BIS2C. Biodiversity and the Tree of Life. At UC Davis Spring 2014. Lecture of Jonathan Eisen. Lecture 35. Symbioses.

1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 35
!
Lecture 35
!
Symbioses in
Symbioses in
Symbioses
!
!
BIS 002C
Biodiversity & the Tree of Life
Spring 2014
! 1

2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where we are going and where we have been
• Previous Lecture:
!34: Really big creatures
• Current Lecture:
!35: Symbioses in Symbioses …
• Next Lecture:
!The Final …
2

3. Napa Vineyard
!3

4. Pierce’s Disease
!4

5. • Pierce’s Disease
• Due to blockage of
xylem circulation
• Caused by
overgrowth of Xylella
fastidiosa, a
bacterium
• Vines, even whole
vineyards, infected
must be destroyed
• Many of world’s
experts at UC Davis
and other UCs
!5
Pierce’s Disease

6. Xylem and Phloem
! Xylem sap: water
and minerals mostly
from roots to rest of
plant.
! Phloem sap:
products of
photosynthesis such
as sugars to sites of
storage or use.
!6
From Lodish et al. 2000

7. Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!9
Symbiosis between Xylella and grapes?
Symbiosis between Xylella and grapes

8. • II: How Pierce’s Disease Gets Around
• How does Xylella get from one plant to another?
!10

9. Plasmodium falciparum- Malaria
kills 700,000-2,000,000 people per year—
75% of them are African children.
Apicomplexans have complex life
cycles, often with two different hosts. !11
Plasmodium

10. • Obligate xylem feeder
• Transmits Xylella
between plants
• Much like mosquitoes
transmit malarial
pathogen
• Only animal listed as
possible “bioterror”
agent by US DHS
!12
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.

11. !13

12. !14http://www.youtube.com/watch?v=xz6kI3SSLJo

13. Symbiosis between Xylella and sharpshooter?
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!16
Symbiosis between Xylella and sharpshooters

14. Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!17
Symbiosis between Xylella and sharpshooter?
Symbiosis between Xylella and sharpshooters

15. Xylem and Phloem
! Xylem sap: water
and minerals mostly
from roots to rest of
plant.
! Phloem sap:
products of
photosynthesis such
as sugars to sites of
storage or use.
!18
From Lodish et al. 2000

16. Conundrum
• Phloem sap is filled with sugar(s) and a variety of other
compounds
• But low in most of the “essential” amino acids that
animals cannot synthesize
!19

17. 35.12 Aphids Live off Phloem Sap
!20

18. !21https://www.youtube.com/watch?v=3rqSWymHc6g

19. Aphids are very successful (> 4000 species, everywhere you look)
!22

20. Plant response to sap feeders
• Possible solutions to low aa in phloem
! Eat other things
! Evolve metabolic pathways to synthesize missing
nutrients
! Find some poor sap to make the stuff for you
!23

21. !24

22. 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)
!25

23. !28
Culturing Field Observations
Key bacteria in
aphid gut have
not been cultured
Studying the microbe-like entities in the aphid gut
Appearance of
limited value
DNA

24. • Who Are They?
!29

25. 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
!30
rRNA1
5’ ...TACAGTATAGG
TGGAGCTAGCGAT
CGATCGA... 3’
PCR and phylogenetic analysis of rRNA genes

26. !32

27. • What Are They Doing?
!33

28. DNA
extraction
PCR
!34
PCR and phylogenetic analysis of rRNA genes
Sequence
the whole
genome
Predict
functions by
comparison
to other
organisms

29. Aphid symbiont genomes
ESSENTIAL
AMINO ACID
SYNTHESIZING
MACHINE
!35

30. Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!37
Symbiosis between Xylella and sharpshooters
Symbiosis between bacteria and aphids?

31. • Obligate xylem feeder
• Transmits Xylella
between plants
• Much like mosquitoes
transmit malarial
pathogen
• Only animal listed as
possible “bioterror”
agent by US DHS
!38
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.

32. !39
Xylem feeding insects also very successful

33. Xylem and Phloem
From
Lodish et
al. 2000
!40

34. Animal nutrition
• Xylem is frequently missing essential amino
acids, vitamins and Co-Factors, and has only
small amounts of carbon skeletons
!41

35. Plant response to sap feeders
• Possible solutions to no aa, vitamins, etc in xylem
! Eat other things
! Evolve metabolic pathways to synthesize missing
nutrients
! Find some poor sap to make the stuff for you
!42

36. !44

37. Moran N. A. PNAS 2007;104:8627-8633
©2007 by National Academy of Sciences
!43
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

38. 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)
!45

39. !48
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)

40. • Who Are They?
!49

41. 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
!50
rRNA1
5’ ...TACAGTATAGG
TGGAGCTAGCGAT
CGATCGA... 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

42. Baumania is close relative of Buchnera symbionts of aphids
Sharpshooters
Aphids
Aphids
Aphids
Ants
Flies
!52

43. !53

44. • What Are They Doing?
!54

45. DNA
extraction
PCR
!56
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

46. Predict metabolic networks from Genome
Wu et al.
2006
PLoS
Biology 4:
e188. !57

47. Baumannia is a Vitamin and Cofactor Producing Machine
Wu et al.
2006
PLoS
Biology 4:
e188. !58
VITAMIN AND
COFACTOR
PRODUCING
MACHINE

48. Baumannia is a Vitamin and Cofactor Producing Machine
Wu et al.
2006
PLoS
Biology 4:
e188. !59
NO PATHWAYS FOR
ESSENTIAL AMINO
ACID SYNTHESIS

49. 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’ ...ACACACATAG
GTGGAGCTAGCGA
TCGATCGA... 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
!61
rRNA2
5’ ...TACAGTATAGG
TGGAGCTAGCGAT
CGATCGA... 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

50. !62

51. Wu et al. 2006 PLoS Biology 4: e188.

52. DNA
extraction
PCR
!64
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

53. Sulcia makes essential amino acids
!65

54. Sulcia makes essential amino acids
!66
ESSENTIAL AMINO
ACID PRODUCING
MACHINE

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

56. Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
!69
Symbiosis between Xylella and sharpshooters
Symbiosis between bacteria & sharpshooters?

57. Pierce’s Disease
!70

58. Bacteria and archaea are key commensals of many eukaryotes
71

59. Examples of mutualisms discussed in class
• 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
!73

60. Don’t Neglect your Symbionts