BIS2C. Biodiversity and the Tree of Life. 2014. L10. Studying Microbes
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 9 continued
1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Different histories within one genome
2
Bacteria Archaea EukaryotesBacteria ArchaeaEukaryotes Bacteria
Nuclear Tree
Mitochondrial Tree
Nucleus
CPST
Bacteria ArchaeaEukaryotes BacteriaMITO
Chloroplast Tree
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
But ….
3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Model Has Limitations
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
BacteriaLUCANM
NMNM
NM
NM
NM
Model like this is inconsistent with much of the data
C
C
C
C
C
C
4
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Scattered distribution of chloroplasts
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N MC
N MC
N MC
N MC
N MC
N MC
Scattered distribution of chloroplasts
6
Hypothesis 1: Ancestral AND Loss
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Cryptomonad
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N MC
N M
N M
N M
N M
N M
Scattered distribution of chloroplasts
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N MC
Scattered distribution of chloroplasts
10
Hypothesis 2: Diversification of Major Lineages !Symbiosis in Plantae Ancestor
“Secondary Symbiosis” in other lineages
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Model for “Secondary” Symbiosis
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Symbiosis between two eukaryotic cells
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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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 14
NM
N M
C
Symbiont
Host
EndosymbiosisEndosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 15
NM
N M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a host of other symbionts.
Endosymbiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 16
NM
N
C
Symbiont
Host
Second mitochondria often lost
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 17
NM
C
Symbiont
Host
Second nucleus often lost
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Secondary Symbioses of Euglenas
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Excavates: Euglenids
• Have flagella. • Some are
photosynthetic, some always heterotrophic, and some can switch.
19
Movement in the euglenoid Eutreptia
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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 MC NMC NMC NMC N MC
N MC
N MC
N MC
N MC
Euglena Nuclear DNA tells us what its phylogenetic backbone is
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Euglena plastid DNA says its plastid is related to those of chlorophytes
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
A lonely excavate ...
N M
22
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
24
Engulfment of Chlorophyte
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
25
Endosymbiosis
N M
N M
N M
N M
N M
N MC NMC NMC NMC N MC
N MC
N MC
N MC
N MCPhylogenetic analysis of plastid DNA reveals that the eukaryote engulfed by euglena was a Chlorophyte
Euglena Nuclear DNA tells us what its phylogenetic backbone is
26
N M
N M
N M
N M
N M
N MC NMC NMC NMC N MC
N MC
N MC
N MC
N MCPhylogenetic analysis of plastid DNA reveals that the eukaryote engulfed by 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
Euglena Nuclear DNA tells us what its phylogenetic backbone is
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Secondary Symbioses of Diatoms
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Stramenopiles: Diatoms
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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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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 MC NMC NMC NMC N MC
N MC
N MC
N MC
N MC
Diatom nuclear DNA tells us what its phylogenetic backbone is
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Diatom plastid DNA says its plastid is related to those of red algae
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
35
N M
N M
N M
N M
N M
N MC NMC NMC NMC N MC
N MC
N MC
N MC
N MCPhylogenetic analysis of plastid DNA reveals that the eukaryote engulfed by diatoms was a red algae
Euglena Nuclear DNA tells us what its phylogenetic backbone is
36
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Secondary Symbioses of Others
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
N M
N M
N M
N MC NMC NMC NMC N MC
N MC
N MC
N MC
N MC
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
N M
N M
N M
N MC NMC NMC NMC N MC
N MC
N MC
N MC
N MC
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Still Can’t Fit Model to Some Eukaryotes
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Dinoflagellate Kryptoperidinium foliaceum
http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full40
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
•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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
•All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine.
Stramenopiles: Brown Algae
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A community of brown algae: The marine kelp forest
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
42
Tertiary Symbioses?
“Normal” eukaryote
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
43
N MN M
C
Tertiary Symbioses?
