Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
oThese techniques are really important for understanding microbes that we
haven’t been able to culture in a lab yet
oThese techniques are far more effective than microscopy, which turns out
to be more of an art than a science
oRemember Buchnera – it’s an obligate symbiont – the only thing that can
grow it is an aphid
oGenomic DNA libraries: variations on a theme:
Small inserts versus larger inserts o Microbial diversity in seawater
Every drop has 106 bacterial cells per ml
Every drop has 107 viruses per ml o “SAR86” 130kb Genome Fragment –
we found a proteorhodopsin, which had never been found in bacteria before (it had
been in archea)
Rhodopsins are photoproteins – they absorb photons
Looking at it on a Phylogenetic tree doesn’t help so much in terms of
function
But you can look at its secondary structure, and you can see that it retains
the elements from functional sensory rhodopsins
Light-driven proton pumping
This looks like a new way that microbes can get energy from light o
Understand the process of looking at an organism from the environment and then
understanding their function by using all these processes
oOnce you know that a particular gene or organism exists, you can go back
out into the environment and ask questions about it.
oPopulation biology, gene distributions, and speciation – hard to do on a
macro-scale
oIt was really a surprise when people realized that different strains of E.
coli can vary by a whole megabase.
oNow that we know that these bacteria have this kind of rhodopsin, when
we look for it we find it all over the place in the ocean
The rhodopsin varies by depth o Lesson: we’ve barely explored
microbial sequence space at all: six years ago we didn’t even know
this rhodopsin existed, and now we know it’s one of the most
common bacterial genes in the ocean.
oMapping organisms to their habitat
Which genes are found at which depth in the ocean? It’s not
random.
Genes associated with flagella and chemotaxis were more highly
represented in the shallow water
Biosynthesis, pili, and attachment genes were more common at the
greater depths
Look at clusters of orthologous genes
Transposases increase with depth – we don’t know why this is, but
it looks like a real trend
• These transposases don’t just all come from one family or
one organism – this trend is spread out across a wide
variety of transposases.
A lot of the viruses in this ocean sample came from cyanophage
Samples from the Sargasso Sea
We’re learning a lot about how these organisms evolve, how they
adapt to their environment, and how they pick up variability
Genomics doesn’t just lead us down a reductionist path – it allows
us to zoom out and look at the larger picture.
Systems Microbiology
¾Exam this week:
¾Lectures Oct 23 (techniques of genomics), 25 (comparitive genomics), 29 (lateral
gene transfer and how genomes evolve), and Nov 1 (Nitrogen cycle from a global
perspective, rhizobium and agrobacterium)
¾Brock Chapters 15 (all), 17(586-591), 19 (656-666), and 31 (989-991) ¾ Today’s
lecture won’t be on the exam.
Environmental Genomics and Microbial Ecology o Natural microbial
diversity o Molecular microbial ecology techniques
oEnvironmental Genomics
Methods for trying to understand bacterial communities – we don’t
normally get pure cultures o If you get a pure culture, it’s much easier
to describe
oBut then you have to be able to describe how it interacts with the larger
mixed environment that it came from
oCounting:
Seawater plate count (hundreds of cells per ml) Direct count –
fluorescence (millions of cells per ml) Why do we get this
difference?
If there are all these microbes that won’t grow on a plate culture in the
lab, then how can we characterize and study them? o Microbial
evolution and phylyogeny
oCultivation independent surveys – Phylogenetic relationships
Polymerase Chain Reaction was invented since this process was
come up with – it allows you to amplify a particular gene from a
complex DNA mixture
That helps with Phylogenetic analysis o Known Bacterial
Phylogenetic Divisions – in 1987, there were only 12. Now there
are around a hundred, most of which we haven’t been able to
culture.
oThe diversity is enormous – but how does that help us understand their
properties and function?
oRemember, Phylogenetic trees are simply measures of genetic difference o
Secondary structure of a small subunit of rRNA – you can design an
oligonucleotide probe
oFluorescent In Situ Hybridization – a species-specific DNA probe – we
can identify cells even at the single-cell level
Beyond just identifying cells, you can start to recognize specific
patterns of environmental interaction
