Introduction to Microbiology & Microorganisms

CHAPTER: 1

Introduction to Microbiology & Microorganisms

·         Microbiology is the study of organisms and agents that are generally too small to be seen clearly by the unaided eye. These organisms include viruses, bacteria, algae, fungi, and protozoa.

·          The study of microorganisms which are very small and cannot be seen by unaided eye

·          A microorganism or microbe  is a microscopic organism, which may be a single cell or multicellular organism .

·          Microorganism is an organism that is too small to be seen by the naked eye — in other words, it is "microscopic." Microorganisms include bacteria, viruses, fungi, parasites, and among others.

Characteristics of microorganisms:

1. Their size is very small.
2. There is no cellular differentiation. They are unicellular and one cell is capable of performing all the functions. Some microorganisms are multicellular with little or no cellular differentiation.
3. Microorganisms are present everywhere on the bodies of animals and humans, on plant surfaces, in the air, water, dust, soil, and even inside the intestinal canal of all insects, birds, animals and human beings.

Taxonomic Groups:

Microorganisms have wide taxonomic distribution and include organisms such as protozoa, algae, fungi, bacteria and virus:

Protozoa :

• These are unicellular eukaryotic organisms, motile having cilia, flagella and pseudopodia, saprophytic or parasitic.
• They are generally present in soil, water and marshy places and their size varies from 5-200 μm.
• They are animal-like in that they ingest particulate food, lack a rigid cell wall, do not contain chlorophyll.
• The study of protozoa is known as protozoology.
• They are differentiated on the basis of morphological, nutritional and physiological characteristics.
• Their role in nature is varied, but the best known protozoa are the few that cause disease in human beings and animals, such as malaria in humans. Some protozoa are beneficial, such as those found in stomach of cattle, sheep and termites that help digest food.
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• Algae :
• These are relatively simple organisms; their size varies from 1 μm to several feet.
• They are considered plant-like because they contain the green pigment chlorophyll, carry out photosynthesis, and have rigid cell walls.
• They are unicellular to multicellular and either motile or non-motile
• The study of algae is known as Algology or Phycology.
• These organisms are autotrophic and are found most commonly in aquatic environments or in damp soil.
• They cause problems by clogging water pipes, releasing toxic chemicals into water bodies, or growing in swimming pools.
• But extracts of some species have commercial uses: as emulsifiers for foods such as ice-creams; as a source of agar used as solidifying agent in microbial medias and as anti-inflammatory drugs for ulcer treatment. 
  
  
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  • Fungi:
  •      These are either saprophytes or parasites.
  •      They have eukaryotic cell structure which, like algae, has rigid cell walls.
  •      They form characteristic hyphae called mycelium which may be septate, nonseptate
  •      They form fruiting structures called conidia or exospores and endospores. Spores of fungi are always present in air, dust and soil.
  •       Multicellular fungi are also called molds while yeast is an important unicellular fungus.
  Molds have considerable value; they are used to produce antibiotics- penicillin, cephalosporin etc, fermented products like soy sauce, cheeses, and many other products. •      But they are also implicated in various human, animal and plant diseases including athlete’s foot and the moldy spoilage of grains and peanuts.
  •      The unicellular yeasts are widely used in Baking industry and for the production of all alcoholic beverages like wine, beer etc. On the other hand, some yeasts cause food spoilage and diseases such as vaginitis and thrush (an oral infection).
  1. Viruses:
  •      These are ultra-microscopic, noncellular obligate parasites of plants, animals and bacteria as well as other protists.
  •      Their size varies from 0.015μm -0.2 μm and shapes from spherical, rod etc. They can be seen only under an electron microscope.
  •      Unlike cells, viruses contain only one type of nucleic acid, either DNA or RNA, which is surrounded by a protein-coat. They lack the cellular components necessary for metabolism or independent reproduction.
  •       viruses can mutiply only on living cells.
  •      The study of viruses is known as virology.
  •       Viruses cause large number of diseases in humans (such as AIDS, common cold, poliomyelitis, SARS, genital herpes, hepatitis etc), plants (tobacco mosaic disease, papaya ring spot disease etc) and foot-and-mouth disease of animals. In addition, some retroviruses have also been implicated in the growth of some malignant tumors.
  2. Bacteria:
  •      These are unicellular microorganisms. Their size varies from 1-5 μm and have rod, coccus or spiral shape.
  •      They have prokaryotic cellular organization and cell division is usually by binary fission. Some bacteria having mycelial morphology are known as Actinomycetes and are very important in production of antibiotics.
  •      Bacteria are important in agriculture and play important role in cycle of biological nitrogen fixation.
  •      With respect to food, they are important in fermentations, food spoilage, food poisoning and food preservation.
  •      The wide range of industrial products derived from bacteria affect the human society in numerous ways. Their activities are of enormous importance and some are beneficial while others are harmful.
  •      The study of bacteria is known as Bacteriology.
  
