Organic materials such as manure, crop residues, and food wastes can decompose through two broad biological pathways: aerobic (with oxygen) and anaerobic (without oxygen). The dominant pathway influences odor, nutrient behavior, biological risks, and the usability of the final material as a soil amendment. Understanding these differences can help farmers make more informed decisions about manure management and technology choices (Haug, 1993).
Under aerobic conditions, microorganisms consume oxygen and release heat as they metabolize organic matter. When moisture, porosity, and air flow are favorable, this microbial activity may produce thermophilic temperatures—often in the range of 55–65°C (131–149°F). This high-temperature phase is commonly associated with what is known as aerobic composting. Over time, this process tends to stabilize organic matter, reduce strong odors, and produce a material that is generally more uniform and easier to handle as a soil amendment (Epstein, 1997).
When oxygen is limited or absent, decomposition shifts toward anaerobic metabolism. In some cases this can be intentionally engineered, such as in controlled anaerobic digestion for biogas production. More commonly on farms, however, it occurs as uncontrolled anaerobic breakdown, often described as putrefaction or “rotting.” This is typical of saturated piles, poorly drained storage areas, and many lagoon systems. Under these conditions, temperatures are often lower and variable, and microbial communities produce gases such as hydrogen sulfide, ammonia, and methane—compounds associated with persistent odors. The resulting material may remain biologically unstable and less predictable as a fertilizer (USEPA, 2003).
For practical purposes, composting is widely described in the scientific literature as an aerobic, heat-generating process that depends on adequate oxygen, moisture, and structure within the material. When these conditions are present—whether in windrows, aerated piles, or enclosed reactors—microbial activity can generate heat that contributes to organic matter stabilization (Haug, 1993).
By contrast, putrefaction refers to uncontrolled anaerobic decomposition that is not managed for oxygen supply or temperature. Because conditions are inconsistent, this pathway is generally not relied upon by regulators or organic certifiers as a dependable method for reducing biological risks (NRCS, 2014).
A frequent misconception is that sunlight helps compost manure. Research and practical experience indicate that this is not correct. Sunlight is essential for plant photosynthesis and can warm the surface of outdoor piles, but it does not drive microbial decomposition. Composting can occur in complete darkness—inside barns, covered windrows, or enclosed systems—provided that oxygen, moisture, and temperature are appropriately managed. The primary drivers of composting are microbial metabolism, not solar radiation (Haug, 1993).
With respect to pathogens, studies show that sustained high temperatures during aerobic composting are associated with reduced survival of many common bacteria of concern, including E. coli and Salmonella. For this reason, compost standards often reference temperature-time relationships rather than simple aging or storage (USEPA, 2003). In uncontrolled anaerobic systems, temperatures are typically lower and less consistent, and pathogens may persist for extended periods, particularly in long-term slurry or lagoon storage.
Weed seed behavior follows a similar pattern. Elevated temperatures achieved during well-managed aerobic composting can reduce the viability of many weed seeds. In anaerobic storage or putrefaction, temperatures rarely reach levels known to damage seeds, which means viable seeds may remain present and germinate after field application (Epstein, 1997).
Odor is often the most visible signal of which pathway is occurring. Aerobic composting, when properly managed, tends to produce mild, earthy smells, whereas anaerobic putrefaction is commonly associated with strong “rotten egg,” ammonia, or swamp-like odors. These odors are frequently a source of neighbor complaints and local regulatory attention.
In response to these concerns, some farms are exploring enclosed treatment systems such as COMPO or KNLL. These systems are designed to maintain controlled airflow, moisture, and temperature with the goal of keeping manure in a predominantly aerobic, heat-generating pathway. Compared with open or lagoon-based storage, enclosed systems may reduce land requirements, limit exposure to weather, and produce a more consistent material that can be reused on fields or marketed. Actual performance, however, depends on proper operation, feedstock characteristics, and site conditions.
From a whole-farm perspective, the key distinction is not simply the technology but the level of biological control. Lagoon-based systems rely heavily on passive, anaerobic processes that can create odor and biological uncertainty. Aerobic composting—whether in windrows or enclosed reactors—seeks to manage oxygen and temperature in a more predictable way, which may offer advantages for nutrient stability, odor management, and community acceptance.
In summary, sunlight does not compost manure—microorganisms do. Effective aerobic treatment depends primarily on oxygen, moisture, and heat, not on exposure to light. Where uncontrolled anaerobic putrefaction may preserve biological risks and generate strong odors, properly managed aerobic approaches—including enclosed systems like COMPO or KNLL—aim to provide a more controlled pathway for converting manure into a usable soil amendment.
MANURE OR ORGANIC WASTE
Is there oxygen?
/ \
YES NO
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AEROBIC ANAEROBIC
( COMPOSTING) (PUTREFACTION / ROT)
References
1. Epstein, E. (1997). The Science of Composting. CRC Press.
2. Haug, R. (1993). The Practical Handbook of Compost Engineering. Lewis Publishers.
3. NRCS (USDA). (2014). Composting and Manure Treatment Standards and Guidance. Natural Resources Conservation Service.
4. USEPA. (2003). Control of Pathogens and Vector Attraction in Sewage Sludge (40 CFR Part 503). U.S. Environmental Protection Agency.