BIS2C: Lecture 35: Symbioses Across the Tree of Life

1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 35:
Interactions Across The Tree of Life
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…
2
•Previous lecture:
•34: Fungi
•Current Lecture:
•35: The End
•Next Lecture:
•36: The Future

3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
The Tree of Life (used in LIFE Version 10)
3

4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 4
BIS2C is ORGANIZED BY THE
TREE OF LIFE
and
PHYLOGENY
The Tree of Life (used in LIFE Version 10)

5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 5
Week 1
Phylogeny
Week 1: Phylogenetic Trees

6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
6
Week 2
Trees of Life?

7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 7
Week 2
The Tree of Life
Week 2: The Tree of Life

8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
8
Week 3
Microbial
Diversity
Week 3: Microbial Diversity

9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 4-5: Plants
9
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 4-5
Plants

10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 4-5: Plants
10
Weeks 4-5
Plants

11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 7-9: Animals
11
Weeks 6-8
Animals

12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 7-9: Animals
12
Weeks 6-8
Animals

13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Week 6: Fungi
13
Week 9
Fungi

14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Week 6: Fungi
14
Week 9
Fungi

15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Napa Vineyard
15

16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 18
Pierce’s Disease

17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Pierce’s Disease
• Caused by overgrowth of
Xylella fastidiosa, a
bacterium
19

18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Pierce’s Disease
• Caused by overgrowth of
Xylella fastidiosa, a
bacterium
19
Xylem

19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Pierce’s Disease
• Caused by overgrowth of
Xylella fastidiosa, a
bacterium
19
Xylem

20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Pierce’s Disease
• Caused by overgrowth of
Xylella fastidiosa, a
bacterium
• Blocks xylem circulation
• Eventually whole plant dies
• Vines, even whole
vineyards, if infected may
be destroyed
• Same bacterial species
causes problems in many
other plants
• Potential for billions of $$
of economic damage
• Many of world’s experts at
UC Davis and other UCs
19
Xylem

21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
• What kind of symbiosis is the one between Xylella and
Grapes?
• A: Mutualism
• B: Pathogenism
• C: Commensalism
• D: Parasitism
• E: Primary
20

22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
• What kind of symbiosis is the one between Xylella and
Grapes?
• A: Mutualism
• B: Pathogenism
• C: Commensalism
• D: Parasitism
• E: Primary
21

23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 22
Pierce’s Disease
Should be easy to contain
Prevent plant to plant contact
Like w/ human infectious diseases

24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Vectors for Blood Borne Diseases
23

25. • Obligate xylem feeder
• Transmits Xylella between
plants
• Much like mosquitoes
transmit malarial pathogen
• Only animal listed as
possible “bioterror” agent
by US DHS
!24
Glassy winged sharpshooter
GLASSY-WINGED
SHARPSHOOTERASeriousThreattoCaliforniaAgriculture
FROM THE
UNIVERSITY OF CALIFORNIA’S
PIERCE’S DISEASE RESEARCH AND
EMERGENCY RESPONSE TASK FORCE
This informational brochure was produced by ANR
Communication Services for the University of Califor-
nia Pierce’s Disease Research and Emergency
Response Task Force. You may download a copy of the
brochure from the Division of Agriculture and Natural
Resources web site at http://danr.ucop.edu or from the
Communication Services web site at
http://danrcs.ucdavis.edu.
For local information, contact your UC Cooperative
Extension farm advisor:
Adults
Egg masses
Glassy-winged Sharpshooter
Generalized Lifecycle
100
80
60
40
20
0
Jan.
Mar.
May
July
Sept.
Nov.
Glassy-winged sharpshooters overwinter as adults
and begin laying egg masses in late February
through May. This first generation matures as
adults in late May through late August. Second-
generation egg masses are laid starting in mid-
June through late September, which develop into
over-wintering adults.

