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BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

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

Lecture 8.
Introduction to Microbial Diversity, part 2.

Slides for Lectures by Jonathan Eisen

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BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 8 ! Lecture 8 ! Introduction to Microbial Diversity Part 2 ! ! BIS 002C Biodiversity & the Tree of Life Spring 2014 ! Prof. Jonathan Eisen 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: !7: Microbial Diversity • Current Lecture: !8: Microbial Diversity part 2 • Next Lecture: !9: Symbioses 2
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Microbial Diversity • Seven major lineages of eukaryotes • Alveolates • Stramenopiles • Rhizaria • Excavates • Amoebozoans • Plantae • Opisthokonts • Complications 1: Endosymbioses • Complications 2: Lateral gene transfer 3
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Microbial Diversity • Seven major lineages of eukaryotes • Alveolates • Stramenopiles • Rhizaria • Excavates • Amoebozoans • Plantae • Opisthokonts • Complications 1: Endosymbioses • Complications 2: Lateral gene transfer 4
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Oversimplification of eukaryotic phylogeny 5
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Phylogenetic diversity of eukaryotes • As with bacteria and archaea, phylogeny of major groups based largely on molecular data. • However, non-molecular data more useful for studies of eukaryotic phylogeny • Major groupings, and the relationships among groups, still being resolved • All organisms other than plants, animals and fungi are sometimes referred to as protists or microbial eukaryotes (note - paraphyletic) 6
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 7 Alveolates Alveolates Have alveoli or sacs beneath surface of plasma membrane. All are unicellular; many are photosynthetic.
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 •Most are marine and are important photoautotrophic primary producers •Mixture of pigments give them a golden brown color. •Have two flagella, one in an equatorial groove, the other in a longitudinal groove. Alveolates: Dinoflagellates 8 Certium tenue Coral symbiont
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 9
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question What is the different between photoautotrophy and photoheterotrophy? ! • A: The source of electrons • B: The source of carbon • C: The source of energy • D: All of the above 10
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question What is the different between photoautotrophy and photoheterotrophy? ! • A: The source of electrons • B: The source of carbon • C: The source of energy • D: All of the above 11
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Alveolates: Apicomplexans • All parasitic • Have a mass of organelles at one tip —the apical complex that help the parasite enter the host’s cells. 12 Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Alveolates: Ciliates 13 Movement in a ciliate from the gut of a termite • All have numerous cilia, the structure is identical to flagella. • Most are heterotrophic; very diverse group. • Have complex body forms and two types of nuclei.
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 14 Stramenopiles Stramenopiles Two flagella, with rows of tubular hairs on the longer one.
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 •All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine. Stramenopiles: Brown Algae 15 A community of brown algae: The marine kelp forest
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Stramenopiles: Diatoms 16 A colony of the diatom, Bacillaria paradoxa •Unicellular, but many associate in filaments. •Have carotenoids and appear yellow or brown. •Excellent fossil record •Most are photoautotrophic •Responsible for 20% of all carbon fixation. •Oil, gas source
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Stramenopiles: Oomcyetes Phytophthora Potato Late Blight • Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but are unrelated. 17 Sudden Oak Death
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 18
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question The similarity in appearance of ooymcetes to fungi is an example of _______ ! • A. Homology • B. Homoplasy • C. Divergent evolution • D. Monophyly 19
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question The similarity in appearance of ooymcetes to fungi is an example of _______ ! • A. Homology • B. Homoplasy • C. Divergent evolution • D. Monophyly 20
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Rhizaria Rhizaria Unicellular, aquatic, with long, thin pseudopods. 21
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Rhizaria: Cercozoans Some cercozoans are aquatic, others live in soil. They have diverse forms and habitats. One group has chloroplasts derived from a green alga by secondary endosymbiosis. Euglyphid 22 Chlorarachnion reptans
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Rhizaria: Foraminiferans Sand beaches in the tropics • Secrete shells of calcium carbonate. • Discarded shells make up limestone. • Create some beach sands • Used to date & characterize sedimentary rocks. • Some live as plankton, others at sea bottom. • Thread-like, branched pseudopods extend through pores in the shell and form a sticky net that captures smaller plankton. 23
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Rhizaria: Radiolarians • Have thin, stiff pseudopods reinforced by microtubules. • The pseudopods increase surface area for exchange of materials; and help the cell float. • Exclusively marine, most secrete glassy endoskeletons, many with elaborate designs. 24
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates 25
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates: Diplomonads and Parabisalids • Unicellular • Lack mitochondria and most are anaerobic. This is a derived condition • Giardia lamblia - a diplomonad - is a human parasite • Trichomonas vaginalis - parabasalid - STD 26
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates: Heteroloboseans • Amoeboid body form. • Naegleria can enter humans and cause a fatal nervous system disease - “brain eating” • Some can transform between amoeboid and flagellated stages. 27
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates: Euglenids • Have flagella. • Some are photosynthetic, some always heterotrophic, and some can switch. 28 Movement in the euglenoid Eutreptia
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates: Kinetoplastids • Unicellular parasites with two flagella and a single mitochondrion. • Mitochondrion contains a kinetoplast - structure with multiple, circular DNA molecules • Includes trypanosomes and agents of chagas, sleeping sickness, Leishmaniasis Trypanosoma sp.! mixed with blood cells 29
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Amoebozoans Amoebozoans Lobe-shaped pseudopods are used for locomotion. 30
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • Not colonial; live as single cells • Some secrete shells or glue sand grains together to form a casing. • Many pathogens 31 Amoebozoans: Loboseans
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Entamoeba histolytica 32 http://www.npr.org/blogs/health/2014/04/09/300991364/gut- eating-amoeba-caught-on-film
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Amoebozoans: Plasmodial Slime Molds • Individual motile cells can form single, multinucleate cell (plasmodium) • Ingest food by endocytosis • Form spores on stalks called fruiting bodies. • Found in cool, moist habitats 33
