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BIS2C_2020. Lecture 8. Phylogenetic Diversity of Microbes

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Slides for BIS2C "Biodiversity and the Tree of Life"
Class at UC Davis Spring 2020.
Lecture 8. Phylogenetic Diversity of Microbes.

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BIS2C_2020. Lecture 8. Phylogenetic Diversity of Microbes

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 8: Phylogenetic Diversity of Microbes Prof. Jonathan Eisen
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Anna’s Hummingbird in Davis, CA April 8, 2020
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals 1. Understand what type of data has been used to infer the overall major structures in the Tree of Life 2. Understand the great plate count anomaly and how it has impacted our view of the phylogenetic diversity of life 3. Understand and be able to give examples of key features present in key ancestors of major branches in the tree of life (e.g., LUCA, BCA, ECA)
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !7: The Domains of Life !8: Phylogenetic Diversity of Microbes !9: Functional Diversity of Microbes Lecture 8 Context
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab Connections • Lab 2 - Intro to Bacteria and Archaea • Lab 2 - Station A - classification • Lab 3 - Intro to microbial eukaryotes • Lab 2 - Great plate count anomaly
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Review of Lecture 7
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cell Structure Observations L7: Prokaryotes vs. Eukaryotes
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There?
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 Prokaryotic Eukaryotic L7: Prokaryotes vs. Eukaryotes Interpreted As Implying This Tree Because That Would Require Only One Event For Nucleus Origin But this is a mistake since this tree, also only requires one event for origin of the nucleus
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes So no reason to assume this is the correct tree, even though many did
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Woese rRNA Tree of Life
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG L7: Woese rRNA Tree of Life
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic L7: Rooted Woese rRNA Tree of Life
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic L7: The Three Domain Tree of Life EukaryaBacteria Archaea Three Domains Re-labelled individual taxa
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Loki’s Castle • Loki’s Castle
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Loki Prokaryotic Eukaryotic EukaryaBacteria Archaea Phylogenetic Trees Using Genomes from Lokiarchaea Look Like This L7: Alternative to Three Domain Tree of Life
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Three Domain Tree of Life Three Domain Tree of Life Archaea Eukarya Note Position of Asgard Archaea New Slide
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Method developments !Same data, with different methods, sometimes gives different results !Some methods are more prone to artifacts and errors than others • Differences between genes • Better taxonomic sampling !Can improve resolution in trees !Can help get around some method problems Reasons for Changes in the Tree of Life L7: Two Domain Tree of Life
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Three Domain Tree of Life Three Domain Tree of Life Archaea Eukarya Note Position of Asgard Archaea New Slide
  28. 28. 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
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  30. 30. 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
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Woese rRNA Tree of Life
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Woese rRNA Tree of Life
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Woese rRNA Tree of Life
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Two Domain Tree of Life
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Two Domain Tree of Life B1 B2 B3 E1 E2 E3 B4 A1 A2 Asgard Bacteria Archaea Eukarya “Prokaryotic Archaea”
  37. 37. 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
  38. 38. 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
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Woese rRNA Tree of Life
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great Plate Count Anomaly
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great Plate Count Anomaly <<<< Culturing Observation CountCount
  42. 42. 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 Lab 2: “Culture Independent DNA Studies”
  43. 43. 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
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  45. 45. 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
  46. 46. 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
  47. 47. 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
  48. 48. 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
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Focus on this reduced subset of the full phylogenetic diversity
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Plants: L14-21 Fungi L 22-23 Animals L 25-36 Choanos: L 24 Everything Else L 8-13 NOOP Not Opisthokonts or Plants Focus on this reduced subset of the full phylogenetic diversity
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates L8: Features and Innovations of Major Groups L9: Functional Diversity L10: Parasites and Pathogens L11: Viruses and Gene Transfer L12: Mutualisms and Microbiomes L13: Endosymbioses and Organelles Everything Else L 8-13 NOOP Not Opisthokonts or Plants Focus on this reduced subset of the full phylogenetic diversity
  52. 52. 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
  53. 53. 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 !LUCA • Bonus Tours
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates LUCA LUCA Last Universal Common Ancestor
  55. 55. 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
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  57. 57. • Made up of cells • Use of DNA as a genetic material • Use of ACTG in DNA • Use of ACUG in RNA • Three letter genetic code • Central dogma (DNA » RNA » protein) • Use water as a solvent • Lipoprotein cell envelope • 20 core amino acids in proteins • Live on Earth • Ribosome for translation • RNA polymerase proteins • Acquires energy from environment • Store energy in chemicals Universal Traits
  58. 58. • Made up of cells • Use of DNA as a genetic material • Use of ACTG in DNA • Use of ACUG in RNA • Three letter genetic code • Central dogma (DNA » RNA » protein) • Use water as a solvent • Lipoprotein cell envelope • 20 core amino acids in proteins • Live on Earth • Ribosome for translation • RNA polymerase proteins • Acquires energy from environment • Store energy in chemicals Universal Traits Infer that LUCA had all of these
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There?
