Soil and microbes



The article Soil and Microbes first gives a brief introduction with properties of different soils and their nature. Then the article deals at length about various microorganisms present in the soils, their detection, isolation and their pathogenic effects followed by references.

Soil and Microbes

Different soils such as sandy soils, soils with clay and silty soils have different levels of acidity, alkalinity, solubility and capability to hold or release nutrients. Soils are basically a mixture of minerals and organic materials. The soil properties such as color, texture and organic content may differ as we go deep. Due care should be taken while handling the soil samples collected from different locations. Preliminary examination of the soil samples can be carried out by wetting the soil sample with water and squeezing them between the fingers to ascertain the type of soil, if the soil is sandy it falls apart, silty soil gives a flour type feeling and if the soil has clay then it holds together (Activity #6, Testing for chemicals in soils).

Soil samples may contain microorganisms such as Bacteria, Fungi, Algae, Actinomycetes and Viruses. All the microorganisms may either exist singly or in colonies. There are various techniques to detect form, pattern and arrangement of microorganisms in soil such as Microscopic methods and Microscopic methods plus culturing.

Microscopic methods involve examination of soil samples under a light microscope by using simple stains such as phenol aniline blue and fluorescent stains such as fluorescein isothiocyanate (FITC), acridine orange, rhodamine (fluoresces red), europium chelate (europium (iii) thenoyltrifluoroacetonate), DAPI (4′-6′-diamidino-2-phenyl-indole), ethidium bromide and Hoechst 33258 (bisbenzimide). While the first method can be adopted with any bright field white light microscope assuming that light can be transmitted through the object under examination but in the second method, the stain emits light at a visible wavelength on illumination with ultraviolet light.

In microscopic methods plus culturing the soil samples are impregnated with agar or polyacrylate resins and sectioned into thin plates and examined by direct microscopy.

One more method called the fluorescent antibody technique is the only technique that can locate and identify microorganisms simultaneously in intact soil samples or sections. In this technique the antibodies to microbial cells are generated by injecting the cells under study into a suitable animal (guinea pigs or rabbits) which produce antibodies to the microbial cells that can be isolated from the serum samples of the animals. The antibodies are proteins that can be reacted with FITC to produce FITC-antibody conjugates which will adhere only to the correct microbial cells if applied to a soil sample. Once the excess FITC-antibody conjugate is washed and removed, only those microbial cells will fluoresce, can be located and identified by epifluorescence microscopy. A recent method uses monoclonal or polyclonal antibodies. Certain other methods like Enzyme-linked immunosorbant assays (ELISA assays) and the Polymerase Chain Reaction (PCR) methods can also used to detect the microbes in soils (Source – United Nations Water Virtual Learning Centre).

Isolating bacteria and viruses or virus like particles (VLP) from the soil samples is being investigated through two techniques i.e., Epifluorescence Microscopy [EFM] and Transmission Electron Microscopy [TEM]             using two elution buffers (1% potassium citrate and 10Mm Sodium pyrophosphate) (Sampling Natural Viral Communities from Soil for Culture-Independent Analyses by Kurt E. Williamson, K. Eric Wommack and Mark Radosevich).

Every possible care should be taken to avoid the microorganisms (Bacteria, Fungi, Algae, Actinomycetes and Viruses) to come into physical contact with the human body or enter into human body through inhalation. Proper protective hand gloves and face masks should be worn while working.

Viruses are called obligate intracellular parasites, since they carry nucleic acids and can replicate inside a host cell. Viruses can be classified into DNA viruses, RNA viruses and Retroviruses (RNA). The pathogenic effects of viruses may cause cell death, acute and chronic tissue damage, triggering of an auto immune response and transformation of cells to form tumors (Pathology – Daniel J O’Connor).

Bacteria can be broadly classified into Gram-positive and Gram-negative based on their reaction towards the Gram stain. The pathogenic effects of bacteria are due to the release of toxins called endotoxin and exotoxin causing acute and chronic inflammation and tissue damage (Pathology – Daniel J O’Connor).

Fungal infections may be superficial (i.e., skin, hair, nails and mucous membranes) or systemic (i.e., lungs, brain or heart). The systemic infections are generally found in immunocompromised patients (Pathology – Daniel  Daniel J O’Connor).


Activity # 6 – Testing for Chemicals in Soils. The site address is given below:

United Nations Water Virtual Learning Centre – Biological treatment of Soil & Ground Water – Overview of Soil Microbiology From: Biology 446 – Module 2 – Methods in Soil Microbiology.   The site address is as follows:

Sampling Natural Viral Communities from Soil for Culture-Independent Analyses – by Kurt E. Williamson, K. Eric Wommack and Mark Radosevich, published in APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 2003, p. 6628–6633, Vol. 69, No. 11

Book titled “Pathology” by Daniel J O’Connor – Chapter 4. Infectious Disease, page numbers 29 to 33.

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