Bacterial Diversity and Response to the Environment Flashcards
Classification requires
the presence of structures
that are conserved across all species.
ALLknown forms of life have
ribosomes and even though there are differences between prokaryotes (archaea and bacteria) and eukaryotes, the basic
structure is conserved
The most conserved sub-unit is the
16S subunit and this is the basis of classifying bacteria
The rRNA genes are duplicated in the
genome as they are needed in large amounts as they form the
basis of the cell’s ability to produce proteins.
Because of the conservation of the 16S
subunit the genes that encode 16S rRNA
are highly
conserved
This conservation in sequence can be
exploited to sequence
16S rRNA genes
Because there are defined areas of
conservation within the rRNA gene we can
design primers that will amplify the gene from many different species of bacteria and compare them by examining to areas of the
gene that are not so strictly conserved.
Conservation can occur in areas that:
- Only bacteria exhibit
- Only eukaryotes exhibit
- Only archaea exhibit
- Or can be conserved across almost
all life
The basic idea of constructing
trees is that
they reflect similarity between sequences.
Those with the greatest similarity
must be
closest related in evolution.
Those with the least similarity
show the
greatest evolutionary divergence.
There is a huge difference between
the number of organisms that can be
seen microscopically in any collection
and
those that can be cultiovated on nutrient media
Only ~1% of bacteria collected are
able to
be cultivated
- Only ~1% of bacteria collected are
able to be cultivated - The rest are
either in a dormant state, require other nutrients, or
require factors produced by other microorganisms
Although we cannot culture many species of bacteria and
archaea, we can
classify them by using oligonucleotide
primers designed to the conserved regions of 16S rRNA
Once amplified from a given environmental sample the
resulting DNA can be
inserted into a gene library and
large scale sequencing of the resultant 16S rRNA genes
can take place
a problem: The species we can sample this way MUST have
the same conserved sequences of their 16S rRNA genes
One of the starkest differences between
bacteria and archaea is
in the composition of the membrane.
Like eukaryotes, bacteria have
ester linkages between the glycerophosphate head and the lipid tail
Like eukaryotes, bacteria have ester
linkages between the glycerophosphate
head and the lipid tail while archaea have
ether linkages
many archaea have lipid
monolayers rather than bilyaers
archaea was orginially thought to only
habit ‘extreme’ environments such as hydrothermal vents, hot springs etc,
archaea was orginially thought to only habit ‘extreme’ environments such as hydrothermal vents, hot springs etc, but now known to…
… be far more widespread – include environments such as the oceans and the mammalian gut.
many of the archae are
extremophiles
Methanopyrus which is capable of reproducing in temperatures up to
120°C
Chemoautotrophic metabolism – produces
methane from reduction of CO2 by hydrogen
Other Archaea are able to withstand
extremely low pH (acidophiles), high temperatures (thermophiles), or salinity (halophiles).
13
17-24 major groups (phyla) on the basis of their
genetic divergence
Recent uses of environmental genomics suggest that there are around
50 phyla - most not culturable
Some groups are
small and ‘obscure’ compared with familiar groups
Proteobacteria and Gram positive contain
best-known species
There is a huge amount of metabolic diversity within
groups
- At the fundamental level there is little diversity within
plants and animals
Photoautotrophy distributed among
5 phyla
Extreme loss of capability in
chlamydia - atp parasite
Traditional bacterial taxonomy:
- cell structure
- ability to take up stains
- biochemistry
- Habitat
But many bacteria have no
distinctive structures
Many large morphological differences are due to
small genetic changes
There has been a large amount of
horizontal gene transfer
the vast majortiy cannot be
cultures
One way of classifying bacteria is in
terms of the
GC content of their genomes
as a general rule those bacteria that live intracellulary have low
gc content whilst those in soil have high gc content
GC content varies from
16.6% in Carsonella ruddi to 74.9% in Anaeromyxobacter dehalogenans.