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Circular DNA Linear DNA
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Circular DNA Linear DNA
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Traits of LUCA = Last Universal Common Ancestor • For characters that differ between prokaryotes and eukaryotes, LUCA likely had the character / character state found in prokaryotes !Circular DNA genome with plasmids !No nucleus or membrane bound organelles !Operons !Binary fission reproduction !Haploid
  64. 64. 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 !LUCA !BCA • Bonus Tours
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates BCA BCA Bacterial Common Ancestor
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BCA = Bacterial Common Ancestor • Likely inherited most of the traits inferred to be in LUCA • A few other key innovations, we are just going to discuss one today
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Peptidoglycan • Unique to bacteria • Polymer that provides a firm, mesh like structure around the cell • Key component of cell wall • Is the target for many antibiotics
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Peptidoglycan • Unique to bacteria • Polymer that provides a firm, mesh like structure around the cell • Key component of cell wall • Is the target for many antibiotics • Why?
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates PG Peptidoglycan is a key innovation of bacteria
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Peptidoglycan variation in bacteria • Two major ways it is used in bacteria • Gram-positive bacteria - thick peptidoglycan layer outside 1 cell membrane • Gram-negative bacteria - thin peptidoglycan layer outside between two cell membranes • This has many impacts on biology, including sensitivity to antibiotics
  71. 71. 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 !LUCA !BCA !ECA • Bonus Tours
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates ECA Eukaryote Common Ancestor
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There?
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates ECA Eukaryote Common Ancestor Tons of innovations thought to have happened here
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Many Other Innovations Associated w/ Origin of Euks • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  77. 77. 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 !LUCA !BCA !ECA !Asgard Archaea and Eukaryotes
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lokiarchaea named after Loki’s Castle Vent Site
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Many Other Innovations Associated w/ Origin of Euks • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Found in Asgard Archaea • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  83. 83. 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
  84. 84. 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
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Tour of Major Clades • You Do Not Need to Know These Details • Really
  86. 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Bacteria Tour
  87. 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Spirochetes • Gram-negative • Motile • Chemoheterotrophic • Unique rotating, axial filaments (modified flagella) • Many are pathogens: !Syphilis !Lyme disease • Others free-living
  88. 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Chlamydias • Gram-negative • Cocci or rod-shaped • Extremely small • Live only as parasites inside cells of eukaryotes & cause various diseases !Trachoma !Multiple sexually transmitted diseases !Pneumonia C. trachomatis
  89. 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cyanobacteria • Photolithoautotrophic • Contain internal membrane system for photosynthesis • Chloroplasts are derived from endosymbiotic cyanobacteria • Colonies can differentiate into vegetative cells, spores, & heterocysts
  90. 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Proteobacteria • Gram-negative • Escherichia coli: model organism and human gut commensal and pathogen • Mitochondria evolved from this group • Includes many human and animal pathogens: plague, cholera, typhoid
  91. 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Low-GC Gram Positives (Firmicutes) • Low G+C/A+T ratio in DNA • Some produce endospores which are resistant “seeds” that germinate when conditions are good • Many agents of diseases (e.g., anthrax, MRSA, Streptococcus, botulism, tetanus) • Many of agricultural and industrial use (e.g., Lactic acid bacteria) • Some (Mycoplasmas) have no cell wall and are extremely small Mycoplasmas
  92. 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 High-GC Gram Positives (Actinobacteria) • High G+C/A+T ratio in DNA • Elaborate branching • Some reproduce by forming chains of spores at tips of filaments • Most antibiotics are from this group • Causative agents of many diseases such as tuberculosis and leprosy • Many originally misclassified as fungi
  93. 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Prokaryotic Archaea Tour
  94. 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Crenarchaeota • Most are both thermophilic (heat loving) & acidophilic (acid-loving) • Sulfolobus lives in hot sulfur springs (70–75°C, pH 2-3) • One species of Ferroplasma lives at pH near 0