26. Clicker
• The glassy winged sharpshooter is an insect. Which of the
following groups are insects part of?
• A. Chordata
• B. Diploblasts
• C. Deuterostomes
• D. Protostomes
• E. None of the above
!25

27. Clicker
• The glassy winged sharpshooter is an insect. Which of the
following groups are insects part of?
• A. Chordata
• B. Diploblasts
• C. Deuterostomes
• D. Protostomes
• E. None of the above
!26

28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

30. Symbiosis between Xylella and sharpshooter?
Symbiosis between Xylella and sharpshooters
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!30

31. Symbiosis between Xylella and sharpshooter?
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!31
Symbiosis between Xylella and sharpshooters

32. Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!32
Symbiosis between Xylella and sharpshooter?
Symbiosis between Xylella and sharpshooters

33. Figure 35.11 The Pressure Flow Model
!33Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Source
cell
Phloem
sieve
tube
Xylem
Sink cell
Sucrose
Sucrose
H2O
H2O
H2O
H2O
Which Would You Choose to Eat?

34. Figure 35.11 The Pressure Flow Model
!34Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Source
cell
Phloem
sieve
tube
Xylem
Sink cell
Sucrose
Sucrose
H2O
H2O
H2O
H2O

35. 35.12 Aphids Live off Phloem Sap
!35

36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Mosquito Feeding
36

37. Aphids are very successful (> 4000 species, everywhere you look)
!37

38. Figure 35.11 The Pressure Flow Model
!38Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Source
cell
Phloem
sieve
tube
Xylem
Sink cell
Sucrose
Sucrose
H2O
H2O
H2O
H2O

39. Figure 35.11 The Pressure Flow Model
!39Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Source
cell
Phloem
sieve
tube
Xylem
Sink cell
Sucrose
Sucrose
H2O
H2O
H2O
H2O

40. !40
Xylem feeding insects also very successful

41. Plant vs. Insect
• Thicken walls
!41
Plant Adaptations Insect Responses
• Better piercing

42. Plant vs. Insect
• Thicken walls
!41
Plant Adaptations Insect Responses
• Better piercing

43. Plant vs. Insect
• Thicken walls
!41
Plant Adaptations Insect Responses
• Better piercing

44. Plant vs. Insect
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Remove key nutrients
!41
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• ????

45. Figure 35.11 The Pressure Flow Model
!42Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Source
cell
Phloem
sieve
tube
Xylem
Sink cell
Sucrose
Sucrose
H2O
H2O
H2O
H2O
• Very low in
sugar

46. How Deal With Very Low Sugar?
!43Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

47. How Deal With Very Low Sugar?
!43Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

48. !44Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

49. !45Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

50. Tree Rain in Tahiti
!46

51. Figure 35.11 The Pressure Flow Model
!47Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Source
cell
Phloem
sieve
tube
Xylem
Sink cell
Sucrose
Sucrose
H2O
H2O
H2O
H2O
• Very low in
sugar
• Remove
essential amino
acids
• Remove
vitamins and
cofactors

52. !48Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Reduced sugar
• Removes key amino acids
• Removes vitamins
• Removes cofactors
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• Pump a lot
• ???
• ???
• ???

53. !49Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Reduced sugar
• Removes key amino acids
• Removes vitamins
• Removes cofactors
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• Pump a lot
• Eat other things
• Eat other things
• Eat other things

54. !50
Severe Feeding Constraints

55. !51Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Reduced sugar
• Removes key amino acids
• Removes vitamins
• Removes cofactors
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• Pump a lot
• ???
• ???
• ???

56. !52Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Reduced sugar
• Removes key amino acids
• Removes vitamins
• Removes cofactors
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• Pump a lot
• Evolve synthetic pathway
• Evolve synthetic pathway
• Evolve synthetic pathway

57. !52Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Reduced sugar
• Removes key amino acids
• Removes vitamins
• Removes cofactors
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• Pump a lot
• Evolve synthetic pathway
• Evolve synthetic pathway
• Evolve synthetic pathway

58. !53Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Reduced sugar
• Removes key amino acids
• Removes vitamins
• Removes cofactors
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• Pump a lot
• ???
• ???
• ???

