Skip to main content

Organic Gardening: Soil Management

Updated May 27, 2021
Professional headshot of Kristine Lang

Kristine Lang

Assistant Professor & SDSU Extension Consumer Horticulture Specialist

Additional Authors: Jason Clark

Original article by Wyatt Brown. Updated by Kristine Lang, Assistant Professor and SDSU Extension Consumer Horticulture Specialist, and Jason Clark, Assistant Professor and SDSU Extension Soil Fertility Specialist.

Professional horticulturists and hobby gardeners throughout South Dakota are experimenting with organic gardening. These methods focus on maintaining and enhancing ecological balance in the garden by increasing biodiversity and crop rotations, improving soil and enhancing water conservation—typically with the exclusion of synthetic fertilizers and pesticides. Although the adoption of organic gardening methods can be daunting at first, readers can be assured that the soil management concepts in this article will set the foundations for successful organic gardening.

Soil Organic Matter

The most-important aspect of growing plants organically is starting with healthy soil. Soil is not lifeless and inert. It is alive! A single teaspoon of healthy soil can house up to a billion bacteria, several yards of fungal filaments, several thousand protozoa, 40-50 nematodes and a variety of smaller insects and arthropods that work harmoniously throughout a complex soil food web that is responsible for life as we know it on this planet. The importance of maintaining fertile soil cannot be overstated. Organic gardeners rely on their knowledge of natural ecosystem cycles to determine the correct soil management techniques for their soil type. They regularly consider the natural inputs required for maintaining high microbial populations and adequate nutrient cycling. Growers utilizing organic practices feed the soil, which in turn feeds and defends their plants.

There are no overnight solutions to improve soils and combat pest issues. Plant enthusiasts must be patient and steadily transition from using synthetic products to organic production methods over a two, three or four-year program, depending on their current situation. This does not mean that growers will not obtain lush, healthy growth from their plants during this time. It just means that growers must provide increased organic amendments and “quick-release” organic fertilizers up front to ensure plant nutrient needs are met while the natural soil ecology improves.

Many gardening publications, whether they promote organic methods or not, all tend to agree on the importance of adding organic matter to soil in lawns and gardens. Organic matter, also known as soil organic matter, is a dynamic mixture of living, dead and decomposing life-forms, and is the “glue” that holds soil together. In general, five to 10 percent organic matter is considered optimal for healthy plant growth; however, most garden soils range from two to three percent soil organic matter. Organic matter can range from kitchen wastes and shredded leaves, to well-rotted manure and compost, to dead insects and grass clippings scattered throughout the soil. According to Rodale’s Growing Fruits & Vegetables Organically, “Feeding your soil a diverse diet of organic matter is an essential part of any management program. … The secret to maintaining a balance between building organic matter and growing crops intensively is to add residues continually. Mulching with organic matter, adding compost and using cover crops (also called green manures) are the most-common ways to add soil organic matter.”

As microbial populations and other insects and animals consume and decompose SOM, we are left with a reasonably stable product known as humus. Humus consists of very long, hard-to-break chains of carbon molecules with a large surface area. These surfaces carry electrical charges, which attract and hold nutrients plants need, making them more available to your plants. If you viewed these molecules through a scanning electron microscope, you would notice these carbon chains resemble a sponge; capable of holding 80–90% of its weight in water and providing housing for crucial beneficial microbes, such as bacteria and fungi.


Young man shoveling a pile of compost.
Annual applications of compost to gardens add nutrients and a diverse population of microbial life to the soil. Courtesy: Karina Walvatne.

The gardener’s equivalent to nature’s humus production is the composting process. Compost is the organic gardener’s secret weapon! Compost is teeming with microbial populations, incorporating organisms from all six biological kingdoms throughout its highly diverse humic profile. However, there are several important considerations when adding compost to your gardens, trees, shrubs and lawns.

First, not all compost is created equal. Compost can vary in its nutrient content from producer to producer, and batch to batch. As a general rule-of-thumb, compost will contain the following Nitrogen (N) – Phosphorus (P) – and Potassium (K) percentages by weight. N: 1.5 to 3.5, P: 0.5 to 1, K: 1 to 2. Compost also provides other nutrients plants need in lower quantities, including calcium (Ca), magnesium (Mg) and sulfur (S), as well as a wide variety of trace elements depending on the starting materials. Second, when applying compost to your growing areas, use compost that is well finished. Finished compost should be dark brown, fairly dry and crumbly, and have an earthy (not rotten) smell. Compost that has not thoroughly broken down will use elements from the soil to finish its decomposition process before the minerals it contains will be available to plants. This means microbes will feed themselves before sharing nutrients with plants, which will be a problem if not managed correctly.

For vegetables and annuals, incorporate one to two inches of compost into the top few inches of soil before seeding or transplanting in existing beds. Gardeners can also apply a side-dressing of compost midway through the growing season as a water-retaining mulch and a source of slow-release nutrients for their food crops and flowers. Compost has a very low danger of burning plants, unlike many synthetic fertilizers. For newly planted trees and shrubs, avoid adding compost directly into a planting hole – this causes roots to ball up instead of spreading out in search of nutrients – thus leaving plants susceptible to waterlogging, disease, insect problems and windthrow (a condition where trees are uprooted or broken by wind). Instead, top-dress existing woody plants or newly planted trees and shrubs with one to two inches of compost across the root zone, then cover with a mulch of wood chips or shredded bark. For lawn applications, apply compost when establishing a new lawn, or when rejuvenating your lawn in spring. Fine compost may be added as an amendment during lawn aeration to provide immediate contact with roots. Compost may be used as an amendment in potting and seedling mix. Screen out any large chunks of compost through a one-quarter inch mesh and add it to either store-bought seedling mix or your own custom-made mix. If you are making custom mix, be sure to include materials, such as peat moss, coconut coir, vermiculite and/or perlite to ensure ample pore space, drainage and water-holding capacity. This will allow the roots of delicate seedlings to penetrate the mix and effectively mine for nutrients. Using garden soil in seedling mix is generally not recommended. Garden soil can contain weed seeds, pathogens and insect pests that will harm the new seedlings.

