In this article we have compiled various notes on microbiology. After reading this article you will have a basic idea about:- 1. Meaning of Microbiology 2. History of Microbiology 3. Scope 4. Branches 5. Industrial Microbiology 6. Microbiology of Soil 7. Microbiology of Air 8. Microbiology of Water 9. Microbiology of Animals 10. Medical Microbiology 11. Space Microbiology and Others.
Contents:
Notes on the Meaning of Microbiology
Notes on the History of Microbiology
Notes on the Scope of Microbiology
Notes on the Branches of Microbiology
Notes on Industrial Microbiology
Notes on the Microbiology of Soil
Notes on the Microbiology of Air
Notes on the Microbiology of Water
Notes on the Microbiology of Animals
Notes on Medical Microbiology
Notes on Space Microbiology
Notes on the Microbiology and Origin of Life
Notes on Geochemical Microbiology
Notes on Microbial Fertilizers
Notes on the Principle of Microbial Interaction
Notes on the Future Prospects of Microbiology
Note # 1. Meaning of Microbiology:
Since both the problems of small size and the methods of study and since unrelated microorganisms frequently occupy the same habitat and thus influence each other, it is convenient to study them within the same discipline, i.e., Microbiology. The science of microbiology is the study of microorganisms and their activities.
It is concerned with the form, structure, metabolism, growth, reproduction and identification of microorganisms. It also includes the study of their distribution in nature, their relationship to each other and to other living organisms. For the most part, microbiology deals with microscopic organisms. Microbiologists are those who specialize to work with the microorganisms.
They have been remarkably successful in exploiting the useful microorganisms and combating the harmful ones and have also successfully solved intricate problems of biochemistry and genetics using microorganisms as tool for their study.
Microbiologists may specialize in the study of different groups of microorganisms. For example, Bacteriology is the study of bacteria often broadly designated as Microbiology; Mycology is the study of fungi; Phycology is the study of algae; Protozoology is the study of protozoa; and Virology is the study of viruses.
Although viruses are not cellular organisms, they are included under microbiology for two reasons:
(i) The techniques that are used to study viruses are very similar to those that are applied in the study of microorganisms; and
(ii) Viruses are causal agents of diseases, hence their diagnostic procedures and identification are also similar to employed in the clinical microbiological laboratory as well as the plant pathology laboratory. There may be further specialization in some aspects of above groups of microorganisms; for example, bacterial genetics, bacterial cytology, algal physiology, medical mycology, etc.
Note # 2. History of Microbiology:
Microbiology or study of microorganisms has an interesting past history. During the thirteenth century Roger Bacon suggested that disease is induced by invisible living organisms. Similar suggestion was made by Fracastoro of Verona (1483-1553) and von Plenciz (1762) without any evidence.
But in the mean time in 1658 Kircher designated the disease inducing living organisms as ‘worms’, which according to him are invisible to the naked eye. It was Kircher who first recognized the importance of microorganisms in disease development. But Antony van Leeuwenhoek (1632-1723) was the first person to report descriptions of microorganisms in detail.
His discovery brought inspiration to many workers to take interest in the origin of living things. The concept of origin of animals spontaneously from the soil, plants, or other unlike animals sponsored by Aristotle (384-322 B.C.) was still accepted in the seventeenth century.
In course of time John Needham (1713-1781), Lazaro Spallanzani (1729-1799), Franz Schulze, (1815-1873) and Zheodor Schwann (1810-1882), Pouchet (1859) spoke for and against the theory that living things can originate spontaneously.
Finally Louis Pasteur (1822-1895) through his series of experiments proved his germ theory by establishing the fact that different germs came into the world from their parent germs and germs induce various diseases which was suggested by earlier workers.
He also founded that fermentation of fruits and grains, resulting in alcohol, was brought about by microbes. Today the pasteurization process, widely used in fermentation industries, is the contribution of Pasteur. Pasteur also tackled the problem of anthrax—a disease of cattle, sheep, and sometimes human beings. In the meantime Robert Koch (1843-1910) was busy with the anthrax problem in Germany.
It was he who discovered the typical bacilli responsible for the anthrax disease of cattle and this was the first time a bacterium had been proved to be the cause of an animal disease.
His series of observations led to the establishment of Koch’s postulates:
(i) A specific organism can always be found in association with a given disease,
(ii) The organism can be isolated and shown in pure culture in the laboratory,
(iii) The pure culture will produce the disease when inoculated into a susceptible animal,
(iv) It is possible to recover the organism in pure culture from the experimentally infected animal.
Again the name of Joseph Lister (1878) is associated with the concept on pure culture technique. Lister obtained pure cultures of bacteria and emphasized the importance of growing an organism (bacterium, fungus, alga, protozoan, or higher forms) in an environment free of any other living organism, i.e., pure culture.
The period from 1880 to 1900 was actually a golden time for microbiology when classical contributions were made leading to the establishment of microbiology as a science.
Besides the classical works of Pasteur and Koch, some of the land marks of the history of microbiology are:
(i) Opening of the field of soil microbiology in the late 1880 by the Russian Serge Winogradsky;
(ii) Application pure culture technique in industrial fermentation by Emil Christian Hansen (1842-1909) of Denmark, Adametz (1889) of Austria, and H. W. Conn of the U.S.A. and H. Weigmann of Germany;
(iii) In 1888 the symbiotic relationship between bacteria and leguminous plants was demonstrated by Hellriegel and Wilfarth;
(iv) A famous Dutch microbiologist, Beijerinck (1851-1981) described the usefulness of free-living nitrogen-fixing bacteria (Azotobacter) in promoting soil fertility; and
(v) In the late nineteenth century Burrill, an American scientist working on fire blight of pears established that bacteria cause plant diseases.
Of late, microorganisms have been used as ideal tools to carry out the study of intricate life processes. This has inspired physicists, geneticists, chemists, and biologists to join with microbiologists in what is known as molecular biology.
Mention may be made of some of the contributors and their contributions in microbiology and molecular biology during the period from 1944 to 1975: Avery and associates (1944)—DNA carries genetic information in pneumococcus; Fritzhipman and Hanskrebs (1953) — physiology and metabolism of living cells; Joshua Lederberg, George Beadle, and Edward Tatum (1958)—genera in bacteria and their recombination.
