Pasteur's swan-neck experiment had controls for each objection. Lazzaro Spallanzani sealed his flasks after boiling, and that drew a reply: perhaps boiling had destroyed the air's life force. Pasteur's open swan-neck flasks answered this by letting fresh air in while blocking germ-carrying dust. Breaking the neck above the bend made the broth putrefy, which showed that the heating had not destroyed some vital property of the broth or the air. Tipping broth into the bend also caused putrefaction, so the source was outside the culture.

Pasteur found that oxygen slowed fermentation, a result now called the Pasteur Effect. From this he theorized that the organisms causing fermentation were anaerobic, meaning that oxygen harmed their development. Historians who read his lab notebooks later found differences between his private work and his public reports. Motivated by rivalry, he altered or exaggerated some results in landmark publications. The published papers and the private notebooks therefore do not always match.

Human activity has changed how much nitrogen reaches soil organisms. In the nitrogen cycle, decomposing bacteria and fungi break down organic nitrogen from dead organisms and release ammonium, and other bacteria turn ammonium into nitrite and nitrate, which plants can absorb. Without the breakdown of dead plants and animals, their nitrogen would remain locked inside. As of September 2014, in some areas near cities and industry, 10 to 1,000 times as much nitrogen was added to soil each year as in 1750. Burning fossil fuels adds nitrogen compounds to the air, and soil organisms are not adapted to this: pine trees in one Harvard Forest test area died from added nitrogen.

Temperature changes how fast decay runs, but not in a simple way. Warm, wet conditions suit decomposers best. As of September 2014, a model showed that as temperatures rise, microbes themselves tend to get less efficient and must work harder for the same result. Warming therefore does not simply speed rot, and predicting future decay is hard.

Food scraps can end up in two places, and the results differ. As of November 2026, municipal landfills were the third largest source of human-related US methane emissions in 2022, about 14%, and wasted food is responsible for 58% of landfill methane emissions. In compost, the material goes back to the soil instead: compost helps soil hold water and feeds plants as it releases nutrients slowly. Rot frees nitrogen, phosphorus and about two dozen other nutrients that living things need to grow, not just carbon. The same kind of scraps can therefore end as methane in a landfill or as slow-release nutrients for plants.

Rot can be measured, and how fast it goes depends on conditions and on size. One way to study rot is to bury blocks of wood in soil at Harvard Forest and time how long they take to rot and disappear. Dead things decay very fast in tropical rainforests, where it is warm and wet. Small pieces rot faster than large ones because microbes have more surface to work on, and a fork used to turn a compost pile lets in air and speeds decomposition. Carbon is always moving between air, plants, soil and rocks, a movement called the carbon cycle, and decomposers release carbon dioxide into the air as they break down dead plants, which plants then use to make food.

Compost heat shows rot at work in a pile. A pile warms in stages: microbes that like mild heat start first, and heat-loving ones that thrive at 115 to 160 degrees F take over. A pile that gets to 130-135 degrees F kills most weed seeds and germs. If a pile goes above about 162-172 degrees F, bacterial activity falls and breakdown slows, so heat has a ceiling as well as a floor. Anaerobic composting works differently. Heat is low, so disease organisms disappear slowly and the material may need to be held for six months to a year, and the lack of heat is a disadvantage when the waste is contaminated. A well-kept pile can finish compost in roughly three to five months, and a pile left alone may need a year or longer. Backyard piles usually do not get hot enough to fully break down dairy, fats and cooked food, and commercial composters reach higher temperatures and can accept them.

The carbon and nitrogen in a pile need a balance, and the balance has numbers. Compost has carbon-rich browns, like dry leaves, and nitrogen-rich greens, like food scraps. Microbes in compost work well at carbon-to-nitrogen ratios from 25:1 to 40:1, and 30 parts carbon to 1 part nitrogen is considered ideal. Finished compost has a ratio of 20 to 25:1, which is below the ideal starting mix of 30 to 1. When carbon and nitrogen are in good balance, nitrogen is released as ammonia, and some ammonia may be converted to nitrate. Too much carbon slows microbes, so several generations are needed to burn it off. For a home pile, the EPA's advice is that browns such as dry leaves should outweigh food scraps by two to three times in volume at the least.

Cells release energy from sugar with oxygen, making carbon dioxide, water and energy. Plants, animals and the bacteria that eat dead plants all do this. Decomposition with oxygen is called aerobic, and composting needs oxygen. With oxygen in the pile, roughly two thirds of the carbon leaves as carbon dioxide, and roughly one third becomes part of the microbes' own cells.

Soil is a huge recycling operation. Dead organisms and wastes are broken down into molecules, ions or elements that become nutrients and energy for living soil organisms. These recyclers then become fodder for the next generation. Earthworms, snails, millipedes and beetles help break down dead plants too. Composting is nature's way of recycling, and decomposers turn dead things back into food for new plants. Nutrients return to the soil as things rot, and living plants take them up to grow.

Words to know

• putrefy: rot with smell
• anaerobic: without oxygen
• ammonium: nitrogen compound
• methane: greenhouse gas
• aerobic: with oxygen