Beneficial Soil Microbes

While compost provides slow-release nutrients, gardeners will find an even better benefit from compost: the delivery of beneficial and diverse microbial populations to the soil. Microbes, in particular beneficial bacteria and fungi, are the organic growers number-one defense against a variety of plant health issues. In natural settings, like old-growth forests, grasslands and mountainous areas, microbes are the primary defenders against a relentless barrage of environmental stressors. Beneficial microbes are nature’s utility player for maintaining plant vigor, influencing drought resistance and nutrient uptake, defending against soil and airborne pathogenic diseases and producing plant growth hormones. In fact, microbes are so important to plant survivability that plants will secrete 20–30% of the food they produce through their roots to feed and attract microbes to the root region. These secretions, known as exudates, consist of carbohydrates (sugars), organic acids, proteins, exoenzymes and other substances. The main benefit of these plant carbohydrate releases is that they ensure microbial carbon (energy) needs are met. Microbes need roughly a 25:1 carbon to nitrogen (C:N) ratio to meet growth needs. These needs can be met by their own decomposition of organic matter, or through sugars exuded by their host plant roots.

Symbiosis is a mutually beneficial relationship between two different organisms living in close proximity. The importance of establishing a healthy plant-microbe symbiotic relationship cannot be overlooked. Nearly every known species of plant forms a relationship with several species of beneficial microbes. Microbes can inoculate every area of a plant, from the root zone below ground, to the exposed, habitable plant tissue above ground and even tissue inside the plant as well. The job of these microbes is simple: protect and nourish the plant at all costs!

Below ground, microbial colonies nourish their hosts in a variety of ways. Just as bacteria protect above-ground plant tissue, soil-dwelling bacteria do the same. They produce enzymes that have an enormous effect on soil and plant health. Many of these enzymes help break down minerals in soil to ionic form, making them available for root uptake. They produce plant hormones that stimulate lateral root growth, produce more flowering sites and activate the plant’s natural defense and response to stress. Other important products of beneficial soil bacteria include antibiotics and antifungal metabolites that keep soil-borne pathogens at bay, amino acids, organic chemicals and other byproducts.

In addition to valuable bacteria, a powerhouse beneficial fungus, known as mycorrhizae, associates with 95% of the world’s plants, forming symbiotic relationships with plant host’s roots. They are well-known for providing host plants with water and nutrients, specifically hard-to-unlock phosphorus. Fungal hyphae extend out into the soil, mining for available nutrients, helping decompose soil organic matter into usable elements and then delivering them directly to the plant root. In exchange, plants provide mycorrhizae with carbohydrates to continue their fungal growth process. Also fascinating is mycorrhizae’s ability to ward off pests. They have been known to trap root enemies, like nematodes, in their hyphae, preventing them from decimating cash crops, such as tomatoes. The nematodes are then consumed by the fungus, which in turn uses the nutrients obtained for growth and feeds the rest to the plants.

Protecting the Soil Food Web

Bacteria, mycorrhizae and other soil food web members require nutrients in the form of either organic matter or exudates to continue their life processes. A great majority of these nutrient requirements are disrupted by the average gardener. Bare soil during both the growing and off-season disturbs nutrient cycling within soil. Use mulch or cover crops to avoid bare soil. Add two to four inches of mulch between plants and across bare soil areas, while avoiding contact with the base of your plants. Sources of organic mulches can include grass clippings, straw or wood chips. Your mulch serves a multifunctional role. It feeds microbes, prevents weed germination, increases SOM and prevents soil erosion and soil water evaporation.

To protect soil microbes, organic gardeners should work to reduce tillage whenever possible. Excessive tilling destroys fungal networks, crushes arthropods and decimates the indispensable worms and the pore spaces they create as they burrow throughout the soil. Soil structure deteriorates from the decline of these important organisms, causing closure of soil pores and leading to possible hardpan issues in the soil. As these issues compound, you’ll notice an increase in soil erosion, a decrease in water absorption, a lack of available nutrients and overall loss of soil productivity. Gardeners can combat the need to till by developing long-term beds in their gardens. They can also use specially designed tools, like broadforks. Broadforks are a large garden tool that is manually inserted into garden beds to gently loosen and turn soil. The broadfork, while requiring more manual labor, allows users to break up any hardpan or compacted soil areas instead of rototilling every season. Additionally, cover crop combinations that incorporate root crops, like turnip and Daikon radish, can help decrease compaction during fallow seasons.

With fewer disruptions to the soil food web, additions of organic matter to growing areas and a better understanding of natural soil fertility, gardeners will witness a noticeable shift in the soil’s water-holding capacity and productivity as they implement organic gardening practices.

Special thanks to SDSU Extension Master Gardeners Tim Schreiner and Stacy Dreis for serving as volunteer copy editors of this article.