Ochoa and Kornberg (1959) isolated and synthesized RNA and DNA: Robert W. Holley, Har Govind Khorana and Marshall W. Nirenberg (1968)—study of genetic code and its function in protein synthesis; Salvador E. Luria (1969)—functions of organisms in terms of molecular structure including elucidation of enzyme structure and mode of action; Gerald M. Edelman and Rodney R. Porter (1972)—chemical structures of antibodies; Renato Dulbecco; Howward M. Temin, and David Baltimore (1975) — enzymes in RNA tumour virus particles. Microbiologists are also engaged in making valuable contributions in medical science, industry, agriculture and in science in general for the welfare of the human society.
The basic knowledge of molecular biology and genetics accumulated during the past few decades is rapidly being translated into practical objectives and is revolutionizing industrial microbiology.
The most outstanding current development in applied microbiology is the ability to alter an organism’s genetic makeup which is commonly referred to as genetic engineering which area of scientific contribution holds great potential for production of drugs and vaccines, for improvement of agricultural crops, and various other areas.
Note # 3. Scope of Microbiology:
i. Microorganisms and Principles of Biology:
Microorganisms help understanding the various principles of biology as they consist of many characteristics which make them ideal for the investigation of important biological phenomena. The microbial metabolism follows almost the same patterns that occur in higher groups of organism.
We can study the metabolic patterns of microorganisms and other life processes at different stages of their growth and reproduction very easily in comparison to higher organisms. It is because of the fact that the microorganisms require less space and can be conveniently grown in test-tubes or flasks; they grow rapidly and reproduce at an unusually high rate (e.g., certain bacteria reproduce within 20 minutes).
ii. Medical Microbiology and Immunology:
Medical microbiology deals with disease producing organisms in human beings whereas immunology deals with the defense the body puts up against the pathogens, the disease causing microorganisms, and the factors which explain resistance to disease.
The medical microbiology and immunology furnishes the basic knowledge on which depend the practical methods employed for the laboratory diagnosis and prevention of microbial diseases. It, therefore, gives us a sound foundation for the intelligent promotion of both, the individual and the public health.
iii. Soil Microbiology:
Soil microbiology deals with the microorganisms present in, and their role in soil. The most important function of soil microorganisms is to decompose various kinds of organic matter.
Second is the process of mineralization of various organic constituents. Mineralization of organic carbon, nitrogen, phosphorus and sulphur via respective cyclic alterations by soil microorganisms makes these elements available for reuse by plants and other organisms.
As we know, microbes improve the fertility of soil by fixing atmospheric nitrogen into nitrogen-compounds which are readily used by plants to synthesize protein and other complex organic nitrogenous compounds. It is generally true, however, that more the microorganisms there are in the soil, the more productive it is.
iv. Industrial Microbiology:
Industrial microbiology is that branch of microbiology which deals with the utility of microorganisms in industrial production of medicines, food supplements, alcohols, beverages, organic acids, vitamins, enzymes etc. Probably the most significant industrial use of microorganisms was the production of antibiotics, the wonder drugs.
However, some 40 years ago only a small group of microorganisms were conveniently referred to as industrially useful microorganisms. But today it is realized that every microorganism has its own industrial importance. The commercially beneficial activities of a large number of bacteria, yeasts, molds, and algae are being exploited, or deserve to be exploited to obtain valuable products.
v. Food Microbiology:
Food microbiology deals with the emphasis upon the relationship of microorganisms to the manufacture, deterioration and preservation of foods. Since man’s food supply consists basically of plants and animals or products derived from them, it is understandable that our food supply can contain microorganisms in interaction with food.
To ensure that food is free of harmful microorganisms and is safe for human consumption, it must be carefully prepared, processed, and stored. Besides, many other microorganisms are of great use to humans because the fermentation of various raw materials by them result in food like oriental foods, bread etc.
vi. Milk and Milk-product Microbiology:
This branch deals with the microorganisms present in and their role in milk and milk-products. Milk is an excellent food for humans or microorganisms. The milk, when it leaves the udder of a healthy cow, contains more or less no microorganisms. It generally becomes contaminated in handling and processing.
Therefore, if it is not properly stored and treated, the microorganisms grow rapidly and spoil and make it unsafe for human consumption. Besides, some microorganisms are used in the manufacture of various milk-products such as cheese, butter etc.
vii. Water Microbiology:
Water has curious and unusual properties, and plays an important role in living systems. The natural source of water is precipitation. As the water precipitates it picks up airborne microorganisms.
When it comes in contact with the soil, other microorganisms get into it from the soil, sewage, organic wastes, dead plants and animals. Therefore, water for human use must be made free from microorganisms by filtration and/or chemical treatment to avoid harm.
viii. Sewage Microbiology:
Raw sewage generally contains millions of microorganisms per millilitre. Many of them are pathogenic, bad odour and taste producing. It is essential that the sewage be treated to remove pathogenic and offensive odour and taste causing microorganisms. This is done by chemical treatment and oxidizing organic material and destroying pathogenic microorganisms.
ix. Air Microbiology:
Although there may be a variety of microorganisms in the air, their number is affected because the air does not contain adequate source of nutrients. The room-air is generally contaminated by sneezing, coughing and talking. The airborne microorganisms give rise to serious problems in scientific experiments via contaminating the equipment’s, materials etc.
They spoil our food and food-products, and they, most significantly, are responsible for many diseases in plants and animals including humans. Therefore air, particularly room-air, must be sanitized by mechanical and chemical treatments to destroy harmful microorganisms.
x. Genetic Engineering:
Genetic engineering deals with the manipulation of genes under highly controllable laboratory conditions. This newly born technique has attracted the attention of microbiologists and is being applied in the food and drug industries, waste disposal, medicine, agriculture, oil pollution, and others.
xi. Microorganisms in Oil Recovery:
Xanthan gum is a polysaccharide produced by the bacterium Xanthomonas campestris. This gum is an inert compound which thickens water and improves its ability to drive out oil trapped underground. When mixed with drilling muds, this gum also serves as a lubricant for the giant drills as they penetrate the rock.
xii. Microorganisms and Energy:
Microbial processes constitute a useful, though unconventional source of energy, especially in developing countries. At present, many microorganisms are being exploited, or being thought to be exploited, as alternative sources of energy.