  
  Reproduction in Bacteria:
  Bacteria reproduces by:
  1. Vegetative
  2. Asexual
  3. Sexual
  
  
  1. Vegetative Reproduction:
  It includes:
  a.       Budding
  b.      Fragmentation
  c.       Binary Fission
  
  
  
  
  1. Budding:
  In this case, a small protuberance, called bud develops at one end of the cell. Genome replication follows & one copy of the genome gets into the bud. Then the bud enlarges, eventually become a daughter cell & finally gets separated from the parent cell.
  Most commonly found in Bacillus.
  2. Fragmentation:
  Mostly during unfavorable conditions, bacterial protoplasm undergoes compartmentalization & subsequent fragmentation, forming minute bodies called gonidia. Under favorable conditions, each gonidium grows to a new bacterium. It becomes apparent that prior to fragmentation the bacterial genome has to undergo repeated replication so that each fragment gets a copy of it.
  3. Binary Fission:
  It is the commonest type of reproduction under favorable conditions in which cell divides into two similar daughter cells. During the process, the bacterial chromosomes get attached to the cell membrane & replicates to the bacterial chromosomes. As the cell enlarges the daughter chromosomes gets separated. A cross wall is formed between the separating daughter chromosomes. It divides the cell into daughter cells. The daughter cells soon grow to maturity within 20-30 minutes. Under favorable conditions many bacteria divide once in 20-30 minutes.

  

  Binary Fision In Bacteria

  
  
  Asexual Reproduction:
  It takes place by endospore formation, conidia, Zoospores & cyst formation.
  a.      Endospore Formation:
  Endospore is resting spores formed in some gram positive bacteria (Bacillus & Clostridium) during unfavorable conditions. They are formed within the cell. During this process a part of the protoplast becomes concentrated round the chromosome. A hard resistant wall is secreted around it. The rest of the bacterial cell degenerates. Endospore is very resistant to extreme physical conditions and chemicals. During favorable conditions the spore wall gets ruptured and the protoplasmic mass gives rise to a new bacterium.
  b.      Conidia Formation:
  ·         Occurs in Stremptomyces
  ·         Conidium germinates and produces filamentous bacteria.
  
  
  c.       Zoospore Formation:
  ·         Occurs in Rhizobium bacteria
  ·         Rarely occurs
  d.      Cyst Formation:
  ·         Occurs in Azotobacter
  ·         The cell which is surrounded by a thick wall of special type of proteins is known as cyst.
  1.      Sexual Reproduction:
  Sexual reproduction occurs in the form of genetic recombination. There are three main methods of Genetic recombination:
  A.    Transformation
  B.     Transduction
  C.     Conjugation  

Distribution of Microorganism

Microorganisms are ubiquitous in nature. They are found everywhere from air to water. Microorganisms occur abundantly where they find suitable food, moisture & temperature. Since the conditions that favor the survival and growth of many microorganisms are those under which people normally live, it is inevitable that we live among a multitude of microbes. They are in the air we breathe and the food we eat. They are on the surfaces of our bodies, in our alimentary tracts, and in our mouth, nose. The distribution of microorganisms can be discussed in the following headings:

Air:

Microorganisms are found everywhere in air. They need suspending particles. Several factors affect the distribution of microorganisms in air. The factors affecting microbial distribution in air may be desiccation, humidity, temperature & radiation. Influenza virus, Mycobacterium tubercolosis, Bacillus spp. Etc.

Water:

In water generally pH, temperature, light intensity, salinity affects the distribution of microorganisms. E. coli, Pseudomonas, Salmonella, Hepatitis virus, Polio virus , Aspergillus  are example of microorganisms found in water.

Food:

Food is major habitat of microbes. The distribution of microorganisms in food depends on type of food. Factors like pH of food, aeration, temperature, nature of food affects microbial distribution. E. coli, Salmonella, Pseudomonas, molds, are the examples.