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Amoebozoans: Cellular Slime Molds • Life cycle consists of individual motile cells that ingest food by endocytosis • This is followed by the formation of single, multicellular fruiting structure • Each cell retains its own plasma membrane and individuality 34 Karyo
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Plantae 35 The Plantae consist of several clades; all chloroplasts trace back to a single incidence of endosymbiosis.
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Plantae: Glaucophytes • Unicellular, freshwater organisms • The chloroplast retains a bit of peptidoglycan between the inner and outer membrane. 36
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 37
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Plantae: Glaucophytes • Unicellular, freshwater organisms • The chloroplast retains a bit of peptidoglycan between the inner and outer membrane. 38 Which of the following groups do not have peptidoglycan in their cell envelopes? •A: Gram positive bacteria •B: Gram negative bacteria •C: Cyanobacteria •D: Crenarchaeota
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Plantae: Glaucophytes • Unicellular, freshwater organisms • The chloroplast retains a bit of peptidoglycan between the inner and outer membrane. 39 Which of the following groups do not have peptidoglycan in their cell envelopes? •A: Gram positive bacteria •B: Gram negative bacteria •C: Cyanobacteria •D: Crenarchaeota
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Plantae: Red Algae 40 • Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores Motile spores from Purpureofilum Audouinella pacifica Spyridia
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Plantae: Chlorophytes • Sister group to charophytes and land plants. • Synapomorphies include chlorophyll a and b, and starch as a storage product. • >17,000 species; marine, freshwater, and terrestrial. Unicellular to large multicellular forms. 41 Movement in the green alga Volvox Micrasterias
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Plantae: Charophytes and Land Plants STAY TUNED 42
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 43 Opisthokonts
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 •Choanoflagellates are sister to the animals. •Some are colonial and resemble a type of cell found in sponges. 44 The choanoflagellate Salpingoeca sp. feeding Opisthokonts: Choanoflagellates
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 45 Opisthokonts: Fungi and Animals STAY TUNED
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Eukaryotic Diversity • Seven major lineages of eukaryotes • Alveolates • Stramenopiles • Rhizaria • Excavates • Amoebozoans • Plantae • Opisthokonts • Complications 1: Endosymbioses • Complications 2: Lateral gene transfer 46
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 47 The Bacteria
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Oversimplification of eukaryotic phylogeny 48
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Diverse Organelles 49 Mitochondrion Chloroplast Nucleus
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Endosymbioses in eukaryotic evolution 50 Prokaryotic cell
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Endosymbioses in eukaryotic evolution 50 Cell wall Prokaryotic cell
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Endosymbioses in eukaryotic evolution 50 DNA Cell wall Prokaryotic cell
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Endosymbioses in eukaryotic evolution 50 DNA Cell wall Prokaryotic cell
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Endosymbioses in eukaryotic evolution 50 DNA Cell wall Prokaryotic cell The protective cell wall was lost.
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Endosymbioses in eukaryotic evolution 50 DNA Cell wall Prokaryotic cell Infolding of the plasma membrane added surface area without increasing the cell’s volume. The protective cell wall was lost.
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Endosymbioses in eukaryotic evolution 50
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51 Endosymbioses
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51 Endosymbioses
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51 Cytoskeleton (micro- filament and micro- tubules) formed. Endosymbioses
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51 Cytoskeleton (micro- filament and micro- tubules) formed. Internal membranes studded with ribosomes formed. Endosymbioses
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51 Endosymbioses
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52 Endosymbioses
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52 Endosymbioses
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52 As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed. Endosymbioses
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52 Early digestive vacuoles evolved into lysosomes using enzymes from the early endoplasmic reticulum. As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed. Endosymbioses
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52 Microtubules from the cytoskeleton formed eukaryotic flagellum, enabling propulsion. Early digestive vacuoles evolved into lysosomes using enzymes from the early endoplasmic reticulum. As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed. Endosymbioses
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52 Endosymbioses
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 53 Endosymbioses
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 53 Proteobacteria Endosymbioses
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 53 Proteobacteria Endosymbioses
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 53 Mitochondria formed through endosymbiosis with a proteo- bacterium. Proteobacteria Endosymbioses
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 53 Endosymbioses
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 54 Endosymbioses
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 54 Cyanobacteria Endosymbioses
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 54 Endosymbiosis with cyanobacteria led to the development of chloroplasts. Endosymbioses
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 54 Flagellum Eukaryotic cell Chloroplast Mitochondria Nucleus Endosymbiosis with cyanobacteria led to the development of chloroplasts. Endosymbioses
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Mitochondrial Symbiosis
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Mitochondrial Symbiosis
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Mitochondrial Symbiosis
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Mitochondrial Symbiosis
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Mitochondrial Symbiosis
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Mitochondrial Symbiosis
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Mitochondrial Symbiosis
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Archaea Mitochondrial Symbiosis
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Archaea Eukaryotes Mitochondrial Symbiosis
  86. 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Archaea Eukaryotes Mitochondrial Symbiosis
  87. 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Archaea Eukaryotes Mitochondrial Symbiosis
  88. 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55 Bacteria Archaea Eukaryotes Mitochondrial Symbiosis
  89. 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 56 Bacteria Archaea Eukaryotes Mitochondrial Symbiosis

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