“Normal” eukaryote
Euglenoid
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
Engulfment
44
N MN M
C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
45
N MN M
C
Host
Symbiont
Endosymbsiosis
This is a “tertiary” symbiosis because the symbiont itself already underwent a secondary symbiosis.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
N M
N M
N M
N MC NMC NMC NMC N MC
N MC
N MC
N MC
N MC
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Brown Algae
Tertiary Endosymbsiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
N M
N M
N M
N MC NMC NMC NMC N MC
N MC
N MC
N MC
N MC
46
Brown Algae
Tertiary Endosymbsiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 10
!
Lecture 10 !
Extremophiles and Methods for Studying Microbes
!!
BIS 002C Biodiversity & the Tree of Life
Spring 2014 !
Prof. Jonathan Eisen48
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where we are going and where we have been
• Previous Lecture: !9: Acquisitions and Mergers
• Current Lecture: !10: Extremophiles
• Next Lecture: !11: Symbioses
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 9 Wrap Up
• Lateral gene transfer
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Case 1: Antibiotic Resistance
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Antibiotic Resistance Evolves Rapidly
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
• http://www.niaid.nih.gov/SiteCollectionImages/topics/antimicrobialresistance/3geneTransfer.gif
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Antibiotic Resistance Can Transfer Between Species
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Case 2: E. coli
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
E. coli genome comparison
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substantial variation in gene content among members of the same species have beenreported in other lineages of bacteria and archaea. Thus, the diminishing number ofcore orthologous genes is simply an extension of something happening among closerelatives.
How do such extensive differences in gene content among close relatives originate?One of the most important clues comes from comparing the genome structures of re-lated species. (A graphical method for aligning circular genomes is introduced in Box7.1; see Figs. 7.8 and 7.9.) In comparing E. coli K12 and O157:H7, the genes that areshared between the two strains not only are highly conserved at the sequence level; but
176 Part I I • THE ORIGIN AND DIVERSIFICATION OF LIFE
Graphical Alignment for Comparing Circular Genomes Using Dotplots
Comparing the arrangement of genomes is a critical tool for un-derstanding how they evolve. This enables scientists to identifyand characterize genome rearrangements (e.g., inversions andtranslocations) and to search for patterns and associations thatmay explain how and why certain events occur. For example,differences in gene order between species are frequently at siteswhere repetitive DNA is found, which suggests that recombina-tion at the repetitive DNA may have led to rearrangements. Oneof the more useful methods compares two genomes on an x–yplot, a procedure commonly referred to as a dotplot.
Dotplots let people use their visual pattern-recognitionskills to identify similarities. Their power and simplicityhave made them a valuable analytical tool in fields beyondbiology, including electrical engineering and computer sci-
ence. Let us illustrate the method using some text-based ex-amples. Figure 7.8A plots a familiar quotation against itself.The central diagonal line is the axis of identity. The outlyingpoints represent text that repeats. A quick examination candistinguish a pattern that is repeated in its entirety (Fig.7.8B) from one with some unique elements (Fig. 7.8C).
Because most bacterial and archaeal chromosomes are cir-cular, a chromosome must first be “opened” before laying it outon the x- or y-axis. Although the circle can be linearized at anypoint, it is preferable to open each chromosome at its origin ofreplication (Fig. 7.9A). One linearized chromosome is thenaligned along the x-axis with the origin of replication placed atthe graphical origin. The other chromosome is similarlyarranged along the y-axis. The two chromosomes are com-
MG1655 (K-12)nonpathogenic
EDL933 (0157:H7)enterohemorrhagic
585
514 204
1932996
1346
1623CFT073uropathogenic
FIGURE 7.7. Number of shared proteins be-tween strains of Escherichia coli. Note thelarge number of genes found in one strainbut not the others (seen in the outer portionsof each circle).
be
A B C
to
not
or
be
to
to be or not to be
edcbaedcba
a b c d e a b c d e
ed
zy
bc
aedcba
a b c d e a b c y z d e
FIGURE 7.8. Dotplots of repeating text.
