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Certificate IV in Food Technology

General Microbiology

Lecture Three

 

Classification

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 reflect true (evolutionary) relatedness among organisms. Such phylogenetic systems not only make organising all of life a lot easier but they also can have profound practical implications. For example, if you discovered a new bacterium, wouldn't you want to know if it were closely related to a deadly pathogen?

One big problem with microbial systematics is that many microbes (especially bacteria) look alike. One rod-shaped bacterium looks pretty much like another under the microscope! Bacteria do not have many fossilised remains to indicate change in characteristics with time.

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. Obviously not much was known about microbes at that time so Linnaeus gave up in frustration and put all microscopic life into one genus, Chaos!  

100 years later 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 "tree" of life has been widely accepted but it is no longer believed to be phylogenetically correct and it implies that all prokaryotes are all closely related to one another (simply because they are small and have simple morphologies) and it also implies that microbes are primitive and haven't been evolving along with everybody else...

Observable features (called phenotypes) were used for most of the classification and certain features were considered more important than others in order to show an evolutionary relationship. Ie. All animals with backbone are placed in the vertebrated group. But with bacteria no single feature could be given precedence so a system of numerical taxonomy was developed where all features were considered equal. Groupings were then made according to the degree of similarity

Eg. 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 rRNA. This molecule occurs in all forms of life and different parts of its sequence are thought to have changed at different rates over evolutionary time.

For classifying bacteria we usually compare the sequence of the 16S region of the ribosome of an unknown bacteria with a database of sequences from known organisms. Most of the classification scheme given in moder text books are based on 16S sequences (or 18S in Eukaryotes). There are also a number of other approaches to microbial classification that support the Genotype scheme. The Genotype is probably as good as we can get to a true phylogenetic scheme for bacteria given the lack of a fossil record.

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 (enter = Gr. for gut), Table 19.2 shows some common genera of Enteric Bacteria (Enterobacteriaceae). Note that the habitat for most of them is indeed in the 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 facultative anaerobes is that they are capable of living dual lives. For example, many bioluminescent bacteria can use their anaerobic capabilities to live in the guts of fish and their aerobic abilities to live in the light organs of fish or to survive in the aerobic waters of the open oceans.

Strict Aerobes or oxidative Organisms (can't ferment organic compounds)

Pseudomonas - polar flagella and oxidase positive.
A very large genus that is now being broken up into many different genera.
Fluorescent Pseudomonads
P. putida
P. aeruginosa (flowers and burn patients)
Fluorescent pigments are iron-chelating compounds (siderophores)
These often cause spoilage of food particularly plant material. And some cause infections

The End

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