier I mentioned the temperature inside the compost pile was over 40°C (120°F). The microorganism are using the compost for fuel using a process called cellular respiration.

Here is a simple outline of cellular respiration used by the microorganisms:

Cellular respiration is an elegant process cells use to utilize almost everything in my compost pile for fuel! 200 grams of dry compost will release about 700 calories of energy! Let's walk through the processes of cellular respiration....

Once the microorganisms take up residence in my 2 bin system they will begin colonizing and releasing enzymes. A first step in digestion kind of like chewing food in your mouth. A variety of microorganisms are in their that can generate (and release) enzymes like protease, lipase, cellulase, and amylase. These enzymes are a critical first step for respiration as it breaks down the larger materials into sugars, fats, and amino acids.

The initial enzymatic hydrolysis of polysaccharides releases heat as glycosidic bonds are cleaved. As you can see from the diagram above, the reaction requires water. For this and other reasons, you will want to make sure your compost piles does not dry out. A good target is 40-60% moisture. If you grab a handful of your compost it should feel like a damp sponge. This will start releasing monosaccharide and disaccharides that fungi, bacteria, and yeasts can use as fuel to grow and multiply. After dark, I like to "water" my compost giving it a shot of nitrogen to help keep things going. As the process requires oxygen, you will need to keep the piles aerated. This is easily accomplished by turning the pile every week or two with a turning fork.

Turning Fork


Bacteria can then use permeases and various transporter proteins in their cell membrane to uptake the sugars, amino acids, and fatty acids. Some bacteria may also be capable of endocytosis but this is traditionally known to be limited to eukaryotes....Once inside the cell, these materials can be used as building blocks, fuel or both. These materials are used for cellular respiration and provide energy and that heat we feel in the compost pile. That is evidence cellular respiration (and composting) is taking place!


A prime example of fuel is glucose. During cellular respiration glucose first enters glycolosis in the in the cytosol releasing some energy (stored at ATP) and is converted to pyruvate. Pyruvate can the be used for fuel in the mitochondria where it is broken down via the Kreb's cycle. NADH and FADH2 generated during the Krebs Cycle is then used in the Electron Transport Chain to produce up to 30 ATP molecules which can be used to power cell activities.


Amino acids are usually used as building blocks. However, amino acids can also fuel cellular respiration. Amino acids can be deaminated (removal of the NH3 group) and then enter the Krebs cycle. At what point they enter the Krebs cycle is determined by the type of amino acid, therefore its not so straight forward to determine the number of ATP that can be ultimately formed. However, most of us are more familiar with the unit of measure in calories. As a general rule of thumb 1 gram of carbohydrate or protein will can yield around 4 calories, whereas fats can deliver 9 calories per gram!


...1 gram of carbohydrate or protein will can yield around 4 calories, whereas fats can deliver 9 calories per gram!



So why do fats have a payload of more than twice that of sugars? Technically, when a fat is digested to glycerol and fatty acid (via lipase etc..), the glycerol can enter glycolysis and the fatty acid enters the Krebs cycle (see the chart above). I like to think of it this way. Here is an example of a fatty acid (left) and sugar (right):

Notice the difference? Many of the carbons in the glucose already have oxygen attached so you can think of it as already partially consumed (or oxidized like a partially burned log). The stearic acid you can see on the left is essentially a raw hydrocarbon. This is the same reason why fuel with ethanol added has less energy than straight up high octane gasoline. But I don't want to get into that! right now.

If the process is 100% efficient you would convert all of your organic waste to carbon dioxide, ammonia, and water. But its not and there are minerals and salts present as well. After the composting process has exhausted you will be left with a carbon, nitrogen and nutrient rich humus like material. Its excellent as a soil conditioner.

Many types of bacteria are present in composting organic waste and species may vary somewhat depending on where you are located. But there a lot of these single celled organisms. In one table spoon of compost you will find billions of bacteria!

My first observation as I dig into the pile is a white fibrous fungi or mold which is present about 3 inches deep under the top surface of compost. Turns out this is actually a fibrous bacterial colony. I identified it as actinomycetes. This is actually a fibrous bacteria indicating optimal active decomposition. Now before you get freaked out about some sort of flesh-eating bacteria, think about this: actinomycetes is responsible for 70% of today antibiotics, including streptomycin. There has been somewhat of a renewed excitement in actinomycetes now that we realize that environmental cues play a critical role in the natural products they produce! There may be natural therapeutics growing in that pile of waste that could cure cancer!

Stale bread goes out to the compost so you can bet that there are molds and fungus growing in their too! These are great to have in there as a compliment to bacteria as they can penetrate, colonize and break down tough plant polymers. They can also tolerate dry compost and varying pH in the soil.

So to wrap things up, its all these microorganisms performing cellular respiration that is generating all this heat and breaking down my kitchen scraps. I'm planning to observe the different organisms via microscopy and stain. I will post some pictures of what I see when I have the time!

If you have a few square feet in your yard, I would encourage you to start your own compost. It does not take much time and you are rewarded with a rich soil conditioner you can use for plants and gardens!

And its kind of fun......well at least for me and the dog..

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