NC State Extension Publications

Soil Management and the Organic Standards

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The USDA rules for certified organic farming include specific objective criteria such as allowable and prohibited practices and inputs, and more subjective criteria such as minimization of erosion and maintenance or enhancement of soil health. Producers should note that international guidelines can differ from USDA guidelines. In certified organic production, certain inputs are allowable, but some inputs will be required to sustain soil fertility. These inputs must be applied in a manner that avoids nutrient excesses and minimizes runoff. Management of weeds, insects, and diseases often depends on several cultural practices, many of which are tied to soil management. Crop rotation and tillage practices must provide an appropriate seedbed and pest control while minimizing erosion. Soil management practices must be developed in consultation with the certifying agent who interprets subjective aspects of the guidelines, approves inputs, and specifies needed documentation.

Crop Rotation: Tilth, Fertility, and Pest Management

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Crop rotation is critical to the maintenance of soil tilth (physical condition), fertility, and organic matter, and as a preventive practice to minimize pest problems. No specific rotations are mandated but recommended crops to include are sods, cover crops, green manures, and catch crops. The rotation adopted must aim to mitigate relevant problems with soil organic matter content, deficient or excess plant nutrients, and soil erosion, and break pest and disease cycles. Defining a rotation is also a key component in designing soil sampling and tillage-management schemes. For short rotations (two to three years), soil samples can be collected once per rotation. For longer rotations, soil samples may still need to be collected every two to three years, preferably prior to planting the most intensively managed crops. Conservation tillage reduces soil erosion, maintains or increases soil organic matter content, and improves soil physical health. Conservation tillage can be alternated with more intense cultivation needed at other times during the rotation, or due to site-specific conditions.

Soil Fertility Management

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Although crop nutritional requirements are the same for organic and conventional farms, organic producers need to be more creative due to the limitations on allowable inputs. Soils throughout the Carolinas differ in texture, organic matter, and past erosion and management history. Additionally, fluctuations in weather patterns and crop yields result in unpredictable residual nutrient status. Periodic soil testing is the only way to understand the current fertility level and sustain the fertility status of each field while avoiding excess nutrient accumulation. Plant tissue analysis can also be used to verify the adequacy of soil fertility management, particularly for nutrients not easily measured in routine soil tests (nitrogen, sulfur, boron). With tissue testing, the appropriate plant part must be collected at the proper growth stage as specified by laboratory guidelines. Contact your local N.C. Cooperative Extension center for more details, or visit the North Carolina Department of Agriculture & Consumer Services website.

North and South Carolina have numerous sources of plant and animal manure and by-products. These states also have favorable climates for growing a diversity of rotational and green manure cover crops. Farmers should study their crops to fully understand production requirements, nutrient needs, and common production problems. Crops differ in their nutrient removal rates (see Table 9-1), and nutrient sources differ in their nutrient contents (Table 9-2).

Certain inputs are allowable on organic production systems, if applied according to guidelines. These include many (but not all) natural and certain synthetic materials. The National List of Allowed and Prohibited Substances under the National Organic Program is available on the USDA Agricultural Marketing Services website. This list specifies synthetic substances allowed for use and non-synthetic substances prohibited for use in crop production. A list of commercially available sources of these materials, which have been OMRI-reviewed and classified as either allowed (A) or regulated (R) is available on the OMRI website. Any other materials not appearing on OMRI’s list should be considered prohibited until further notice. In all cases, input use should be included in their organic system plan and confirmed by the certifying authority prior to application.

Critical aspects of soil fertility management include pH, major nutrients (N, P, K, S, Ca, Mg), and micronutrients (especially B, Cu, Mn, Zn; but also Fe, Mo, and Cl). A summary of soil fertility parameters and organic management options is given in Table 9-3.