Soil:

There great varieties of microbes found in soil. Soil texture, soil aeration, soil fertility, moisture, pH etc affects microbes distribution. Nitrogen fixing bacteria like Azotobacter, Azospirilium, Nitrobacter, Clostridium are found in soil.     

Historical Background and Development:

History:

A. Discovering the "organisms”:

1.         1676: A. Leeuwenhoek – first to observe and describe microbes accurately

2.         1884: C. Chamberland – constructed a bacterial filter that allowed the identification of viruses

3.         1898: Loeffler and Frosch – identified filterable infectious agent as cause of foot-and-mouth disease in cattle

4.         1898-1900: M. Beijerinck – identified tobacco mosaic virus

5.         1982: S. Prusiner – described prions (infectious protein that causes a particular normal protein to alter its shape and become a prion)

B. Disproving spontaneous generation (that living organisms could develop from nonliving matter):

1. 1688: F. Redi – first to challenge theory of spontaneous generation by    showing that if raw meat was protected from flies, the formation of    =>   maggots was prevented

2. 1748: R. Needham – supported spontaneous generation of microbes by showing that even after boiling mutton broth and pouring into  => sealed containers, growth of microbes occurred

3. 1776: L. Spallanzani - challenged spontaneous generation as it pertained to => microbes by showing that sealed containers that were boiled do not produce microbes

4. 1861: L. Pasteur – rigorously disproved spontaneous generation

a)      filtered air => showed that air contained microbial organisms

b)   constructed flasks with curved neck that allowed air into the flasks while dust, etc. remained in the neck => placed broth into the flasks and boiled => showed that no microbial growth resulted unless flasks were tipped to allow the broth into the neck .

      

C. The germ theory of disease:

1.      Previously, people thought that disease was punishment for an individual's crimes, due to poisonous vapors.

2.      The idea that invisible organisms caused disease were given by Lucretius  and Fracastoro (1546).

3.      1835: A. Bassi showed that silkworm disease was due to a fungus.

4.      1867: J. Lister showed that antiseptic surgical procedures reduced the frequency of wound infections.

5.      1876/1884: R. Koch definitively proved that Bacillus anthracis caused the disease anthrax in cows and Mycobacterium tuberculosis caused the disease tuberculosis using Koch's postulates:

            a) The suspected pathogen should be present in ALL cases of the disease

            and NOT present in healthy animals.

            b) The suspected pathogen should be grown in vitro in pure culture.

            c) Cells from a pure culture of the putative pathogen should cause disease

            in healthy animals.

            d) The putative pathogen should be re-isolated from the infected animal.

D. Preventing disease by vaccination:

1.         E. Jenner inoculated people with cowpox to protect against smallpox.

2.         1885 – Pasteur developed the rabies vaccine.

3.         1890: von Behring and Kitasato produced antibodies to purified toxins to

            protect against diphtheria and tetanus.

4.         1884: E. Metchnikoff described phagocytosis of bacteria.

E. Discovering the effect of microbes on organic and inorganic matter:

1. 1856: Pasteur described lactic acid fermentation; contributions to wine industry.

2. 1887-1900: S. Winogradsky and M. Beijerinck studied soil microbes and their role in the biochemical cycles of sulfur, carbon, nitrogen

Recent history of microbiology – the 20th century:

A.    Infectious diseases: The etiological agent of most infectious diseases has been ascertained. Current research focuses on understanding the molecular mechanisms by which disease is caused.

B.   Chemotherapy: Discovery of antibiotics; antibiotic resistance

C.   Immunology develops as a science.

D.     Physiology and biochemistry: Using microbes as a model, many physiological and biochemical processes have been elucidated.

E.     Genetics: Many of the advances in molecular genetics were made using bacteria as models. A few of the many:

                         1. 1941: Beadle and Tatum – 1 gene = 1 enzyme

                        2. 1943: Luria and Delbruck – mutations are spontaneous in nature

                        3. 1944: Avery, MacLeod, and McCarty – DNA is the genetic                                material

                        4. 1961: Jacob and Monod – the operon and gene regulation

F. Molecular biology:

                         Many of the advances in molecular biology were made using

                          bacteria as models. A few of the many:

                                    1. 1970: Restriction enzymes discovered

                                    2. 1979: Insulin synthesized using recombinant techniques

                                    3. 1990: Gene therapy trials begin

                                    4. 1995: The nucleotide sequence of the first free-living                               organism (Haemophilus influenzea) published

Scope of Microbiology:

1. Agricultural Microbiology/ soil Microbiology:

                        Microorganisms related to soil fertility, plant diseases, transformation of matter, biological nitrogen fixations etc are studied.

