Slides for BIs2C at UC Davis Spring 2016. Lecture by Jonathan Eisen. Topic: Microbial Growth and Functions

1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 11:
Microbial Growth and Functions
BIS 002C
Biodiversity & the Tree of Life
Spring 2016
Prof. Jonathan Eisen
1

2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Where we are going and where we have been
• Previous Lecture:
!10: Not a Tree
• Current Lecture:
!11: Microbial Growth and Functions
• Next Lecture:
!12: Symbiosis
2

3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• What are the ranges of conditions in which
life on Earth lives?
• What are the ranges of conditions in which
life on Earth prefers to live?
• What are the key ways that living systems
acquire carbon and energy?
3

4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Key Concepts and Topics
• Culturing
• Extremophily
!Thermophiles
!Halophiles
• Trophies
• Oxygen
• More on organelles
4

5. 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
!5

6. General approach to culturing
! Collect sample
! Make an environment with 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
!6

7. Culturing
!7

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

9. Mitosis
!9

10. Binary fission and Mitosis Clonal Growth
10

11. 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.
!11

12. Function Example I:
Extremophily
!12

13. Example 1: Thermophiles
!13

14. Figure 26.16 Some Crenarchaeotes Like It Hot
!14

15. Figure 26.14 What Is the Highest Temperature Compatible with Life?
!15
Some prokaryotes can survive at temperatures above the 120°C
threshold of sterilization.
1. Seal samples of unidentified, iron-reducing, thermal vent prokaryotes in tubes with a medium
containing Fe3+ as an electron acceptor. Control tubes contain Fe3+ but no organisms.
2. Hold both tubes in a sterilizer at 121°C for 10 hours. if the iron-reducing organisms are metabolically
active, they will reduce the Fe3+ to Fe2+ (as magnetite, which can be detected with a magnet).
Archaea of “Strain 121” can survive at temperatures above the
previously defined sterilization limit.

16. Set up some
flasks with
growth media
60° 70° 80° 90°
1 2 3 4 Use different
flasks for
different
conditions
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time

17. 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° 80° 90°
1h 1h 1h 1h
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time

18. 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° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time

19. 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° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
1 2 3 4
60° 70° 80° 90°
3h 3h 3h 3h
Determining Optimal Growth Temperature
!1633
Grow starter culture
Add a small
portion of the
starter culture
to flasks
Monitor growth over time

20. 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 Elapsed
DensityofGrowth

21. 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
GrowthRate

22. Optimal growth temperature (OGT) for Different Species
!19

23. Optimal growth temperature (OGT) for Different Species
!21
A > B >> E
Mesophile Optimum at 15-45 °C
Thermophile Optimum at 45-80°C
Hyperthermophile Optimum at > 80°C

24. 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.doi.org/10.1038/nmicrobiol.2016.48

25. Hug et al 2016
!24
Thermophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
What are some possible
evolutionary scenarios
that would account for this
pattern of presence of
thermophily across the
Tree of Life?

26. Thermophile Adaptations
!30
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

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

28. Determining Optimal Salt Concentrations
!3233
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

29. Determining Optimal Salt Concentrations
!3233
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 4
1M 2M 3M 4M
1h 1h 1h 1h

30. Determining Optimal Salt Concentrations
!3233
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 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h

31. Determining Optimal Salt Concentrations
!3233
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 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

32. 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
DensityofGrowth

33. 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

34. Optimal salt concentration for different species
!35

35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Euryarchaeota: Halophiles (Salt lovers)
• Pink carotenoid
pigments – very visible
• Have been found at
pH up to 11.5.
• Unusual adaptations
to high salt,
desiccation
• Many have
bacteriorhodopsin
which uses energy of
light to synthesize ATP
(photoheterotrophs)
36

36. Hug et al 2016
!38
Extreme Halophiles Across the Tree
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
What are some possible
evolutionary scenarios
that would account for this
pattern of presence of
halophily across the Tree
of Life?

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

38. • 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
!40
H20
H20

39. • 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
!42
High internal salt requires ALL cellular components to be
adapted to salt, charge. For example, all proteins must
change surface charge and other properties.

40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Uses of extremophiles
!43
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

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

42. Function Example I:
Trophies
!45

43. Incredible diversity in forms of nutrition in bacteria and archaea
• Bacteria and archaea exhibit incredible diversity in how
they obtain nutrition (i.e., the processes by which an
they assimilates chemicals and energy and uses them for
growth)
• Generally referred to with the suffix “trophy”
• Origin: Greek -trophiā, from trophē, from trephein, to
nourish.
• Examples:
! autotrophy
! chemotrophy
! phototrophy
! heterotrophy
!46

44. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• Three main components to “trophy”

45. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• E. coli • Chemo organo hetero trophy
• Chemo hetero trophy

46. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• Humans? • Chemo organo hetero trophy
• Chemo hetero trophy

47. Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Forms of nutrition (trophy)
• Cyanobacteria • Photo litho auto trophy
• Photo auto trophy

48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51
αProteo
Genome
Bacterial cell envelope
Cell
membrane
Genome
A Symbiosis with a Proteobacterium

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

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

51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Symbiosis with Free Living Cyanobacterium
54
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Engulfment
55
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

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

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

55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
What is the different between
chemoautolithotrophy and
chemoheterolithotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above
58

56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
What is the different between
chemoautolithotrophy and
chemoheterolithotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: A, B and C
59

57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Growth vs. Oxygen
60
Aerobes vs. Anaerobes
Microbes differ in their use and tolerance of oxygen.
1. Aerobes- Require oxygen
2. Anaerobes- Vary in their tolerance/ use of oxygen
Obligate anaerobes – oxygen is toxic.
Aerotolerant anaerobes – can’t
use oxygen, but are not
damaged by it.
Facultative anaerobes – don’t need
oxygen, but use it when available.

58. Organelle Evolution
61

59. Simple Species Tree for Three Domains
62
Archaea Eukaryotes Bacteria

60. 63
Archaea Euks BacteriaTACK
Eocyte Species Tree for Three Domains

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

62. Endosymbiosis Shown on Species Tree
65
Archaea Euks BacteriaTACK

63. Continued Evolution After Endosymbiosis
66
Archaea Euks BacteriaTACK

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

65. 68
Suppose we built
phylogenetic trees
with different genes
from each of these
species
A2 E1 PBT E2 B2 B3 B4A1 A3
Simple Model Showing Some Diversification within Eukaryotes

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

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

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

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

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

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

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

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

74. Mitochondrial Genes
78
A2 E1 PBT E2 B2 B3 B4A1 A3 E3
The topology of the tree within
Eukaryotes is the same
regardless of which genes.
They differ in where
eukaryotes placed in the tree.

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

76. 80
Another Symbioses - with a CB - Cyanobacterium
Archaea T PBEukaryotes CB B3 B4

77. 81
Continued Evolution - Diversification of Plants
Archaea T PBE1 CB B3 B4E2 Plants
Suppose we built
phylogenetic trees
with different genes
from each of these
species