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BIS2C_2020. Lecture 9. Form and function

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BIS2C_2020. Lecture 9.

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BIS2C_2020. Lecture 9. Form and function

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 9: Diversity of Form and Function Prof. Jonathan Eisen
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some insects from my yard in Davis Western HoneyBee
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some insects from my yard in Davis Argentine ant
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some insects from my yard in Davis Tiger fly?
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some insects from my yard in Davis Carpenter bee
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 iNaturalist • Take pictures • Upload them !http://iNaturalist.org !Inaturalist App !Seek App (real time identification) • Use their AI system and also community to help with identification • My observations here: https:// www.inaturalist.org/observations/ phylogenomics
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals • Understand general patterns of diversity of form seen in Bacteria, “Prokaryotic Archaea” and Eukarya • Understand key ways that organisms acquire carbon and use energy and electrons • Understand how one can use culturing to study extremophiles in the lab • Understand example patterns of the evolution of extremophily
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !8: Phylogenetic Diversity !9: Diversity of Form and Function !10: Pathogens and Parasites Lecture 9 Context
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function !Form !Trophy !Extremophily
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function !Form !Trophy !Extremophily
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab Connections • Lab 2 Station B: Microbial Metabolic Diversity • Lab 2 & 3 Microscopy • Lab 2 Station F: Winogradsky columns
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Review Lecture 8
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus tours
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Key Lesson #1 • The overall structure of the tree of life has been determined by analysis of molecular sequence data • Molecular data particularly important for placing most microbes into the tree of life
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Two Domain Tree of Life with Some Major Subbranches Shown
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Key Lesson #2 • Most microbes were only included in the tree of life if they could be grown in the lab
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great Plate Count Anomaly <<<< Culturing Observation CountCount
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great Plate Count Anomaly <<<< Culturing Observation CountCount http://www.google.com/url? sa=i&rct=j&q=&esrc=s&source=images&cd =&docid=rLu5sL207WlE1M&tbnid=CRLQYP 7d9d_TcM:&ved=0CAUQjRw&url=http%3A% 2F%2Fwww.biol.unt.edu%2F~jajohnson%2F DNA_sequencing_process&ei=hFu7U_TyCtO qsQSu9YGwBg&psig=AFQjCNG-8EBdEljE7- yHFG2KPuBZt8kIPw&ust=140487395121142 4 DNA “Culture Independent DNA Studies”
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Environmental Sampling genome genomegenome ACUGCACCUAU CGUUCGACUGCACC UAUCGUUCGACUGC ACCUAUCGUUCGAC UGCACCUAUCGUUC GACCUAUCGUUCGA CUGCACCUAUCGUU CGACCUAUCGUUCG ACUGCACCUAUCGU UCG ACUGCACCUAU CGUUCGACUGCACCU AUCGUUCGACUGCAC CUAUCGUUCGACUGC ACCUAUCGUUCGACC UAUCGUUCGACUGCA CCUAUCGUUCGACCU AUCGUUCGACUGCAC ACUGCACCUAU CGUUCGACUGCACCU AUCGUUCGACUGCAC CUAUCGUUCGACUGC ACCUAUCGUUCGACC UAUCGUUCGACUGCA CCUAUCGUUCGACCU AUCGUUCGACUGCAC CUAUCGUUCG
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Most of the phylogenetic diversity of bacteria only known through DNA from environmental samples Same is true for Archaea Also true for the microbial lineages in eukaryotes No way to cover all this diversity in this class
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates LUCA LUCA Last Universal Common Ancestor Can infer traits using character state reconstruction methods
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates BCA BCA Bacterial Common Ancestor
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates ECA Eukaryote Common Ancestor
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Some features previously thought to be “Eukaryotic” innovations were likely present in the Eukaryote- Asgard ancestor Cytoskeleton Chromatin
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function !Form !Trophy !Extremophily
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function !Form !Trophy !Extremophily
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Unicellularity & Multicellularity continuum • Unicellular: one cell does everything R • Colonial: collections of many attached cells (usually of the same genotype); no differentiation or division of labor or reproduction capabilities • Multicellular: collection of many attached cells (usually of same genotype); differentiation and division of labor and reproductive capabilities
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria & “Prokaryotic Archaea” : Major Cell Forms • Among the Bacteria and Archaea, three shapes are common: ! Sphere or coccus (plural cocci), occur singly or in plates, blocks, or clusters. ! Rod—bacillus (plural bacilli) ! Helical • Rods and helical shapes may form chains or clusters. Cocci = Spheres Bacilli = Rods Spirilla = Curved
