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BiS2C: Lecture 11: Microbial Growth and Functions

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Slides for BIs2C at UC Davis Spring 2016.
Lecture by Jonathan Eisen.
Topic: Microbial Growth and Functions

Published in: Science
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BiS2C: Lecture 11: Microbial Growth and Functions

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Lecture 11: Microbial Growth and Functions BIS 002C Biodiversity & the Tree of Life Spring 2016 Prof. Jonathan Eisen 1
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Where we are going and where we have been • Previous Lecture: !10: Not a Tree • Current Lecture: !11: Microbial Growth and Functions • Next Lecture: !12: Symbiosis 2
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • What are the ranges of conditions in which life on Earth lives? • What are the ranges of conditions in which life on Earth prefers to live? • What are the key ways that living systems acquire carbon and energy? 3
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Key Concepts and Topics • Culturing • Extremophily !Thermophiles !Halophiles • Trophies • Oxygen • More on organelles 4
  5. 5. Culturing • Culturing (or cultivation) is the growth of microorganisms in controlled or defined conditions. • A pure culture (which is the ideal if possible) is one in which only one type of microbe is present !5
  6. 6. General approach to culturing ! Collect sample ! Make an environment with specific growth conditions " Energy " Electrons " Carbon " Other conditions (e.g., O2, temperature, salt, etc) ! Dilution/passaging until one obtains a “pure” sample with just a single clone !6
  7. 7. Culturing !7
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Prokaryotic Cell Division (Part 1) 8
  9. 9. Mitosis !9
  10. 10. Binary fission and Mitosis Clonal Growth 10
  11. 11. Examples of Benefits of Culturing: • Allows one to connect processes and properties to single types of organisms • Enhances ability to do experiments from genetics, to physiology to genomics • Provides possibility of large volumes of uniform material for study • Can supplement appearance based classification with other types of data. !11
  12. 12. Function Example I: Extremophily !12
  13. 13. Example 1: Thermophiles !13
  14. 14. Figure 26.16 Some Crenarchaeotes Like It Hot !14
  15. 15. Figure 26.14 What Is the Highest Temperature Compatible with Life? !15 Some prokaryotes can survive at temperatures above the 120°C threshold of sterilization. 1. Seal samples of unidentified, iron-reducing, thermal vent prokaryotes in tubes with a medium containing Fe3+ as an electron acceptor. Control tubes contain Fe3+ but no organisms. 2. Hold both tubes in a sterilizer at 121°C for 10 hours. if the iron-reducing organisms are metabolically active, they will reduce the Fe3+ to Fe2+ (as magnetite, which can be detected with a magnet). Archaea of “Strain 121” can survive at temperatures above the previously defined sterilization limit.
  16. 16. 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 !1633 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  17. 17. 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 !1633 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  18. 18. 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 !1633 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  19. 19. 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 !1633 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  20. 20. Growth vs. Time !17 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
  21. 21. Growth Rate !18 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
  22. 22. Optimal growth temperature (OGT) for Different Species !19
  23. 23. Optimal growth temperature (OGT) for Different Species !21 A > B >> E Mesophile Optimum at 15-45 °C Thermophile Optimum at 45-80°C Hyperthermophile Optimum at > 80°C
  24. 24. Hug et al 2016 !22 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
  25. 25. Hug et al 2016 !24 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 What are some possible evolutionary scenarios that would account for this pattern of presence of thermophily across the Tree of Life?
  26. 26. Thermophile Adaptations !30 Stresses of High Temperature Examples of common adaptations Denatures proteins, RNA and DNA Make proteins more stable Speeds up reactions Slow down enzyme rates Liquifies membranes Decrease fluidity of membranes
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Example 1: Extreme Halophiles 31
  28. 28. Determining Optimal Salt Concentrations !3233 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
  29. 29. Determining Optimal Salt Concentrations !3233 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
  30. 30. Determining Optimal Salt Concentrations !3233 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
  31. 31. Determining Optimal Salt Concentrations !3233 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
  32. 32. Growth vs. Time Plot Growth vs. Time for Each Condition !33 0.0 20.0 40.0 60.0 80.0 0h 1h 2h 3h 1M 2M 3M 4M Time Elapsed DensityofGrowth
  33. 33. Growth Rate !34 0.0 12.5 25.0 37.5 50.0 1M 2M 3M 4M Calculate and Plot Growth Rate vs. Conditions Salinity GrowthRate
  34. 34. Optimal salt concentration for different species !35
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 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) 36
  36. 36. Hug et al 2016 !38 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 What are some possible evolutionary scenarios that would account for this pattern of presence of halophily across the Tree of Life?
  37. 37. • Some stresses of high salt ! Osmotic pressure on cells ! Desiccation Halophile adaptations !39 H20
