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Soil Organic Carbon
Agroforestry may improve the amount of carbon in the soil compared to conventional crops. The addition of leaf litter from trees and the integration of carbon from roots both contribute carbon to soil in agroforestry systems. Tree management activities such as pruning can contribute carbon into the soil when trimmings are applied as a mulch.

In temperate settings, silvoarable and silvopasture can improve soil organic carbon. In silvopasture and silvoarable systems, the addition of organic carbon is spatially distributed in the treed portion of the field, as opposed to the adjacent herbaceous crop area. The addition of carbon in the soil from agroforestry is in the top 30 cm of the soil. Despite the fact that trees root deep into the soil compared to annual crops, the contribution of carbon from roots in the deeper soil is not significant.

In tropical systems, forest farming and homegardening are associated with improvement of soil organic carbon. Soil depth, aggregate size, land use system, the spatial arrangement of plants, species assemblage and soil texture are all factors that have an effect on soil organic carbon stocks in tropical forest farming systems. Species rich homegardens with high density have more soil organic carbon than their less diverse and dense counterparts. Results vary as to whether soil organic carbon decreases or increases with soil depth in tropical systems, and this may depend on the system and characteristics of the site. In tropical forest farming systems, carbon is contributed from the shade tree leaf litter and roots, as well as from the crop leaves and roots. Organic matter is rarely removed from the system, which allows for continuous inputs of carbon into the soil between harvests. Soil organic carbon stocks in tropical forest farms can be as high as in uncultivated forest.

Soil Nutrients
Agroforestry systems can enhance soil nutrient availability as compared to a crop monoculture. Leaf litter from trees can supply nutrients to crops, such as nitrogen through the processes of decomposition and mineralization. Agroforestry trees are associated with reduced leaching of nutrients, and nutrients that are contributed to the soil by agroforestry trees may be less likely to be leached.

In a temperate setting, agroforestry practices such as boundary cropping and alley cropping can have higher concentrations of nutrients compared to conventional crops. In boundary cropping systems, there may be significantly higher soil nutrient concentrations of N, P, K, Mg, and Na observed in the vicinity of trees in the field boundary, probably due to leaf litter inputs. The nutrient concentration associated with the trees decreases as the distance from the tree increases, and this effect may be observed up to 30 m away from the boundary trees. Trees in a boundary or alley cropping system that are more mature may have an increased effect on nutrient concentration within the agroforestry system than trees that are younger.

In tropical systems,  forest farming, homegardening, and the use of silvoarable practices can improve soil nutrition. Tree cover in tropical agricultural systems is associated with greater nutrient concentrations in the soil compared to conventional monocultures. Diversity of plants in forest farms is positively correlated with phosphorus concentration in soils. There are high concentrations if inorganic nitrogen in tropical forest farming soils compared to conventional monocultures due to the return of nitrogen through leaf litter inputs. Soil inorganic nitrogen is higher when leguminous tree species are included in tropical agroforestry systems. Adding pruning residues of nitrogen fixing trees to crop fields can increase the amount of inorganic nitrogen in the soil. In some cases, the nutrient concentrations in a tropical forest farming system may be comparable to the nutrient concentrations in the uncultivated forest. Spatially, the improvements to soil nutrition in tropical agroforestry systems extends to the area under the crown of the tree or shrub. Concentrations of N, P, K, Ca all higher directly under the crown than in adjacent area.

Soil Biota
Agroforestry can improve soil biota on farms compared to farms without integrated trees. The abundance of soil fauna in agroforestry systems depends on the plant species, the soil fauna species, the climate, and the agroforestry practice. Although converting a conventional crop stand to an agroforestry system can improve soil biota, converting from a productive forest to an agroforestry system can damage the diversity of soil biotic communities. In silvopasture systems that are created by thinning second growth forests to stand densities low enough for grazing, there may be long-term reductions in earthworm abundance. Alley-cropping systems that are established by thinning existing forest may result in reduced abundance of fungal diversity and microbial activity. However, temperate agroforestry systems that are established by the addition of trees into an agricultural landscape can improve soil biotic abundance and diversity. Providing greater landscape heterogeneity on farms creates more habitat for soil organisms that may increase the rates of competition, nutrient and energy exchange, and movement of soil organisms.