Soil pH

Soil pH is important since it influences nutrient solubility, microbial activity, and root growth. Low pH levels common in native Carolina soils can kill developing root tips and prevent root colonization of the soil. Low soil pH continues to be the most common limiting factor for plant development seen in samples submitted to the North Carolina Department of Agriculture & Consumer Services’ Agronomic Division Laboratory. Correcting low soil pH should be based on soil test recommendations that consider both the soil pH and the residual acidity levels, crop pH requirement, target pH based on soil class, and whether calcitic or dolomitic lime should be used. Most agricultural lime is derived from naturally occurring minerals of relatively low solubility, and its use is generally allowed in organic production systems. Hydrated limes, burnt limes, lime-stabilized biosolids, and industrial wastes or slags are not allowed. In rare cases when soil pH is too high to permit optimum crop growth, elemental sulfur can be used to lower soil pH. The amount of sulfur required to lowering the pH can be calculated using the equations presented in NC State’s Calculating the Rate of Acidifiers to Lower the pH of North Carolina Soils (AG-439-88).

Nitrogen (N)

Nitrogen is the most frequently limiting nutrient for crop production. Organic farms need to supply N through sources such as legumes, animal wastes or by-products, plant processing by-products, or limited additions of mined mineral deposits. It is possible for a nitrogen-fixing legume or legume-grass mixture cover crop to provide adequate N for certain following cash crops. The amount of N provided will depend on the legume species, nodulation effectivity, biomass produced, and termination timing. A seed inoculum is recommended for legumes unless an adequate native inoculum is present; adequate soil fertility is needed to insure no other factors limit legume growth. It is important that producers make sure inoculums are organically approved, and must not be mixed with any prohibited substances such as pesticides or inorganic fertilizers.

Many farmers in North Carolina use composted or uncomposted poultry litter to supply the N needed for their organic field crops. Poultry litter and poultry by-products are available in many parts of the state. Mined nitrates, such as sodium nitrate (NaNO3, often referred to as Chilean nitrate), may be used in certain places, but are limited to a maximum of 20% of the crop’s total N requirement. Constantly relying upon NaNO3, a restricted substance in organic agriculture, will be questioned by a certification agency. Since many international certifiers, including those in the European Union, Japan, Australia, and even some US certifiers prohibit any use of Chilean nitrate, producers should verify its acceptability with their certifier and to their prospective markets.

Other Nutrients

Phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), copper (Cu), manganese (Mn), and zinc (Zn) can generally be supplied in adequate amounts through additions of lime (Ca, Mg), animal or plant by-products or wastes (P, K, S, micronutrients), or permissible mineral inputs. Naturally occurring minerals of relatively low solubility (lime, gypsum, rock phosphate, rock dusts, mined humates) are generally allowed.

In addition, the following naturally occurring minerals of relatively high solubility may be applied if used in compliance with the National List.

  • Magnesium sulfate (Epsom salt), with a documented soil deficiency.
  • Sulfate of potash and potassium magnesium sulfate, if from an approved source and with a documented soil deficiency.
  • Muriate of potash, if derived from a mined source and applied in a manner that minimizes chloride accumulation in the soil. This may be acceptable for most crops in the Carolinas with a soil test documenting the deficiency and recommending an application rate.
  • Many micronutrient salts, with documented soil deficiency and if not in the form of nitrate or chloride salts. This includes various soluble boron products and sulfates, carbonates, oxides, or silicates of zinc, copper, iron, molybdenum, selenium, and cobalt.

Numerous animal and plant by-products are available to provide essential crop nutrients (Table 9-2). It is important to check with the certifying agency, and the prospective market if possible, before using any input.

Tillage Practices

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Management of soil’s physical health, organic matter, and fertility is an important aspect of a successful organic production system. Organic farming systems traditionally relied on pre-plant tillage and cultivation following planting to control weeds and reduce the incidence of seedling diseases and insect pests. However, tillage decreases organic matter and increases soil erodibility, both critical aspects of soil fertility, water-holding capacity, and general soil health. Following annual grain crops with cover crops where the soil surface is protected by a growing crop for most of the year makes it easier to maintain soil organic matter content. The use of roller-crimpers to kill cover crops, and heavy residue cultivators for additional weed control, also provides soil and water conservation benefits while reducing tillage. Cover crop species should be selected based on the producer’s soil type, climate, and management goals. Soils that hold significant amounts of moisture may not be best suited for roller-crimping. Tillage should occur when soil moisture is low enough to prevent compaction. Since primary tillage operations often occur a month before a crop is planted, careful planning is required. The ability to take advantage of dry weather periods will be extremely helpful. This also means that fields with soils that are poorly drained or that have low spots may not be good choices for organic production. These are also the soils which get compacted over the time due to field traffic; every pass on these soils will contribute to soil compaction. Recommendations for the types of primary and secondary tillage practices for specific soil types and field conditions can be found in greater detail in the “Weed Management” chapter of this guide. More information about tillage and the use of cover crops can also be found on NC State’s Soil Health and Management extension portal.