59. How Do Eukaryotes Get Many New Biochemical Functions?
• Eukaryotic organelles (plastids and mitochondria)
• Secondary symbioses (eukaryote with another eukaryote)
• Lichens (fungi and photosynthetic microbe)
• Coral & dinoflagellates (zooxanthellae)
• Ant - fungus farming
• Pogonophoran worms and chemosynthetic bacteria
• Legumes and N2 fixing bacteria
• Herbivores and cellulolytic gut microbes
• Wood eating organisms and gut microbes
!54

60. !55Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Thicken walls
• Fill up xylem with toxins
• Immune response
• Reduced sugar
• Removes key amino acids
• Removes vitamins
• Removes cofactors
Plant Adaptations Insect Responses
• Better piercing
• Detoxify
• Immune suppression
• Pump a lot
• Symbiosis
• Symbiosis
• Symbiosis

61. !56

62. Moran N. A. PNAS 2007;104:8627-8633
©2007 by National Academy of Sciences
!57
Sharpshooter:
Cuerna sayi
bacteriomes
symbionts in their bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbio
Candidatus “Baumannia cicadellinicola” (Gammaproteobacteria)
Candidatus “Sulcia muelleri” (Bacteroidetes)
D Takiya
10!m
“Candidatus Baumannia cicadellinicola” (Gammaproteoba
in “red” portion of bacteriome of Homalodisca vitripennis
N=host nucleus B=Bacteriocyte membrane E=Endosym
Irregu
~2 !m

63. Studying the microbe-like entities in the aphid gut
!58
Field Observations
Sharpshooter:
Cuerna sayi
bacteriomes
Sharpshooters harbor two obligate
symbionts in their bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
Candidatus “Baumannia cicadellinicola” (Gammaproteobacteria)
Candidatus “Sulcia muelleri” (Bacteroidetes)
D Takiya
0.1mm
Bacteriome dissected from anterior abdomen of H. vitripennis
Orange-red portion- Baumannia only
Yellow portion- Baumannia and Sulcia
(Moran et al. 2003 Environmental Microbiology)

64. Studying the microbe-like entities in the aphid gut
!59
Field Observations
Appearance of
limited value
Sharpshooter:
Cuerna sayi
bacteriomes
Sharpshooters harbor two obligate
symbionts in their bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
Candidatus “Baumannia cicadellinicola” (Gammaproteobacteria)
Candidatus “Sulcia muelleri” (Bacteroidetes)
D Takiya
0.1mm
Bacteriome dissected from anterior abdomen of H. vitripennis
Orange-red portion- Baumannia only
Yellow portion- Baumannia and Sulcia
(Moran et al. 2003 Environmental Microbiology)

65. !60
Culturing Field Observations
Studying the microbe-like entities in the aphid gut
Appearance of
limited value
Sharpshooter:
Cuerna sayi
bacteriomes
Sharpshooters harbor two obligate
symbionts in their bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
Candidatus “Baumannia cicadellinicola” (Gammaproteobacteria)
Candidatus “Sulcia muelleri” (Bacteroidetes)
D Takiya
0.1mm
Bacteriome dissected from anterior abdomen of H. vitripennis
Orange-red portion- Baumannia only
Yellow portion- Baumannia and Sulcia
(Moran et al. 2003 Environmental Microbiology)

66. !61
Culturing Field Observations
Key bacteria in
sharpshooter gut have
not been cultured
Studying the microbe-like entities in the aphid gut
Appearance of
limited value
Sharpshooter:
Cuerna sayi
bacteriomes
Sharpshooters harbor two obligate
symbionts in their bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
Candidatus “Baumannia cicadellinicola” (Gammaproteobacteria)
Candidatus “Sulcia muelleri” (Bacteroidetes)
D Takiya
0.1mm
Bacteriome dissected from anterior abdomen of H. vitripennis
Orange-red portion- Baumannia only
Yellow portion- Baumannia and Sulcia
(Moran et al. 2003 Environmental Microbiology)

67. !62
Culturing Field Observations
Studying the microbe-like entities in the aphid gut
Appearance of
limited value
DNA
Key bacteria in
sharpshooter gut have
not been cultured
Sharpshooter:
Cuerna sayi
bacteriomes
Sharpshooters harbor two obligate
symbionts in their bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
Candidatus “Baumannia cicadellinicola” (Gammaproteobacteria)
Candidatus “Sulcia muelleri” (Bacteroidetes)
D Takiya
0.1mm
Bacteriome dissected from anterior abdomen of H. vitripennis
Orange-red portion- Baumannia only
Yellow portion- Baumannia and Sulcia
(Moran et al. 2003 Environmental Microbiology)

