BIS2C. Biodiversity and the Tree of Life. 2014. L10. Studying Microbes

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 9 continued
1

Different histories within one genome
2
Bacteria Archaea Eukaryotes
Bacteria ArchaeaEukaryotes Bacteria
Nuclear
Tree
Mitochondrial
Tree
Nucleus
CPST
Bacteria ArchaeaEukaryotes Bacteria
MITO
Chloroplast
Tree

But ….
3

Model Has Limitations
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
Bacteria
LUCA
NM
NM
NM
NM
NM
NM
Model like this is
inconsistent with much
of the data
C
C
C
C
C
C
4

Scattered distribution of chloroplasts
55

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
6
Hypothesis 1:
Ancestral AND Loss

Cryptomonad

N M
C
N M
N M
N M
N M
N M
8
Hypothesis 2:
Diversification of Major
Lineages
!
Symbiosis in Plantae
Ancestor

N M
C
N M
C
N M
C
N M
C
Each lineage accumulates
some unique properties,
such as sequences of
some of their genes (N, M
or C genes).
N M
C
N M
C
N M
C
N M
C
N M
C

N M
C
10
Hypothesis 2:
Diversification of Major
Lineages
!
Symbiosis in Plantae
Ancestor
“Secondary Symbiosis” in
other lineages

Model for “Secondary” Symbiosis
11

Symbiosis between two eukaryotic cells
12
N
M
“Normal” eukaryote
Plantae representative with chloroplast
N M
C

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 13
N
M
N M
C
Engulfment

N
M
N
M
C
Symbiont
Host
Endosymbiosis
Endosymbiosis: when an organism (the host) bring another organism (the
symbiont) inside of its cell.

N
M
N
M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a
host of other symbionts.
Endosymbiosis

N
M
N
C
Symbiont
Host
Second mitochondria often lost

N
M
C
Symbiont
Host
Second nucleus often lost

Secondary Symbioses of Euglenas
18

Excavates: Euglenids
• Have flagella.
• Some are
photosynthetic,
some always
heterotrophic, and
some can switch.
19
Movement in the euglenoid Eutreptia

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
Euglena Nuclear DNA tells
us what its phylogenetic
backbone is
20

Euglena plastid
DNA says its
plastid is related to
those of
chlorophytes
21

A lonely excavate ...
N
M
22

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N
M
23
Engulfment of Chlorophyte

N
M
N M
C
24
Engulfment of Chlorophyte

N
M
N M
C
25
Endosymbiosis

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
Phylogenetic analysis of
plastid DNA reveals that the
eukaryote engulfed by
euglena was a Chlorophyte
backbone is
26

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
euglena was a Chlorophyte
Note - in some cases a
“relic” nuclear genome of
the symbiont is also still
present and this can also be
used to determine what type
of organism the symbiont
was
backbone is
27

Secondary Symbioses of Diatoms
28

Stramenopiles: Diatoms
29
A colony of the diatom,
Bacillaria paradoxa
•Unicellular, but many associate in
filaments.
•Have carotenoids and appear yellow or
brown.
•Excellent fossil record
•Most are photoautotrophic
•Responsible for 20% of all carbon fixation.
•Oil, gas source

N M
N M
N M
N M
N M
Many lines of evidence indicate that it occurred in the
common ancestor of the “Plantae” lineage.
!One line of evidence for this is that all organisms on this
branch have chloroplasts and the cells of these
organisms resemble the “primary” symbiotic cell.
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
Diatom nuclear DNA tells
backbone is
30

Diatom plastid
DNA says its
plastid is related to
those of red algae
31

A lonely stramenophile ...
N
M
32

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N
M
Engulfment of a red algae
33

N
M
N M
C
34

N
M
N M
C
35

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
diatoms was a red algae
backbone is
36

Secondary Symbioses of Others
37

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
38

Still Can’t Fit Model to Some Eukaryotes
39

Dinoflagellate Kryptoperidinium foliaceum
http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full
40

•All are multicellular; some get very large
(e.g., giant kelp).
•The carotenoid fucoxanthin imparts the
brown color.
•Almost exclusively marine.
Stramenopiles: Brown Algae
41
A community of brown algae: The marine kelp forest

N
M
42
Tertiary Symbioses?