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria & “Prokaryotic Archaea” : Major Cell Forms • Among the Bacteria and Archaea, three shapes are common: ! Sphere or coccus (plural cocci), occur singly or in plates, blocks, or clusters. ! Rod—bacillus (plural bacilli) ! Helical • Rods and helical shapes may form chains or clusters. Cocci = Spheres Bacilli = Rods Spirilla = Curved These are the most common forms seen but there are all sorts of other forms What follows is a brief tour of this diversity. You do not have to know the details unless presented elsewhere in class
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR BEGINS Diversity of Form in Bacteria and “Prokaryotic Archaea”
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates “Full Tree”
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR Compressed Tree Compressed Tree of Life
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Many are single celled but not all have the “simple” sphere, rod, or spiral shapes TOUR Diversity of Form in Bacteria and “Prokaryotic Archaea”
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR Endospores: Only Seen in Firmicutes Phylum Resistant to Everything Diversity of Form in Bacteria and “Prokaryotic Archaea”
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR Heterocysts Unique to Cyanobacteria Used for N2 fixation Diversity of Form in Bacteria and “Prokaryotic Archaea”
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR “Spiral” shape comes in many kinds Diversity of Form in Bacteria and “Prokaryotic Archaea”
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR Some Chlamydia species change forms during life cycle Diversity of Form in Bacteria and “Prokaryotic Archaea”
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thiomargarita Epulopiscium TOUR Some Bacteria are not microbial (can see with eyes without aids) Diversity of Form in Bacteria and “Prokaryotic Archaea”
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR Square Archaea Diversity of Form in Bacteria and “Prokaryotic Archaea”
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Some are colonial Diversity of Form in Bacteria and “Prokaryotic Archaea” TOUR
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR Clumps of Cocci Seen in Many Phyla Diversity of Form in Bacteria and “Prokaryotic Archaea”
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOURFilaments Seen in Many Phyla Diversity of Form in Bacteria and “Prokaryotic Archaea”
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • A few may be truly multicellular Diversity of Form in Bacteria and “Prokaryotic Archaea” TOUR
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR More Complex Structure in Some Taxa Fruiting body of gliding bacterium Stigmatella aurantiaca. SEM. Diversity of Form in Bacteria and “Prokaryotic Archaea”
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Vibrio Cyanobacterium Many are Motile TOUR Diversity of Form in Bacteria and “Prokaryotic Archaea”
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR ENDS Diversity of Form in Bacteria and “Prokaryotic Archaea” Need to Know Material not in the “Tours”
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • More than just cocci, bacilli, and spirals but these are common • Most are single celled but some are colonial and a few may be multicellular • Many are motile • Some can be identified from morphology • In most cases morphology does not match phylogeny and is more related to ecology or functions • Most phylogenetic studies are based on sequence data Diversity of Form in Bacteria and “Prokaryotic Archaea”
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotic Diversity of Form
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR BEGINS Eukaryotic Diversity of Form
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Many are single celled Eukaryotic Diversity of Form TOUR
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Dinoflagellates TOUR
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Apicomplexans Apical complex TOUR
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Ciliates TOUR
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Rhizarians: Cercozoans TOUR
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Rhizarians: Foraminiferans TOUR
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Rhizarians: Radiolarians TOUR
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Amoebozoans: Loboseans TOUR
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Trypanosoma sp. mixed with blood cells Excavates: Kinetoplastids TOUR
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates: Euglenids TOUR Movement in the euglenoid Eutreptia TOUR
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates: Diplomonads and Parabasalids TOURTOUR
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates: Heteroloboseans TOUR
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Many are colonial Eukaryotic Diversity of Form TOUR
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Diatoms TOUR
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts: Choanoflagellates The choanoflagellate Salpingoeca sp. feeding TOUR
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Many are multicellular Eukaryotic Diversity of Form TOUR
  68. 68. Multicellular Eukaryotes TOUR Plants, Animals, Many Fungi
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Brown Algae A community of brown algae: The marine kelp forest TOUR
