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Lecture Three

 

Classification & Nomenclature

Nomenclature

Bacteria are named using the binomial system used for other living thins whereby each species is given two names The first name is the Genus name (equivalent to your surname) and the second name is the species name (equivalent to your Christian name)

Bacteria belong to the one species if they have 90% similarity of all observed characteristics

A group of similar species that have 80% similarity is called a Genus
The genus name always start with a capital letter and the species name is in lower case and in singular
e.g. Staphylococcus aureus
Such binomial species names are always underlined or written in Italics
e.g. Staphylococcus aureus

It is important to remember these rules because often a word used in a genus or species name is the same as a word used to describe itís cellular morphology

e.g. not all streptococci are Streptococcus in fact some streptococci are Leuconostoc

not all staphylococci are Staphylococcus in fact some streptococci are Micrococcus

not all bacilli are Bacillus in fact some bacilli are Chlostridium etc etc.

 
The relationship between evolution and classification.

It is the goal of systematic biologists to develop classification schemes that indicate true evolutionary relationship between organisms. Such phylogenetic systems not only make organizing organisms a lot easier but they also can suggest important  characteristic that may not appear obvious. For example, if  a newly discovered bacterium was found to have evolved from the same ancestor as  a deadly pathogen it may that it has some latent abilities that may become important in a new environment.

A big problem with microbial taxonomy is that most  bacteria look the same. One rod shaped bacterium looks much like another rod under  the microscope. Phyogenic taxonomy of higher plants and animals has been aided by reference to fossilized remains that show a gradual change in morphology of may millions of years. Bacteria however do not have many fossilized remains ..

A botanist named Linnaeus in his 1759 treatise divided the world into Animal, Vegetable and Mineral and named all organisms that he knew of using the binomial (Genus species) system that we still use today. He  put all microscopic life into one genus, Chaos!

In 1969 Whittaker and others introduced the 5 kingdom system for classifying all life (Plants, Animals, Fungi, Protists and Bacteria). This system was based mostly on the 3 main modes of nutrition: photosynthesis, absorption, and ingestion. This system is no longer considered to be appropriate as it implies that all prokaryotes are l closely related to one another (just because they are small ) and it  implies that microbes are primitive and haven't  evolved over the many millions of years. In fact because of there rapid generation time bacteria are able to evolve more rapidly than higher organisms. Just because they look simple does not mean that they are.

In higher organisms observable features ( phenotypical characteristics) were used for most of the classification and some features were considered more important than others in order to show an evolutionary relationship. I.e.. All animals with backbone are placed in the vertebrate group. But with bacteria no single feature can be given precedence over the others  so a system of numerical taxonomy was developed where all features were considered equal. Groupings were then made according to the degree of similarity

E.g.. Members of a Species have 90% similar characteristics

All species in a Genus have 80% similarity

All Genera in an Family have 70% similarity

All Families in an Order have 60% similarity

Microbiologists have long known that the phenotype of a bacterium is not a good character to use in classifying them. Recent progress has been made using methods that compare the Genotype of the bacteria. (The sequences of bases in DNA). Many such molecules have been sequenced and a few are now used to classify microbes. Perhaps the most useful sequences have been those of  ribosomal RNA (rRNA). This molecule occurs in all forms of life and  its sequence are thought to have changed at different rates over  time.

For classifying bacteria we can compare the sequence of the 16S region of the ribosome of an unknown bacteria with a database of sequences from known bacteria. Most of the classification scheme given in modern text books are based on 16S sequences or rRNA .

OTHER METHODS OF GROUPING BACTERIA

Gram Stain

One morphological observation that is used extensively is the colour obtained by bacteria when treated with the gram stain technique

Gram positive (+ve) bacteria are very different from Gram negative (-ve) bacteria

Physiological groupings.

Heterotrophs - use organic carbon compounds as their carbon and energy sources (we are heterotrophs as are the fungi and many bacteria).
Autotrophs can fix carbon dioxide (CO2) from the air and turn it into organic molecules.
Photoautotrophs use light energy to do this (plants, cyanobacteria and many other bacteria are photoautotrophs).
Chemoautotrophs use chemical energy to fix CO2 (e.g. sulfur oxidizing bacteria and nitrifiers are chemoautotrophs).
Anaerobes and aerobes Aerobes are bacteria the use oxygen when it is available

Anaerobic organisms use several different physiological ways of making a living, including fermentation reactions and anaerobic respiration, the details of which we will explore in a few weeks.

Facultative anaerobes are organisms that can grow anaerobically or aerobically.

GRAM ĖVe BACTERIA:
Enteric Bacteria (Enterobacteriaceae). Note that the habitat for most of these is usually an intestines of some sort of animal.
Some Famous genera:
Salmonella (S. typhi causes typhoid fever)
Escherichia (E. coli)
Shigella (S. dysenteriae is closely related to E. coli)
Yersinia (Y. pestis causes plague)
Klebsiella (fixes N2 and can cause pneumonia)
Serratia
Erwinia (live on plants - some plant pathogens)
One common attribute of most of the G -Ve. facultative anaerobes is that they are capable of living dual lives. For example, many enterics can use their anaerobic capabilities to live in the guts of animals and their aerobic abilities to live in the soil or on plant material.

Strict Aerobes or oxidative Organisms (can't liver anaerobically)

Pseudomonas - have  polar flagella and are oxidase positive.
A very large order that is now  broken up into many different genera.
Fluorescent Pseudomonads
P. putida
P. aeruginosa (flowers and burn patients)
Fluorescent pigments are iron-chelating compounds (siderophores)
These organisms are adapted for living in soil and are ably to digest many substrates . They often cause food spoilage and break down fats and protein producing really bad smells and colour changes.. And some cause serious infections including food born infections. Because they are adapted for living in soil they are often resistant to antibiotics.

The End

Prepared by Barry Brazier