2. Food Microbiology:

                        Microorganisms important with respect to food viz., food fermentations, food spoilage, food poisoning and food preservation are studied in this area.

3. Industrial Microbiology:

                        Microbial production of useful products like antibiotics, fermented beverages, alcohols, industrial chemicals, organic acids, enzymes, hormones etc are studied in this area.

4. Medical Microbiology:

                         Besides their usefulness, microorganisms are casual agents of several diseases of plants, animals and human beings. Many diseases are caused by viruses also. Medical Microbiology deals with studies on causative agents of disease, diagnostic procedures, identification of disease causing organisms, development of effective vaccines and preventive measures etc.

5. Exo-Microbiology:

                        It deals with exploration of existence of biomolecules and microbial life in outer space.

6. Geochemical Microbiology:

                         Prospects for deposits of coal, mineral and gas, recovery of minerals from low grade ores, sea water mining operations, coal, mineral and gas formation and exploration are studied in this area.

7. Molecular Biology:

                        It is the program of interpreting the specific structure and function of organisms in terms of their molecular structures. Microorganisms have been used as a tool to explore fundamental life processes because of many advantages; their fast rate of reproduction, their growth can be easily manipulated, and lysed cells can be studied in terms of specific chemical reactions, specific products and specific structures involved.

8. Genetic Engeneering & Biotechnology:

                        This is an important development in applied Molecular Biology which refers to the human capability to alter the genetic makeup of an organism. It has been possible because of the detailed knowledge of structure and function of DNA and discovery of the restriction enzymes which can cleave or cut the DNA at specific sites along the chain length. Use of genetically engineered microorganisms has opened great potential for production of drugs, vaccines, improvement of agricultural crops etc.

9. Environmental Microbiology:

                        It deals with use of microorganisms to protect the environment from the toxic pollutants, reduction of microbial load in the sewage and industrial wastes, pesticides, insecticides, heavy metals etc. and to develop suitable methods for treatment of these wastes and their recycled use.

Application of Microorganism:

                        Microorganisms play an important role in sustaining life on this planet and in our daily life through the following activities:

1. Transformation of matter:

                        Microorganisms degrade dead organic matter and return to the atmosphere in inorganic form. They complete the cycle of matter and are responsible for transformation of C, N and S and other important elements which are essential for life.

2. Biological nitrogen fixation:

            They fix nitrogen from atmosphere and make it available to the plants in usable form. Important microorganisms under this category include, Rhizobium, Azotobacter, Azospirillum etc.

3. Mycorrhiza:

                        Association of roots of many plants with fungi forms a composite structure called mycorrhiza. Fungus helps in absorption of mineral salts from soil and plant in turn provides carbohydrates for the growth of fungus.

4. Silage:

                        This method is used to preserve feed with its characteristic flavor, taste and nutritive value. Leaves of green plants are compacted in size and some molasses is added. Lactic acid bacteria develop and produce lactic acid which helps to conserve the cattle feed.

5. Cellulose degradation in Rumen:

                        Ruminants feed on straw and grass which contains about 50 % cellulose. There is symbiotic association of microorganisms with rumen for degradation of cellulose and about 10¹⁰ – 10 ¹¹ cells/ml of different bacteria are usually present in the rumen. Most important of these include Ruminococcus and Clostridium.

6. Biogas:

                        Animal waste products and cellulose containing waste is fermented by microorganisms (Methanogens). Animal excreta is preserved in rotting sediment and methane gas so formed is used as a fuel.

7. Composting:

                        Decomposition of organic matter by microorganisms to convert it into nutrient rich manure is known as composting. Bacillus, Aspergillus and Thermoactinomyces are important in this process.

8. Industrial uses:

                        Different microorganisms are used for the production of wide range of products at industrial scale. These include alcoholic beverages, antibiotics, enzymes, pharmaceuticals etc.

Importance of Microbiology in Agriculture:

•      Involved in nutrient transformation process

•      Decomposition of resistant components of plant and animal tissue

•      Role in microbial antagonism

•      Participate in humus formation

•      Predator to nematodes

•      Improves soil structure

•      Maintenance of biological equilibrium