Of the major groups of saprotrophs, fungi are among the most efficient at decomposing complex organic molecules and recycling those nutrients back into the ecosystem. Fungi are some of the most-significant decomposers of plant matter, which makes up the vast majority of detritus in terrestrial environments. The bulk of plant tissue consists of cell-wall material, which is made up largely of a complex carbohydrate called cellulose. Cellulose consists of multiple glucose molecules, arranged in such a way that most organisms are unable to efficiently metabolize the compound. Fungi, however, have evolved a suite of enzymes that enable them to digest the complex structure, converting cellulose into simple carbohydrates. That ability plays a critical role in the carbon cycle by enabling the release of carbon dioxide from decaying organisms, and it transforms plant organic matter into substances that both fungi and other organisms can utilize for nutrition.

Fungi that decompose leaves and twigs in organic litter, such as that found on the forest floor, include species of Marasmius and many familiar garden and forest mushrooms. Some fungi, such as Pilobolus, feed primarily on the dung of herbivores. Wood-decomposing fungi, including species of turkey tails (Trametes), oyster mushrooms (Pleurotus), and Ganoderma, can have negative economic consequences to the lumber industry, decomposing both cut timber and the dead bark of living trees. Damage to homes from “dry rot” is caused by the wood-decay species Serpula lacrymans.

Bacteria are well-known decomposers of dead animal flesh and are efficient at converting animal tissues to simpler organic compounds. A number of saprotrophic bacteria, including Escherichia coli, are associated with food-borne illnesses, since meat and other food products are also the kinds of resources they would consume in nature.

Some bacteria, such as Spirochaeta cytophaga, have the capacity to decompose cellulose through absorptive nutrition. Symbiotic cellulose-degrading bacteria are found in the rumen of cows and aid digestion through the fermentation of the cellulose in grass. Similar to fungi, these organisms also have the capacity to partially break down cellulose into intermediate molecules and facilitate the process of decomposition.

Water molds, or Oomycetes, are common in fresh- and saltwater environments throughout the world. Some species, particularly those found in the order Saprolegniales, are saprotrophs and decompose both plant and animal material. Those organisms are considered some of the most-important decomposers in freshwater aquatic environments.