Soil and Microbes
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.
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