Identification of Bacteria, Filamentous Fungi and Yeast Fungi in Soil

Soil is a living ecosystem teeming with multitudes of invisible residents. One cup of native soil supports billions of microscopic organisms, says Colorado State University, including bacteria and fungi. These unseen creatures have great influence on plant growth and can be beneficial, neutral or harmful. Identifying soil-supported bacteria, filamentous fungi and yeast considers form and function of the organisms.

  1. Microbiological Function

    • Symbiotic, antagonistic or innocuous relationships exist between plants and soil microbes. The soil zone surrounding plant roots is the rhizosphere, a highly concentrated area of microbial activity. Plant roots exude nutrients into soil that feed bacteria and fungi. In turn, rhizobial bacteria form nodules on leguminous roots, making nitrogen available to plants. Mycorrhizal fungi colonize roots to assist in the transfer of nutrients from soil to plants. Function helps identify these beneficial microbes and other pathogenic microbes that cause plant diseases.


    • Bacteria are microscopic unicellular organisms having rod, sphere and spiral shapes. The United States Department of Agriculture reports that an acre of soil can contain a ton of bacteria. Identification of bacteria falls into four categories: decomposers, mutualists, pathogens and lithotrophs, or chemoautotrophs. Decomposers break down plant matter and soil-borne pesticides. Mutualists form beneficial nitrogen-fixing root nodules. Pathogens are bacteria that cause diseases, such as fire blight on apple and pear trees. Utah State University lists bacterial fire blight as one of the top 10 pathogenic diseases of woody ornamentals. Lithotrophic bacteria facilitate breakdown of chemical soil pollutants.

    Filamentous Fungi

    • Fungi form two groups: filamentous multi-cellular fungi, or hyphae, and unicellular yeasts. The unique behavior and distinctive cellular organization of filamentous fungi present special challenges in describing their form and function, say microbiologists at Colorado State University. Cytoplasm within their tubular filaments can move in response to environmental conditions, electrical fields, surfaces and gravity. This unusual cellular form distinguishes filamentous fungi from all other soil organisms and enables them to form hyphal networks that are predominantly beneficial to most plants.

    Yeast Fungi

    • Mycologists at A.T. Still University use laboratory tests to identify yeasts. Biochemical tests and growth-behavior tests in broth, serum and on cornmeal agar isolate specific strains of yeast. In 1988, field-grown Walla Walla onions displayed bulb rot. Laboratory tests isolated Kluyveromyces marxianus var. marxianus, the first-reported pathogenic yeast at Washington State University. This finding was significant in helping Washington onion growers distinguish this fungal yeast infection from a similar onion infection caused by bacteria.

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