Documenting Crop Nutrient Deficiencies and Soil Health Maintenance

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Since use of some soil amendments is limited to cases of nutrient deficiency, organic producers should maintain soil testing and plant tissue analysis records documenting specific nutrient deficiencies that need correction. Soil test records can also be useful in documenting soil quality maintenance, as they indicate changes in stable organic matter fractions and nutrient levels over time. Of particular concern are avoiding topsoil erosion, which could result from excessive cultivation for weed control (declines in soil organic matter are indicative of erosion losses) and avoiding excess phosphorus and micronutrient accumulation following application of manures and composts. Reducing tillage, cover crop mulching, and roller-crimping can provide good residue coverage, and can help with weed management, erosion, and building soil health. Leguminous cover crop species can also act as an alternative source of nitrogen.

Composts and Manures

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Specific guidelines must be followed when applying compost and manure in organic production systems. Materials should not contain excess nutrients and must be applied at agronomic rates in compliance with any applicable nutrient management guidelines. Raw animal manures must either be: 1) composted according to specific criteria, 2) applied to land used for a crop not intended for human consumption, 3) incorporated into the soil at least 90 days prior to the harvest of an edible product not contacting soil or soil particles, or 4) incorporated into the soil at least 120 days prior to the harvest of an edible product that does contact soil or soil particles. The guidelines for compost production for organic agriculture state that the initial C:N ratio must be between 25:1 and 40:1, and a temperature between 131° and 170°F must be achieved. This temperature must be maintained for at least three days for in-vessel or static aerated pile systems, or for at least 15 days during which there are at least five turns for windrow systems. Composts not meeting these criteria must be applied based on other raw manure criteria, which also apply to lagoon liquids, lagoon solids, and stockpiled poultry litter. Manure ash may not be used, but ashes from other untreated plant and animal materials may be applied if not combined with any prohibited substances.

Avoid over-reliance on animal manures, as this could lead to accumulation of excess P, Cu, and Zn in soils. For example, based on the general nutrient data shown in Table 9-1 and Table 9-2, stockpiled turkey litter applied at a rate of 5 tons per acre would supply the approximate amount of N removed by a 150-bushel-per-acre corn crop. Note that the amount of phosphorus added (as P2O5 equivalent) would be 360 pounds per acre, while crop removal would only be 53 pounds per acre. Similarly, 2.8 pounds per acre of zinc would be added, while crop removal would only be 0.15 pound per acre. Sporadic use of manures in conjunction with more frequent use of legume cover crops, green manures or other N sources is an excellent way to supply several plant nutrients in appropriate amounts.

NC State provides several fact sheets describing specific types of manures (swine, poultry, dairy). Since nutrient composition of animal manures and composts can vary widely, submit a sample to the Plant and Waste Analysis Laboratory of the North Carolina Department of Agriculture Agronomic Division before using. Sewage sludge and composted municipal wastes are not allowable on organic fields.

Table 9-1. Nutrient removal (in pounds) by different crops. Approximate removal rates can be adjusted based on comparison with the crop yield level shown. Missing values indicate no data available.

