When nitrogen and phosphorus leave a farm, the loss affects both farm performance and downstream water quality. Nutrients that were purchased, produced in manure or stored in soil are no longer available to the crop when they move beyond the root zone. They may also contribute to algal growth, oxygen depletion and other water-quality problems in streams, lakes and estuaries.
Fungi are part of the soil and water-management picture, but they are not a stand-alone cure. Fungal networks can support soil structure, decomposition, plant nutrient uptake and microbial treatment processes. Their greatest value is usually as one component of a broader system that first prevents unnecessary nutrient loss, then slows and intercepts water where nutrients are already moving.
How nutrients leave productive land
Nutrients enter farm systems through commercial fertiliser, manure, crop residues, soil organic matter, legumes, irrigation water and approved organic amendments. Some are taken up by crops, while others remain in soil or are transformed by biological activity. Loss occurs when rainfall, irrigation or drainage moves them away from the productive root zone.
Nitrogen commonly leaves as nitrate dissolved in subsurface drainage or groundwater. It can also move in surface runoff, attached to sediment or organic particles, and may be released as gases such as ammonia and nitrous oxide. Tile drainage can carry nitrate rapidly toward a stream or ditch, sometimes bypassing a vegetated riparian area.
Phosphorus is generally less mobile through soil than nitrate, but it can be environmentally important in both dissolved and particulate forms. Dissolved phosphorus, including orthophosphate, can be readily available to algae. Particulate phosphorus is attached to eroded soil and organic matter. It may be deposited elsewhere and remain a longer-term source, particularly if conditions later release it into the water.
Bare or compacted soil, intense rainfall, concentrated flow, excessive nutrient applications, recent manure spreading and high soil-phosphorus levels can all increase risk. Manure application based only on a crop’s nitrogen requirement can also gradually build soil phosphorus if the manure supplies more phosphorus than the crop removes.
Prevention comes before biological treatment
The most reliable nutrient-management strategy begins at the source. Farmers and land managers should use soil tests, manure analysis and realistic yield goals to match nutrient applications with crop demand. The commonly used 4R approach—right source, right rate, right time and right place—provides a practical framework.
- Account for residual soil nutrients, manure mineralisation, legumes, irrigation water and previous applications.
- Avoid spreading fertiliser or manure before heavy rain, on saturated or frozen ground, or when crop uptake is unlikely.
- Store manure securely and prevent direct livestock access to streams and drainageways.
- Manage grazing to maintain plant cover and avoid pugging, compaction and bare soil.
- Use cover crops, crop residues, perennial vegetation and suitable rotations to keep living roots or protective cover in place.
- Reduce erosion and manage compaction so that rainfall can infiltrate rather than rapidly becoming runoff.
These measures reduce the amount of nutrient available to be transported. Edge-of-field practices such as buffers and drainage treatment are important, but they should not be used to justify continued over-application.
Soil organic matter and the fungal network
Soil organic matter stores carbon and nutrients, including nitrogen and phosphorus. Decomposition and mineralisation release some of these nutrients into forms plants can use, while immobilisation incorporates some inorganic nutrients into microbial or plant biomass. Bacteria, fungi and other soil organisms work together in this food web.
Active biological communities and adequate organic matter can contribute to stable soil aggregates, better infiltration, greater water-holding capacity and improved resistance to crusting and erosion. Those changes may reduce the volume of runoff and the amount of sediment-bound phosphorus leaving a field.
Fungal hyphae—the fine threads that make up mycelium—help connect soil particles and organic residues. Decomposer, or saprotrophic, fungi process complex materials such as cellulose and lignin. Mycorrhizal fungi live in association with plant roots; their hyphae can extend beyond the root system and help plants explore more soil for water and nutrients, particularly phosphorus.
However, fungal uptake is not automatically nutrient removal. Nitrogen or phosphorus held in fungal biomass is a temporary biological store. When fungal material dies or is consumed, nutrients can return to the soil. Likewise, organic matter may retain nutrients for a time but release them again as it decomposes, becomes saturated or is eroded.