68. • What is this issue with the difficulty in culturing organisms been
called?
• A. Great microscope anomaly
• B. Great count anomaly
• C. Great plate count anomaly
• D. Grate cheese anomaly
• E. Great plating anomaly
!63

69. • What is this issue with the difficulty in culturing organisms been
called?
• A. Great microscope anomaly
• B. Great count anomaly
• C. Great plate count anomaly
• D. Grate cheese anomaly
• E. Great plating anomaly
!64

70. • Who Are These Microbes?
!65

71. DNA
extraction
PCR
Sequence
rRNA genes
Sequence alignment = Data matrixPhylogenetic tree
PCR
rRNA1
Yeast
Makes lots of
copies of the
rRNA genes
in sample
E. coli
Humans
A
T
T
A
G
A
A
C
A
T
C
A
C
A
A
C
A
G
G
A
G
T
T
C
rRNA1
E. coli Humans
Yeast
!66
rRNA1
5’ ...TACAGTATAGGTG
GAGCTAGCGATCGAT
CGA... 3’
PCR and phylogenetic analysis of rRNA genes
bacteriomes
r two obligate
bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
cola” (Gammaproteobacteria)
roidetes)
D Takiya
mm
domen of H. vitripennis

72. DNA
extraction
PCR
Sequence
rRNA genes
Sequence alignment = Data matrixPhylogenetic tree
PCR
rRNA1
rRNA2
Makes lots of
copies of the
rRNA genes
in sample
rRNA1
5’ ...ACACACATAGGTG
GAGCTAGCGATCGAT
CGA... 3’
E. coli
Humans
A
T
T
A
G
A
A
C
A
T
C
A
C
A
A
C
A
G
G
A
G
T
T
C
rRNA1
E. coli Humans
rRNA2
!67
rRNA2
5’ ...TACAGTATAGGTG
GAGCTAGCGATCGAT
CGA... 3’
PCR and phylogenetic analysis of rRNA genes
3)/,0+
bacteriomes
r two obligate
bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
cola” (Gammaproteobacteria)
roidetes)
D Takiya
mm
domen of H. vitripennis

73. Baumania is close relative of Buchnera symbionts of aphids
Sharpshooters
Aphids
Aphids
Aphids
Ants
Flies
!68

74. !69

75. !70

76. • What Are They Doing?
!71

77. !72

78. DNA
extraction
PCR
!73
Genome sequencing
Sequence the
whole genome
Predict
functions by
comparison to
other
organisms
bacteriomes
r two obligate
bacteriomes
Moran et al. 2003 Environ. Microbiol.
Moran et al. 2005 Appl. Environ. Microbiol.
cola” (Gammaproteobacteria)
roidetes)
D Takiya
mm
domen of H. vitripennis

79. Predict metabolic networks from Genome
Wu et al.
2006 PLoS
Biology 4:
e188.
!74

80. Baumannia is a Vitamin and Cofactor Producing Machine
Wu et al.
2006 PLoS
Biology 4:
e188.
!75
BAUMANNIA IS A
VITAMIN AND
COFACTOR
PRODUCING MACHINE

81. Sulcia
!76

82. Sulcia makes essential amino acids
!77
SULCIA IS AN
ESSENTIAL AMINO
ACID PRODUCING
MACHINE

83. Wu et al. 2006 PLoS Biology 4: e188.
Baumannia makes vitamins
and cofactors
Sulcia makes essential amino acids

84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
• What kind of symbiosis is the one between Baumania and
Sharpshooters?
• A: Endemism
• B. Commensalism
• C. Mutualism
• D: Parasitism
• E: Pathogenism
79

85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
• What kind of symbiosis is the one between Baumania and
Sharpshooters?
• A: Endemism
• B. Commensalism
• C. Mutualism
• D: Parasitism
• E: Pathogenism
80

86. !81

87. • Where else have we seen microbes that are used in control of
pests or pathogens?
!82

88. Pierce’s Disease
!83

89. Don’t Neglect your Symbionts

90. Find the Right Partner(s) and Work
With Them …