Biogas is a good example. Alcohol produced by microbial fermentation is added to petroleum products to supplement the scarce fuels. Microorganisms synthesize hydrocarbons and oxygenated hydrocarbons either of which may serve as liquid fuel.
xiii. Microorganisms and Mining:
Deposit of many important high grade ores are diminishing at an alarming rate, and traditional methods of mining low grade ores are often prohibitively expensive. Microbial mining may provide a viable alternative in some cases such as copper and uranium.
Note # 4. Branches of Microbiology:
Microbiology is not a mere study of the structural diversity and classification of microbes, but encompasses the whole gamut of microbial life. The knowledge of the various aspects of microbes has been accumulating since the last century and has become so vast that no microbiologist can claim familiarity with all aspects of the subject.
The various aspects of microbiological study can be divided basically into the following branches:
i. Aero-microbiology:
Dispersal of disease causing microbes through air, microbial population in air, their quality and quantity in air comes under the preview of this branch.
ii. Agricultural Microbiology:
In this branch, the role of microbes in agriculture is studied from the point of view of both harm and usefulness. Many microbes—fungi, bacteria and viruses—cause a number of plant diseases. From the point of view of benefit—N2 fixing activity, use of microbes as bio -fertilizers and several other aspects are studied.
iii. Aquatic Microbiology:
Microbiological examination of water, water purification, biological degradation of waste are studied in this branch.
iv. Bacteriology:
This is the largest group among microbes not only in number but also in importance. Bacteria of both kinds—eubacteria and cyanobacteria (also known as blue green algae)—are studied here. Bacteria have a profound influence on various human endeavours including health, industry, agriculture, etc.
v. Biotechnology:
This is the most significant branch which may even change the course of life as we know today. Microbes are used as gene carriers to deliver specific genes to function in a different environment. New, genetically engineered microbes can produce drugs (human insulin), or in agriculture-N2 fixing ability may be transferred to all the plants. The potentialities of biotechnology are immense.
vi. Environmental Microbiology:
This is one of the most important branches of microbiology. The role of microbes in maintaining the quality of the environment is studied in this branch. Microbial influence in degradation and decay of natural waste; their role in biogeochemical cycles are all studied.
Some of the recent researches have shown that certain bacteria can help in cleaning the oil spill, and this gives added significance to the study of environmental microbiology.
vii. Food and Dairy Microbiology:
Various aspects such as food processing, food preservation, canning, pasteurization of milk, study of food borne microbial diseases and their control is studied.
viii. Geochemical Microbiology:
Role of microbes is coal, gas and mineral formation, prospecting for coal, oil and gas and recovery of minerals from low grade ores using microbes, is included here.
ix. Immunology:
Studied in this branch are the immune responses in organisms. How toxins are produced? How the antigens influence the formation of antibodies? How protective vaccination helps in combating the diseases? How immune system collapses (as in AIDS), are some of the questions for which immunology as a branch of microbiology is trying to find out answers.
x. Industrial Microbiology:
The role of microbes in Industrial Production is studied here. Many microbes produce industrial alcohols and acids as a part of their metabolism. The study of fermentation by microbes has contributed a lot to alcohol manufacturing. Breweries have greatly benefitted by understanding the role of specific microbes in fermentation.
xi. Medical Microbiology:
This branch deals with the pathogenic microbes—their life-cycle, physiology, genetics, reproduction, etc., Many of the microbes also provide remedies for microbial diseases. All these aspects are studied in this branch. Some of the diseases like tuberculosis, leprosy, typhoid, etc. are caused by microbes, and cure for them is provided by other microbes in the form of antibiotics.
xii. Mycology:
The study of eukaryotic, achlorophylous organisms generally referred to as fungi is included in this branch. Some of the common fungi are yeasts, moulds, mushrooms, puffballs, etc. Fungi are not only harmful but beneficial also.
xiii. Phycology:
Deals with the study of autotrophic eukaryotic organisms. Members are generally called algae. Algae include both microscopic as well as macroscopic members. Only the microscopic algae are studied as a part of microbiology.
xiv. Protozoology:
Study of Protozoans in all their aspects comes under the preview of protozoology. Protozoans are known to cause many diseases like malaria, amoebic dysentery, sleeping sickness, etc.
xv. Virology:
Viruses are neither eukaryotic not prokaryotic. In fact, they are on the border line between living and non-living. Viruses cause disease to plants and animals including human beings. The dreaded AIDS is also caused by a virus.
Note # 5. Industrial Microbiology:
Microorganisms were used in industrial processes even before their existence was known. The production of fermented beverages and vinegar, and the baking of bread are all traditional processes which have come down to use from time immemorial.
From an industrial view point the substrate in which microorganism is grown is regarded as raw material and the microorganism as the “chemical factory” since it converts the raw material into new products.
The microorganisms possess three outstanding qualities:
(i) Rapid growth in large quantities in suitable organic substrate,
(ii) Maintain physiological constancy of growth to produce approximate amounts of products, and
(iii) Can convert cheap raw materials into useful products.
This is why they have been exploited on commercial scale to obtain valuable products like alcoholic beverages, food supplements, medicine, organic acids, enzymes, etc. Microorganisms that are chiefly employed in various industrial processes include fungi (yeasts and molds) and bacteria. Again production of bacteria and viruses on a commercial scale for the preparation of vaccines is also one of the industrial processes.
Industrial microbiology may be grouped in the following manner:
I. Alcoholic Beverage Industry:
One of the oldest and largest microbial industries is the production of ethyl alcohol from carbohydrate materials by fermentation process. This process is used by brewers of malt, beverages, distillers, wine makers, and many others. Starches and other complex carbohydrates are used as raw material which should be hydrolyzed to simple fermentable sugar.
The source of raw material may be molasses, sugar beets, grapes, etc. The hydrolysis can be accomplished with enzymes from molds or by heat treatment of acidified material.
Strains of Saccharomyces cerevisiae are used for fermentation. They must be vigorously growing with high tolerance for alcohol having a capacity for producing a large yield of alcohol. Next to the production of ethyl alcohol is the production of alcoholic beverages—beer, wine, run, whisky, and gin.
Beer is prepared from barly malt by using strains of S. cerevisiae or S. carlsbergensis, rum and whisky are prepared from molasses and maize starch respectively by using strains of S. cerevisiae, and wine from grape juice by using strains S. ellipeoideus.
II. Bakery Industry:
Pure cultures of selected strains of Saccharomyces cerevisiae (bakeries’ yeast) are mixed with bread dough to bring about desired changes in texture and flavour in the bread. Bakers’ yeast has the ability to ferment sugar in the dough vigorously and to grow rapidly. The carbon dioxide produced during fermentation is responsible for the rising of the dough.