More organic material is not always beneficial. Fresh, nutrient-rich manure, compost or mulch can release soluble nitrogen or phosphorus, especially when applied excessively or before major rainfall. Organic amendments should be tested and included in the farm nutrient budget. “Natural” and “biological” do not mean nutrient-free.
Buffers, riparian areas and woody filter zones
Vegetated buffers slow overland flow and increase contact between runoff, soil, roots and microbes. Grasses, sedges, forbs, shrubs and trees can trap sediment, stabilise banks, take up nutrients and create conditions that support microbial processing. Wet, carbon-rich areas may also support denitrification, in which microbes convert nitrate into gaseous nitrogen compounds.
Riparian forest buffers add woody roots, leaf litter and other carbon-rich material. These resources support decomposer organisms, including fungi, and can create biologically active zones beside streams and drainageways. Woody vegetation also helps reduce bank erosion and can improve habitat.
Buffers work best when runoff enters as dispersed sheet flow. Concentrated flow can cut channels through vegetation, while livestock access, excessive sediment, poor maintenance or inadequate width can reduce performance. Surface buffers may also have limited effect on nitrate carried through buried drainage pipes. Site-specific design is therefore essential.
Wood-based treatment systems offer another opportunity. In a woodchip bioreactor, drainage water is routed through a trench or contained zone filled with woodchips. The main established purpose is to provide carbon and low-oxygen conditions that support microbial denitrification of nitrate.
Woodchip bioreactors contain mixed microbial communities. Bacteria commonly drive much of the denitrification, while fungi and other organisms help break down lignocellulose and release carbon that can support the wider process. Recent research indicates that wood-rotting fungi may be especially active in parts of saturated bioreactors where oxygen is more available. This supports a complementary fungal role, not the claim that fungi alone remove nitrate.
Performance depends on temperature, flow rate, residence time, carbon availability and system design. Sediment can clog the treatment zone, woodchips eventually degrade, and water quality should be monitored for possible side effects. Similar caution applies to proposed “fungal filters,” mycelial mats or inoculated mulches: visible fungal growth does not prove that a system is removing a measured nutrient load.
Cycling, storage and removal are different
These terms are often used interchangeably, but they describe different outcomes:
- Nutrient cycling means nutrients are transformed or moved among soil, plants, residues, microbes and water.
- Immobilisation means nutrients are temporarily incorporated into microbial or plant biomass.
- Storage or retention means nutrients remain in soil, organic matter, sediment or vegetation and may be released later.
- Removal means nutrients leave the treatment pathway, such as nitrate converted predominantly to nitrogen gas through denitrification.
Denitrification must also be managed carefully because incomplete reactions can produce nitrous oxide. For phosphorus, biological uptake and sediment trapping may retain nutrients, but they do not necessarily destroy them. Harvesting biomass or removing accumulated sediment may be needed if long-term removal is the objective.
A practical sequence for farms
For most farms, a sensible sequence is to reduce surplus at the source, keep soil covered, manage manure and grazing, control erosion, and then intercept remaining flows. Possible measures include grassed waterways, filter strips, contour practices, terraces, prairie strips, riparian buffers, controlled drainage, saturated buffers and woodchip bioreactors.
Fungi fit within this sequence by helping maintain biologically active soils, supporting plant nutrient acquisition, contributing to decomposition and soil aggregation, and participating in carbon-rich drainage-treatment systems. Their contribution is most credible when it is evaluated alongside the whole system—measured nutrient loads, hydraulic performance, soil condition and management records—rather than inferred from the presence of mycelium.
The practical message is simple: fungi may help farms retain, transform and manage nutrients, but they do not magically remove excess fertiliser. Sound nutrient planning, soil cover, erosion control, manure management, grazing management and careful water control remain the foundation.
Further guidance
Useful technical guidance is available from the U.S. Environmental Protection Agency, USDA Natural Resources Conservation Service, Penn State Extension and Iowa State University Extension. Local conservation advisers can help match practices to soil, slope, drainage layout, rainfall, crop system and regulatory requirements.