N
M
43
N
M
N M
C
Tertiary Symbioses?
Euglenoid

N
M
Engulfment
44
N
M
N M
C

N
M
45
N
M
N M
C
Host
Symbiont
Endosymbsiosis
This is a “tertiary” symbiosis because the symbiont itself already underwent a
secondary symbiosis.

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
46
Brown Algae
Tertiary Endosymbsiosis

Plants and Animals Get Many Functions from Symbionts
• Endosymbioses (only really work with
eukaryotic cells as hosts)
!Legumes with nitrogen fixing bacteria
!Aphids with amino acid synthesizing
bacteria
!Tubeworms with chemosynthetic bacteria
!Lichens - fungi with algae or cyanobacteria
!100s more
• Other symbioses
!Cellulose digestion in the guts of termintes,
ruminants
47

Lecture 10
!
Lecture 10
!
Extremophiles and Methods for
Studying Microbes
!
!
BIS 002C
Biodiversity & the Tree of Life
Spring 2014
!
Prof. Jonathan Eisen
48

Where we are going and where we have been
• Previous Lecture:
!9: Acquisitions and Mergers
• Current Lecture:
!10: Extremophiles
• Next Lecture:
!11: Symbioses
49

Lecture 9 Wrap Up
• Lateral gene transfer
50

Case 1: Antibiotic Resistance
51

Antibiotic Resistance Evolves Rapidly
52

• http://www.niaid.nih.gov/
SiteCollectionImages/topics/
antimicrobialresistance/3geneTransfer.gif
53
Antibiotic Resistance Can Transfer Between Species

Case 2: E. coli
54

E. coli genome comparison
55
substantial variation in gene content among members of the same species have been
reported in other lineages of bacteria and archaea. Thus, the diminishing number of
core orthologous genes is simply an extension of something happening among close
relatives.
AND DIVERSIFICATION OF LIFE
MG1655 (K-12)
nonpathogenic
EDL933 (0157:H7)
enterohemorrhagic
585
514 204
193
2996
1346
1623
CFT073
uropathogenic
FIGURE 7.7. Number of shared proteins be-
tween strains of Escherichia coli. Note the
large number of genes found in one strain
but not the others (seen in the outer portions
of each circle).

Binary ﬁssion
56

Binary fission
57

Mutations happen…
Mutation =
heritable change
in the genome
(i.e., some change
in DNA bases)
58

Differential reproduction
59

Recombination in bacteria and archaea
DNA gets passed from
one cell to another
60

61
This movement of DNA from one lineage to another, is
known as lateral (or horizontal) gene transfer.

Vertical Transmission Continues

Sexual recombination in eukaryotes
63
In eukaryotes, the variants produced by mutation can “recombine” via sex
meiosismeiosis
fertilization

Lateral gene transfer
64

Lecture 10 Outline
• Methods for studying microbes:
! Extremophiles as an example
! Field observations
! Culturing
! CSI Microbiology
65

Lecture 10 Outline
! Culturing
! CSI Microbiology
66

105°C
CH3
CO, 80°CH2S, pH 0, 95°C High salt
CO2 4°Clow pH
!67
Diversity: The Unusual

How to study microbes
• Key questions about microbes in environment:
! Who are they? (i.e., what kinds of microbes are they)
! What are they doing? (i.e., what functions and
processes do they possess)
• Will use extremophiles as an example
• The principles here apply to any bacteria, archaea or
eukaryotic microbes
!68

Lecture 10 Outline
! Culturing
! CSI Microbiology
69

Field Observations an Important Tool
!70

Field Observations an Important Tool
!71

Observe Via Microscopy
!72
! Can look at
organisms in
a microscope
!
! Can observe
behaviors
and
responses to
stimuli
!
! Can try to
identify them
by
appearance

Method 1: Observe in the Field
• For bacteria and archaea appearance is not very helpful
in identifying organisms
• For some microbial eukaryotes it is more useful because
of the synapomorphies outlined in Ch 27, Lecture
• In many cases, there is not enough material to work with
for field observed microbes (e.g., a few cells in a pond
water sample)
• Difficult to determine what is going on inside cells
!73

Lecture 10 Outline
! Culturing
! CSI Microbiology
74

Method 2: Culturing
• Culturing (or cultivation) is the growth of microorganisms
in controlled or defined conditions.
• A pure culture (which is the ideal if possible) is one in
which only one type of microbe is present
!75

