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BIS2C: Lecture 35: Symbioses Across the Tree of Life

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BIS2C: Lecture 35: Symbioses Across the Tree of Life

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BIS2C: Lecture 35: Symbioses Across the Tree of Life

  1. 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. 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. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 The Tree of Life (used in LIFE Version 10) 3
  4. 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. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 5 Week 1 Phylogeny Week 1: Phylogenetic Trees
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Life on Mars 6 Week 2 Trees of Life?
  7. 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. 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. 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. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Weeks 4-5: Plants 10 Weeks 4-5 Plants
  11. 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. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Weeks 7-9: Animals 12 Weeks 6-8 Animals
  13. 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. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Week 6: Fungi 14 Week 9 Fungi
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Napa Vineyard 15
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 18 Pierce’s Disease
  17. 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. 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. 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. 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. 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. 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. 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. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Vectors for Blood Borne Diseases 23
  25. 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. 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. 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. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
  30. 30. Symbiosis between Xylella and sharpshooter? Symbiosis between Xylella and sharpshooters Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !30
  31. 31. Symbiosis between Xylella and sharpshooter? Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !31 Symbiosis between Xylella and sharpshooters
  32. 32. Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !32 Symbiosis between Xylella and sharpshooter? Symbiosis between Xylella and sharpshooters
  33. 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. 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. 35.12 Aphids Live off Phloem Sap !35
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Mosquito Feeding 36
  37. 37. Aphids are very successful (> 4000 species, everywhere you look) !37
  38. 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. 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. !40 Xylem feeding insects also very successful
  41. 41. Plant vs. Insect • Thicken walls !41 Plant Adaptations Insect Responses • Better piercing
  42. 42. Plant vs. Insect • Thicken walls !41 Plant Adaptations Insect Responses • Better piercing
  43. 43. Plant vs. Insect • Thicken walls !41 Plant Adaptations Insect Responses • Better piercing
  44. 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. 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. 46. How Deal With Very Low Sugar? !43Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
  47. 47. How Deal With Very Low Sugar? !43Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
  48. 48. !44Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
  49. 49. !45Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
  50. 50. Tree Rain in Tahiti !46
  51. 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. 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. 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. 54. !50 Severe Feeding Constraints
  55. 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. 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. 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. 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. 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. 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. 61. !56
  62. 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. 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. 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. 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. 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. 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. 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. 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. 70. • Who Are These Microbes? !65
  71. 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. 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. 73. Baumania is close relative of Buchnera symbionts of aphids Sharpshooters Aphids Aphids Aphids Ants Flies !68
  74. 74. !69
  75. 75. !70
  76. 76. • What Are They Doing? !71
  77. 77. !72
  78. 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. 79. Predict metabolic networks from Genome Wu et al. 2006 PLoS Biology 4: e188. !74
  80. 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. 81. Sulcia !76
  82. 82. Sulcia makes essential amino acids !77 SULCIA IS AN ESSENTIAL AMINO 
 ACID PRODUCING MACHINE
  83. 83. Wu et al. 2006 PLoS Biology 4: e188. Baumannia makes vitamins and cofactors Sulcia makes essential amino acids
  84. 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. 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. 86. !81
  87. 87. • Where else have we seen microbes that are used in control of pests or pathogens? !82
  88. 88. Pierce’s Disease !83
  89. 89. Don’t Neglect your Symbionts
  90. 90. Find the Right Partner(s) and Work With Them …

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