TAXONOMY AND IDENTIFICATION

TAXONOMY AND IDENTIFICATION
 
TAXONOMY•Taxonomy is the science of classification.
•It is an attempt to classify biological organisms in an orderly manner.
•Usually organisms with similar physical, biochemical and genetical properties are grouped together.

 
 IMPORTANCE OF TAXONOMY•Classification is important because it establishes criteria for identifying organisms.
•It is essential for grouping together similar organisms and it also provides information on how organisms evolved.
•Taxonomy consists of two major disciplines which are identification and nomenclature

 TERMS IN CLASSIFICATION OF ORGANISM
 •Taxonomy is the science of biological classification.
•Classification is the arrangement of organisms into groups or taxa (s. taxon) based on mutual similarity or evolutionary relatedness.
•Nomenclature is the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules.
•Identification is the process of determining that a particular isolate belongs to a recognized taxon.
•Systematics is the scientific study of organisms with the ultimate object of characterizing and arranging them in an orderly manner
•Classification i.e. Description of a taxon of bacteria is therefore based on biochemical, physiologic, genetic and morphologic properties
•Nomenclature is the naming of an organism according to international rules contained in the Bacteriological Code e.g. Escherichia coli
•Identification refers to practical use of a classification scheme.

 CLASSIFICATION OF PROKARYOTES AND VIRUSES
•The genus and species names must be derived from Latin or Greek and in print are written either in bold face in italics or underlined.
•The first letter of the generic name must be a capital letter e.g. Bacillus cereus.
•In some instances where no confusion may arise, the generic name may be abbreviated to its initial capital letter e.g. B. cereus.
  
BACTERIAL TAXONOMY
Depending on the organism and facilities available, there are different approaches in classifying bacteria. The different approaches are:

• Conventional (or classical) taxonomy
• Numerical taxonomy
• Genetic or molecular taxonomy

 CONVENTIONAL TAXONOMY
•This type of bacterial taxonomy has been practiced for more than 100 years now.
•In conventional taxonomy of the bacteria, various characteristics are used in classifying bacteria.

The characteristics used include the followings:

•  Morphology
• Gram reaction
• Nutritional classification
• Cell wall chemistry
• Presence of cell inclusions and storage products
• Endospore formation
• Capsule chemistry
• Pigments
• Nutritional requirements
• Ability to use various carbon, nitrogen and sulphur sources
• Fermentation products
• Gaseous needs
• Temperature and PH ranges
• Antibiotic sensitivity
• Pathogenicity
• Symbiotic relationship
• Immunological characteristics
• Habita

 Morphology
• Bacteria cells can be spherical (i.e. coccus); cylindrical shaped (i.e. bacillus or simply rods); they can be spiral (i.e. spirilla); also can be spiral helix (i.e. spiro-chaeters).
•The spiral bacteria are actually curved rods, while the spirochaetes are actually coiled bacteria.
•Some bacteria do have extensions their cells as long tubes or stalks.
•Such bacteria are said to be appendaged bacteria.
•The bacterial cells can sometimes form groups or clusters such as rods or cocci in chains. The cocci can also form sheets or form three dimensional cubes.

 Gram reaction
•In this characteristics, bacterial cells are treated with a gram stain.
•The result is that, they are either gram-positive (i.e. appear purple under the microscope) or gram- negative (appear red).

 Nutritional classification
•The bacteria can either be
1) Phototrophs i.e. obtanining energy from light or
2) Heterotrophs i.e. obtaining energy and carbon from organic compounds or
3) Lithotroph i.e. obtaining energy from oxidising inorganic compounds.

 Cell wall chemistry
•That is the types of derivatives of the peptidoglycan, lipopolysaccharides, the binding proteins etc. of the bacterial cell wall

 Presence of cell inclusions and storage products
•Nature of substances included or stored in different bacteria differ.
•In procaryotes in general, one of the common inclusion substnces is poly-ß-hydroxy butyric acid (PHB)
•It usually forms granules in the cells as revealed by electron microscope
•Other storage products include glycogen which is a polymer of glucose subunits.
•It resembles starch, Polyphosphate granules i.e. granules of inorganic phosphate are accumulated and stored by many microorganisms.
•Furthermore, elemental sulphur is also accumulated and form granules in some microorganisms.

 Endospore formation
•Bacterial endospore (i.e. a spore formed within the cell) is usually heat resistant.
•Endospores are also resistant to other harmful agents such as drying, radiation, acids and chemical disinfectants.
•The position of the endospore in the bacterial cell is also characteristic. It can be:-
       a)Central spore without distention of mother cell
       b)Terminal spore without distention of mother cell
       c)Terminal spore with mother cell distended ovally.
       d) Central spore, with mother cell distended
              to spindle shape.
       e) Terminal spherical spore, with mother
           cell distended to drumstick shape.
       f)Lateral spore, with mother cell distended to spindle


Capsule chemistry
•The capsule or slime layer occur on the surface of most procaryotic cells.
•It is secreted by the cells.
•The general term glycocalyx is defined as the polysaccharide – containing material lying outside the cell.
•The chemical composition of the glycocalyx varies in different microorganism


 Pigments
•These are usually present in photosynthetic bacteria, the colours of the pigment include, green, brown, purple-red, purple-violet, orange-green etc.
•Different carotenoids make up the different pigments.