General approach to culturing
!
! Collect field sample
! Provide specific growth conditions
" Energy
" Electrons
" Carbon
" Other conditions (e.g., O2, temperature, salt, etc)
! Dilution/passaging until one obtains a “pure” sample
with just a single clone
!76

Examples of Benefits of Culturing:
• Allows one to connect processes and properties to single
types of organisms
!
• Enhances ability to do experiments from genetics, to
physiology to genomics
!
• Provides possibility of large volumes of uniform material
for study
!
• Can supplement appearance based classification with
other types of data.
!78

!
“Who is out there?”
via Culturing
!79

Woese Tree of Life
80

Woese Tree of Life
80
rRNA rRNArRNA

Woese Tree of Life
80
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG

Woese Tree of Life
80
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
S ACUGCACCUAUCGUUCG!
!
E ACUCCAGCUAUCGAUCG!
!
C ACCCCAGCUCUCGCUCG

Woese Tree of Life
80
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
R ACUCCACCUAUCGUUCG!
F ACUCCAGGUAUCGAUCG!
C ACCCCAGCUCUCGCUCG!
W ACCCCAGCUCUGGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG

Woese Tree of Life
80
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
W ACCCCAGCUCUGGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaebacteria

!
“What Are They Doing?”
via Culturing
!81

Determining “Optimal Growth Conditions” in the lab
• Culture specific type (usually referred to as a strain)
• Take single clone of that organism
• “Inoculate” multiple flasks that have different conditions
! 0.5M, 1M, 1.5M, 2M, 2.5M, 3M, 3.5M, 4M Salt
! 20°C, 30°C, 40°C, 50°C, 60°C, 70°C, 80°C, 90°C ...
• Measure concentration of cells in each condition over
time.
• Change in concentration over time = growth rate
!83
TextText

!8433
Grow starter culture
Set up some
flasks with
growth media

!8433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks

!8433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
1 2 3 4 Use different
flasks for
different
conditions

!8433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M

!8433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M
Monitor growth over time

!8433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h

!8433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h

!8433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h
1 2 3 4
1M 2M 3M 4M
3h 3h 3h 3h

Plot Growth vs. Time for Each Condition
!85
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
1M 2M 3M 4M

!86
0.0
12.5
25.0
37.5
50.0
1M 2M 3M 4M
Growth Rate
Calculate and Plot Growth Rate vs. Conditions

Optimal salt concentration for different species
!87

• Some stresses of high salt
! Osmotic pressure on cells
! Desiccation
Halophile adaptations
!88
H20

! Desiccation
• Halophile adaptations
! Increased osmolarity inside cell
" Proteins
" Carbohydrates
" Salts
! Membrane pumps
! Desiccation resistance
!89
H20
H20

! Desiccation
" Proteins
" Carbohydrates
" Salts - only done in extremely halophilic archaea
! Membrane pumps
!90

! Desiccation
" Proteins
" Carbohydrates
" Salts - only done in extremely halophilic archaea
! Membrane pumps
!91
High internal salt requires ALL cellular components to be
adapted to salt, charge. For example, all proteins must
change surface charge and other properties.

Extreme halophiles are a monophyletic group
!92

!9433
Set up some
flasks with
growth media

!9433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks

!9433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions

!9433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
20° 30° 40° 50°

!9433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
20° 30° 40° 50°
1 2 3 4
20° 30° 40° 50°
1h 1h 1h 1h

!9433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
20° 30° 40° 50°
1 2 3 4
20° 30° 40° 50°
1h 1h 1h 1h
1 2 3 4
20° 30° 40° 50°
2h 2h 2h 2h

!9433
Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
20° 30° 40° 50°
1 2 3 4
20° 30° 40° 50°
1h 1h 1h 1h
1 2 3 4
20° 30° 40° 50°
2h 2h 2h 2h
1 2 3 4
20° 30° 40° 50°
3h 3h 3h 3h

!95
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
20° 30° 40° 50°
Plot Growth vs. Time for Each Condition

!96
0.0
12.5
25.0
37.5
50.0
20° 30° 40° 50°
Growth Rate
Calculate and Plot Growth Rate vs. Conditions

