Visualizing Soil Microorganisms via the Contact Slide Assay and Microscopy

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona
Demonstrating Author: Bradley Schmitz

Soil comprises the thin layer at the earth’s surface, containing biotic and abiotic factors that contribute to life. The abiotic portion includes inorganic particles ranging in size and shape that determine the soil’s texture. The biotic portion incorporates plant residues, roots, organic matter, and microorganisms. Soil microbe abundance and diversity is expansive, as one gram of soil contains 10^7-8 bacteria, 10^6-8 actinomycetes, 10^5-6 fungi, 10³ yeast, 10^4-6 protozoa, 10^3-4 algae, and 5³ nematodes. Together, the biotic and abiotic factors form architectures around plant roots, known as the rhizosphere, that provide favorable conditions for soil microorganisms.

Biotic and abiotic factors promote life in soils. However, they also contribute stressful dynamics that limit microbes. Biotic stress involves competition amongst life to adapt and survive in environmental conditions. For example, microbes can secrete inhibitory or toxic substances to harm neighboring microorganisms. Penicillium notatum is a notorious fungus, as it reduces competition for nutrients by producing an antimicrobial, which humans harvest to create the pharmaceutical penicillin. Abiotic stresses arise from physical or chemical properties limiting microbial survival, such as light, moisture, temperature, pH, nutrients, and texture.

1. Soil Slide Microcosm Preparation

Collect garden soil from the surface (0-6” depth), and weigh 150 g soil into two separate cups.
1. If soil has high density of organic matter, weigh 100 g.
Label one cup “Treatment” and the other “Control.”
Calculate amount of water needed to alter moisture content.
1. Moisture content is often close to field capacity.
  
  Log in or to access full content. Learn more about your institution’s access to JoVE content here

Fungi display thick, filamentous hyphae (Figure 2). Actinomycetes display thin, filamentous hyphae. Bacteria display small cocci or rod shapes. They’re often found in clumps, on soil particles, or lining fungal hyphae. Soil particles display irregular, dark shapes (Figure 3).

Figure 2. Contact slide image using 100X objective lens.
Photo courtesy W.H. Ful

The contact slide assay, also referred to as the buried-slide, is a simple technique utilized to qualitatively observe soil biota. This assay qualitatively shows the spatial interactions between fungal hyphae, actinomycete filaments, bacteria, and soil particles. Individuals or industry can employ this assay to gather knowledge on a particular soil’s health in regards to agriculture, gardening, composting, teaching, and studying. However, this technique does not quantify soil micro biota, as it only encompasses a s

Pepper, I. L., & Gerba, C P. 'Contact Slide Assay.' Environmental Microbiology A Laboratory Manual. 2nd ed. Elsevier 19-25 (2004).
Pepper, I. L., Gerba, C. P., & Gentry, T. J. 'Earth Environments.' Environmental Microbiology. 3rd ed. Elsevier 59-88 (2014).
Rossi, G., Ricardo, S., Gesue, G., Stanganelli, M., and Want, T.K. Direct Microscopic and bacteriological investigations of the soil. Soil Science. 41, 52 – 66 (1936).

Transcript