The principles of microbial phylogeny, classification and
identification
13 August 2020 14:12
Bacterial taxonomy/ Pseudomonadaceae
Understanding taxonomy and phylogeny (classification and evolution of bacterial species)
Topic 1: Taxonomy and phylogeny: Bacteria and Archaea
Bacteria and Archaea are two different single groups of organisms.
Definitions
Taxonomy: Classification based on the shared characteristics (phenetic, overall similarity).
Phylogeny: Measures the evolutionary relationships between organisms.
Classification of bacteria:
Traditional properties used in classification:
- Microscopy/ Morphology
- Response to oxygen
- Mode of energy synthesis/ source of carbon
- Biochemical, enzymatic tests
Molecular and genetic methods:
- Choose appropriate molecular markers for a gene family
- Amplify and sequence
- Create evolutionary model
- Phylogenetic tree analysis and construction
All living organisms have genes which mature randomly (base changes) at low frequency.
All progeny (offspring) will carry the mutation (base changes)
Organisms differing by a few DNA base changes have diverged more recently in evolutionary
time than organisms that differ by more bases.
Steps in taxonomic classification of microbes:
Carl Linnaeus (founder of modern taxonomy 1708-1778)
He is the first to originate the seven of the kingdoms, phylum and so on down to species.
1) Classification:
Ordering organisms into groups, based on shared properties.
2) Nomenclature:
Naming the classified organisms
3) Identification:
Obtaining data on the properties of an unknown organism and determining which species it
belongs to, based on direct comparison to known groups.
The taxonomic characteristics are generally changing throughout evolution but its
specifically changing for bacteria because of how difficult it is to assess their shared
Microbial phylogeny and Classification Page 1
, specifically changing for bacteria because of how difficult it is to assess their shared
characteristics given that they're microscopic. There is another main method used to
classify organisms to species level, which is whether or not they can inter breed.
This is if two animals can't produce any young, they're generally regarded as different
species or if they can't produce fertile young, that's generally considered to be different
species. But that’s incredibly difficult to make sure of with bacteria because we are dealing
with plasmids of organisms that would normally reproduce asexually.
So, Carl Linnaeus regarded classification of the microbial world as chaos because you simply
couldn't apply the same rule as you can to multicellular organisms.
For a long period of time there was only crude differences in morphology. For example,
based on very simple light microscopes or early versions of light microscopes.
In addition to staining and varying microbes, there are range of tests which can be used to
categorise microbes whether it's to do with appearance, morphology, atmospheric
condition for growth or any other kinds of nutrition or enzyme production enables nutrient
utilisation.
There are molecular and genetic methods which allow to characterise microbes. For
example, there are molecular markers for a particular sequence of genes and which allows
you to amplify sequences, work out the distant and common ancestors from which current
species separated.
The basis of phylogenetic relationships is that they rely on the principle called molecular
clocks. Using the number of base pairs difference you can work out how much of difference
and similarities each species have as they evolved.
Internal nodes- which represent an extinct ancestor from which two species have
separated.
External nodes- which represent the existing strains of species.
Formally, bacteria are named under archaea. Carl Woese (July 15, 1928- December 20,
2012) defined that archaea as separate domain of life in 1977 by phylogenetic taxonomy of
16s ribosomal RNA. Carl Woese realised through more modern genetic analyst that how we
were regarding bacteria was actually incorrect because there were actually a separate
category called the archaea, which were very distinct and completely different branch of
that phylogenetic tree.
The system had all these single cell prokaryotes as monera and eukaryotes as protists. The
monera are known to be separate and they constitute the bacteria and the archaea which is
more closely related to eukaryotes. Archaea are more closely related to eukaryotes than
Microbial phylogeny and Classification Page 2
identification
13 August 2020 14:12
Bacterial taxonomy/ Pseudomonadaceae
Understanding taxonomy and phylogeny (classification and evolution of bacterial species)
Topic 1: Taxonomy and phylogeny: Bacteria and Archaea
Bacteria and Archaea are two different single groups of organisms.
Definitions
Taxonomy: Classification based on the shared characteristics (phenetic, overall similarity).
Phylogeny: Measures the evolutionary relationships between organisms.
Classification of bacteria:
Traditional properties used in classification:
- Microscopy/ Morphology
- Response to oxygen
- Mode of energy synthesis/ source of carbon
- Biochemical, enzymatic tests
Molecular and genetic methods:
- Choose appropriate molecular markers for a gene family
- Amplify and sequence
- Create evolutionary model
- Phylogenetic tree analysis and construction
All living organisms have genes which mature randomly (base changes) at low frequency.
All progeny (offspring) will carry the mutation (base changes)
Organisms differing by a few DNA base changes have diverged more recently in evolutionary
time than organisms that differ by more bases.
Steps in taxonomic classification of microbes:
Carl Linnaeus (founder of modern taxonomy 1708-1778)
He is the first to originate the seven of the kingdoms, phylum and so on down to species.
1) Classification:
Ordering organisms into groups, based on shared properties.
2) Nomenclature:
Naming the classified organisms
3) Identification:
Obtaining data on the properties of an unknown organism and determining which species it
belongs to, based on direct comparison to known groups.
The taxonomic characteristics are generally changing throughout evolution but its
specifically changing for bacteria because of how difficult it is to assess their shared
Microbial phylogeny and Classification Page 1
, specifically changing for bacteria because of how difficult it is to assess their shared
characteristics given that they're microscopic. There is another main method used to
classify organisms to species level, which is whether or not they can inter breed.
This is if two animals can't produce any young, they're generally regarded as different
species or if they can't produce fertile young, that's generally considered to be different
species. But that’s incredibly difficult to make sure of with bacteria because we are dealing
with plasmids of organisms that would normally reproduce asexually.
So, Carl Linnaeus regarded classification of the microbial world as chaos because you simply
couldn't apply the same rule as you can to multicellular organisms.
For a long period of time there was only crude differences in morphology. For example,
based on very simple light microscopes or early versions of light microscopes.
In addition to staining and varying microbes, there are range of tests which can be used to
categorise microbes whether it's to do with appearance, morphology, atmospheric
condition for growth or any other kinds of nutrition or enzyme production enables nutrient
utilisation.
There are molecular and genetic methods which allow to characterise microbes. For
example, there are molecular markers for a particular sequence of genes and which allows
you to amplify sequences, work out the distant and common ancestors from which current
species separated.
The basis of phylogenetic relationships is that they rely on the principle called molecular
clocks. Using the number of base pairs difference you can work out how much of difference
and similarities each species have as they evolved.
Internal nodes- which represent an extinct ancestor from which two species have
separated.
External nodes- which represent the existing strains of species.
Formally, bacteria are named under archaea. Carl Woese (July 15, 1928- December 20,
2012) defined that archaea as separate domain of life in 1977 by phylogenetic taxonomy of
16s ribosomal RNA. Carl Woese realised through more modern genetic analyst that how we
were regarding bacteria was actually incorrect because there were actually a separate
category called the archaea, which were very distinct and completely different branch of
that phylogenetic tree.
The system had all these single cell prokaryotes as monera and eukaryotes as protists. The
monera are known to be separate and they constitute the bacteria and the archaea which is
more closely related to eukaryotes. Archaea are more closely related to eukaryotes than
Microbial phylogeny and Classification Page 2