Box 7.1
169-194_Evo_Ch07.qxd:13937_C05.qxd 12/15/08 11:05 AM Page 176
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Binary fission
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Binary fission
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Binary fission
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Binary fission
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Binary fission
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Binary fission
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Binary fission
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
58
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
58
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
58
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
58
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
58
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
58
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Differential reproduction
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Recombination in bacteria and archaea
DNA gets passed from one cell to another
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Recombination in bacteria and archaea
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This movement of DNA from one lineage to another, is known as lateral (or horizontal) gene transfer.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 62
Vertical Transmission Continues
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Sexual recombination in eukaryotes
63
In eukaryotes, the variants produced by mutation can “recombine” via sex
meiosis meiosis
fertilization
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lateral gene transfer
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 10 Outline
• Methods for studying microbes: ! Extremophiles as an example ! Field observations ! Culturing ! CSI Microbiology
65
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 10 Outline
• Methods for studying microbes: ! Extremophiles as an example ! Field observations ! Culturing ! CSI Microbiology
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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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 10 Outline
• Methods for studying microbes: ! Extremophiles as an example ! Field observations ! Culturing ! CSI Microbiology
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Field Observations an Important Tool
!70
Field Observations an Important Tool
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Field Observations an Important Tool
!70
Field Observations an Important Tool
!70
Field Observations an Important Tool
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Field Observations an Important Tool
!70
Field Observations an Important Tool
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Field Observations an Important Tool
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Field Observations an Important Tool
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Field Observations an Important Tool
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Field Observations an Important Tool
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Field Observations an Important Tool
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Field Observations an Important Tool
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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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 10 Outline
• Methods for studying microbes: ! Extremophiles as an example ! Field observations ! 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
Method 2: Culturing
!77
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
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rRNA rRNArRNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
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rRNA rRNArRNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
80
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
80
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
80
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
80
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
80
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaebacteria
!“What Are They Doing?”
via Culturing
!81
Example 1: Halophiles
!82
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
!8433
!8433
!8433
Grow starter culture
!8433
Grow starter culture
Set up some flasks with growth media
!8433
Grow starter culture
Set up some flasks with growth media
Add a small portion of the starter culture to flasks
!8433
Grow starter culture
Set up some flasks with growth media
Add a small portion of the starter culture to flasks
!8433
Grow starter culture
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
Grow starter culture
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
1M 2M 3M 4M
!8433
Grow starter culture
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
1M 2M 3M 4M
Monitor growth over time
!8433
Grow starter culture
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
1M 2M 3M 4M
Monitor growth over time
1 2 3 41M 2M 3M 4M1h 1h 1h 1h
!8433
Grow starter culture
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
1M 2M 3M 4M
Monitor growth over time
1 2 3 41M 2M 3M 4M1h 1h 1h 1h
1 2 3 41M 2M 3M 4M2h 2h 2h 2h
!8433
Grow starter culture
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
