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It's All About the Soil Lisa & Kathleen Putnam

Updated: Nov 14, 2019

When we first started gardening, we were concerned about the chemistry of the soil — the amount of nitrogen, phosphorus and potassium in the soil. We soon figured out, though, that the chemistry would take care of itself if we focused on the soil’s biology: the microorganisms, or soil bugs, within. The soil is a living, breathing organism that needs to be nurtured. When you start feeding the soil, instead of the plant, you are well on your way to the foundation of organic gardening.  The Soil Food Web Through photosynthesis, plants convert light energy into chemical energy. That chemical energy is stored as carbon chains in the form of carbohydrates in the plant, especially in the roots. The plant will slough off extra carbohydrates, called exudates, to attract and feed surrounding beneficial microorganisms (bacteria, fungi, nematodes, etc.). In return, the microorganisms feed the plant nutrients. Bacteria are like small bags of fertilizer containing nitrogen, phosphorous, potassium and other trace elements the plant needs to thrive. Fungal hyphae, a structure of hair-like filaments from the fungi, act as root extenders and literally go and find what a plant needs at any given time and bring that nutrient back to the plant. Scientists have found fungal hyphae five miles from a plant they were feeding.

The plants feed the people and the microbes and, in return, the microbes feed the plant. It is a wonderful symbiotic relationship!

How do you feed the soil and not the plant? In your vegetable garden, the best thing you can do for your soil is to feed it a steady stream of high-quality compost and grow cover crops. After you add your compost, cover it up with some mulch, like grass hay or grass clippings. For your perennial borders, put down a 2- to 3-inch layer of wood chips as mulch to protect your soil. This slowly feeds the soil and protects it from the elements.

Cover crops: You always want to have something growing in your soil. As we just learned, the roots of plants feed your soil microbes, so you don’t want fallow/bare soil, which will not support life. Thus, when you are not growing a crop to eat, you should be growing a cover crop. We like to grow legumes as a cover crop, as they add nitrogen to the soil. A legume (fava beans, peas, clover, alfalfa, etc.) will take atmospheric nitrogen and store it in small nodules on its roots, and a microbe will convert the nitrogen into a plant-ready form. This is formally known as nitrogen fixation.

Synthetic fertilizers can provide some of these necessary nutrients, too, however, they ultimately will kill the life in the soil. They also will harm the environment. In addition, plants become dependent on humans (via synthetic fertilizers) to give them the nutrients they need vs. the Soil Food Web naturally providing them with their necessary nutrients.

No-till: If you are interested in sequestering carbon and keeping the carbon in the soil to feed the microbes, the best gardening/farming practice is “no-till.” When you rototill your soil, you slice and dice microbes and you release a lot of carbon into the atmosphere. No-till farming is gaining in popularity as farmers realize the benefits of keeping their soil alive and feeding the microbes as well as reducing the amount of carbon released into the atmosphere.

The DOs and DON'Ts


  • Grow a diversity of plants — this will attract a greater variety of microbes.

  • Feed your soil with compost and keep it covered with mulch — compost is rich with life, which will add more good microbes to your soil. The mulch will keep the microbes safe — it protects them from the beating sun and the compaction of the rain.

  • Rotate crops — this will increase the diversity of the microbes and reduce the chance that a pathogen will take hold; i.e., it reduces the inoculant of the pathogens.

  • Grow cover crops — always grow something in your soil. When you are not growing an edible crop, grow cover crops like fava beans, bell beans, alfalfa, clover, buckwheat, etc. This will keep roots in your soil, which will attract and feed the microbes. If your cover crop is a legume, you have the added advantage that it will fix nitrogen in your soil.


  • Don’t till your soil; it kills the fungal hyphae, destroys soil structure and releases carbon into the atmosphere.

  • Don’t step on your soil or compact it — this reduces oxygen in the soil and suffocates microbes.

  • Don’t over-water — the microorganisms need oxygen as well as moisture.

  • Don’t use chemical fertilizers, pesticides, herbicides or fungicides — these all kill microbes.

By feeding the Soil Food Web you will increase organic matter, soil organisms, water-holding capacity and infiltration, improve soil structure, and most importantly, the soil will feed your plant. Ultimately, this will result in plants that will be super healthy and able to fend for themselves against disease and pests, thereby eliminating the need for pesticides, herbicides, insecticides and fertilizers.

By optimizing soil integrity, more nutrient-dense plants result. Bountiful fruits, vegetables and legumes provide the healthiest way to nourish the human body and improve the health of our planet.


  • The Art of Composting:

  • Soil Solutions to Climate Problems, Narrated by Michael Pollan:

  • Mycelium Running: How Mushrooms Can Help Save the World by Paul Stamets

  • Soil Biology Primer.  Published by the Soil and Water Conservation Society in cooperation with the USDA Natural Resource Conservation Service

  • Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web by Jeff Lowenfels & Wayne Lewis

Lisa and Kathleen Putnam

Lisa has a BS in Agricultural Economics from UC Davis. She also studied nutrition science there. She currently operates a small sustainable organic farm in Woodside and is a lifetime gardener, a UC Master Gardener (1999) and Master Composter (2010). Lisa’s passions are composting and the Soil Food Web. She teaches both summer and winter vegetable gardening at Lyngso, Common Ground and several local garden clubs.

Kathleen is a professional organic vegetable gardener and an ISA Certified Arborist serving the Mid-Peninsula region. She has a degree in Environmental Horticulture from City College of San Francisco and is a UC Master Gardener. She teaches classes about vegetable gardening and fruit tree pruning throughout the Bay Area, at Common Ground, Lyngso, San Francisco Community Gardens, Los Altos Garden Club, Portola Valley Garden Club, San Mateo Master Gardeners and the San Francisco Professional Gardeners Association. 

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