Phylogenetic analysis can be
confused by
the presence of horizontal gene transfer by either conjugation,
transduction, or transformation.
Gram negative bacteria e.g. proteobacteria have an
outer and inner membrane which surround a periplasmic space
A separate family of bacteria are
gram positive
The Gram stain attaches to
Gram-positive bacteria but as this layer is shielded in
Gram-negative bacteria the stain is easily washed away with ethano
notable gram-positive bacteria include:
Bacillus. staphylococcus, and clostridium.
proteobacteria are the largest…
… group (phylum) of bacteria
proteobacteria include many of the
familar species important in medicine, agriculture, and industry
proteobacteria is metabolically very
diverse
all proteobacteria are
gram negative
proteobacteria is divided into
5 groups
important members of proteobacteria?
- Purple sulphur bacteria
- Nitrosomonas – Rhizobium,
Agrobacterium, Beggiatoa, Pseudomonas - Purple non-sulphur bacteria
- E. coli
Regardless of the type of metabolism
all have
common elements
all bacteria require a
- a carbon source (CO2 or organic).
- an energy source (light, organic compounds, or inorganic compounts)
- Electron donor with higher energy than the electron acceptor.
Energy gained by
using
electrons with high energy
Energy gained by using electrons with high energy and
converting the energy into useful biological energy via ATP synthesis which can then be used to drive biosynthetic pathways.
The redox tower illustrates the
comparative redox potential of
redox pairs
Chemoheterotrophs exhibit
the most familiar means of obtaining energy and converting carbon into useable compounds
like animals and fungi chemoheterotrophs require
the intake of ready made organic compounds in order to grow
They cannot fix
carbon dioxide themselves
Carbon sources are converted to
a useable energy source (glucose) which then goes through glycolysis
Chemoheterotrophs can range from
obligate anaerobes to obligate aerobes.
what kind of anaerobe is e. coli ?
E. coli is a facultative anaerobe.
what are photoautotrophs also known as?
purple sulphur bacteria
how do photoautotrophs obtain energy?
energy is obtained by light but rather than the electron donor being water as in the case of normal photosynthesis, the electron donor in this case is hydrogen sulphide
photoautotrophs crucially
fix carbon dioxide
the pigmentation of Photoautotrophs is produced by
bacteriochlorophylls and carotenoids
it is the absorption spectra that are responsible for
the colours of photoautotrophs
elemental sulphur is further oxidised to
SO4^2-
Beggiatoa species live in
sulphur springs, the soil, and mud at the bottom of lakes
Beggiatoa exist as
filaments of around 50 cells
Beggiatoa can grow as
chemoheterotrophs or as chemoautotrophs
Chemoautotrophy depends on a cell using
the energy from oxidation of inorganic compounds (e.g. H2S, Fe2+) rather than energy from light in order to drive splitting of
water molecules and the fixation of carbon
dioxide.
The levels of hydrogen sulphide required by purple sulphur bacteria are
toxic to purple non-sulphur bacteria
Photoheterotrophs use light and an autotrophic mechanism to
fix carbon dioxide but they are also capable of photoheterotrophy
Light is used as the energy source but
organic carbon compounds are used as the
carbon source rather than just carbon dioxide
Rhodobacter obtains hydrogen from
small fatty acids it has obtained by heterotrophic
nutrition
The hydrogen is then used as an
electron donor to drive the photosynthetic reaction centre
Cyanobacteria formally known as
blue green algae.
however, they are bacteria, not algae
cyanobacteria are the ancestral bacteria which
were endosymbiosed by eukaryotic cells and evolved into chloroplasts in algae and plants
As cyanobacteria are the ancestors of chloroplasts their
photoautotrophic metabolism is the same as in plants
In cyanobacteria, light energy is harvested by
pigments (chlorophyll)
Light energy is harvested by pigments (chlorophyll), water
molecules are
split, and the resultant electrons are passed along an electron transport chain generating ATP
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