Denitrifiers are anaerobic, meaning they are active where oxygen is absent, such as in saturated soils or inside soil aggregates. They are responsible for the characteristically earthy smell of freshly turned, healthy soil. Fungi are more important in degrading these compounds at low pH. A number of antibiotics are produced by actinomycetes such as Streptomyces. Various species of bacteria thrive on different food sources and in different microenvironments. This includes fresh, young plant residue and the compounds found near living roots.
Bacteria are especially concentrated in the rhizosphere, the narrow region next to and in the root.
There is evidence that plants produce certain types of root exudates to encourage the growth of protective bacteria. Bacteria alter the soil environment to the extent that the soil environment will favor certain plant communities over others. Before plants can become established on fresh sediments, the bacterial community must establish first, starting with photosynthetic bacteria. These fix atmospheric nitrogen and carbon, produce organic matter, and immobilize enough nitrogen and other nutrients to initiate nitrogen cycling processes in the young soil. Then, early successional plant species can grow.