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Amoebozoans: Plasmodial Slime Molds TOUR
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Kary Amoebozoans: Cellular Slime Molds TOUR
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Red Algae Motile spores from Purpureofilum Audouinella pacificaSpyridia TOUR
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Chlorophytes Movement in the green alga Volvox Micrasterias TOUR
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 TOUR ENDS Eukaryotic Diversity of Form
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Range from single celled to colonial to multicellular • Incredible diversity in form & motility among Eukaryotes • For many, but not all taxa, morphology (aka form) is a valuable trait for identification and phylogeny Eukaryotic Diversity of Form (Need to Know This)
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lesson: Convergence of Form is Common
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Fungal Hyphae
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Oomycetes Phytophthora Sudden Oak Death Potato Late Blight
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Actinobacterial Branching Filaments
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question The similarity in appearance of ooymcetes to fungi is an example of _______ • A. Homology • B. Homoplasy • C. Divergent evolution • D. Monophyly • E. Synapomorphy
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question The similarity in appearance of ooymcetes to fungi is an example of _______ • A. Homology • B. Homoplasy • C. Divergent evolution • D. Monophyly • E. Synapomorphy
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function !Form !Trophy !Extremophily
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Trophy
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Trophy • Organisms exhibit incredible diversity in how they obtain nutrition (i.e., the processes by which an they assimilates chemicals and energy and uses them for growth) • Generally referred to with the suffix “trophy” • Origin: Greek -trophiā, from trophē, from trephein, to nourish.
  85. 85. Component Different Forms Energy source Light Photo Chemical Chemo Electron source (reducing equivalent) Inorganic Litho Organic Organo Carbon source Carbon from C1 compounds Auto Carbon from organics Hetero Trophy • Three main components to “trophy” Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  86. 86. Component Different Forms Energy source Light Photo Chemical Chemo Electron source (reducing equivalent) Inorganic Litho Organic Organo Carbon source Carbon from inorganics Auto Carbon from organics Hetero • E. coli • Chemo organo hetero trophy • Chemo hetero trophy Trophy Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  87. 87. Component Different Forms Energy source Light Photo Chemical Chemo Electron source (reducing equivalent) Inorganic Litho Organic Organo Carbon source Carbon from inorganics Auto Carbon from organics Hetero • Humans? • Chemo organo hetero trophy • Chemo hetero trophy Trophy Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  88. 88. Component Different Forms Energy source Light Photo Chemical Chemo Electron source (reducing equivalent) Inorganic Litho Organic Organo Carbon source Carbon from inorganics Auto Carbon from organics Hetero Cyanobacteria • Photo litho auto trophy • Photo auto trophy Trophy Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  89. 89. Trophy • Bacteria and “prokaryotic archaea” are very diverse in types of trophy • There are many distinct mechanisms to carry out each form of “trophy” • Also a great deal of diversity in some eukaryotes groups Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  90. 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question What is the difference between chemolithoautotrophy and chemolithoheterotrophy? • A: The source of electrons • B: The source of energy • C: The source of carbon • D: A and B • E: All of the above
  91. 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Clicker Question What is the difference between chemolithoautotrophy and chemolithoheterotrophy? • A: The source of electrons • B: The source of energy • C: The source of carbon • D: A and B • E: All of the above
  92. 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Clicker Question What is the difference between chemolithoautotrophy and chemolithoheterotrophy? • A: The source of electrons • B: The source of energy • C: The source of carbon • D: A and B • E: All of the above
  93. 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Clicker Question What is the difference between chemolithoautotrophy and chemolithoheterotrophy? • A: The source of electrons • B: The source of energy • C: The source of carbon • D: A and B • E: All of the above
  94. 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Clicker Question What is the difference between chemolithoautotrophy and chemolithoheterotrophy? • A: The source of electrons • B: The source of energy • C: The source of carbon • D: A and B • E: All of the above
  95. 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function !Form !Trophy !Extremophily
  96. 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Extremophiles Extremophile: Organism that survives and thrives extreme conditions (as compared to conditions where other forms of life survive and thrive).
