Week 2 - Microbial Classification and Diversity, and Bacterial Growth and
Replication
LO1: Understand the role of DNA sequencing in modern taxonomy
LO2: Describe the basic classification of microbes and appreciate their place in the tree of life
LO3: Understand the different modes of bacterial cell division and the requirements for successful cell division
in bacteria
LO4: Appreciate the different ways to measure microbial growth rates
LO5: Understand the constraints to bacterial growth in different environments
Microbial Classification
History of Classification
Historical corner; a history of classification schemes
Current thinking is all based on Carl Woese's 3-domain scheme from 1990
Carl Woese's said you can take all living things on Earth and split them up into these 2 groups of bacteria,
archaea and eukarya, and that has superseded all the past classification schemes
The evidence for Woese's scheme comes primarily from comparing sequences for the RNA molecule in the
small subunit of the ribosome (this is called the 16S subunit in prokaryotes and the 18S subunit in
eukaryotes)
They are slightly different sizes in prokaryotes and eukaryotes
Why SSU rRNA?
Present in all cells, therefore comparable
Essential for cell survival
Changes at DNA level acquired slowly, i.e. its conserved
Different parts of DNA sequence will change at different rates, you can find parts of the SSU rRNA where the
sequence changes much more rapidly, it gives you a ways to compare things that are much more closely
related, hence making it an excellent molecule for comparison to build the tree of life
Changes that do not affect function; relatively rapid mutation
Changes that affect function; relatively slow mutation (some mutations will kill cells)
Therefore non-functional sequences mutate more rapidly than functional sequences
Functional sequences can alter but at a slower rate
Only using SSU rRNA is limited but why is this
It's only 1 gene out of thousands. It's not a bad choice as everything has one and it is very central to life.
But other genes might give you different trees - this is particularly the case in prokaryotes where horizontal
gene transfer is widespread
Classification
, Comparison of part of the SSU rRNA sequence, shows parts that are absolutely conserved for the last 3 1/2
billion years; the yellow boxes identical nucleotide, blue boxes at least one difference
Methanococcus/ Thermococcus/Sulfolobus = Archaea
E.coli/Thermotoga = Bacteria
A.nidulans/yeast/humans/Zeamays = Eukarya
SSU rRNA functions as a molecular clock
The more genetic differences between 2 sequences, the less related they are (1 mutation, 1 "tick"
of the clock)
Any DNA/RNA or protein sequence can be used as a molecular clock but few things are as universal as
ribosomes, some things tend to mutate much quicker making it harder to compare things that are
distantly related
Housekeeping genes make good clocks for classification
o Found in most/all organisms, under pressure to acquire few mutations
Some clocks tick faster than others
Difficult to make direct and reliable correlations to actual timescales as different organisms will have
different mutation rates
Taxonomic Ranking
Nb. There are some problems with applying the "species" concept to prokaryotes
Taxonomic ranking illustrates different degrees of relatedness
Tree of Life
, Analysis of SSU rRNA allows construction of "The Tree of Life"
Notice how archaea and eukarya are slightly more closely related to each other than they are with bacteria,
meaning that the first great split was between bacteria and everything else
This tree's branch length
represents the degrees of
genetic difference
Most of the tree of life is
made up of microbes
(highlighted in blue), so
most of the genetic diversity
is in the microbial world
Prokaryotic microbes = bacteria, archaea
Eukaryotic microbes = fungi, protozoa, algae
Table below shows the principle differences between prokaryotic and eukaryotic microbes
Replication
LO1: Understand the role of DNA sequencing in modern taxonomy
LO2: Describe the basic classification of microbes and appreciate their place in the tree of life
LO3: Understand the different modes of bacterial cell division and the requirements for successful cell division
in bacteria
LO4: Appreciate the different ways to measure microbial growth rates
LO5: Understand the constraints to bacterial growth in different environments
Microbial Classification
History of Classification
Historical corner; a history of classification schemes
Current thinking is all based on Carl Woese's 3-domain scheme from 1990
Carl Woese's said you can take all living things on Earth and split them up into these 2 groups of bacteria,
archaea and eukarya, and that has superseded all the past classification schemes
The evidence for Woese's scheme comes primarily from comparing sequences for the RNA molecule in the
small subunit of the ribosome (this is called the 16S subunit in prokaryotes and the 18S subunit in
eukaryotes)
They are slightly different sizes in prokaryotes and eukaryotes
Why SSU rRNA?
Present in all cells, therefore comparable
Essential for cell survival
Changes at DNA level acquired slowly, i.e. its conserved
Different parts of DNA sequence will change at different rates, you can find parts of the SSU rRNA where the
sequence changes much more rapidly, it gives you a ways to compare things that are much more closely
related, hence making it an excellent molecule for comparison to build the tree of life
Changes that do not affect function; relatively rapid mutation
Changes that affect function; relatively slow mutation (some mutations will kill cells)
Therefore non-functional sequences mutate more rapidly than functional sequences
Functional sequences can alter but at a slower rate
Only using SSU rRNA is limited but why is this
It's only 1 gene out of thousands. It's not a bad choice as everything has one and it is very central to life.
But other genes might give you different trees - this is particularly the case in prokaryotes where horizontal
gene transfer is widespread
Classification
, Comparison of part of the SSU rRNA sequence, shows parts that are absolutely conserved for the last 3 1/2
billion years; the yellow boxes identical nucleotide, blue boxes at least one difference
Methanococcus/ Thermococcus/Sulfolobus = Archaea
E.coli/Thermotoga = Bacteria
A.nidulans/yeast/humans/Zeamays = Eukarya
SSU rRNA functions as a molecular clock
The more genetic differences between 2 sequences, the less related they are (1 mutation, 1 "tick"
of the clock)
Any DNA/RNA or protein sequence can be used as a molecular clock but few things are as universal as
ribosomes, some things tend to mutate much quicker making it harder to compare things that are
distantly related
Housekeeping genes make good clocks for classification
o Found in most/all organisms, under pressure to acquire few mutations
Some clocks tick faster than others
Difficult to make direct and reliable correlations to actual timescales as different organisms will have
different mutation rates
Taxonomic Ranking
Nb. There are some problems with applying the "species" concept to prokaryotes
Taxonomic ranking illustrates different degrees of relatedness
Tree of Life
, Analysis of SSU rRNA allows construction of "The Tree of Life"
Notice how archaea and eukarya are slightly more closely related to each other than they are with bacteria,
meaning that the first great split was between bacteria and everything else
This tree's branch length
represents the degrees of
genetic difference
Most of the tree of life is
made up of microbes
(highlighted in blue), so
most of the genetic diversity
is in the microbial world
Prokaryotic microbes = bacteria, archaea
Eukaryotic microbes = fungi, protozoa, algae
Table below shows the principle differences between prokaryotic and eukaryotic microbes
