Soil fungi are microscopic organisms that form extensive, threadlike networks within the earth. These networks, known as mycelium, are composed of fine threads called hyphae. Fungi are a component of soil’s microbial ecology and can be found in nearly every soil environment across the globe. Their presence significantly impacts the health and function of terrestrial ecosystems.
The Role of Fungi in Soil
Soil fungi are categorized into three functional groups based on their environmental interactions. The largest group is decomposers, or saprophytic fungi, which are responsible for breaking down dead organic material. These fungi release enzymes to decompose complex substances like cellulose and lignin in woody debris. This process cycles nutrients by converting dead matter into fungal biomass and making them available for other soil organisms.
A second group is the mutualists, which form beneficial relationships with plants. The most well-known are mycorrhizal fungi, which colonize plant roots in a symbiotic partnership. The fungus extends its hyphae into the soil, far beyond the plant’s roots, to absorb water and nutrients like phosphorus and nitrogen. In exchange, the plant provides the fungus with sugars produced through photosynthesis, which enhances plant health.
The third functional group is the pathogens, which cause disease in plants. Genera such as Fusarium, Rhizoctonia, and Pythium are examples of soil-borne pathogenic fungi that negatively impact plant health. These fungi attack plant roots, leading to rot and other diseases that inhibit growth or kill the plant. Understanding the fungi present is important for managing soil and plant health.
Visual Identification Methods
Identifying soil fungi can begin with visual inspection. The most obvious signs are the macroscopic fruiting bodies some fungi produce, such as mushrooms, puffballs, or truffles. These are the reproductive structures of a larger underground mycelial network. The presence of mold on the soil surface or on decaying organic matter is another visible indicator, and its color and texture can offer clues for identification.
Closer inspection of the soil can reveal the mycelium itself, which appears as a mass of fine, white or yellow threads. These networks of hyphae bind soil particles together into a web-like structure. Fungal hyphae are significantly finer than plant roots, about 1/60th the diameter of a typical root hair. The appearance of this mycelium can hint at the type of fungus present.
For a more detailed examination, a strong magnifying glass or a basic microscope can be used to observe general hyphal structures. Another technique is creating a spore print. By placing a mushroom cap on a piece of paper for several hours, it will release its spores. Their collective color—which can range from white to brown to black—is a characteristic used in identification.
Laboratory Identification Techniques
When visual methods are insufficient, laboratory techniques provide more definitive identification. Culture-based identification involves growing fungi from a soil sample on a nutrient-rich medium, like a potato dextrose agar (PDA) plate. The isolated fungus forms a colony with distinct macroscopic characteristics, including its color, shape, and growth rate, which are used for preliminary identification.
Microscopic examination of the cultured fungus offers further detail. Technicians use high-powered microscopes to observe specific structures invisible to the naked eye. These include the shape and size of spores, the structure of spore-producing bodies called conidiophores, and hyphal characteristics, such as being septate (divided by cross-walls). These morphological details are compared against taxonomic keys to determine the fungus’s genus and species.
Molecular techniques are the most precise method for fungal identification. Scientists extract DNA from a soil sample or a cultured fungus to analyze specific gene sequences. The internal transcribed spacer (ITS) region of ribosomal DNA is a common genetic marker, or “barcode,” for fungi. By sequencing this region and comparing it to international databases, researchers can achieve highly accurate identification, even for species that are difficult to culture.
Common Soil Fungi Examples
Trichoderma is a genus of fungi commonly found in soils and known for its beneficial role. Many species are used as biocontrol agents because they are aggressive parasites of pathogenic fungi like Rhizoctonia. Trichoderma coils around the hyphae of these pathogens and secretes enzymes that dissolve their cell walls. In culture, Trichoderma colonies often appear as a green mold and are identified microscopically by their bottle-shaped phialides and small, oval conidia.
Rhizoctonia is a pathogenic fungus that causes a variety of plant diseases, including damping-off and root rot. It does not produce airborne spores, instead spreading through soil via its mycelium and small, hardened masses of hyphae called sclerotia. The fungus attacks the roots and lower stems of plants, creating characteristic lesions. Lab identification relies on observing its distinctive mycelial characteristics, such as the right-angle branching of its hyphae.
Mycorrhizal fungi are a broad group of mutualistic fungi that partner with most plant species. Ectomycorrhizae grow on the surface of plant roots, primarily with tree species. In contrast, arbuscular mycorrhizae penetrate the root cells of most agricultural and herbaceous plants. Their presence is a sign of a healthy soil ecosystem, though they are difficult to identify visually without observing their association with plant roots.