III. Food supplements Industry:
In recent years various microbial proteins (single-cell protein) are produced by using waste hydrocarbon from industrial wastes. These proteins are useful for animal feed. Yeasts, molds, bacteria and algae are used for this purpose. Of all these organisms, yeasts are better suited for single-cell protein extraction.
Mass cultivation of these organisms offers a food supplement for animals bridging ‘the protein gap’. Methophilus methylatrophus acted upon methyl alcohol derived from oil and natural gas treated with various chemical substances produces large quantities of protein from the substrate. Such proteins are used to produce a milk substitute for calves, thus releasing more cow’s milk for human consumption.
IV. Pharmaceutical Industry:
Most important aspect of this category is the production of antibiotic substances used for the therapeutic purpose by utilizing the source of microorganisms belonging to the groups of Fungi (molds) and Bacteria. Penicillin was the first antibiotic to be produced commercially.
The remarkable chemotherapeutic effectiveness of penicillin was demonstrated by Florey and Chain during 1939 and 1941 and subsequently due to pressure of war yield of penicillin was increased may times.
Initially Penicillium notatum was used for penicillin production, but in course of time a better penicillium-producing species P. chrysogenum was isolated. Besides penicillin, tetracyclines are produced by using Streptomyces rimosus and S. aureofacieus. In addition to these, various other antibiotic substances are prepared commercially.
V. Industrial production of Acids and Enzymes:
(a) Citric acid is an important chemical used in medicines, flavouring extracts, food, manufacture of ink, and engraving. It is manufactured industrially by converting sugar (molasses) to citric acid by Aspergillus niger incorporated in a medium containing inorganic nitrogen compound and inorganic salts under aerobic condition.
(b) Perhaps the most famous of all industrial fermentations is that of acetone- butanol production by Clostridium acetobutylicum needed for the manufacture of cordite.
(c) Enzymes (amylases, invertase, proteases, and pectinase) synthesized and excreted in large quantities by species of Aspergillus, Penicillium, Mucor and Rfuzopus are industrially purified and used in the processing or refining of variety materials for example, amylases and pectinases in clarifying fruit juices, proteases used for treatment of hides to provide finer texture and grain.
(d) Lactic acid essential for food and pharmaceutical industries is prepared from hydrolysed starch with barley, molasses with nitrogenous material by the use of Lactobacillus delberueckii.
(e) Vinegar, Cider vinegar, apple vinegar are the various types of vinegar that are prepared by fermenting fruit juices, sugar containing syrups and starchy materials with Acetobacter.
(f) In paper industry, paper manufacture involves: the physical or chemical treatment of cellulosic material (e.g. wood, cotton, etc.) for separating and purifying the cellulose, fibres; and fabrication of the resulting fibrous pulp, after further refinement for redeposition of the fibres in the form of sheet. Microbes play a vital role in the paper industry for the preparation of paper-pulp slime.
VI. Industrial production of Vaccines:
Certain groups of microorganisms (bacteria and viruses) are put to large scale cultivation for the commercial production of vaccines.
Note # 6. Microbiology of Soil:
Early work in soil microbiology was almost entirely confined to the study of soil bacteria. The poioneer workers of the late nineteenth century in this line are: Beijerinck and Winogradsky. But it was not until about thirty years later that comparable interest was shown in the soil fungal flora and its activities. The soil micro- fauna was neglected for even longer and only recently attention has been drawn in the” soil algae.
Soil, water and air which contain living organisms are collectively known as biosphere. It is produced due to interaction of parental material (rock itself), climate, age, and growth and interaction of microorganisms.
Soil is an excellent medium for the growth of microorganisms which include bacteria, fungi, algae, protozoa and various insects whose number and kinds in the soil depend mainly on the nature and depth of soil, seasonal condition, state of cultivation, temperature, amount of organic matter, moisture content and aeration.
A fertile soil has various components—mineral materials, organic materials and organisms. The mineral materials are derived from the parent rock by weathering to which organic materials are added from plant and animal sources. The organic materials are always associated with soil organisms.
The amount of the above components in the soil varies greatly from one situation to another. The organic materials are incorporated into the soil by the action of soil organisms and if it is not first oxidized, is converted to humus—the dark amorphous colloidal material.
Assessment of microbial population:
The complexity of soil environment and the diversity of its population make sampling and assessment of the microbial population very difficult. There are three main methods: cultural studies, direct examination, and activity measurement. No information on the species of organisms is obtained by these methods.
Cultural studies however, permit identification of the isolates though not very satisfactory for fungi. Direct examination method is time consuming and it is difficult to locate and count organisms in opaque soil. Activity measurement study is even more difficult and inconclusive.
Although bacteria are more numerous than any other group of organisms, the biomass of the fungi is larger than that of bacteria and also the combined biomass of protoeoa, nematodes and other soil animals are quite different.
Interaction and distributional pattern of microorganisms:
The behaviour and distributional pattern of microorganisms depend on the nutrients available, temperature, moisture, gas content, pH, and depth of soil. Generally there is decrease in numbers with depth.
a. Interaction among microorganisms:
The microorganisms that inhabit the soil exhibit different types of associations or interactions which depend upon the biotic and abiotic components of soil. An association is neutral when two different species of microorganisms occupy the same environment without affecting each other without producing metabolic end products that are inhibitory.
When an association involves symbiotic relationship between two species, it is mutualism. The benefits derived by the associated organisms are extremely variable. An association involving the exchange of nutrients between two species is syntrophism.
Again a relationship between organisms in which one partner receives benefit, the other is not affected. Such a relationship is designated as commensalism encountered in association between fungi and bacteria, where fungi breakdown cellulose to glucose.
Many bacteria are unable to utilize cellulose, but they utilize the fungal breakdown products of cellulose. The association is said to be antagonism when one species affects the environment for another species by producing antibiotics or other inhibitory substances. There may be competition among species for essential nutrients. The best adapted microbial species will predominate eliminating other species.
A relation between microorganisms may also be parasitic when one organism lives in or on another organism encountered in case of Gram-negative bacteria Bdellovibrio bacteriovorus which is widespread in soil and sewage. Again viruses which attack bacteria, fungi, and algae are intracellular parasites.
b. The Rhizosphere:
Plant roots cause an increase in the population of microorganisms in the soil adjacent to them. The region of soil under the influence of roots is the rhizosphere, where many types of reactions occur. The influence of the root effects on the soil population and is expressed as the R/S ratio, that is, the number of organisms in rhizosphere soil as compared with the number of the same in soil beyond the influence of the roots.
