eChapters

4.1 From Soil

Soil contains varied group of microorganisms such as fungi, bacteria, actinomycetes, algae and protozoa. The type of nutrients available, moisture, temperature and pH of the soil determine the nature of microbial population in soil. Different laboratory techniques for isolation of microorganisms have been detailed in chapter-III. These are used in particular for the isolation of specific type of microorganisms. All the techniques adopted are just to segregate the pathogens/ microorganisms from the mixture of microbial population present in nature.

(a) Isolation of Fungi

Soil contains large number of fungi and constitutes a major place of microbial population. They can be isolated in pure form by following the methods given below:

Under natural habitats microorganisms usually grow in mixed populations containing several species. This is really a problem for microbiologists because a single type of microorganism can not be studied adequately in a mixed culture. In laboratories these populations can be separated into pure cultures. The pure cultures contain only one type of organism and are thus suitable for studying the cultural, morphological and biochemical characters of an individual species. In the present days there are several ways of developing pure cultures in laboratories. Some of which are as follows:

Microorganisms, being ubiquitous, are found in soil, air, water, food, sewage, on body surfaces as well as on degrading and decomposing substances. Their survival and continued growth mostly depend on an adequate supply of nutrients and favourable growth environments. The culture media (nutrients) consisting of chemicals support the growth of microorganisms in a given condition. They are devised in such a way that the organism should get all the nutritional requirements. These are usually prepared in laboratory by weighing and dispensing the individual ingredients. Generally, the common media contain both inorganic and organic nutrients; however, for the cultivation of large number of microorganisms, specialized media are required.

Basically the culture media are of three types: (1) Natural, (2) Semi synthetic and (3) Synthetic.

Microbiology is a branch of science dealing with the study of organisms which are too small to be seen clearly by unaided eye. Roughly the organisms with a diameter of 0.1mm or less, which can not be seen by the human eyes unaided, come under the domain of microorganisms.

Thus, the laboratory work dealing with the microorganisms needs special care to avoid infection and infusion for maintaining good health. In fact all microorganisms should be treated as potential pathogens. Thus, for working with microorganisms aseptic techniques must be followed by students as well as by the laboratory assistants and teachers.

Microorganisms live as single cells in nature in association with other cells in assemblage that we call “Population”. Such populations are composed of group of related cells generally derived by successive cell divisions from a single parent cell. The location in an environment where a population generally lives in association with other populations of cells called “Microbial communities”. Environmental microbiology deals with the study of these microbial communities in different habitats, naturally occurring on earth.

Natural habitats of microorganisms are exceedingly diverse. Any habitat that is suitable for the growth of microorganisms can also support the growth of other microorganisms. But in addition, there are many habitats where, extreme environment, due to chemical and physical factors, higher organisms cannot grow but microorganisms can grow and flourish. In this chapter, different habitats of microorganisms are discussed briefly.

Because microorganisms are so small, their habitats are also small. The term microenvironment is often used in ecology to describe where a microorganism actually lives and metabolites within its habitat.

Development of sophisticated procedures for the isolation, manipulation and expression of genetic materials is a field called genetic engineering. Genetic engineering has applications in both basic and applied research. In basic research, genetic engineering techniques are used to study the mechanisms of gene replication and expression in prokaryotes, eukaryotes and viruses. For applied research, genetic engineering used for development of microbial cultures capable of producing valuable products such as human insulins, growth hormones, interferons, vaccines, enzymes etc. The commercial application of genetic engineering is sometimes referred as Biotechnology. In broad sense, Biotechnology refers the use of living organisms to carry out defined chemical processes for industrial application.

The process of isolation, purification and replication of specific DNA fragment is called molecular cloning or gene cloning. Molecular cloning is the base of most of the genetic engineering procedures. The purpose of molecular cloning is to isolate large quantity of specific genes in pure form. Thus molecular cloning is very important in genetic engineering and can be divided into several steps depends on the purpose. The steps are as follows:

The pathogenicity of an organism varies form mild attack to severe fatal attacks. The host has many mechanisms to resist or to avoid the pathogens apart from immune systems. One or few of these will be activated when the pathogen enters into the body. Following are some of the listed natural host defense mechanisms.

Industrial Microbiology is the discipline that uses micro organisms, usually grown on large scale, to produce commercial products or carry out important chemical transformations.

The products derived from such processes are

1 Alcohols and alcoholic beverages.
2 Production of pharmaceutical agents like antibiotics, vaccines etc.
3 Food additives
4 Enzymes
5 Chemicals
6 Single cell proteins

Genetics is the study of what genes are, how they carry information, how their information is expressed, and how they are replicated and passed to subsequent generations or other organisms.

DNA in cells exists as a double-stranded helix; the two strands are held together by hydrogen bonds between specific nitrogenous base pairs: A-T and C-G.

A gene is a segment of DNA, a sequence of nucleotides, that code for a functional product, usually a protein.

When a gene is expressed, DNA is transcribed to produce RNA; mRNA is then translated into proteins. This is also referred as Central Dogma of Life. The DNA in a cell is replicated before the cell divides, so each daughter cell receives the same genetic information.

Sterilization refers the complete removal or elimination of microorganisms from an environment. Physical and chemical agents are available to remove the microorganisms from the environment. Heat, irradiation and filtration are the three physical agents and various chemicals are available for sterilization.

Terms related to control of microorganisms

Cide or cidal means to kill the microorganism (Ex. Bactericidal refers the killing of bacteria).

