A 2012 study proposed that white rot fungi helped end the Carboniferous coal age, and the proposal runs like this: once these fungi evolved to break down lignin, wood that would have been buried and fossilized as coal was rotted instead. Two kinds of wood-rotting fungi matter to the story. White rot fungi break down lignin and the cellulose in wood, while brown rot fungi take the cellulose and leave the lignin behind, which leaves the crumbly brown logs seen in temperate forests. Plant cell walls are built of three fibers, with hemicellulose softest, cellulose sturdier and lignin toughest. Lignin sits in a tough matrix with cellulose, and once white rot fungi destroy the lignin, the matrix collapses and the cellulose is freed for the fungi to eat.
Behind the white rot story is the basic chemistry of how a fungus eats wood. A fungus grows thin threads called hyphae into wood and leaves, and together the threads are called mycelium. Fungi make special chemicals called enzymes, which are molecules that speed up chemical reactions, and the enzymes break down the wood so that the fungus can take in the nutrients. Cellulose is essentially glucose rings attached to one another, so the enzymes break the bond between two glucose molecules, and the freed glucose is taken up as food. After a tree falls, fungi that specialize in wood usually begin the work, using their hyphae. Enzymes from white rot fungi break down complex organic molecules, and they have been studied for bioremediation, which uses living things to clean up contaminants, and for releasing sugars from plants to make biofuels.
Researchers have also looked for other organisms that can use plant waste. As of September 2014, scientists were looking for microbes that could make biofuel from plant waste, and a bacterium found near the Quabbin Reservoir in Massachusetts can turn hemicellulose and cellulose into ethanol in one step. Bacteria from Puerto Rico's rainforest did more than eat lignin, because they also used it to produce energy by respiration. Fungi usually break down lignin in forests, but they are too costly to grow at factory scale. Lignin is the toughest of the three fibers, so the finding that bacteria can use it as food shows that fungi are not the only organisms that can do so. Termites offer a related case: they eat wood but cannot digest cellulose alone, and bacteria, fungi and protozoa living in their guts break the cellulose down so the termites can absorb the nutrients.
The 2012 white rot study was led by David Hibbett of Clark University, with 71 researchers from 12 countries, and it appeared in Science on June 29, 2012. It built on a 1990 paper by Jennifer Robinson that proposed white rot's rise helped end the Carboniferous, so the 2012 study came 22 years after that paper. To date the change, the researchers compared 31 fungal genomes and used a molecular clock, which assumes that genes gain mutations at fairly steady rates. They traced lignin-breaking ability back roughly 290 to 300 million years. The date depends on the assumption inside the method, because a clock gives a date only as far as the mutation rates are fairly steady, and the 31 genomes are the data on which the clock was run, so the method turns differences between genomes into dates.
Fossils give a second line of evidence, and as of the 2012 study they matched the clock only loosely. The clock puts the start of lignin-breaking at roughly 290 to 300 million years ago, but the first definitive white rot fossil is only about 260 million years old, so the gap is about 30 to 40 million years. The two dates differ. Two kinds of evidence were therefore pointing at different dates, one from genes and one from rock, and the distance between them was tens of millions of years. One more piece was missing. As of the 2012 study, how white rot breaks down lignin was unknown. The fungi release reactive molecules and enzymes that seem to tear lignin apart by "brute force", and that marks the limit of what was known in June 2012.
The fungal explanation for the end of coal is a hypothesis, not settled. Older explanations blamed swampy conditions that buried lignin-rich plants, and Hibbett said the ideas are not mutually exclusive, which means both could be partly right. He also said that more fungal fossils are needed. As of June 2012, then, the case stood as a hypothesis with a gap between its two kinds of dates, and the older swamp explanation remained on the table beside it. A hypothesis is a proposed explanation that can still be tested, and this one was still in that state. The 1,000 Fungal Genomes Project aimed to sequence many more fungi, but in 2012 that still covered less than 0.1 percent of estimated fungal species, and Hibbett said fungi play a huge role in the carbon cycle but do not get enough attention.