In a tropical system, silvopasture and forest farming are practice that may increase soil biota. Forest farms created by the addition of shade trees over a crop such as coffee can have higher densities of nematodes and detritivorous micro-arthropods than in conventional fields. As with the trends in temperate agroforestry systems, the effect of agroforestry practices on soil fauna can be positive when compared to conventional crops, but neutral or negative when compared to uncultivated forests. In a tropical system, the abundance of soil fauna depends on the plant species, the soil fauna species, the climate, and the agroforestry practices in place. Tropical agroforestry systems such as homegardening and forest farming that support crown closure can create a microclimate in the soil that is beneficial to soil organisms. The microclimate created by crown closure in forest farming systems is associated with increased abundance of soil fauna.

Soil Erosion
Agroforestry practices integrated into agricultural systems can function to reduce water erosion. Agroforestry practices that promote canopy closure, such as forest farming and homegardening, can reduce water erosion. Areas with reduced amount of tillage are associated with less soil loss; farms that have trees in the landscape will have less area under tillage because trees occupy that space. Silvopasture, agrisilvopasture, and silvoarable are practices that can be used to cover soils with leaf litter, which is also associated with reduced erosion. Canopy closure intercepts rainfall and slows its descent to the soil and leaf litter can prevent rainfall from hitting the soil directly. Agroforestry systems provide tree residues that can be mulched after pruning or harvesting to provide soils with cover.

Agroforestry practices that function in space, such as silvopasture and agrisilvopasture, reduce erosion more than practices that function in time, such as swidden. Practices that result in no net soil loss can also reduce nutrient leaching in the soils. In some cases, agroforestry systems can even have less net erosion than natural forests. The use of hedgerows in pasture or crop fields can reduce erosion as hedgerow networks provide protection against soil loss. Hedgerows, like other treed areas, provide a sediment sink; in contrast, areas with intensive cropping and pasture with no perennials in the landscape are often sediment sources. The practice of using hedgerows can result in decreased erosion, increased deposition on hillslopes with hedgerows, and increasing carbon input from the aboveground and belowground biomass of the hedgerow.

Soil Moisture
Agroforestry practices may result in either increased or decreased soil moisture. Trees in the landscape can lead to greater rainfall interception because soil aggregation under trees may be greater, which results in higher soil moisture holding capacity. Scattered trees can improve water infiltration and macropore flow, as well as reduce soil evaporation due to shading. Evapotranspiration and canopy interception of rainfall due to tree cover can also reduce soil moisture. Forest farms have relatively higher soil organic matter, more stable aggregates, improved filtration, and reduced drainage of water compared to monoculture cropping systems.

Agroforestry systems have different spatial and temporal soil moisture regimes than monoculture cropping systems and natural forest. Practices that include boundary planting, such as shelterbelts or hedgerows, results in spatial variation where soil moisture is greatest near the boundary planting. Spatial variation in the depth of soil is also observed in boundary planting and forest farming systems. Variation in soil moisture in deep soils is relatively more stable in agroforestry systems that use boundary planting than in monocultures. In forest farming systems, soil moisture in the topsoil is greater and relatively more stable as compared to monocultures. Deeper soil is drier than topsoil forest farming systems, indicating complimentary use of the soil water by crop plants and shade trees.

Microclimates in agroforestry systems can affect soil moisture. Agroforestry practices can create microclimates resulting variation in soil moisture over small areas. The spatial arrangement of the trees in an agroforestry system creates microclimates that affects the spatial distribution of soil moisture, as well as the infiltration of water by soil. In forest farming systems, the shade trees buffer temperature extremes that can lead to soil water evaporation in shaded areas, creating variation in microclimates. Shade trees can mitigate microclimate extremes within the system so that soil moisture is greater overall during the dry season.