Erosion by physical, chemical, and climatic factors combined with the additions of organic matter from animals, plants, and microorganisms living both within and above the earths surface all combine in the natural process that develops soils. With strong influences from the millions of years of geologic changes that have occurred in the region, these soils have developed in the recent past in a semi-arid climate with a grassland/sagebrush steppe vegetation community.
Hard parent material like the basalt layers common to the monument takes many years to break down to soil size particles. The soft tuffs and claystones from ancient volcanic ash erodes more readily, but their chemical properties resist the development of the types of soil needed for plants and microorganisms to become established.
Other factors, such as the 9-16 inch rainfall, put limits on weatherization of parent material and on plant establishment. Steep slopes (2% to 120% on some of the rock outcroppings) allow erosion by water and wind to quickly remove any developing soils to other locales.
The John Day Fossil Beds has many areas in the Sheep Rock and Painted Hills Units of exposed tuffs and claystones that only support a few very specialized plants.
The rest of the monument is covered with healthy native plant communities, each adapted to the soil types, aspects, topography, and availability of water unique to that particular area. These plant communities range from cottonwood/sedge/basin wildrye communities along the rivers edge, to greasewood and saltgrass on the alluvial fans, and to mountain mahogany/Idaho fescue/hedgehog cactus in high elevation rocky outcroppings.
Cryptobiotic crusts comprised of algae, lichens, mosses, microfungi, and bacteria are also important components of many of the plant communities. They are often seen as a black crust or covering on the soils beneath the plants. These small organisms play an integral role in binding and protecting the soils from erosion, in fixing nitrogen for the plants to use, in storing water, and in the nutrient cycling process that further develops the soils.