Optimal growth temperature (OGT) for Different Species
!97

Temperature limits
Mesophile = Optimum at moderate temps
Thermophile = Optimum at 45-80°C
Hyperthermophile = Optimum at > 80°C
!99

Temperature limits
A > B >> E
!100
Mesophile = Optimum at moderate temps
Thermophile = Optimum at 45-80°C
Hyperthermophile = Optimum at > 80°C

Thermophiles found throughout the bacteria and archaea
!101

Thermophile Adaptations
!102
Stresses of High
Temperature
Examples of common
adaptations
Denatures proteins, RNA
and DNA
Make proteins more
stable
Speeds up reactions Slow down enzyme rates
Liquifies membranes Decrease fluidity of
membranes

!104
Uses of extremophiles
Type of
environment
Examples Example of
mechanism of
survival
Practical Uses
High temp
(thermophiles)
Deep sea vents,
hotsprings
Amino acid
changes
Heat stable
enzymes
Low temp
(psychrophile)
Antarctic ocean,
glaciers
Antifreeze
proteins
Enhancing cold
tolerance of crops
High pressure
(barophile)
Deep sea vents,
hotsprings
Solute changes Industrial processes
High salt
(halophiles
Evaporating
pools
Incr. internal
osmolarity
Soy sauce
production
High pH
(alkaliphiles)
Soda lakes Transporters Detergents
Low pH
(acidophiles)
Mine tailings Transporters Bioremediation
Desiccation
(xerophiles)
Deserts Spore formation Freeze-drying
additives
High radiation
(radiophiles)
Nuclear reactor
waste sites
Absorption,
repair damage
Bioremediation,
space travel

Lecture 10 Outline
! Culturing
! CSI Microbiology
106

Great Plate Count Anomaly
!107

Culturing Microscopy
!108

CountCount
!109

<<<<
!110
CountCount

!111
Problem because
appearance not
effective for “who
is out there?” or
“what are they
doing?”
<<<<
CountCount

!112
Problem because
appearance not
is out there?” or
“what are they
doing?”
<<<<
CountCount
Solution?

!113
Problem because
appearance not
is out there?” or
“what are they
doing?”
<<<<
CountCount
Solution?
DNA

Collect from
environment
Analysis of uncultured microbes
!114

Collect from
environment
!115

Polymerase Chain Reaction- PCR
!118

Woese Tree of Life
119

Woese Tree of Life
119
DNA DNADNA

Woese Tree of Life
119
DNA DNADNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG

Woese Tree of Life
119
DNA DNADNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG

Woese Tree of Life
119
DNA DNADNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
W ACCCCAGCUCUGGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG

!120
NOTES 3419
A. pisum P
A. piswn S Tx. nivea
L awaaasym
LL equizenata syr
Cud orbgcdar s,ym
rs. gesgosterorn - I/ -- V
I
N. gonorrhoeae B. Uhar.opkiuns sym
5% C. magncisca sym
Tns. sp. L-12
A. tnefaciens
R. ricketsil
1992
JOURNAL OF BACTERIOLOGY, May 1992, p. 3416-3421 Vol. 174, No. 10
0021-9193/92/103416-06$02.00/0
Copyright © 1992, American Society for Microbiology
Phylogenetic Relationships of Chemoautotrophic Bacterial
Symbionts of Solemya velum Say (Mollusca: Bivalvia) Determined
by 16S rRNA Gene Sequence Analysis
JONATHAN A. EISEN,lt STEVEN W. SMITH,2 AND COLLEEN M. CAVANAUGH`*
Department of Organismic and Evolutionary Biology, 1 and Harvard Genome Laboratory,2
Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138
Received 4 November 1991/Accepted 9 March 1992
The protobranch bivalve Solemya velum Say (Mollusca: Bivalvia) houses chemoautotrophic symbionts
intracellularly within its gills. These symbionts were characterized through sequencing of polymerase chain
of an Escherichia coli gene probe to S. velum

Collect from
environment
!121

Woese Tree of Life
122

Woese Tree of Life
122
DNA DNADNA

Woese Tree of Life
122
DNA DNADNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG

Woese Tree of Life
122
DNA DNADNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG

Woese Tree of Life
122
DNA DNADNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
W ACCCCAGCUCUGGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG

