Santa Fe Extension Master Garden Edition - September 2026

In a soil sample under a microscope, the organisms that matter most are not the bacteria—they are the predators. Bacteria are almost never the problem in degraded soil, even in the worst cases. What is missing are the protozoa, nematodes, and amoebas that eat bacteria and release the nutrients locked inside them. That process—sometimes called the “poop loop”—is what makes nutrients plant-available. Josh Waybright, a soil health specialist and owner of Brightway Agriculture, walked through this on the Santa Fe Extension Master Gardener Edition of the Garden Journal, explaining how gardeners can restore their soil by feeding and protecting the full soil food web.

The soil food web: a predator-prey relationship below ground

The soil food web starts with plants. Using energy from the sun, plants convert atmospheric carbon into sugars and push those sugars down through their roots. This exudate attracts bacteria and fungi to the root zone. In exchange, the microbes weather mineral particles and break down organic matter. Then predators—flagellates, ciliates, amoebas, and nematodes—eat the bacteria and fungi. When they excrete, the nutrients that were held inside the microbial bodies become available to plants. This is the core mechanism: plants feed microbes, and microbes, through predation, feed plants.