What Role Do Microorganisms Play in Composting? The Biology Explained Simply
Why does our partnership matters
For every purchase, we plant 1 TREE to nurture our planet 🌲Together, we are sowing the seeds of change and cultivating a greener, more sustainable world.
Anything else?
Anything else?You willl also receive an official certificate from Greenspark as a token of appreciation for your commitment to the environment! 📜
How do we see the progress?
How do we see the progress?Join us on this remarkable journey towards an impact dashboard.You can see how your eco-smart choice made the world a better place
View more
Your support empowers reforestation, fights climate change,
and paves the way for a brighter, eco-friendly future.
Join us on this remarkable journey towards a cleaner,healthier planet.
Shop with a purpose, shop with Reencle! 🛒💚
Microorganisms are the engine of composting — without them, you'd just have a pile of slowly rotting food.
Bacteria do most of the heavy lifting, consuming organic carbon and nitrogen and releasing heat as a byproduct.
Fungi break down tougher materials like lignin and cellulose that bacteria can't access easily.
Actinomycetes — a specialized group that looks like white threads — finish the job in the later stages, producing that characteristic earthy compost smell.
These groups work in a predictable sequence, and understanding the sequence tells you exactly why temperature, moisture, and aeration matter so much to a successful compost pile.
Why Microorganisms Are the Real Composters
When you turn a compost pile and feel the rush of warmth, or find the center of your bin hot to the touch, you're experiencing microbial metabolism directly.
That heat is the byproduct of billions of microscopic organisms consuming organic matter, respiring, and reproducing — all powered by the carbon and nitrogen in your food scraps and garden waste.
A teaspoon of healthy compost can contain more microorganisms than there are people on Earth — including bacteria counts in the hundreds of millions to billions per gram, thousands of species of fungi, and complex communities of protozoa, nematodes, and actinomycetes [Cornell Composting, Cornell University].
This biological richness is also why finished compost is so valuable as a soil amendment. When you add compost to a garden bed, you're introducing a living, diverse community of microorganisms that improve soil structure, suppress plant pathogens, and make nutrients available to plant roots.
Bacteria: The Primary Decomposers
Bacteria are responsible for the vast majority of decomposition in a compost pile — estimated at 80–90% of total organic matter breakdown in an active pile [Haug, R.T., 1993].
Bacteria are classified in composting science by their preferred temperature range:
Psychrophilic Bacteria (Below 10°C / 50°F)
These cold-tolerant bacteria are active at very low temperatures and are the first responders when a compost pile is assembled in cool conditions. They work slowly — decomposition at psychrophilic temperatures proceeds at a fraction of the rate seen in warm conditions. Most home compost piles in winter are primarily psychrophilic, which is why cold-weather composting is slow rather than stopped.
Mesophilic Bacteria (10–40°C / 50–104°F)
Mesophilic bacteria are the most diverse and abundant group in a compost pile during its early and late stages. They activate quickly when fresh organic matter is added, consume simple sugars and starches first, and produce the initial heat that warms the pile from ambient temperature into the thermophilic range.
The critical contribution of mesophilic bacteria: they create the conditions that allow thermophilic bacteria to take over.
Thermophilic Bacteria (40–70°C / 104–158°F)
This is where composting really happens. Thermophilic bacteria are heat-loving specialists that become active once the pile reaches around 40°C.
Their metabolism is extremely rapid — they can double their population in minutes under optimal conditions — generating intense heat as a byproduct of aerobic respiration.
Thermophilic temperatures (typically 55–65°C in a well-managed pile) accomplish two critical functions:
1. Rapid decomposition: The rate of organic matter breakdown at 60°C is many times faster than at 20°C.
2. Pathogen and weed seed destruction:
Most human and plant pathogens, and most weed seeds, cannot survive sustained temperatures above 55°C.
Holding the pile at 55–65°C for at least 3 consecutive days (or 15 days in windrow composting, turned 5 times) is sufficient to eliminate most biological hazards [U.S. EPA, 2023].
Haug's comprehensive engineering analysis of composting systems establishes that thermophilic activity is the defining characteristic of "hot composting" and is the mechanism responsible for producing hygienically safe finished compost [Haug, R.T., 1993].
The Temperature Shift: Mesophilic to Thermophilic
Understanding this temperature progression helps you diagnose what's happening in your pile at any given moment.
The typical temperature arc of an active compost pile:
1. Day 1–3 (Assembly): Temperature rises from ambient as mesophilic bacteria multiply rapidly on fresh organic material.
2. Day 3–7 (Heating phase): Temperature climbs into the thermophilic range (40–65°C). This is the most active decomposition period.
3. Week 2–3 (Peak thermophilic): Center of pile reaches 55–65°C. Turning the pile during this phase brings outer cooler material to the center for exposure to high temperatures.
4. Week 3–6 (Cooling): As easily available carbon and nitrogen are consumed, microbial activity slows. Temperature drops back toward the mesophilic range.