1M 2M 3M 4M
Monitor growth over time
1 2 3 41M 2M 3M 4M1h 1h 1h 1h
1 2 3 41M 2M 3M 4M2h 2h 2h 2h
1 2 3 41M 2M 3M 4M3h 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
• Some stresses of high salt ! Osmotic pressure on cells ! Desiccation
• Halophile adaptations ! Increased osmolarity inside cell
" Proteins " Carbohydrates " Salts
! Membrane pumps ! Desiccation resistance
Halophile adaptations
!89
H20
H20
• Some stresses of high salt ! Osmotic pressure on cells ! Desiccation
• Halophile adaptations ! Increased osmolarity inside cell
" Proteins " Carbohydrates " Salts - only done in extremely halophilic archaea
! Membrane pumps ! Desiccation resistance
Halophile adaptations
!90
• Some stresses of high salt ! Osmotic pressure on cells ! Desiccation
• Halophile adaptations ! Increased osmolarity inside cell
" Proteins " Carbohydrates " Salts - only done in extremely halophilic archaea
! Membrane pumps ! Desiccation resistance
Halophile adaptations
!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
Example 2: Thermophiles
!93
!9433
!9433
!9433
Grow starter culture
!9433
Grow starter culture
Set up some flasks with growth media
!9433
Grow starter culture
Set up some flasks with growth media
Add a small portion of the starter culture to flasks
!9433
Grow starter culture
Set up some flasks with growth media
Add a small portion of the starter culture to flasks
!9433
Grow starter culture
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
!9433
Grow starter culture
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
20° 30° 40° 50°
!9433
Grow starter culture
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
20° 30° 40° 50°
Monitor growth over time
!9433
Grow starter culture
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
20° 30° 40° 50°
Monitor growth over time
1 2 3 420° 30° 40° 50°1h 1h 1h 1h
!9433
Grow starter culture
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
20° 30° 40° 50°
Monitor growth over time
1 2 3 420° 30° 40° 50°1h 1h 1h 1h
1 2 3 420° 30° 40° 50°2h 2h 2h 2h
!9433
Grow starter culture
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
20° 30° 40° 50°
Monitor growth over time
1 2 3 420° 30° 40° 50°1h 1h 1h 1h
1 2 3 420° 30° 40° 50°2h 2h 2h 2h
1 2 3 420° 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
!98
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
\
!103
!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
Novozymes in Davis
!105
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 10 Outline
• Methods for studying microbes: ! Extremophiles as an example ! Field observations ! Culturing ! CSI Microbiology
106
Great Plate Count Anomaly
!107
Culturing Microscopy
Great Plate Count Anomaly
!108
Culturing Microscopy
CountCount
Great Plate Count Anomaly
!109
<<<<
Great Plate Count Anomaly
!110
Culturing Microscopy
CountCount
Great Plate Count Anomaly
!111
Problem because appearance not
effective for “who is out there?” or “what are they
doing?”
<<<<
Culturing Microscopy
CountCount
Great Plate Count Anomaly
!112
Problem because appearance not
effective for “who is out there?” or “what are they
doing?”
<<<<
Culturing Microscopy
CountCount
Solution?
Great Plate Count Anomaly
!113
Problem because appearance not
effective for “who is out there?” or “what are they
doing?”
<<<<
Culturing Microscopy
CountCount
Solution?
DNA
Collect from environment
Analysis of uncultured microbes
!114
Collect from environment
Analysis of uncultured microbes
!115
Deep Sea Ecosystems
!116
Deep Sea Ecosystems
!117
Polymerase Chain Reaction- PCR
!118
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaebacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaebacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
119
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaebacteria
Analysis of uncultured microbes
!120
NOTES 3419
A. pisum P
A. piswn S Tx. nivea
L awaaa symLL equizenata syrCud orbgcdar s,ym
rs. gesgosterorn - I/\ -- V IN. gonorrhoeae
B. Uhar.opkiuns sym
5% C. magncisca sym
Tns. sp. L-12
A. tnefaciens
R. ricketsil
FIG. 4. Unrooted phylogenetic tree showing the position of the S. velum symbionts in relation to that of other Proteobacteria species onthe basis of 16S rRNA gene sequences. The tree was constructed from evolutionary distances in Table 1. Members of the alpha and betasubclasses of the Proteobacteria are bracketed; all others are of the gamma subclass. Chemoautotrophic symbionts (sym) are listed inboldface type. Full species names listed in Table 1. Scale bar represents percent similarity.
dicted size bands for S. velum genomic DNA (Fig. 3A): AvaIand BclI, 1,080 bp; EcoNI, 1,109 bp; and Nco and Stul, 998bp (data not shown). We suggest that this technique isgenerally useful for the confirmation of the presence ofPCR-generated sequences in cells with multiple types ofDNA.The restriction patterns of 16S rRNA coding regions for
DNA extracted from S. velum gills were identical for all nineclams examined; representative results are shown in Fig. 3.This, along with the lack of variability in the partial sequenceof 16S rDNA for three individuals, suggests that there is asingle dominant bacterial species within S. velum and thatthe host-symbiont association is species specific. This resultis in agreement with the findings of Distel et al. (12) forlamellibranch bivalve and tubeworm chemoautotrophic sym-bionts.