R/S values of over 100 are sometimes known for some bacteria. In genera’, bacterial response to the rhizosphere condition is greater than that of other groups of microorganisms. Again with a high bacterial response the R/S ratio for protozoa is also high. But fungal population increases only slightly in the rhizosphere.
As a whole the micro-flora benefits from the presence of plant roots in the soil. Again micro-flora also influences plant root branching and root hair production.
c. Distributional pattern:
A general account of the distributional pattern of the microorganisms is given below:
i. As to the bacterial types, members of the genera Pseudomonas, Achromobacter, and Bacillus are found in most aerobic soils; where conditions are anaerobic, Clostridium spp. occur.
But when suitable substrates are added to the-soil, a multiplication of chemoautotrophic organisms such as the nitrifying bacteria—Nitrosomonas and Nitrobacter and the sulphur oxidizers of the genus Thiobacillus takes place. Organisms whose numbers increase in this way as a result of special soil conditions may be regarded as showing a zymogenous (fermentative) response.
ii. Most actinomycetes are soil inhabitants. Their numbers increase with the warmth of the climate and decrease with depth of the soil. They breakdown the residual nutrients remaining in the soil.
iii. Isolation experiments suggest that in general, species of Mucor, Penioillum, Trichoderma, and Aspergillus predominate and those of Rhizopus, Zygerhynchus, Fusarium, Cephalosporium, Cladosporium, and Verticillium are also often present in the soil. Addition of organic matter to a soil stimulates the growth of fungal flora in soil in the same way as it does the zymogenous bacterial population.
The fungal population of arid environments is greater than that of bacteria. Majority of filamentous fungi are aerobes and their mycelium is interwoven among the soil particles and it binds these together, thus improving the texture of soil. Again the major part of the fungal flora occurs in the upper soil horizons where there is most organic matter.
iv. Algal species living in soil include flagellate, coccoid, or filamentous ones. Some of the common algae are: Oscillatoria, Nostoc, Anabaena, Cylindrospermum, Chloro- coccum, Chlorella and certain diatoms (e.g., Hantzschia and Navicola). The growth of soil algae affects the surface soil by depletion of some nutrients. The algal biomass on surface soil is great.
v. The soil fauna contains numerous protozoa and representative of metazoa. The smallest species, protozoa and nematodes are widely distributed in the soil. The former generally occur in the water film surrounding soil particles and the latter usually in the soil of the upper horizons among plant roots.
The more microorganisms there are in the soil, the more productive it is. These soil inhabiting microorganisms play important roles in the soil.
Some of them are:
(a) Decomposition of organic matter, transformations in the soil and maintenance of soil fertility balance;
(b) Improvement of soil fertility, reclamation of barren soil and check soil erosion; and
(c) Biological control of diseases and afforestation.
Decomposition of organic matter and transformations in soil:
The soil population is responsible for the removal of natural litter from the surface of the earth and also for transformations which are important for continued soil fertility. The natural litter comprises of complex organic residues of plant and animal remains which are chiefly different forms of carbohydrates, proteins, fats, waxes, etc.
They are attacked by soil microorganisms which serve as biogeochemical agents for this conversion into simple inorganic compounds or into their constituent elements. The overall process is called mineralization. It provides for the continuity of elements (or their compounds) as nutrients for plants and animals including humans.
Since the constituent elements of carbohydrates, proteins, fats, etc. cannot be utilized by plants or animals in the elemental form, microorganisms through various cycles of transformations (Nitrogen Cycle, Carbon Cycle, Sulphur Cycle, Oxygen Cycle etc.) convert them into complex forms.
Nitrogen Cycle is the one in which free molecular Nitrogen of the atmosphere passes through a cycle of transformations mediated by microorganisms to fixed inorganic Nitrogen, to simple organic compounds, to complex organic compounds in the tissues of plants, animals, and microorganisms. Eventually this Nitrogen is released back to the atmosphere through microbial action.
Microorganisms thus perform an essential role in maintaining a cyclic process for the reutilization of elements under natural conditions. The predominant microbial types involved and the rate of attack depend on the chemical nature of the residues, the environmental conditions and the nature of the underlying soil.
For example, nitrogenous materials are generally degraded more rapidly than residues with high C: N ratios. Of the environmental conditions, moisture is particularly important as in dry conditions the attack will be slow. Temperature also affects the rate of degradation and the composition of the attacking flora. Again the underlying soil determines to a large extent the microbial population available for degradation.
Proteins, nucleic acids, purine and pyrimidine bases, and amino sugars represent the complex organic nitrogenous substances which are deposited in soil in the form of animal and plant wastes or their tissues. Synthetic processes of microorganisms also contribute some amount of complex organic nitrogen compounds.
The nitrogen that is locked in proteins is not available to plants as a nutrient. Hence to set free this organically bound nitrogen, enzymatic hydrolysis of protein—proteolysis must take place.
This is accomplished by microorganisms capable of converting protein to smaller units—peptides with the help of enzymes—proteinases. The peptides are attacked by enzymes peptidases resulting in the release of amino acids. These proteolytic enzymes are produced by Clostridium histolyticum and C. sporogenes and species of the genera
Proteus, Pseudomonas, and Bacillus; and many fungi and actinomycetes. The amino acids are degraded by microbial attack to produce ammonia, a process known as ammonification. Ammonia being volatile, some portion leaves the soil and the rest is solubilized to form NH4+ which is utilized by plants and. microorganisms and, under favourable conditions is oxidized to nitrates by nitrifying bacteria by a process referred to as nitrification.
This happens in two steps:
(i) Oxidation of ammonia to nitrite by ammonia-oxidizing bacteria and
(ii) Oxidation of nitrite to nitrate by nitrite-oxidizing bacteria.
Ammonia oxidizers are:
Nitrosomonas europaea, Nitrosovibrio tenuis, Nitrosococcus nitrosus, and Nitrosococcus oceanus; and nitrite-oxidizing bacteria are: Nitrobacter winogradskyi and Nitrospina gracilis.
Again under anaerobic conditions, in waterlogged soil heterotrophic bacteria convert nitrates into nitrites or ammonia, the process known as denitrification, an undesirable process which results in loss of nitrogen from the soil declining nutrient level for plant growth.