Key Finding 1: Major phyla of bacteria and archaea (as of 2002)
No cultures
Some cultures
!123

Key Finding #2: Biogeography
!124

Key Finding #3: Microbiomes
125

• Endosymbioses continued
• Lateral gene transfer
• Symbioses
!127
Lecture 11 Outline

Symbioses
• Symbiosis is an intimate association between at least
two different organisms in which at least one of them
benefits
!128

Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!129

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
!130

• Eukaryotes as a group are somewhat metabolically
limited in their capabilities
• Eukaryotes appear less able to “acquire” metabolic
processes from other species via lateral gene transfer
• However, eukaryotes are remarkably adept at “acquiring”
capabilities by engaging in symbioses with bacteria and
archaea
• This may be related to their propensity for phagocytosis
!131

• Mutualistic symbioses involving bacteria and archaea abound in
eukaryotes and take many forms
• Digestive
! Ruminants
! Cellulolytic insects
• Defensive
• Behavioral
! Squid light organs
• Autotrophic
! Photosynthetic
! Chemosynthetic in deep sea
• Nutritional
! Aphids
! Nitrogen fixation in legumes
!134

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
!135

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
!136

II. Some terms
• Pathogens are infectious agents that cause a disease
(can be considered a subclass of parasites)
• Pathogenicity = ability to enter a host and cause disease
• Virulence = degree of pathogenicity
• Note - not all parasites are pathogens but all pathogens
are parasites
!137

No archaeal pathogens
• Lots of types of pathogens
! Bacteria that infect eukaryotes
! Viruses that infect eukaryotes, archaea and
bacteria
! Eukaryotes that infect other eukaryotes
• No known archaeal pathogens of any organism
! No clear explanation of why
! If you discover one, you will become famous
(well, among scientists)
!138

Symbioses
• Endosymbiosis is a symbiosis (could be mutualism,
commensalism or parasitism) in which one of the
organisms live inside the cells of the other
!139

Case 1: Antibiotic Resistance
141

Antibiotic Resistance Evolves Rapidly
142

• http://www.niaid.nih.gov/
SiteCollectionImages/topics/
antimicrobialresistance/3geneTransfer.gif
143
Antibiotic Resistance Can Transfer Between Species

Case 2: E. coli
144

substantial variation in gene content among members of the same species have been
reported in other lineages of bacteria and archaea. Thus, the diminishing number of
core orthologous genes is simply an extension of something happening among close
relatives.
AND DIVERSIFICATION OF LIFE
MG1655 (K-12)
nonpathogenic
EDL933 (0157:H7)
enterohemorrhagic
585
514 204
193
2996
1346
1623
CFT073
uropathogenic
FIGURE 7.7. Number of shared proteins be-
tween strains of Escherichia coli. Note the
large number of genes found in one strain
but not the others (seen in the outer portions
of each circle).

Transmission of traits in bacteria and archaea
• Trait transmission in bacteria and archaea is simpler in
some ways and more complex in others than in
eukaryotes.
• Sexual reproduction with crossing over and gamete
fusion does not occur in bacteria and archaea.
• Two main features to discuss:
! Binary fission (clonality)
! Lateral gene transfer
!146

Binary fission
149
Binary fission
generates a
cell lineage
“tree” =
analogous to a
phylogenetic
tree

Mutations happen…
Mutation =
heritable change
in the genome
(i.e., some change
in DNA bases)
150

Differential reproduction
151
Not all variants
reproduce equally well

Note - equivalent processes happen in eukaryotes
152

152
Binary fission is a form of
asexual reproduction

152
Leads to “clonality”

152
Also known as
“vertical transmission”Leads to “clonality”

one cell to another
153

The recipient can mix
the new DNA with its
own 154
one cell to another
This movement of DNA from one lineage to another, is
known as lateral (or horizontal) gene transfer.

Normal vertical
transmission cont.
155
The recipient can mix
the new DNA with its
own
one cell to another

Lateral inheritance I: Competence
157

Lateral inheritance II: Conjugation
158

Lateral inheritance III: Transduction
159

BIS2C. Biodiversity and the Tree of Life. 2014. L10. Studying Microbes

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BIS2C. Biodiversity and the Tree of Life. 2014. L10. Studying Microbes