BiS2C: Lecture 11: Microbial Growth and Functions

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 11:
Microbial Growth and Functions
BIS 002C
Biodiversit...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Where we are going and where we have been
• Previous Lecture:
!...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• What are the ranges of condit...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Key Concepts and Topics
• Culturing
• Extremophily
!Thermophile...

Culturing
• Culturing (or cultivation) is the growth of microorganisms
in controlled or defined conditions.
• A pure cultu...

General approach to culturing
! Collect sample
! Make an environment with specific growth conditions
" Energy
" Electrons
...

Culturing
!7

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotic Cell Division (Part 1)
8

Mitosis
!9

Binary fission and Mitosis Clonal Growth
10

Examples of Benefits of Culturing:
• Allows one to connect processes and properties to single
types of organisms
• Enhance...

Function Example I:
Extremophily
!12

Example 1: Thermophiles
!13

Figure 26.16 Some Crenarchaeotes Like It Hot
!14

Figure 26.14 What Is the Highest Temperature Compatible with Life?
!15
Some prokaryotes can survive at temperatures above ...

Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
Determining Opt...

Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70°...

Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70°...

Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
1 2 3 4
60° 70°...

Growth vs. Time
!17
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
60° 70° 80° 90°
Plot Growth vs. Time for Each Condition
Time Elaps...

Growth Rate
!18
0.0
12.5
25.0
37.5
50.0
60 °C 70 °C 80 °C 90° C
Calculate and Plot Growth Rate vs. Conditions
Temperature
...

Optimal growth temperature (OGT) for Different Species
!19

Optimal growth temperature (OGT) for Different Species
!21
A > B >> E
Mesophile Optimum at 15-45 °C
Thermophile Optimum at...

Hug et al 2016
!22
Hug et al. 2016 Tree of Life
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx....

Hug et al 2016
!24
Thermophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx....

Thermophile Adaptations
!30
Stresses of High
Temperature
Examples of common
adaptations
Denatures proteins, RNA
and DNA
Ma...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Example 1: Extreme Halophiles
31

Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portio...

Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portio...

Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portio...

Determining Optimal Salt Concentrations
!3233
Grow starter culture
Set up some
flasks with
growth media
Add a small
portio...

Growth vs. Time
Plot Growth vs. Time for Each Condition
!33
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
1M 2M 3M 4M
Time Elapsed
D...

Growth Rate
!34
0.0
12.5
25.0
37.5
50.0
1M 2M 3M 4M
Calculate and Plot Growth Rate vs. Conditions
Salinity
GrowthRate

Optimal salt concentration for different species
!35

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Euryarchaeota: Halophiles (Salt lovers)
• Pink carotenoid
pigme...

Hug et al 2016
!38
Extreme Halophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http...

• Some stresses of high salt
! Osmotic pressure on cells
! Desiccation
Halophile adaptations
!39
H20

• Some stresses of high salt
! Osmotic pressure on cells
! Desiccation
• Halophile adaptations
! Increased osmolarity insi...

• Some stresses of high salt
! Osmotic pressure on cells
! Desiccation
• Halophile adaptations
! Increased osmolarity insi...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Uses of extremophiles
!43
Type of
environment
Examples Example ...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Novozymes in Davis
44

Function Example I:
Trophies
!45

Incredible diversity in forms of nutrition in bacteria and archaea
• Bacteria and archaea exhibit incredible diversity in ...

Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
O...

Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
O...

Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
O...

Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
O...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51
αProteo
Genome
Bacterial cell envelope
Cell
membrane
Genome
...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Engulfment
52
αProteo
Cell
membrane
Genome
Genome
Bacterial cel...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What Does This Provide Host?
53

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Symbiosis with Free Living Cyanobacterium
54
N
Mitochondrion
Mi...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Engulfment
55
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Ce...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What Does This Provide Host?
56

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
57

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
What is the different between
chemoautolithotr...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
What is the different between
chemoautolithotr...

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Growth vs. Oxygen
60
Aerobes vs. Anaerobes 
Microbes differ in ...

Organelle Evolution
61

Simple Species Tree for Three Domains
62
Archaea Eukaryotes Bacteria

63
Archaea Euks BacteriaTACK
Eocyte Species Tree for Three Domains

Acquisition of Mitochondria At Base of Eukaryotic Branch
64
Archaea Euks BacteriaTACK

Endosymbiosis Shown on Species Tree
65
Archaea Euks BacteriaTACK

Continued Evolution After Endosymbiosis
66
Archaea Euks BacteriaTACK

Simple Model Showing Some Diversification within Eukaryotes
67
A2 E1 PBT E2 B2 B3 B4A1 A3

68
Suppose we built
phylogenetic trees
with different genes
from each of these
species
A2 E1 PBT E2 B2 B3 B4A1 A3
Simple M...

Gene Set 1
69
A2 E1 PBT E2 B2 B3 B4A1 A3
Some Genes with
Show This Pattern
with Eukaryotes
Sister to TACK

Gene Set 2: Organellar Genes
70
A2 E1 PBT E2 B2 B3 B4A1 A3
Some Genes with Show
Alternative Pattern With
“Eukaryotes” Bran...

After Additional Speciation in the Eukaryote Portion of the Tree
71
A2 E1 PBT E2 B2 B3 B4A1 A3 E3

Gene transfer model
72
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
Suppose we built
phylogenetic trees
with different genes
from each of...

Nuclear Genes
73
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
Some Genes with
Show This Pattern
with Eukaryotes
Sister to TACK

Nuclear Genes
74
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
Note - Branching of
E2 sister to E3

Mitochondrial Genes
76
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
Some Genes with Show
Alternative Pattern With
“Eukaryotes” Branching
...

Mitochondrial Genes
77
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
Note - Branching of
E2 sister to E3

Mitochondrial Genes
78
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
The topology of the tree within
Eukaryotes is the same
regardless of ...

Another Symbioses - with a CB - Cyanobacterium
79
Archaea T PBEukaryotes CB B3 B4

80
Another Symbioses - with a CB - Cyanobacterium
Archaea T PBEukaryotes CB B3 B4

81
Continued Evolution - Diversification of Plants
Archaea T PBE1 CB B3 B4E2 Plants
Suppose we built
phylogenetic trees
wi...

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