Single bands were evident for all enzymes predicted to cutoutside or near the ends of the gene such as AvaI, Bcll,EcoNI, PvuII, XhoI (Fig. 3), and NcoI (band size, 9,600 bp;data not shown). Some of these enzymes generated restric-tion fragments larger than that of a typical bacterial ribo-somal operon (which includes the 5S, 16S, and 23S rRNAgenes [-5 kb]), indicating that the single bands observedwere not generated by double cuts within multiple operons.Furthermore, only two bands were observed for enzymespredicted to cut near the middle of the 16S rRNA gene suchas EcoRI (Fig. 3B) and StuI (bands of 4,400 and 19,500 bp;data not shown). Thus, all enzymes in all animals generatedpatterns consistent with the presence of only one copy of the16S rRNA gene in the symbiont genome (Fig. 3). However,
it should be noted that a large duplication of the regioncontaining the rRNA operon with no subsequent changes atany of the nine restriction sites could escape detection bythis analysis.These results suggest that the symbiont genome contains
but a single rRNA operon. Bacterial rRNA operons (rm),which include the 5S, 16S, and 23S rRNA genes, varyconsiderably in number among bacteria. In contrast tofree-living species of Proteobacteria, which have 4 to 7 rmloci (18), only one copy has been detected in other endosym-bionts including both the primary (P) and secondary (S)symbionts of the pea aphid, Acyrthosiphon pisum (33) (in-cluded in Fig. 4). Multiple rRNA operons have generallybeen thought necessary to support a high rate of rRNAsynthesis in rapidly dividing cells (3, 22). Unterman andBaumann (32) suggested that the aphid symbionts thereforegrow slowly, with doubling times of 2 days to parallel thegrowth rate of the aphid host. They further speculated thatthe single rRNA operon in the aphid symbiont genome is aconsequence of the adaptation to a symbiotic existence,which necessitates a slow growth rate. Although the divisionrate of S. velum symbionts is not known, it is unlikely thatthey grow slowly, since they must produce all of the biomassfor their invertebrate host. Studies of rn copy number andgrowth rates of endosymbionts and their free-living relativesfrom a variety of phylogenetic groups may help resolve thesignificance of rRNA operon redundancy.
Phylogenetic analysis of the S. velum symbionts. Phyloge-netic analysis was conducted using the Genetic Data Envi-ronment program (Steve Smith, Harvard Genome Laborato-
VOL. 174, 1992
JOURNAL OF BACTERIOLOGY, May 1992, p. 3416-3421 Vol. 174, No. 100021-9193/92/103416-06$02.00/0Copyright © 1992, American Society for Microbiology
Phylogenetic Relationships of Chemoautotrophic BacterialSymbionts of Solemya velum Say (Mollusca: Bivalvia) Determined
by 16S rRNA Gene Sequence AnalysisJONATHAN 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 symbiontsintracellularly within its gills. These symbionts were characterized through sequencing of polymerase chainreaction-amplified 16S rRNA coding regions and hybridization of an Escherichia coli gene probe to S. velumgenomic DNA restriction fragments. The symbionts appeared to have only one copy of the 16S rRNA gene. Thelack of variability in the 16S sequence and hybridization patterns within and between individual S. velumorganisms suggested that one species of symbiont is dominant within and specific for this host species.Phylogenetic analysis of the 16S sequences of the symbionts indicates that they lie within the chemoautotrophiccluster of the gamma subdivision of the eubacterial group Proteobacteria.
Procaryote-eucaryote associations in which marine inver-tebrates harbor chemoautotrophic bacteria as endosym-bionts appear to be widespread in marine habitats such asdeep-sea hydrothermal vents and coastal sediments (8, 15).In such symbioses, the procaryotes utilize the energy re-leased by the oxidation of reduced inorganic substrates, suchas hydrogen sulfide, to fix carbon dioxide via the Calvin-Benson cycle (7, 13). The hosts appear to derive nutritionfrom their endosymbionts and in turn provide the symbiontssimultaneous access to the substrates from anoxic and oxicenvironments which are necessary for energy generation.Maintenance of such intracellular symbionts presents anovel metazoan acquisition of procaryotic energy generationand autotrophic carbon fixation.While the existence of chemoautotroph-invertebrate sym-
bioses is now generally accepted, little is actually knownabout the symbionts observed in the tissues of any of thehosts because none have been cultured. Comparison ofrRNA sequences has greatly facilitated the identification ofbacteria, including unculturable microorganisms, and theelucidation of their natural relationships (38). Phylogeneticanalysis of 16S rRNA sequences enabled Distel et al. (12) toestablish that the chemoautotrophic symbionts of the hydro-thermal vent tubeworm and five species of bivalves of thesubclass Lamellibranchia are related and cluster in thegamma subdivision of the Proteobacteria (formerly purplephotosynthetic bacteria), one of the 11 major groups ofeubacteria (30).
