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BIS2C. Biodiversity and the Tree of Life. 2014. L35. Symbioses

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

Lecture 35. Symbioses.

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BIS2C. Biodiversity and the Tree of Life. 2014. L35. Symbioses

  1. 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. 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. 3. Napa Vineyard !3
  4. 4. Pierce’s Disease !4
  5. 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. 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. 7. Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !9 Symbiosis between Xylella and grapes? Symbiosis between Xylella and grapes
  8. 8. • II: How Pierce’s Disease Gets Around • How does Xylella get from one plant to another? !10
  9. 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. 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. 11. !13
  12. 12. !14http://www.youtube.com/watch?v=xz6kI3SSLJo
  13. 13. Symbiosis between Xylella and sharpshooter? Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !16 Symbiosis between Xylella and sharpshooters
  14. 14. Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !17 Symbiosis between Xylella and sharpshooter? Symbiosis between Xylella and sharpshooters
  15. 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. 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. 17. 35.12 Aphids Live off Phloem Sap !20
  18. 18. !21https://www.youtube.com/watch?v=3rqSWymHc6g
  19. 19. Aphids are very successful (> 4000 species, everywhere you look) !22
  20. 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. 21. !24
  22. 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. 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. 24. • Who Are They? !29
  25. 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. 26. !32
  27. 27. • What Are They Doing? !33
  28. 28. DNA extraction PCR !34 PCR and phylogenetic analysis of rRNA genes Sequence the whole genome Predict functions by comparison to other organisms
  29. 29. Aphid symbiont genomes ESSENTIAL AMINO ACID SYNTHESIZING MACHINE !35
  30. 30. Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !37 Symbiosis between Xylella and sharpshooters Symbiosis between bacteria and aphids?
  31. 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. 32. !39 Xylem feeding insects also very successful
  33. 33. Xylem and Phloem From Lodish et al. 2000 !40
  34. 34. Animal nutrition • Xylem is frequently missing essential amino acids, vitamins and Co-Factors, and has only small amounts of carbon skeletons !41
  35. 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. 36. !44
  37. 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. 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. 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. 40. • Who Are They? !49
  41. 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. 42. Baumania is close relative of Buchnera symbionts of aphids Sharpshooters Aphids Aphids Aphids Ants Flies !52
  43. 43. !53
  44. 44. • What Are They Doing? !54
  45. 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. 46. Predict metabolic networks from Genome Wu et al. 2006 PLoS Biology 4: e188. !57
  47. 47. Baumannia is a Vitamin and Cofactor Producing Machine Wu et al. 2006 PLoS Biology 4: e188. !58 VITAMIN AND COFACTOR PRODUCING MACHINE
  48. 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. 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. 50. !62
  51. 51. Wu et al. 2006 PLoS Biology 4: e188.
  52. 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. 53. Sulcia makes essential amino acids !65
  54. 54. Sulcia makes essential amino acids !66 ESSENTIAL AMINO 
 ACID PRODUCING MACHINE
  55. 55. Wu et al. 2006 PLoS Biology 4: e188. Baumannia makes vitamins and cofactors Sulcia makes essential amino acids
  56. 56. Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - !69 Symbiosis between Xylella and sharpshooters Symbiosis between bacteria & sharpshooters?
  57. 57. Pierce’s Disease !70
  58. 58. Bacteria and archaea are key commensals of many eukaryotes 71
  59. 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. 60. Don’t Neglect your Symbionts

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