The number of fungi is itself uncertain, and the estimates have changed. A 2012 NSF release said almost 1.5 million species exist and only about 5% were classified, while Kew's 2023 estimate was about 2.5 million, with about 155,000 named. As of November 2026, about 6 percent of the estimated species have names, which leaves about 2.3 million species without a formal name, so most are still unknown. The estimate rose by about 1 million species between the 2012 release and Kew's 2023 figure.
Mould shows another side of the fungi. Mould is one kind of fungus, and it shows as fuzzy growth on old bread or cheese. Mould spores are microscopic, 2 to 100 microns across, and many are so small that they float through the air; they are found indoors and outdoors, but they grow only where moisture is present. Mould digests whatever it grows on, and because moisture is the most important factor for mould growth indoors, controlling moisture is the key to controlling mould. Yeasts, which are fungi, make the bubbles in bread. Chemically and genetically, fungi are closer to animals than other organisms are.
The coal question is about rot at the largest scale, and smaller experiments test rot in forests today. In the DIRT experiments, scientists move leaf litter from one forest plot to another each fall. Plots without litter lose organic matter and release fewer nutrients back to plants, while plots given extra litter become more fertile. Carbon is always moving between air, plants, soil and rocks, which is called the carbon cycle, and rot is one of its steps. Decomposers release carbon dioxide into the air as they break down dead plants, and plants then use that carbon dioxide to make food, so the litter plots measure one step of that cycle. Where a pile has oxygen, about two thirds of the carbon is breathed out as carbon dioxide, while about a third is built into microbe cells.
Another long experiment measured rot under heat. In Harvard Forest, scientists warmed soil plots 5 degrees C with buried cables, and after about 25 years the top organic layer had shrunk by about a third, because warmer microbes were releasing more carbon dioxide. As of September 2014, the result was reported in that form. A simpler way to study rot is also used at Harvard Forest, where scientists bury blocks of wood in soil and see how long they take to rot and disappear. Warming could speed rot, release more carbon dioxide and cause more warming, but a computer model suggested that after a few years microbes may adjust to higher temperatures, so the size of this feedback is uncertain. Too much nitrogen from pollution also seemed to slow decomposition, because microbes make fewer of the enzymes needed to break down dead tissue, so nutrients stay locked in the litter, and whether this holds over longer times is not clear.
Cold changes rot as well. Frozen northern soil called permafrost holds rich deposits of plant carbon because cold slows decay, and when the soil warms, the organic matter decays and carbon seeps out as methane and carbon dioxide. Dead things decay very fast in warm, wet places such as tropical rainforests. Oxygen changes decay as well, because without oxygen, decay is a different process, and it makes smelly gases such as hydrogen sulfide and releases carbon mainly as methane.
Decay with oxygen gives off far more heat than decay without it, so the same dead plants can leave different gases behind, depending on whether oxygen is present. A landfill is a place with no air, and food and yard waste there rot without oxygen and give off methane, a powerful greenhouse gas. The same living things and the same dead plants produce different results when the air is taken away, and the difference is in the gases that come out and in the heat that is given off. A pile with air is the kind that composting aims for, and turning a compost pile with a fork lets in air and speeds up decomposition.
Not everything rots the way leaf litter does. NOAA says some plastics fragment into smaller and smaller pieces and may never fully go away, and even plastics labeled biodegradable could last an indefinite time in the ocean. As of November 2026, that is NOAA's statement. Scientists cannot say exactly how long marine plastics last, because heat, light, oxygen and location all matter and lab results may differ from the ocean. As of September 2020, plastics had only been mass produced for about 75 years, so long-term data were lacking. Seventy-five years of mass production is short next to the roughly 290 to 300 million years that lignin-breaking has been traced back, which is more than 3 million times as long. A question about how long something lasts is a question about decay, and for plastics in the ocean it was still open in 2020.
Words to know
- lignin: tough wood fiber
- hypothesis: tested idea
- bioremediation: cleanup with life
- matrix: framework
- genomes: full gene sets