Corn, grain

(150 bu)


(60 bu)


(50 bu)

Tobacco, flue-cured

(3000 lb)

Irish potato

(15 tons)


(300 bu)


(3.5 tons)


(5 tons)


(8 tons)

N 112 75 188 85 90 40 135 215 319
P2O5 53 38 41 15 48 18 65 85 122
K2O 40 22 74 155 158 96 185 240 467
S 10 4 23 12 7 6 20 46
Ca 2 2 10 75 5 4 60
Mg 8 9 10 15 7 4 13 40 47
B 0.1 0.05 0.06 0.05 0.08 0.05
Cu 0.06 0.04 0.05 0.03 0.06 0.02
Mn 0.08 0.14 0.06 0.55 0.14 0.06
Zn 0.15 0.21 0.05 0.07 0.08 0.03

Table 9-2. Nutrient content of selected natural sources. These are general values and may not accurately represent the content of any specific source. Laboratory analysis should be performed prior to utilizing these materials. Missing values indicate no data available. Use of any specific source should be approved by the certifying authority prior to application to an organic farm.
Source Units N [a] P2O5 K2O S Ca Mg B Cu Mn Zn
Swine lagoon liquid lb/acre-inch 102

64 [b]

37 93 10 26 83 0.2 0.3 0.34 1.5
Broiler, fresh manure lb/ton 16 17 11 2 10 4 0.1 0.7 0.6 0.5
Broiler, stockpiled litter lb/ton 22 80 34 12 54 8 0.04 0.3 0.6 0.6
Layer, fresh manure lb/ton 73 42 40 12 124 9 0.05 0.2 0.7 0.9
Layer, composted manure lb/ton 44 38 39 6 87 8 0.05 0.1 0.5 0.5
Turkey, fresh manure lb/ton 16 25 12 10 27 2 0.6 0.6
Turkey, stockpiled litter lb/ton 22 72 33 10 42 7 0.05 0.3 0.6 0.6
Feather meal lb/ton 128 8 2 15 5 1 0.03 0.03 0.1
Blood, dried lb/ton 240 to 300 (total N) 60 6
Bone meal, raw lb/ton 70 (total N) 440 4 440 12
Mushroom compost lb/ton 10 8 4 9 47 4 1 0.2 0.1
Shrimp process waste lb/ton 58 (total N) 200
Cotton motes lb/ton 40 (total N) 10 60 12 80 14
Peanut hull meal lb/ton 24 (total N) 12 16
Wood ash lb/ton 0.0 40 120 400 20

[a] Values shown represent plant available N estimate for material incorporated into the soil, unless specified otherwise.

[b] Sprinkle-irrigated and not incorporated.

Table 9-3. Soil fertility parameters and management options.
Parameter Effect on Plants Problem Documentation Supply Options [1] Not Allowed
pH Nutrient solubility, root development, microbial activity Soil test Standard calcitic or dolomitic agricultural ground limestone; pH can be lowered by adding elemental sulfur. Hydrated or burnt lime

[Ca(OH)2, CaO], industrial wastes, slags

Major Nutrients



Component of proteins, chlorophyll Tissue analysis Legumes, manures [3], animal by-products (blood, fish), plant by-products (cotton, apple, fermentation wastes), mined sodium nitrate (NaNO3) [3] Synthetic fertilizers, sewage sludges, municipal waste composts


Component of nucleic acids Soil test, tissue analysis Manures [3], rock phosphate, animal by-products (bone meal; fish, shrimp, & oyster scraps; leather) Processed rock phosphates


Water, salt, & pH balance; enzyme activation; protein synthesis; photosynthesis Soil test, tissue analysis Manures [3], plant by-products (ash, dried seaweed), greensand, sulfate of potash (K2SO4) [4], possibly muriate of potash (KCl) [3,4] KCl if excess chloride


Component of proteins; volatile compounds of mustard, garlic, onion Tissue analysis Manures [3], plant by-products (cotton motes, peanut meal), elemental sulfur [4], gypsum (CaSO4), Epsom salt (MgSO4) [4], sulfate of potash (K2SO4) [4] Synthetic fertilizers


Cell wall & membrane stabilization, cell growth, osmoregulation Soil test, tissue analysis Standard calcitic or dolomitic agricultural ground limestone, gypsum (CaSO4), bone meal, ash Ca(OH)2, CaO, calcium nitrate [Ca(NO3)2]


Component of chlorophyll, cell pH and cation balance, enzyme activation Soil test, tissue analysis Standard dolomitic agricultural ground limestone, Epsom salts (MgSO4) [4], sulfate of potash magnesium, bone meal, plant by-products (cottonseed meal, wood ash) Synthetic fertilizers

Micronutrients [2]