  95. 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Euryarchaeota: Methanogens • Only known methanogens (produce methane (CH4) by reducing CO2 ) - a form of chemoautotrophy • Methanogens release 2 billion tons of methane per year • Many live in the guts of grazing mammals • Many such as Methanopyrus live in deep- ocean hydrothermal vents
  96. 96. 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)
  97. 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Eukarya Tour
  98. 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae The Plantae consist of several clades; all chloroplasts trace back to a single incidence of endosymbiosis.
  99. 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Glaucophytes • Unicellular, freshwater organisms • The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.
  100. 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Red Algae • Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores Motile spores from Purpureofilum Audouinella pacifica Spyridia
  101. 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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. Movement in the green alga Volvox Micrasterias
  102. 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Charophytes and Land Plants STAY TUNED
  103. 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts
  104. 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •Choanoflagellates are sister to the animals. •Some are colonial and resemble a type of cell found in sponges. The choanoflagellate Salpingoeca sp. feeding Opisthokonts: Choanoflagellates
  105. 105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts: Fungi and Animals STAY TUNED
  106. 106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates Alveolates Have alveoli or sacs beneath surface of plasma membrane. All are unicellular; many are photosynthetic.
  107. 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •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 Certium tenue Coral symbiont
  108. 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Apicomplexans • All parasitic • Have a mass of organelles at one tip—the apical complex that help the parasite enter the host’s cells. Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children
  109. 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Ciliates 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.
  110. 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles Stramenopiles Two flagella, with rows of tubular hairs on the longer one.
  111. 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine. Stramenopiles: Brown Algae A community of brown algae: The marine kelp forest
  112. 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Diatoms 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
  113. 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Oomcyetes Phytophthora Potato Late Blight • Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but are unrelated. Sudden Oak Death
  114. 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Rhizaria Rhizaria Unicellular, aquatic, with long, thin pseudopods.
  115. 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Chlorarachnion reptans
  116. 116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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.
  117. 117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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.
  118. 118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates
  119. 119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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
  120. 120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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.
  121. 121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates: Euglenids • Have flagella. • Some are photosynthetic, some always heterotrophic, and some can switch. Movement in the euglenoid Eutreptia
  122. 122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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
  123. 123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Amoebozoans Amoebozoans Lobe-shaped pseudopods are used for locomotion.
  124. 124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Not colonial; live as single cells • Some secrete shells or glue sand grains together to form a casing. • Many pathogens Amoebozoans: Loboseans
  125. 125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Entamoeba histolytica http://www.npr.org/blogs/health/2014/04/09/300991364/gut-eating-amoeba- caught-on-film
  126. 126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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
  127. 127. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Karyog
  128. 128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 End of The Tours • End of the Tours
  129. 129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !7: The Domains of Life !8: Phylogenetic Diversity of Microbes !9: Functional Diversity of Microbes Lecture 8 Context • See you Monday for Functional Diversity of Microbes

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