5. Month 2+ (Curing): Mesophilic and psychrophilic bacteria continue slowly. Actinomycetes become visible. The pile stabilizes into mature compost.
> Practical implication: If your pile never heats up, it's missing something the thermophilic bacteria need — usually nitrogen (add greens), moisture (add water), mass (pile needs to be at least 1 cubic meter), or oxygen (turn the pile).
The Cornell Waste Management Institute identifies pile size and moisture as the two most common limiting factors in home piles that fail to reach thermophilic temperatures
[Cornell Composting, Cornell University].
Fungi: Breaking Down What Bacteria Can't
Bacteria are extraordinarily capable, but they struggle with the toughest plant materials: lignin (the compound that gives wood and straw their rigidity), cellulose (the structural component of plant cell walls), and chitin (found in insect exoskeletons and mushroom cell walls).
Fungi are the specialists for these materials. Their long filamentous structures (hyphae) physically penetrate woody material, and they secrete enzymes — particularly ligninases and cellulases — that break down the chemical bonds in lignin and cellulose that bacteria cannot access enzymatically.
You can often see fungal activity in a compost pile as:
• White or gray fluffy growth on the surface of the pile, particularly on cardboard or woody material
• A fine white network threading through decomposing organic matter
This visible growth is almost always beneficial — these are saprophytic (decomposer) fungi at work.
Common species include Trichoderma, Penicillium, and various Basidiomycetes (related to the mushroom family).
The Rodale Institute's long-term studies on organic matter decomposition note that fungal diversity in compost positively correlates with the finished compost's disease-suppressive properties in soil — another reason to value and protect fungal activity in your pile [Rodale Institute, 2023].
Actinomycetes: The Final Stage Specialists
Actinomycetes are a fascinating group — they're technically bacteria, but they grow in a filamentous (thread-like) way that makes them look like fungi, sitting biologically between the two kingdoms.
They are the composting community's cleanup crew, specialized for the final stages of decomposition.
What actinomycetes do:
• Break down tough materials that even fungi leave behind: lignin, chitin, and complex organic polymers
• Produce antibiotics and antifungal compounds that suppress plant pathogens in finished compost
• Generate the characteristic "earthy" smell of finished compost — caused by a volatile compound called geosmin, produced almost exclusively by actinomycetes
How to recognize them:
Actinomycetes appear as fine white, gray, or powdery threads visible in the outer layers of an aging compost pile — particularly in the 2–4 month range.
They thrive at slightly lower temperatures than thermophilic bacteria (30–45°C) and are most prominent in the curing and maturation phases.
The presence of visible actinomycete threads and the earthy geosmin smell are among the most reliable indicators that compost is maturing correctly and approaching a usable state [Golueke, C.G., 1972]
Most pathogens and pest eggs can be killed in a properly managed hot compost pile that reaches 55–65°C throughout. The problem is that most backyard piles don't achieve those temperatures uniformly. Outer layers and corners often stay at ambient or mesophilic temperatures [Haug, R.T., 1993].
If diseased material survives composting and is applied to garden beds, you reintroduce the pathogen — sometimes in higher concentration than if you had simply disposed of it.
Safe to compost: lightly wilted or spent plants with no signs of disease, healthy prunings, vegetable tops (carrot tops, bean plants after harvest).
Best practice: When in doubt, bag it and send it to a municipal green waste program, which uses industrial hot composting.
How the Microbial Stages Work in Sequence
Composting is not a single process — it's a succession of microbial communities, each creating conditions that favor the next group:
| Stage | Dominant Organisms | Temperature | What Happens |
|---|---|---|---|
| Initial (Days 1–7) | Mesophilic bacteria | 10–40°C | Simple sugars and starches consumed; pile heats |
| Active (Weeks 1–4) | Thermophilic bacteria | 40–70°C | Rapid decomposition; pathogens/seeds killed |
| Cooling (Weeks 4–8) | Mesophilic bacteria return | 25–40°C | More complex materials broken down; fungi increase |
| Maturation (Months 2–6) | Actinomycetes, fungi | Ambient | Lignin/cellulose breakdown; earthy smell develops |
| Finished compost | Diverse, balanced community | Ambient | Stable humus; high microbial diversity; ready to use |
Sources: Haug (1993); Golueke (1972); Cornell Composting
What Microorganisms Need to Work at Peak Performance
The four environmental factors that control microbial activity in composting:
1. Oxygen (Aerobic vs. Anaerobic)
Composting bacteria that produce fast, odor-free decomposition are aerobic — they require oxygen. Without regular turning or aeration, the center of a pile becomes anaerobic, slowing decomposition dramatically and producing methane and hydrogen sulfide (the rotten-egg smell associated with bad compost).
Turn your pile every 1–2 weeks during active decomposition.
2. Moisture (40–60% Water Content)
Microorganisms live in the thin film of water surrounding organic particles. Too dry (below 40%) and they become dormant.
Too wet (above 65%) and oxygen is excluded from the pores between particles, creating anaerobic conditions.