Cell wall & membrane stabilization, cell growth, carbohydrate & protein metabolism, pollen germination Tissue analysis Manures, animal and plant by-products, soluble boron fertilizers [4]


Enzyme component, photosynthesis, respiration, cell wall lignification, pollen formation Soil test, tissue analysis Manures, animal and plant by-products, sulfates & oxides [4] chlorides


Enzyme activation, protein component, photosynthesis, cell growth Soil test, tissue analysis Manures, animal and plant by-products, sulfates & oxides [4] chlorides


Enzyme component & activation, protein synthesis

Soil test, tissue analysis Manures, animal and plant by-products, sulfates & oxides [4] chlorides
Co, Fe, Mo, Se Tissue analysis [5] Manures, animal and plant by-products, sulfates, carbonates, oxides, or silicates [4] Chlorides, nitrates

[1] Inputs must be on the National Organic Program or the OMRI-approved source list and approved by the certifying agents.

[2] Avoid over-application of micronutrients as toxicities can occur.

[3] See restrictions in text.

[4] Documentation of nutrient deficiency required.

[5] Deficiencies of Co, Mo, and Se are not common in North Carolina, and these elements are not included in routine tissue analyses performed by the North Carolina Department of Agriculture and Consumer Services. Consult a Cooperative Agricultural Extension office for information regarding private agricultural laboratories.

Farm Profile: Looking Back Farms

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Looking Back Farms, located in northeastern North Carolina, is a 350-acre organic grain farm located mostly on Arapaho fine, sandy loam soil. This farm has been certified organic for nearly 15 years. Currently, the farm employs a two-year rotation of corn-oats-soybeans, with oats and soybeans double-cropped.

Corn is planted in May and is seeded at a rate of 32,000 seeds per acre on 36-inch rows. This rate is about 10% higher than a conventional rate for the area. The higher plant population reduces weed competition and allows the population to compensate for any plants lost during cultivation. Soybeans are planted on the same row spacing, and oats are drilled using a seed drill on 6-inch spacing, and planted at 80 pounds per acre.

Fertility Management: Looking Back Farm applies chicken litter from a neighboring farm on corn and oats. The litter is applied pre-plant at 3 to 4 tons per acre. Mushroom compost (2:2:4 analysis) is used when available before soybeans (applied on top of oat stubble when double-cropping) and is eventually applied to all fields over two years. The compost contains liming agents and helps raise the soil pH, keeping soil life and nutrients in balance, which in turn allows maximum crop health and growth. Cover crops are also used on this farm as part of the fertility management plan. Rye, crimson clover, Austrian winter pea, and triticale have all been grown as cover crops after corn. The cover crops increase soil organic matter, soil microbiology, water infiltration, and water holding capacity. Legume crops, Austrian winter pea, and crimson clover also fix nitrogen, adding it to the soil so it is available for subsequent crops. The cover crops are broadcast seeded in October after corn has been harvested and fields tilled. The cover crops are cut and tilled into the soil in March, allowing enough time for the cover crop residue to break down before soybeans or corn are planted.

The farmers try to avoid a build-up of phosphorus and heavy metals from poultry litter in their soil by rotating compost and litter fertility amendments and by using cover crops. They see the benefits of one application of a fertility amendment for up to three years after the application because the organic amendments take much longer than conventional fertilizers to decompose and release N and other nutrients. They often do not see the benefits of applying litter or compost in the spring to their oats because of this. Nitrogen from the litter or compost becomes available slowly, as the amendment breaks down, and the plants cannot take advantage of a nitrogen boost since the nutrients are released more slowly than conventional fertilizers. However, their yields do not suffer. It is likely that the organic amendments applied at planting (and years before) provide enough fertility as they slowly break down for the crop. Lime does not have to be applied often; the last application of lime was three years ago, and the pH of soils in all fields ranges between 6.0 and 6.5.

Acknowledgment of Previous Contributing Authors

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Carl R. Crozier, Soil Science Extension Specialist, NC State University


Extension Soil Fertility Specialist and Associate Professor
Crop & Soil Sciences
Extension Soil Management Specialist and Assistant Professor
Crop & Soil Sciences

Find more information at the following NC State Extension websites:

Publication date: March 19, 2024

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