Static or stasis means inactivation or inhibition, but not killing. They prevent multiplication of the organism. (Ex. Fungistatic refers the inhibition of growth of fungi.).

Sepsis refers break down of a living tissue by organisms and is accompanied by inflammation and pus formation.

Antispetic is an agent applied externally on living tissues to kill or inhibit the growth of the organisms.

Disinfectant is an agent applied externally on inanimate objects (not living tissues) to destroy harmful pathogens in their vegetative stage.

(Antiseptics are milder than disinfectants because to avoid the side effects)

Sanitation refers removal of organisms from a location by cleaning but not by sterilization.

The essential nutrients and their function in microbial cells

Virus can be defined as a genetic element containing either DNA or RNA that replicates in host cells as intracellular parasites but is characterized by having an extracellular state.

Virus can use the metabolic machinery of the host cell and can modify the genetics of the host cell. Virus has both extracellular and intracellular state.

Extracellular State

Outside the host cell, the virus is a minute particle containing nucleic acid surrounded by protein, which is referred as virions or virus particles. Virions are inert and have no biosynthetic and metabolic functions. Extracellular state or virus particle is the perfect stage of virus to study the morphology and chemistry.

Intracellular State

The active state in which the virus replicate in the host cell. When the virus nucleic acid is introduced to host cell and replication starts, the process is referred as infection. The cell in which infection of virus and replication takes place is referred as host cell.

Proto – first; Zoon – animal

Protozoa are single celled eukaryotic organisms, which lack cell wall and ability to move at some stage of their life cycle.

They are referred as the first animals.

There are about 65000 described species grouped into 7 phyla. Among them, 50 per cent are not available as living forms (as fossils) and out of remaining 50%, 22,000 species are free-living and 10,000 species are parasitic forms.

The protozoa are distinguished from other organisms by following characters

Algae are a large and diverse group of eukaryotic organisms that contain chlorophyll and carry out the oxygenic photosynthesis.

Study of algae is referred as phycology or algalogy

They vary from cyanobacteria or blue green algae by their eukaryotic nature.

Eukaryotic, spore – producing, achlorophyllous organisms with absorptive nutrition that generally reproduce both sexually and asexually and whose thallus is usually filamentous, branched somatic structures known as hyphae, typically surrounded with cell wall.

Mycology – Study of fungi

The fungi can be divided into two groups namely

True fungi: Chytridiomycota, Zygomycota, Ascomycota, Basidiomycota

Additional phyla: Myxomycota, Dictyosteliomycota, Acrasiomycota, Plasmodiophoromycota, Oomycota, Labyrinthulomycota, Hypochitridomycoya.

Size – Shapes - Arrangements – Morphology

Bacteria are very small, most being approximately 0.5 to 1.0 mm diameter. Smallest bacteria are Mycoplasmas, as small as 0.2 micrometers (almost as small as largest poxviruses).

Accepted wisdom is that bacteria are smaller than eukaryotes. But certain cyanobacteria are quite large; Oscillatoria cells are 7 micrometers diameter, size of red blood cells. And certain eukaryotes (e.g. Nanochlorum eukaryotum) are very small, only 1 to 2 micrometers, but true eukaryotes (nucleus, chloroplast, mitochondrion are present). So size difference is, like many generalizations, only a useful yardstick, not an absolute truth.

Epulopiscium fishelsoni, discovered in 1985 in intestinal tract of sturgeonfish, is an enormous, cigar-shaped cell, as large as 80 x 600 micrometers (that’s 0.6 mm, large enough to be seen by the naked eye). Amazingly, this cell is prokaryotic! Initial evidence by EM was hard to believe, but confirmed rRNA comparisons with other organisms, a cousin of Gram-positive Clostridium genus.

The relative size of the bacteria are as follows :

Place of Microorganisms in Living World

Haeckel’s kingdom Protista

E.H. Haeckel, 1866 proposed this concept. Apart from plant and animal kingdom, the third kingdom “Protista” was developed by him. The protista includes unicellular organisms that are typically neither plant nor animal. These organisms, the protists, include bacteria, algae, fungi and protozoa. Bacteria are referred as lower protists and others are called as higher protists.

Whittaker’s five kingdom concept

R.H.Whittaker (1969) proposed the concept of five kingdom. He divided the living things in to 5 kingdoms.

Microscope is an instrument to magnify and enable to see the microorganisms by us.

Microscopes are of two types. Light and Electron microscope.

Basic Principles of light microscope

The light is the primary source on which magnification is performed. The magnification is obtained by a system of optical lenses using light waves. These light microscopes can be further classified into

Obviously human have had to deal with microbes even before the recorded history. The first record of human using microorganisms comes from ancient tablets from mid east.

Babylonians were using yeast to make beer over 8000 years ago and acetic acid bacteria to make vinegar over 6000 years ago. About 5000 years ago, Persia (Now Iran) region recorded the wine making.

The Romans had God for specific microorganisms. The roman God of mold and mildew were “Robigus” and “Robigo” which mean crop rust. (Rust is one of the plant disease caused by fungus). God Robigus was very much feared because of crop lost. About 2000 years ago, Romans proposed that diseases were caused by tiny animals. But, fundamentalist religions had a strong hold over the progress. The real microbiology history starts from 1600s, when people began to make crude lenses and microscopes.

The following are the scientists and their role in the development of microbiology:

Microbiology

Study of microorganisms, a large and diverse group of microscopic organisms, that exist as single cell or cluster. It also includes virus, which are microscopic, but not cellular.