Besides these, the microorganisms also convert atmospheric molecular nitrogen into ammonia by a process known as nitrogen fixation.
They belong to two groups:
(i) Symbiotic microorganisms, those living in roots of plants; and
(ii) Nonsymbiotic microorganisms, those living freely and independently in the soil.
During bacterial nitrogen fixation the nitrogen fixing enzyme—nitrogenase enzyme complex characterized by two components which react together along with a strong- reducing agent—ferredoxin or fiavodoxin and ATP.
Symbiotic nitrogen fixation is accomplished by bacteria of the genus Rhizobium in association with leguminous plants with some degree of specificity between the bacteria and legumes. Again non-symbiotic nitrogen fixation is done by Clostridium pasteurianum and species of the genus Azotobacter.
Although green plants and algae are the most important agents of assimilation of carbon dioxide present in the atmosphere or dissolved in water, bacteria are also capable of synthesizing organic matter from inorgaic carbon through Carbon Cycle. The organic carbon compounds so formed are deposited in the soil due to annual litter fall and death of different groups of plants and animals.
They are degraded by microbial activity. The end product, carbon dioxide, is released into the air and soil.
The micro-flora is responsible for the evolution of 95 per cent of carbon dioxide and animals are only 95 per cent. Most of the microorganisms involved in the carbon cycle in terrestrial environments are heterotrophic. Some portion of carbon contained organic residues is incorporated in microbial tissues which themselves will eventually be decomposed.
The remainder is incorporated into humus—the dark-coloured amorphous organic material which is important for soil fertility. The soil fauna is also associated with humus formation. The humus is not a single chemical substance, it is essentially polyphenolic in nature and contains some amino acids and amino sugars. Bacteria and fungi are the principal microorganisms that degrade organic carbon compounds.
The most abundant organic material in plants is, cellulose which is readily attacked by bacteria and fungi. During cellulose decomposition fungal hyphae rapidly colonize the surface of the organic residues and hydrolyse cellulose. Some of the genera of fungi taking part in the process are: Botryotrichum, Chaetomium, Humicola, Stachybotrys, and Stysanus.
After a few weeks the mycelium dies off and there appear bacteria and animals to cause decomposition and degradation of these organic materials. The initial enzymatic attack by enzyme cellulase splits cellulose to cellobiose. Again cellobiose is split to glucose by the enzyme β-glucosidase; glucose is metabolized readily by many microorganisms.
Complete oxidation yields carbon dioxide and water. Similar degradation paths occur for the other plant tissue substances such as hemi- cellulose, lignin and pectin. Carbon dioxide may also originate from the decarboxylation of amino acids, as well as from the dissimilation of fatty acids. All of these transformations may occur in the soil.
Sulphur in its elemental form cannot be utilized by plants or animals. It passes through a cycle of transformations like nitrogen and carbon mediated by microorganisms.
Many of the microorganisms taking part in the Sulphur Cycle are not active in the soil, e.g., the photosynthetic bacteria involved in the oxidation of sulphides. In most agricultural soils sulphur is present in sufficient concentrations to meet the requirements of the soil population and crop plants.
This supply is derived from the parent rock, from organic residues and from volatile compounds in the industrial regions. Microorganisms are, as a group, more versatile and can utilize most of the sulphur compounds and are instrumental in making sulphur available to higher plants in a utilizable form.
Again some microorganisms oxidize and others reduce various sulphur compounds. Thiobacillus thiooxidans, an autotroph can oxidize sulphur to sulphate which is assimilated by plants and is incorporated into sulphur-containing amino acids and then into proteins.
Whereas, members of the genus Desulfovibrio are responsible for reducing sulphate in the soil. In water-logged paddy field soil where anaerobic conditions prevail, they are responsible for the generation of hydrogen sulphide which may damage the roots of rice plants growing there. They are also responsible for causing extensive erosion to underground iron pipes.
Again degradation of proteins liberates amino acids, some of which contain sulphur. This sulphur is released from amino acids by enzymatic activity of many heterotrophic bacteria.
Examples of bacteria involved in the sulphur cycle in various ways are: species of the genus Desulfotomaculum; purple and green sulphur bacteria Chromatium and Chlorobium; nonsulphur purple bacteria Rhodospirillum, Rhodopseudomonas and Rhodomicrobium.
Trace elements (e.g., Zn, Cu, Co, etc.) are released by microorganisms during decay and their uptake by higher plants can be affected by bacteria growing on the root surface. Some of the bacteria taking part in the above process are: Pseudomonas, Corynebacterium, and Flavobacterium.
The metabolic activity of the microorganisms also solubilizes phosphate from insoluble Calcium, Iron, and Aluminium phosphates. Phosphates are released from organic compounds such as nucleic acids by microbial degradation. Bacteria change insoluble oxides of Iron and Manganese to soluble ferrous and manganous salts. The reverse is also possible.
Thus it is apparent that microorganisms perform numerous and essential functions that contribute to the productivity of soil.
The wide-scale application of herbicides and pesticides for improving crop yield produces certain side effects which need careful consideration and fruitful solution. These substances when deposited in soil cause destruction of soil microorganisms, they run off with rainwater and thereby also cause pollution to streams and rivers and as such affect aquatic flora and fauna.
Improvement of soil fertility and other aspects of soil:
Blue-green algae— Oscillatoria princeps; O. formosa; species of Anabaena; Spirulina; Nostoc; Cylindrospermum increase soil fertility by fixing atmospheric nitrogen. Besides this, blue-green algae are also used in the reclamation of barren and alkaline soils.
Both blue-green and green algae which grow on soil surface check soil erosion preventing the upper fertile layer of soil from getting washed during rainy season and thereby playing an essential role in agricultural soil improvement.
Biological control of diseases and afforestation:
Soil microorganisms like Arthrobotrys oligospora, Dactylella cinopaga are very effectively utilized to catch and destroy nematodes in the soil as a programme of biological control of diseases of agricultural crops.
Besides these, mycorrhizal fungal microorganisms associated with the roots of forest trees, e.g., Boletus subtomentosus with Pinus montana and Lactarius deliciosus with Pinus sylvestris increase the absorption surface and absorption rate of various minerals and also make them immune to the attack of diseases. This group of microorganisms is profitably utilized in afforestation programme.