  97. 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Extreme Environments 105°C CH3 CO, 80°CH2S, pH 0, 95°C High salt CO2 4°Clow pH
  98. 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Methods for Studying Microbes Observation What Next? Collect Sample Look in Microscope See Cells
  99. 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Methods for Studying Microbes Culturing Observation What Next? Collect Sample Look in Microscope See Cells
  100. 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Methods for Studying Microbes <<<< Culturing Observation What Next? The Great Plate Count Anomaly Collect Sample Look in Microscope See Cells
  101. 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Methods for Studying Microbes <<<< Culturing Observation DNA What Next? The Great Plate Count Anomaly Culture independent DNA studies Collect Sample Look in Microscope See Cells
  102. 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Methods for Studying Microbes <<<< Culturing Observation DNA What Next? The Great Plate Count Anomaly Culturing can work, and this allows all sorts of studies Culture independent DNA studies Collect Sample Look in Microscope See Cells
  103. 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Culturing Microbes
  104. 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Example 1: Thermophiles
  105. 105. Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
  106. 106. Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
  107. 107. Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture
  108. 108. Set up some flasks with growth media Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture
  109. 109. Set up some flasks with growth media Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks
  110. 110. Set up some flasks with growth media Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks
  111. 111. Set up some flasks with growth media 1 2 3 4 Use different flasks for different conditions Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks
  112. 112. Set up some flasks with growth media 60° 70° 80° 90° 1 2 3 4 Use different flasks for different conditions Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks
  113. 113. Set up some flasks with growth media 60° 70° 80° 90° 1 2 3 4 Use different flasks for different conditions Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  114. 114. Set up some flasks with growth media 60° 70° 80° 90° 1 2 3 4 Use different flasks for different conditions 1 2 3 4 60° 70° 80° 90° 1h 1h 1h 1h Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  115. 115. Set up some flasks with growth media 60° 70° 80° 90° 1 2 3 4 Use different flasks for different conditions 1 2 3 4 60° 70° 80° 90° 1h 1h 1h 1h 1 2 3 4 60° 70° 80° 90° 2h 2h 2h 2h Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  116. 116. Set up some flasks with growth media 60° 70° 80° 90° 1 2 3 4 Use different flasks for different conditions 1 2 3 4 60° 70° 80° 90° 1h 1h 1h 1h 1 2 3 4 60° 70° 80° 90° 2h 2h 2h 2h 1 2 3 4 60° 70° 80° 90° 3h 3h 3h 3h Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  117. 117. Growth vs. Time Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 0.0 20.0 40.0 60.0 80.0 0h 1h 2h 3h 60° 70° 80° 90° Plot Growth vs. Time for Each Condition Time Elapsed DensityofGrowth
  118. 118. Growth Rate Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 0.0 12.5 25.0 37.5 50.0 60 °C 70 °C 80 °C 90° C Calculate and Plot Growth Rate vs. Conditions Temperature GrowthRate
  119. 119. Optimal growth temperature (OGT) for Different Species Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  120. 120. Optimal growth temperature (OGT) for Different Species Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Extremophile Type Low High Psychrophile -20 °C 10 °C Mesophile 11 °C 40 °C Thermophile 41 °C 80 °C Hyperthermophile 81 °C 122 °C
  121. 121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Two Domain Tree of Life with Some Major Subbranches Shown
  122. 122. Hug et al 2016 Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hug et al. 2016 Tree of Life Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 Two Domain Tree of Life with Some Major Subbranches Shown Laura Hug U. Waterloo Jill Banfield UC Berkeley
  123. 123. Hug et al 2016 Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thermophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 41 - 80 °C Thermophiles Across Tree of Life