  38. 38. • Some stresses of high salt ! Osmotic pressure on cells ! Desiccation • Halophile adaptations ! Increased osmolarity inside cell " Proteins " Carbohydrates " Salts ! Membrane pumps ! Desiccation resistance Halophile adaptations !40 H20 H20
  39. 39. • Some stresses of high salt ! Osmotic pressure on cells ! Desiccation • Halophile adaptations ! Increased osmolarity inside cell " Proteins " Carbohydrates " Salts - only done in extremely halophilic archaea ! Membrane pumps ! Desiccation resistance Halophile adaptations !42 High internal salt requires ALL cellular components to be adapted to salt, charge. For example, all proteins must change surface charge and other properties.
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Uses of extremophiles !43 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
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Novozymes in Davis 44
  42. 42. Function Example I: Trophies !45
  43. 43. Incredible diversity in forms of nutrition in bacteria and archaea • Bacteria and archaea 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. • Examples: ! autotrophy ! chemotrophy ! phototrophy ! heterotrophy !46
  44. 44. 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 Forms of nutrition (trophy) • Three main components to “trophy”
  45. 45. 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 Forms of nutrition (trophy) • E. coli • Chemo organo hetero trophy • Chemo hetero trophy
  46. 46. 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 Forms of nutrition (trophy) • Humans? • Chemo organo hetero trophy • Chemo hetero trophy
  47. 47. 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 Forms of nutrition (trophy) • Cyanobacteria • Photo litho auto trophy • Photo auto trophy
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51 αProteo Genome Bacterial cell envelope Cell membrane Genome A Symbiosis with a Proteobacterium
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Engulfment 52 αProteo Cell membrane Genome Genome Bacterial cell envelope
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 What Does This Provide Host? 53
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Symbiosis with Free Living Cyanobacterium 54 N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Cyanobacterial Cell envelope Cyanobacterial Genome Cyano
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Engulfment 55 N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Cyanobacterial Cell envelope Cyanobacterial Genome Cyano
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 What Does This Provide Host? 56
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 57
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question What is the different between chemoautolithotrophy and chemoheterolithotrophy? • A: The source of electrons • B: The source of energy • C: The source of carbon • D: A and B • E: All of the above 58
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question What is the different between chemoautolithotrophy and chemoheterolithotrophy? • A: The source of electrons • B: The source of energy • C: The source of carbon • D: A and B • E: A, B and C 59
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Growth vs. Oxygen 60 Aerobes vs. Anaerobes
 Microbes differ in their use and tolerance of oxygen. 1. Aerobes- Require oxygen 2. Anaerobes- Vary in their tolerance/ use of oxygen Obligate anaerobes – oxygen is toxic. Aerotolerant anaerobes – can’t use oxygen, but are not damaged by it. Facultative anaerobes – don’t need oxygen, but use it when available.
  58. 58. Organelle Evolution 61
  59. 59. Simple Species Tree for Three Domains 62 Archaea Eukaryotes Bacteria
  60. 60. 63 Archaea Euks BacteriaTACK Eocyte Species Tree for Three Domains
  61. 61. Acquisition of Mitochondria At Base of Eukaryotic Branch 64 Archaea Euks BacteriaTACK
  62. 62. Endosymbiosis Shown on Species Tree 65 Archaea Euks BacteriaTACK
  63. 63. Continued Evolution After Endosymbiosis 66 Archaea Euks BacteriaTACK
  64. 64. Simple Model Showing Some Diversification within Eukaryotes 67 A2 E1 PBT E2 B2 B3 B4A1 A3
  65. 65. 68 Suppose we built phylogenetic trees with different genes from each of these species A2 E1 PBT E2 B2 B3 B4A1 A3 Simple Model Showing Some Diversification within Eukaryotes
  66. 66. Gene Set 1 69 A2 E1 PBT E2 B2 B3 B4A1 A3 Some Genes with Show This Pattern with Eukaryotes Sister to TACK
  67. 67. Gene Set 2: Organellar Genes 70 A2 E1 PBT E2 B2 B3 B4A1 A3 Some Genes with Show Alternative Pattern With “Eukaryotes” Branching within Bacteria
  68. 68. After Additional Speciation in the Eukaryote Portion of the Tree 71 A2 E1 PBT E2 B2 B3 B4A1 A3 E3
  69. 69. Gene transfer model 72 A2 E1 PBT E2 B2 B3 B4A1 A3 E3 Suppose we built phylogenetic trees with different genes from each of these species
  70. 70. Nuclear Genes 73 A2 E1 PBT E2 B2 B3 B4A1 A3 E3 Some Genes with Show This Pattern with Eukaryotes Sister to TACK
  71. 71. Nuclear Genes 74 A2 E1 PBT E2 B2 B3 B4A1 A3 E3 Note - Branching of E2 sister to E3
  72. 72. Mitochondrial Genes 76 A2 E1 PBT E2 B2 B3 B4A1 A3 E3 Some Genes with Show Alternative Pattern With “Eukaryotes” Branching within Bacteria
  73. 73. Mitochondrial Genes 77 A2 E1 PBT E2 B2 B3 B4A1 A3 E3 Note - Branching of E2 sister to E3
  74. 74. Mitochondrial Genes 78 A2 E1 PBT E2 B2 B3 B4A1 A3 E3 The topology of the tree within Eukaryotes is the same regardless of which genes. They differ in where eukaryotes placed in the tree.
  75. 75. Another Symbioses - with a CB - Cyanobacterium 79 Archaea T PBEukaryotes CB B3 B4
  76. 76. 80 Another Symbioses - with a CB - Cyanobacterium Archaea T PBEukaryotes CB B3 B4
  77. 77. 81 Continued Evolution - Diversification of Plants Archaea T PBE1 CB B3 B4E2 Plants Suppose we built phylogenetic trees with different genes from each of these species

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