Note # 7. Microbiology of Air:
The atmosphere of the earth contains many particles of solid matter, a large proportion of which being of biological origin. Most viable air born<; particles are spores of different organisms which are to some extent suited for survival in such an environment.
Not only spores of fungi, myxomycetes, bryophytes and pteridophytes, but also pollen grains, moss gemmae, propagules of lichens, cells of algae, vegetable cells and cells and spores of bacteria, cysts of protozoa, and virus particles may occur in the air and constitute the air spora which pollute the air we breathe.
Spores remain suspended in the air for as long as their fall speeds are less than the speeds of frequently recurring upward air currents.
Air borne microorganisms constitute mainly viruses (influenza, measles, etc.); bacteria (species of Streptococcus, Mycobacterium, Corynebacterium, etc.) and spores of Ther- moactinomyces vulgaris and Micropolyspora faerti; and spores of fungi (Aspergillus fumigatus, Cladosporium herbarum, etc.).
They are responsible for various diseases (pulmonary or otherwise) of humans. It is essential to study the nature, origin, and behaviour of the aerial microorganisms to prevent the incidence of the diseases induced by them.
Source and distribution of air spora:
Most of the air spora derives from the surface of vegetation or vegetable debris above ground level or dust. True, numerous organisms expell their spores forcibly for distances ranging from a few to many millimetres by active mechanisms, but most air borne microorganisms have no special structures to facilitate their dispersal into the atmosphere.
They are dependent on physical disturbance for their take-off and dust serves as vehicle of air borne contamination.
Nature of air spora:
The nature of air spora is extremely variable as it is governed by various physical and physiological factors.
(i) Air spora in external air:
Air spora constituting fungal spores near ground level display a diurnal periodicity. Spores of yeasts are most abundant in the air spora before dawn, spores of Phytophthora infestans late in the morning and spores of Cladosporium, Alternaria, and Ustilago in the afternoon.
Often after rain near the ground level—wet-air-spora is rich in basidiospores and ascospores which is replaced by dry air spora which consists of pollen grains and dry spores of powdery mildews, Alternaria, smuts and rusts.
Air borne fungal spores are responsible for pulmononary disease. These spores are derived from moldy crains, straw, damp vegetation and compost heaps. Aspergillosis in pigs develops through straw contaminated with Aspergillus fumigatus which can also produce many human diseases.
Spores of the fungus Cladosporium herbarum, thermophilic actinomycetes, e.g., Thermoactinomyces vulgaris, and Micropolyspora faeni and pollen grains penetrate deeply into the respiratory tract producing allergic symptoms in man. Besides these, there are many more bacteria whose spores contribute to form air spora in the external air and when inhaled cause serious diseases.
(ii) Air spora inside buildings:
The microbial content of the air inside buildings may include viruses, pathogenic and nonpathogenic bacteria and fungi. Many viruses including those of influenza, the common cold, measles, smallpox, etc. are dispersed by air and may produce infection when inhaled. Endospores of the genera Bacillus and Cladosporium, especially CI. perfringens, are commonly found in occupied rooms, hospital wards.
Rhodotorulla and other yeasts, and spores of the species of Apergillus, Penicillium, Mucor and other molds are commonly present. These may contaminate food and moist perishable organic materials, such as leather, and inhalation may cause respiratory infections of man and animals and allergic reactions, such as asthma.
In buildings housing animals, the air pollution is particularly high owing to the presence of hay, straw or other fodder, bedding and dried excreta and contamination from animal coats. The spores of Aspergillus fumigatus have been found in 80 per cent or more of samples of dust examined from city houses. When inhaled there is development of aspergillosis of lung. Some of the air borne bacterial pathogens
include the organisms causing tonsillitis (Streptococcus pyogenes); tuberculosis (Mycobacterium tuberculosis); diphtheria (Corynebacterium diphtheriae); and Q-fever (Rickettsia burnetii). The denser particles settle rapidly but of lighter ones remain suspended permanently.
The dry sweepings of floors, the dusting of objects, shaking clothes, making beds, movement of people and droughts can break up the original substrates into finely divided particles or disturb settled dust and cause it to become air borne.
Survival of air spora:
The survival of air borne microorganisms depends on many factors. Spores which can tolerate dehydration will survive longer than vegetative cells. The length of the survival of all microorganisms is increased in humid atmospheres away from the bacteriacidal rays of sunlight which penetrate glass windows to only a limited extent.
Microorganisms as air purifiers:
Large number of microorganisms work as air purifiers-forming one of the active components of ecosystems in nature.
For example, photosynthetic bacteria (Chromatium sp., Rhodospirillum molischianum, etc.) with bacteriochlorophyll; and blue-green algae and green algae with chlorophyll convert atmospheric carbon dioxide to various forms of carbohydrate and thereby purify air, maintain gas equilibrium taking part in the ecosystem in the nature.
Note # 8. Microbiology of Water:
Microbiology of water comprises the study of nature, distribution, and activities of microorganisms in fresh, estuarine, and marine waters. The earth’s moisture is in continuous circulation. This process of circulation of moisture is known as water cycle or hydrologic cycle which has different stages atmospheric, surface, and ground water.
The volume of moisture and the nature of microorganisms in each stage are extremely variable. The microbial flora of atmospheric moisture is contributed by the air along with particles of dust. It is removed from the earth’s surface in large numbers by rain and hail.
The surface water includes waters of lakes, streams, rivers, and oceans. These waters are susceptible to periodic contamination with microorganisms from atmospheric water by precipitation, surface washings of soil, and any wastes that are dumped into them.
The composition of microbial flora in the surface water is dependent upon the microbial nutrients that are present in the water, geographical, biological, and climatic conditions. Ground water is subterranean water that occurs in the soil or rock-containing materials.
Depending upon the permeability of the soil and the depth to which the water penetrates, the microbes are removed by filtration and as such the groundwater may be free from any microbes.
The microbial population in a body of surface water is largely determined by the physical and chemical conditions which prevail in that habitat. Some of these conditions are: temperature, hydrostatic pressure, light, salinity, turbidity, pH, and inorganic and organic constituents.
Again optimum growth of microbes depends upon the interaction between these conditions and the nature of surface water (fresh or marine). Besides these, the distribution of microorganisms varies according to the depth of water. In deep waters, the top layers and the bottom sediments harbour the higher concentration of microorganisms than the rest.