  124. 124. Hug et al 2016Thermophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 What are some possible evolutionary scenarios that would account for this pattern of presence of thermophily across the Tree of Life? Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  125. 125. Hug et al 2016 Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hyperthermophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 Hyperthermophiles Across Tree of Life No Eukaryotes Only a few Bacteria 81 - 122 °C
  126. 126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Example 2: Halophiles
  127. 127. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
  128. 128. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33
  129. 129. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture
  130. 130. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media
  131. 131. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks
  132. 132. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks
  133. 133. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks 1 2 3 4 Use different flasks for different conditions
  134. 134. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks 1 2 3 4 Use different flasks for different conditions 1M 2M 3M 4M
  135. 135. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks 1 2 3 4 Use different flasks for different conditions 1M 2M 3M 4M Monitor growth over time
  136. 136. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks 1 2 3 4 Use different flasks for different conditions 1M 2M 3M 4M Monitor growth over time 1 2 3 4 1M 2M 3M 4M 1h 1h 1h 1h
  137. 137. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks 1 2 3 4 Use different flasks for different conditions 1M 2M 3M 4M Monitor growth over time 1 2 3 4 1M 2M 3M 4M 1h 1h 1h 1h 1 2 3 4 1M 2M 3M 4M 2h 2h 2h 2h
  138. 138. Determining Optimal Salt Concentrations Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Set up some flasks with growth media Add a small portion of the starter culture to flasks 1 2 3 4 Use different flasks for different conditions 1M 2M 3M 4M Monitor growth over time 1 2 3 4 1M 2M 3M 4M 1h 1h 1h 1h 1 2 3 4 1M 2M 3M 4M 2h 2h 2h 2h 1 2 3 4 1M 2M 3M 4M 3h 3h 3h 3h
  139. 139. Growth vs. Time Plot Growth vs. Time for Each Condition Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 0.0 20.0 40.0 60.0 80.0 0h 1h 2h 3h 1M 2M 3M 4M Time Elapsed DensityofGrowth
  140. 140. Growth Rate Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 0.0 12.5 25.0 37.5 50.0 1M 2M 3M 4M Calculate and Plot Growth Rate vs. Conditions Salinity GrowthRate
  141. 141. Optimal salt concentration for different species Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  142. 142. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Euryarchaeota: Halophiles (Salt lovers) • Pink carotenoid pigments – very visible • Have been found at pH up to 11.5. • Unusual adaptations to high salt, desiccation • Many have bacteriorhodopsin which uses energy of light to synthesize ATP (photoheterotrophs)
  143. 143. Hug et al 2016 Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Extreme Halophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 Most extreme halophiles are from a single clade of “prokaryotic Archaea”
  144. 144. Hug et al 2016Extreme Halophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 What are some possible evolutionary scenarios that would account for this pattern across the Tree of Life? Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  145. 145. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Uses of extremophiles Type of environment Examples Example of mechanism of survival Practical Uses High temp (thermophiles) Deep sea vents, hotsprings Amino acid changes Heat stable enzymes Low temp (psychrophile) Antarctic ocean, glaciers Antifreeze proteins Enhancing cold tolerance of crops High pressure (barophile) Deep sea vents, hotsprings Solute changes Industrial processes High salt (halophiles) Evaporating pools Incr. internal osmolarity Soy sauce production High pH (alkaliphiles) Soda lakes Transporters Detergents Low pH (acidophiles) Mine tailings Transporters Bioremediation Desiccation (xerophiles) Deserts Spore formation Freeze-drying additives High radiation (radiophiles) Nuclear reactor waste sites Absorption, repair damage Bioremediation, space travel
  146. 146. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Novozymes in Davis
  147. 147. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !8: Phylogenetic Diversity !9: Diversity of Form and Function !10: Pathogens and Parasites Lecture 9 Context

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