In this investigation we sought to establish the phyloge-netic relationships and the species specificities of the sym-bionts of the protobranch bivalve Solemya velum Say, anAtlantic coast clam which has been studied as a shallow-water model of invertebrate-chemoautotroph associations(7, 9, 10). The phylogenetic placement of the S. velumsymbionts, to date limited to sequence analysis of the 5SrRNA, indicates that these symbionts also fall in the Proteo-bacteria gamma subdivision (31). However, the small size of
* Corresponding author.t Present address: Department of Biological Sciences, Stanford
University, Stanford, CA 94305.
the 5S rRNA molecule (-120 bp) precludes resolution thatcan be attained with larger molecules such as 16S rRNA(-1,550 bp) (16). Species of the genus Solemya are, to date,the only bivalves of the subclass Protobranchia in whichchemoautotrophic symbiosis has been documented. Theprotobranchs represent an important component of studiesof chemoautotrophic symbioses, since they may be theclosest living group to the ancestral bivalve condition, be-cause they dominate the deep sea and are present along agradient from the deep sea bottom to the shore (1).PCR amplification. We used the polymerase chain reaction
(PCR) (28) to amplify 16S rRNA coding regions from amixture of procaryotic and eucaryotic DNA extracted fromthe symbiont-containing gills of S. velum. S. velum werecollected from eelgrass beds near Woods Hole, Mass., andplaced in filtered (passed through filters with a pore size of0.2 ,um) seawater to cleanse body surfaces prior to dissec-tion. The gills, which contain -109 bacterial symbionts per g(wet weight), and feet, in which symbionts have not beenobserved (7), were dissected, frozen in liquid nitrogen, andstored at -85° C. Frozen tissue was homogenized in lysisbuffer, and DNA was isolated by using hexadecyltrimethy-lammonium bromide (4). DNA from Escherichia coli JM109,prepared by the miniprep method (4), was used as a positivecontrol.
Amplification of 16S rRNA genes by PCR was carried outessentially by the method of Weisburg et al. (34) usingeubacterial universal primers and 200 ng of template DNA.DNA products (Fig. 1) amplified from S. velum gill tissue(lane 1) and from the positive-control E. coli (lane 4) wereprominent single bands of approximately 1,500 bp. Amplifi-cation was not detected when DNA template was not added(lane 2), nor when DNA from S. velum foot tissue was usedas the template (lane 3).The strong amplification from gill tissue DNA and lack of
amplification from foot tissue DNA (Fig. 1) supports theconclusions from studies of enzyme activity, electron mi-croscopy (9), and 5S rRNA sequences (31) that the bacteriaare abundant within, and specific to, the gill tissue. Thisconclusion was further supported by lack of hybridization of
3416
Collect from environment
Analysis of uncultured microbes
!121
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaebacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Woese Tree of Life
122
DNA DNADNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
EukaryotesBacteria Archaebacteria
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
Censored
Censored
!126
• 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
Classes of symbiosis
Organism
Class of symbiosis A B
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
Deep Sea Ecosystems
!132
Deep Sea Ecosystems
!133
• 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
Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!135
Classes of symbiosis
Organism
Class of symbiosis A B
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
Lateral Gene Transfer
!140
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Case 1: Antibiotic Resistance
141
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Antibiotic Resistance Evolves Rapidly
142
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
• http://www.niaid.nih.gov/SiteCollectionImages/topics/antimicrobialresistance/3geneTransfer.gif
143
Antibiotic Resistance Can Transfer Between Species
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Case 2: E. coli
144
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 145
substantial variation in gene content among members of the same species have beenreported in other lineages of bacteria and archaea. Thus, the diminishing number ofcore orthologous genes is simply an extension of something happening among closerelatives.