 Nutritional requirements
•These are substances in the environment which are useful for the growth of the microorganisms.
•These are known as nutrients and can be divided into two classes

Ability to use various carbon, nitrogen and sulphur sources
•Sources of carbon for microorganisms include CO2 and organic compounds.
•Nitrogen can be obtained from ammonia (NH3), Nitrate (NO3-) and organic compounds like amino acids.
•Sources of sulphur include hydrogen sulphide (H2S), sulphate (SO42-) and organic compounds like cystein.trients and can be divided into two classes:
 
 Fermentation products
•Fermentation is a process whereby catabolic (biochemical processes involved in the breakdown of organic compounds usually leading to energy production) reaction occur, producing ATP in which organic compounds serve as both primary electron donor and ultimate electron acceptor.
•Different fermenting microorganisms produce different fermentation products which include ethanol, lactic acid, proprionic acid butyric acid.

 Gaseous needs
•Some bacteria need oxygen so as to grow while anaerobic bacteria will grow in the absence of oxygen.
•Methanogenic bacteria need H2 and CO2 mostly at a ratio of 80%:20%.
•While some sulphur bacteria need SO2.
•Nitrogen fixing bacteria will need N2 and CO2 so as to grow in a culture medium that does not have any other source of nitrogen

 Temperature and PH ranges
•Different bacteria will grow under different temperature and PH ranges.
•Each microorganism has a minimum, an optimum and a maximum value for its growth.
•Organisms that grow at low PH (i.e. acidic ranges) are called acidophiles.
•However most bacteria grow best at neutral PH.
•With regards to the temperature at which the bacteria will grow, it is possible to divide the bacteria into four groups; viz:
a)Psychrophiles i.e. those with low temperature optima (0-200C).
b)Mesophiles i.e. with mid temperature optima (150C – 450C).
c)Thermophiles i.e. with high temperature optima (400C – 700C).
d)Extreme thermophiles i.e. with very high temperature optima (650C – 950C

 Antibiotic sensitivity
•Different bacteria have different sensitivity to different types of antibiotics at different dilutions of the antibiotics.
•The antibiotics tested include Ampicillin, Chloramphenicol, Gentamicin, Penicillin, Streptomycin, Tetracycline etc.

Pathogenicity
•That is the amount of damage the bacteria will cause onto its host.
•In other words, it means the ability of a parasite to cause a disease.
•Pathogenicity is a property of a species and thus also useful in bacterial taxonomy.

 Symbiotic relationship
•Many bacteria live in a symbiotic association with plants and animals.
•In many cases the symbiosis is very specific.
•For example, the nitrogen fixing species of Rhizobium trifolli occurs only in the root nodules of the plants of genus Trifolium.

 Immunological characteristics
•Bodies of higher animals can develop resistance to certain bacteria, viruses and other microorganisms.
•The mechanism is the immune response.
•Foreign substances (e.g. bacteria) called antigens stimulate the body to produce specific proteins called antibodies or specific cells called activated T. cells.

 Habitat
•This is the location in the environment where a population is living.
•There are various types of microorganisms living in various environments. These environment include:
(a) Aquatic: Bacteria can be found to live in such aquatic environments as oceans, estuarines, salt marshes, lakes, ponds, rivers and springs
•These environments differ a lot in their physical and chemical properties and thus the composition of microorganisms in them will differ also.
•The sea water environment has 3.5% NaCl plus small amounts of many other minerals and elements.
•Thus microorganisms living optimally in the sea, are living optimally in the high osmotic environment.
•Such microorganisms are called moderate halophiles.
•This is to distinguish from exterme halophiles which live in very salty environments.
 (b) Cold habitat: In cold places, such a bacterium as Flavobacterium is living.
(c) Dry environments: Organisms capable of living in dry environments are known as xerophiles.
(d) High temperature environments: Even at very high temperatures, bacteria have been found to live. For example in such places as boiling hot springs.


Intracellular and extracellular
Microorganisms can live and multiply inside cells of their hosts (e.g. malaria parasite Plasmodium vivax). While others, live in the plasma of their hosts (i.e. extracellularly)
(f) Anaerobic or aerobic environments: Some bacteria require oxygen (aerobic) so as to live.
(g) Soil: In the soil many microorganisms are found to live. The environment at which the bacterium is living can be used as a criterion for classifying the microorganisms.