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Soil Science

What Your Soil Is
Trying to Tell You

On reading soil structure, understanding what's happening biologically, and how to rebuild what's been depleted.

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Garden at Good Land Seed Co.
Photo: Brigham Stoehr, 2026

Pull a handful of soil from your garden and look at it. Not at the color, though that matters — look at the structure. Does it hold together loosely, with visible aggregates and some give? Does it compact into a dense clay-filled clod? Does it fall apart into powder? The physical structure of soil is a proxy for everything happening inside it biologically, and once you learn to read it, you stop thinking about soil as dirt and start thinking about it as a framework for nearly 60% of all species on Earth.1

Healthy soil is not primarily a chemical environment, but a biological one. A single teaspoon of productive garden soil contains more microorganisms than there are people on earth, give or take. Bacteria, fungi, protozoa, nematodes, arthropods, earthworms — all of them moving nutrients, breaking down organic matter, building aggregates, and suppressing pathogens. The chemistry follows from the biology. Feed the biology and the chemistry tends to sort itself out.

the organic matter problem

The Organic Matter Problem

Most residential garden soils are depleted. Decades of tilling, synthetic fertilizer use, and the removal of plant matter have thinned the organic matter content below the threshold at which soil biology can sustain itself. The average American lawn soil has somewhere around one to two percent organic matter. Productive agricultural soils in good condition run three to five percent. Prairie soils that have never been cultivated can exceed eight percent. The difference in soil health isn't just cosmetic — it is deeply structural, biologically diverse, and cumulative in nature.

Organic matter is the primary food source for the microbial community. It also holds water, buffers pH, improves aeration, and provides a slow-release reservoir of nutrients. You cannot substitute it with synthetic inputs. Nitrogen fertilizer feeds the plant directly but bypasses soil biology entirely, which is efficient in the short term but detrimental over the long term. The plant grows. The soil starves.

The fix is clear, even if it's slow: return organic matter consistently. Compost. Cover crops. Mulch. Chopped plant debris left on the surface. Every layer of organic material that breaks down adds to the biological capital of the soil. This is an endeavor that requires diligent stewardship and care of the land. Reasonable people disagree about how long it takes to meaningfully rebuild depleted soil, but three to five years of consistent amendment is a realistic baseline.

what amendments actually do

What Amendments Actually Do

Compost is the workhorse. It supplies a diverse microbial community, adds humus directly, and improves structure in both sandy and clay-heavy soils. Make it yourself from garden and kitchen waste, or source it from a reliable supplier.

Liquid fertilizers derived from food waste occupy an interesting niche. Some producers take material that would otherwise enter the waste stream, process it through a managed natural digestion method that destroys pathogens, and produce a liquid amendment rich in available nitrogen and phosphorus (along with a more extensive micronutrient profile).

There's something enjoyable about this logic: food that fed people, then processed into something that feeds soil, that feeds more food. These products tend to be immediately available to plants while also supporting microbial activity, which is a combination that synthetic fertilizers don't achieve.

Worm castings, kelp meal, fish emulsion, and biochar all have genuine value in certain circumstances. The evidence is thinner than I'd like for some of the more aggressive marketing claims around biochar in particular, but the fundamentals hold. Varied organic inputs build varied soil biology.

reading your soil's signals

Reading Your Soil's Signals

Garden soil and plants at Good Land Seed Co.
Photo: Brigham Stoehr, 2026

Earthworms are a reliable indicator. A shovelful of healthy garden soil should turn up several. No earthworms, or very few, suggests low organic matter or a chemical environment antagonistic to soil life.

Crusting on the soil surface after rain means low organic matter and poor aggregate stability. Water runs off rather than infiltrating.

Persistent drainage problems in clay soil often improve markedly with organic matter addition over time, because the fungal mycelium and bacterial glues that form aggregates create macropores that clay alone doesn't produce.

Weeds can divulge some useful information as well. Dock and plantain favor compacted, wet soils. Lambsquarters tend to appear in nitrogen-rich ground. Oxalis frequently signals low calcium or pH imbalance. These are rough signals, but they're worth paying attention to before you reach for an amendment.

Soil health cannot simply be purchased; it must be stewarded: composting, reducing disturbance, keeping the soil covered, and keeping roots in the ground year-round when possible. The plant and the ground are in a deep conversation. Your job is mostly to stay out of the way.

about the authors

Brigham and Alicia Stoehr are co-founders of Good Land Seed Company, an heirloom and open-pollinated seed company in Southwest Idaho. Brigham writes and grows from an ecological perspective, focusing on soil health, native plants, and seed saving. Alicia is an oncology RN who has spent years growing food and flowers for everyone she knows, bringing the same precise care to the garden that she brings to her patients. Every variety in their catalog is variety-stable, meaning the seed you buy can be saved, replanted, and passed on indefinitely. Explore their seed catalog and free resources on seed saving and soil biology at goodlandseed.com.

Citations

1. Anthony, M. (2023, July 2). Enumerating soil biodiversity. PNAS. https://www.pnas.org/doi/10.1073/pnas.2304663120

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