We’re transforming the way we think about gardening by placing the health of soil microorganisms front and center. We use 100% microbe-rich compost as soil and microbe-rich worm castings (worm poop) as fertilizer. Both are teeming with healthy microorganisms that feed and support our plants.

Why Microorganisms Matter

Healthy soil is the foundation for healthy plants, and the secret lies beneath the surface. Microorganisms - bacteria, fungi, and other tiny invisible critters - form symbiotic relationships with plant roots, providing essential nutrients that plants can’t access on their own. This interaction is key to plant nutrition, resilience, and overall health.

In just one gram of soil, there can be millions to billions of microbes, depending on the soil's condition. There are tens of thousands of species of soil micro-organisms that do a vast number of nature's tasks. The microbe expansion continues every year and every planting. Let’s enable the trillions of microflora (microbes and fungi) in our gardens to feed our plants for us.

These microscopic helpers feed on organic matter and transport nutrients to plant roots in a form that plants can efficiently use. The soil microbes and plants engage in a mutual aid pact—plants feed microbes through root exudates, and microbes, in turn, nourish the plants.

Microbe-Rich Soil: The Foundation of Success

Deep Roots uses a combination of 100% microbe-rich compost as our “new soil” and microbe-rich worm castings as our fertilizer to foster this microbial life. Our compost is crafted using a “thermophilic” process, where heat-loving microbes break down organic matter (plant waste and manure), creating nutrient-rich aggregates that provide both nutrients and structure to the soil. This process also eliminates weed seeds and pathogens, setting our compost apart from many commercial options.

Worm castings (worm poop), a cornerstone of our method, supercharge the soil with even more microbial life. These castings, produced from worms fed primarily on organic livestock bedding (straw and manure), are added when planting seedlings and seeds. Fish emulsion can also be applied throughout the season to provide short-term boosts of organic matter, stimulating microbial populations and helping plants thrive.

Key Principles of Our Approach

1. Cultivating thriving soil microbial communities: Creating a thriving ecosystem within the soil itself is more important than growing your plants. Although the specifics for growing each veggie or herb is important, it is secondary to the task.

2. No till, no dig, no pull rule: Tilling and digging disrupt the delicate fungal and bacterial networks that have built up in your soil. Instead of pulling plants out by the roots, cut them at the soil level, leaving the roots to decompose and feed the soil microbes. Root crops are the exception to this rule. For most plants, this method preserves soil structure and microbial health. No till rule blog post.

3. Biodiversity is essential: We encourage planting a variety of vegetables, flowers, and herbs together in raised beds, which boosts microbial diversity and makes the garden more resilient against pests and diseases. The greater the variety of plant roots, the more microbial interactions occur beneath the surface. It also makes it harder for pests to find their favorite plants. But make sure that large plants don’t block sun from the smaller plants. Biodiversity blog post.

4. Grow in raised beds: We highly recommend growing in raised beds and not growing in the ground. The most important benefit is that with raised beds YOU choose the soil rather than accepting the soil you have in your yard. Raised beds allowed Deep Roots to start using a completely new kind of soil – 100% microbe-rich compost.

5. Use 100% compost as the growing medium: All composts are not equal. Highest microbe density is in compost made with a natural  “thermophilic” (microbe generated heat) process in giant piles at a local farm. Deep Roots sells microbe-rich compost that is powerful and gentle. Many of the bagged commercial soils contain lumber industry waste (a cheap “organic” ingredient) without essential nutrients and microbes. Our compost is certified for food growing by Organic Materials Research Institute (OMRI) and by the U.S. Composting Council (USCC).

6. Adding organic matter regularly: Every fall and spring before planting a new crop spread 2 inches of compost over your raised beds and containers. See our post Putting Your Bed to Bed (for the winter). Add a half to a whole cup of worm castings to seedling holes and short seed furrows. Adding worm castings around plant stems during the growing season is optional. These materials decompose slowly, providing a steady source of food for the microbes. Avoid "miracle" solutions like compost teas, which may offer little benefit compared to simply adding microbe-rich compost directly to the soil. Planting seeds and seedlings blog post.

7. Managing compaction and moisture: To protect the air and water balance that microbes need, avoid compacting your soil. Permanent pathways and mulching help keep the soil structure intact, allowing oxygen to reach the microbes. Additionally, maintain proper soil moisture through mulching and regular watering, but be careful not to over water, as microbes need both air and water to thrive. And never walk on your soil

A Paradigm Shift in Gardening

Transformational gardening requires a shift away from conventional gardening techniques. Instead of focusing on the individual needs of plants, we focus on nurturing the soil. When we feed and protect the microbial populations in the soil, the plants grow naturally strong and healthy.

In conventional gardening, there's often an over-reliance on fertilizers and commercial soils that don’t support microbial life. Our method encourages you to move away from these products and instead focus on building a living soil ecosystem. Avoid bagged soils that contain decomposing wood chips, which consume nitrogen needed by plants. Instead, choose microbe-rich compost that fosters microbial health.

Nurturing Microbes for Soil and Plant Health

At Deep Roots Project, we know that the secret to a thriving garden lies not in what you see above the ground but in the microbial universe beneath it. Our methods emphasize growing soil first and plants second, using the natural power of microbes to create sustainable, vibrant gardens.

By focusing on these principles—no-till practices, biodiversity, 100% compost as soil, and proper soil care—you can unlock the true potential of your garden. Let’s work with nature to build a healthier, more resilient world from the ground up.

Happy Gardening!

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