How do such extensive differences in gene content among close relatives originate?One of the most important clues comes from comparing the genome structures of re-lated species. (A graphical method for aligning circular genomes is introduced in Box7.1; see Figs. 7.8 and 7.9.) In comparing E. coli K12 and O157:H7, the genes that areshared between the two strains not only are highly conserved at the sequence level; but
176 Part I I • THE ORIGIN AND DIVERSIFICATION OF LIFE
Graphical Alignment for Comparing Circular Genomes Using Dotplots
Comparing the arrangement of genomes is a critical tool for un-derstanding how they evolve. This enables scientists to identifyand characterize genome rearrangements (e.g., inversions andtranslocations) and to search for patterns and associations thatmay explain how and why certain events occur. For example,differences in gene order between species are frequently at siteswhere repetitive DNA is found, which suggests that recombina-tion at the repetitive DNA may have led to rearrangements. Oneof the more useful methods compares two genomes on an x–yplot, a procedure commonly referred to as a dotplot.
Dotplots let people use their visual pattern-recognitionskills to identify similarities. Their power and simplicityhave made them a valuable analytical tool in fields beyondbiology, including electrical engineering and computer sci-
ence. Let us illustrate the method using some text-based ex-amples. Figure 7.8A plots a familiar quotation against itself.The central diagonal line is the axis of identity. The outlyingpoints represent text that repeats. A quick examination candistinguish a pattern that is repeated in its entirety (Fig.7.8B) from one with some unique elements (Fig. 7.8C).
Because most bacterial and archaeal chromosomes are cir-cular, a chromosome must first be “opened” before laying it outon the x- or y-axis. Although the circle can be linearized at anypoint, it is preferable to open each chromosome at its origin ofreplication (Fig. 7.9A). One linearized chromosome is thenaligned along the x-axis with the origin of replication placed atthe graphical origin. The other chromosome is similarlyarranged along the y-axis. The two chromosomes are com-
MG1655 (K-12)nonpathogenic
EDL933 (0157:H7)enterohemorrhagic
585
514 204
1932996
1346
1623CFT073uropathogenic
FIGURE 7.7. Number of shared proteins be-tween strains of Escherichia coli. Note thelarge number of genes found in one strainbut not the others (seen in the outer portionsof each circle).
be
A B C
to
not
or
be
to
to be or not to be
edcbaedcba
a b c d e a b c d e
ed
zy
bc
aedcba
a b c d e a b c y z d e
FIGURE 7.8. Dotplots of repeating text.
Box 7.1
169-194_Evo_Ch07.qxd:13937_C05.qxd 12/15/08 11:05 AM Page 176
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
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Binary fission
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Binary fission
149
Binary fission generates a cell lineage “tree” = analogous to a phylogenetic tree
Binary fission
149
Binary fission generates a cell lineage “tree” = analogous to a phylogenetic tree
Binary fission
149
Binary fission generates a cell lineage “tree” = analogous to a phylogenetic tree
Binary fission
149
Binary fission generates a cell lineage “tree” = analogous to a phylogenetic tree
Binary fission
149
Binary fission generates a cell lineage “tree” = analogous to a phylogenetic tree
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
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
150
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
150
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
150
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
150
Mutations happen…
Mutation = heritable change in the genome (i.e., some change in DNA bases)
150
Differential reproduction
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Differential reproduction
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Not all variants reproduce equally well
Note - equivalent processes happen in eukaryotes
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Note - equivalent processes happen in eukaryotes
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Binary fission is a form of asexual reproduction
Note - equivalent processes happen in eukaryotes
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Binary fission is a form of asexual reproduction
Leads to “clonality”
Note - equivalent processes happen in eukaryotes
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Binary fission is a form of asexual reproduction
Also known as “vertical transmission”Leads to “clonality”
DNA gets passed from one cell to another
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Recombination in bacteria and archaea
The recipient can mix the new DNA with its own 154
DNA gets passed from one cell to another
Recombination in bacteria and archaea
This movement of DNA from one lineage to another, is known as lateral (or horizontal) gene transfer.
Normal vertical transmission cont.
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The recipient can mix the new DNA with its own
DNA gets passed from one cell to another
Recombination in bacteria and archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 156
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lateral inheritance I: Competence
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lateral inheritance II: Conjugation
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lateral inheritance III: Transduction
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 160
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