The aggregation of floating and drifting microbial group in the surface of water is known as plankton which when comprising .primarily of algae is phytoplankton, when protozoa and other minute animals predominate it is zooplankton, and when there is a mixture of both plant and animal life it is zoophytoplankton.
Macrobial inhabitants of the bottom region (benthic zone) of a body of water are the benthic organisms, richest in an estuarine-marine system. In the benthos two distinct life forms are found, one attached and non-motile, the other unattached and capable of horizontal and vertical movements. The attached species growing on rock or stone surfaces are epilithic, on plants are epiphytic, and on animals are epizooic.
Owing to the intensive concentration of biomass of benthic organisms, it forms one of the most important grazing ground for protozoa, vegetarian fish, etc. In between the benthic zone and the zone of producers (photosynthetic algae) is the pro-fundal zone of open water where photosynthetic activity decreases progressively.
In fresh water, the pro-fundal zone and benthic zone are largely populated by heterotrophic organisms. Whereas, in marine water, the area between the upper strata and the area just above the sea floor is relatively barren, a vast microbiological oceanic desert region.
Note # 9. Microbiology of Animals:
Certain microorganisms remain regularly associated with animals (including insects) constituting the ‘normal flora’ exhibiting a dynamic equilibrium. Such equilibrium may be disbalanced when the host resistance is lowered and the normal flora assumes a pathogenic role.
The types of microorganisms of normal flora are influenced by the kind of animal body and environmental conditions:
i. Microorganisms associated with human body:
Normal flora of human skin includes Gram-positive cocci mainly Staphylococcus albus and Sarcina spp. In the secretions of skin Pityrosporum ovalis and P. orbiculare are present. In the secretions of ears saprophytic acid-fast Mycobacterium smegmatis is common.
The tears secreted on the conjunctiva of the eyes contain the enzyme lysozyme, which attacks bacterial cell walls causing lysis, and this keeps the number of organisms in this site at a low level.
Human nostrils are always heavily colonized with Staphylococcus albus and S. aurens. Again the normal flora of the upper respiratory tract is represented predominantly by Streptococcus salivatius, S. pyogenes, Neisseria pharyngis, and Haemophilus influenzae. There is no normal flora of the trachea and bronchi.
Flora of human alimentary tract includes nonhaemolytic streptococci, nonpathogenic species of Neisseria, anaerobic spirochaetes, Fusobacterium and lactobacilli. Besides these, Candida albicans is also present. The small intestine flora includes: Escherichia coli, Clostridium perfringens, species of the genera Bacillus and Bacteroides. But in general, diet influences the intestinal flora.
ii. Microorganisms associated with other animals:
Besides human body, one of the major habitats for microorganisms is other animals. As such there exist many different types of interaction between them. These interactions are traditionally classified into: symbiotic, parasitic and commensal.
Approximately 10 per cent of all insects exist in a symbiotic association with one or frequently more kinds of microorganism.
Some of the common examples are: fungi (Termitomycetes spp) and termites; flagellate (Hypermastigina and Polymastigina) as weir as bacteria and rickettsia’s with termites; mycoflora (Saccharomyces spp. Aspergillus spp.) of beehives; wood-inhabiting insects (bark-boring beetles) and ambrosia fungus (Ceratocystis ulmi).
An interesting aspect is the rumen (first chamber of stomach of herbivorous animals) symbiosis of microorganisms. Microorganisms like Bacteroides succinogenes, B. ruminicola, Streptococcus bovis, Selenomonas ruminantium grow in the first chamber (rumen) of multi-chambered stomachs of cows along with stored forage.
They digest cellulose, synthesize proteins and vitamins and alter fats of the forage in the rumen and make them suitable for nutritional requirements of the cows.
In the rumen, microorganisms also synthesize amino acids, proteins, and vitamins used by the host as well as by some species of the rumen microflora. Again rumen has an atmosphere suitable for development of continuous crop of microorganisms. This is how both the components of the symbiotic association are benefited.
Study of the nature and activities of the microorganisms and their quality improvement is useful for the benefit of dairy animals. Pasteur did not believe that animals could live in the absence of microorganisms.
The parasitic relationship between microorganisms and animals is exhibited by different pathogenic microorganisms. Again the relationship between aerobic bacteria (species of the genera Pseudomanas, Achromobacter, Vibrio, etc.) and marine fish may be cited as one of the best examples of commensal interactions of microorganisms.
Note # 10. Medical Microbiology:
This is the branch of Microbiology that deals with disease-producing microorganisms in human beings, other animals, and plants. Microorganisms are best known to the average person by the disease they cause. Medical Microbiology is concerned with the prevention and control of diseases.
The importance of the various types of microorganisms in causing diseases will be clear only with the study of the concerned microorganisms.
This branch of Microbiology is treated separately as:
(a) Study of diseases of plants (Plant Pathology) and
(b) Study of diseases of animals including humans.
It is essential to treat biological wastes by chemicals or by microorganisms to remove disease-producing microorganisms which cause offensive odour. Proper treatment which varies with the type and source of wastes, can eliminate health hazards and remove the compounds harmful to fish and other aquatic life. Knowledge of these organisms is essential to maintain balance of life forms.
Some of the microorganisms associated with sewage are: species of Enterobacter, Pseudomonas, Escherichia, Methano- bacterium, Methanococcus.
Note # 11. Space Microbiology (exobiology):
It is the study of possible occurrence of microorganisms in the outer space and on planets (extra-terrestrial life), or the establishment of earth types of planets through space vehicle. It also includes the study of the potential use of microorganisms for food and energy and for maintenance of a suitable oxygen-carbon dioxide balance in the space vehicle, e.g., use of species of Chlorella.
Note # 12. Microbiology and Origin of Life:
Many explanations have been offered for the origin of life on planet earth. One of the more acceptable of these proposals suggests that life originated in the sea following- million years of chemical evolutionary process.
The wide range of biochemical capabilities found among the microorganisms, the great simplicity of some types make microorganisms attractive “experimental tools” for the study of the transition between chemical synthesis and living forms.
Note # 13. Geochemical Microbiology:
Study of microorganisms has answered many vital questions like the role of microorganisms in the formation of coal, petroleum, and utilization of raw materials (hydrocarbon;) for transformation into valuable chemicals. Organic matters derived from microorganisms accumulated in mud deposits of the ocean floor were buried in course of time by sedimentary action and were gradually converted into oil and gas.
Continued