The target is the "wrung sponge" state — moist but not dripping when squeezed [Rynk, R. (Ed.), 1992].
3. Temperature
As described above, thermophilic temperatures drive the fastest, safest decomposition.
Maintaining adequate pile mass (minimum 1 cubic meter), moisture, and nitrogen content will naturally produce these temperatures.
4. Carbon-to-Nitrogen Ratio (25:1 to 30:1)
Bacteria need carbon for energy and nitrogen for protein synthesis.
At the ideal C:N ratio, their population growth is unrestricted.
Too much carbon starves them of nitrogen; too much nitrogen leads to ammonia production and inhibits activity.
The Macroorganisms: Worms, Beetles, and Friends
Microorganisms get the most attention, but a healthy compost pile also hosts a visible community of macroorganisms — organisms you can actually see — that contribute meaningfully to decomposition:
• Earthworms: Particularly red wigglers (Eisenia fetida) in cooler, moist layers.
They physically fragment organic matter, dramatically increasing surface area for microbial attack.
• Sowbugs and pillbugs: Fragment woody material and create channels for airflow.
• Centipedes and beetles: Predators that feed on other decomposers, maintaining the community's balance.
• Fly larvae (maggots): Present when the pile has meat or protein sources; fast decomposers but attract concerns.
Their presence in a well-managed pile without prohibited materials usually indicates anaerobic pockets or surface exposure of food.
Quick Reference Summary
• Bacteria do the majority of decomposition; they work in temperature-dependent stages
(psychrophilic → mesophilic → thermophilic → mesophilic again)
• Thermophilic bacteria (40–70°C) drive the fastest decomposition and kill pathogens and weed seeds
• Fungi break down lignin, cellulose, and other tough materials that bacteria cannot easily access
• Actinomycetes finish the job in the curing phase, producing the earthy smell of finished compost
• The four essentials: oxygen (turn regularly), moisture (40–60%), correct C:N ratio (25–30:1), sufficient mass (1 m³ minimum)
Frequently Asked Questions
Q: Do I need to add a compost starter or activator to introduce microorganisms?
A: In most cases, no. Microorganisms are naturally present on all organic matter — on fruit peels, garden soil, and in the air. A new pile inoculates itself quickly. Commercial compost activators or starters can theoretically speed up early decomposition, but the scientific evidence for their benefit over a well-balanced pile is limited. The most effective "starter" is a shovelful of finished compost or healthy garden soil from your yard, which introduces a diverse microbial community at no cost.
Q: Is the white mold I see in my compost pile harmful?
A: Almost certainly not. White mold or white thread-like growth in a compost pile is typically saprophytic fungi (decomposers) or actinomycetes — both beneficial. The white growth on cardboard and woody material is fungi digesting cellulose and lignin.
The powdery white threads visible in older, cooling sections are usually actinomycetes working on stable organic compounds.
Only worry if the growth appears on seedlings or living plants — in a compost pile, white biological growth is almost always a sign that decomposition is proceeding well.
Q: Why does my compost smell bad if microorganisms are responsible for it?
A: Odor in compost is produced by anaerobic microorganisms — a different community that thrives when oxygen is depleted.
Anaerobic decomposers produce hydrogen sulfide (rotten egg), ammonia, and other volatile compounds that cause bad smells.
This happens when the pile is too wet, too compacted, or has too much nitrogen without enough aeration.
Turning the pile to introduce oxygen shifts the microbial community back to the aerobic bacteria and fungi that produce the desirable earthy smell.
Q: How long do microorganisms survive in finished compost?
A: Finished compost maintains a diverse, active microbial community for months when stored properly (slightly moist, covered from rain and direct sun).
As compost dries out or is exposed to extreme temperatures, microbial populations decline.
This is why fresh compost is more biologically active than compost that has been stored for a long time — and why it's best applied to garden beds shortly after it reaches maturity.
References
1. Haug, R.T. (1993). The Practical Handbook of Compost Engineering. Lewis Publishers.
2. Golueke, C.G. (1972). Composting: A Study of the Process and Its Principles. Rodale Press.
3. Cornell Waste Management Institute. Cornell Composting: Biology of Composting.
4. Rynk, R. (Ed.). (1992). On-Farm Composting Handbook (NRAES-54). Northeast Regional Agricultural Engineering Service.
5. U.S. Environmental Protection Agency. (2023). Composting at Home.
6. Rodale Institute. (2023). Compost Science and Soil Biology.
7. Cooperband, L. (2002). The Art and Science of Composting. University of Wisconsin-Madison Extension.
About the Author: [Author Name] is a composting educator and soil science writer with [X] years of experience studying microbial ecology and organic matter decomposition. They contribute to the Reencle blog on the science of composting and soil health. [Author credentials here.]
Related Posts:
• What is the carbon-to-nitrogen ratio in composting, and why does it matter?
• What food scraps are best for composting? A complete guide to green and brown materials
• What should you never put in a compost bin? A complete list of what to avoid