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Lecture 01 (3 20-2018) slides

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Introduction to microbial diversity

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Lecture 01 (3 20-2018) slides

  1. 1. Microbial Diversity Microbiology 480 Microbial Physiology & Diversity Instructor: Dr. Kristen DeAngelis Office: Life Science Labs (LSL) N435 Office Hours: Tuesdays and Thursdays 12:30 to 1:30 pm OR by appointment (RSVP appreciated) Email: deangelis@microbio.umass.edu Phone: 413-577-4669
  2. 2. Microbial Diversity schedule 2
  3. 3. What to expect • How we spend our class time – 5-10 mins: logistics, questions, social bookmarking – 3 parts: 15 m lecture, 5 m activity – Last 5 minutes: write minute papers • How to meet the course learning goals Attend lectures Listen to lecture recordings on moodle Re-read lecture slides with notes on moodle Read the assigned chapters, before class Read & annotate the shared notes doc or graphical syllabus • How to get help – Work in groups – Come to my office hours – Email me with questions 3
  4. 4. Social bookmarking • Optional • New science or news articles that relate to topics were discussing • Email to me before class or bring into class to discuss at the beginning. • We want to talk about the most current science possible! 4
  5. 5. Activities for Review of each unit… 1. Instructions for the activity will be provided. 2. Reviews last 5 minutes, with about 3 per class. 3. You might be asked to type/write, discuss, debate, sketch, or connect new information to course materials. 4. These questions are the orthologs to the ones on the exam. 5
  6. 6. Shared Notes Doc • Google doc link shared on moodle • Take notes here during class • Everyone in our class can edit & there is version control • I will review these note docs for accuracy & completeness • These will serve as the review sheets for the exams 6
  7. 7. Minute papers Names are optional 1. What do you think you know about next class’s topic? 2. Is there anything from today’s class that you do not understand? Turn your papers in to me as you leave; you may email them to me, as long as I get them before the end of office hours (Tu-Th 11:30-12:30pm, LSL N435) 7
  8. 8. Bacteroidetes Green sulfur bacteria Chlamydia Planctomycetes Proteobacteria Cyanobacteria Spirochaetes Firmicutes Actinobacteria Deinococcus/ Thermus Thermotoga Aquifex Green nonsulfur bacteria Euryarchaea Nanoarchaea Crenarchaea Korarchaeum Chromalveolates Plantae Unikonts Rhizaria Excavata Unit 6. Diversity of Microbial Mats Unit 7. Diversity of Soils and Sediments Unit 8. Diversity of Rare and Uncultivable Species Unit 9. Diversity of the Human Microbiome Unit 10. Diversity of Permafrost Unit 11. Diversity of Acellular Life: V iruses & Prions Part 2. Exploring Microbial Diversity BacteriaArchaeaEukarya Units in this section will apply concepts from Part 1 to example ecosystems as a way to explor e microbial groups; groups covered in each unit are shown in the tree by open circles ( ). Unit 1. Microbial Diversity Introduction ... what is diversity? Why does it matter? How do you mea sure it? Unit 3. Phylogenetic Diversity, or Taxonomy and Trees Unit 2. Origins of Diversity, or Microbiology of Ea rly Earth Unit 5. Morphological Diversity, or Biofilms and Motilit y Unit 4. Funcitonal Diversity, or the Baas Becking hyp othesis, “ Everything is everywh ere, but the environment selects.” Part 1. Measuring Microbial Diversity Units in this section will explore origins of diversity and how diversity is understood and applied. Graphical Syllabus 8
  9. 9. HOW TO MEASURE DIVERSITY Unit 01, 3.20.2018 Reading for today: Brown Ch. 1 & 2 Reading for next class: Brown Ch. 4, 5 & 6 Dr. Kristen DeAngelis Life Science Labs (LSL) N435 Office Hours Tu & Th 12:30 to 1:30 pm OR by appointment (RSVP appreciated) deangelis@microbio.umass.edu, 413-577-4669 9
  10. 10. Unit 1. How to measure diversity LECTURE LEARNING GOALS 1. Identify the important historical founders of modern microbiology and describe their contributions to our science. 2. For common measures of microbial diversity, explain how diversity is measured. 3. Recognize the abundance and diversity of organisms we cannot see, microbes, in all natural and manufactured environments. 10
  11. 11. Unit 1. How to measure diversity LECTURE LEARNING GOALS 1. Identify the important historical founders of modern microbiology and describe their contributions to our science. 2. For common measures of microbial diversity, explain how diversity is measured. 3. Recognize the abundance and diversity of organisms we cannot see, microbes, in all natural and manufactured environments. 11
  12. 12. What are microbes?  Any living thing you need a microscope to see... 12
  13. 13. Antonie van Leeuwenhoek Dutch trader & scientist (1632 –1723) “Father of Microbiology,” made the first microscope Figures of bacteria from the human mouth (letter 39, 17 Sept. 1683) 13
  14. 14. Louis Pasteur  French chemist & microbiologist (1822-1895)  Pasteurization  Described anaerobic bacteria (butyric acid, lactic acid fermentation)  Role of yeast in alcohol fermentation  Swan-necked flask experiments conclusively disproved spontaneous generation 15
  15. 15. Robert Koch  German scientist and physician (1843-1910)  Established causative agents of disease  Koch's postulates  THE way to establish causation  Developed methods for studying bacteria in pure culture using agar plates  named after his assistant, Julius Richard Petri 16
  16. 16. Sergei Winogradsky  Discovered that microbes were capable of geochemical transformations  Discovered chemolithotrophs  Isolated anaerobic nitrogen fixing bacteria 18
  17. 17. Carl Woese Discovered that the sequence of the small subunit ribosomal RNA gene is a phylogenetic marker. Woese, Candler & Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 19
  18. 18. Activity for Review of Unit 01.1 Founders of Microbiology On your own: for each major advance in the history of microbiology, a. name the scientist responsible and b. describe how they made their contribution 1. Visualizing microbes 2. Sterile technique 3. Culturing single colonies 4. Method for defining causative agents 5. Sequencing methods for true phylogenies After ~2m, turn to your neighbor and compare notes. At the end, we will review answers as a class. 21
  19. 19. Unit 1. How to measure diversity LECTURE LEARNING GOALS 1. Identify the important historical founders of modern microbiology and describe their contributions to our science. 2. For common measures of microbial diversity, explain how diversity is measured. 3. Recognize the abundance and diversity of organisms we cannot see, microbes, in all natural and manufactured environments. 22
  20. 20. What are some different kinds of diversity? • Taxonomic diversity • Phylogenetic diversity • Genetic diversity • Functional diversity • Morphological • Structural • Metabolic • Ecological • Behavioral THERE ARE MANY DIFFERENT WAYS OF MEASURING DIVERSITY. 23
  21. 21. Microbial metabolisms that define functional groups... or what we call microbes 25
  22. 22. The Central Dogma of Biology DNA → RNA → Protein 26
  23. 23.  Small subunit (16S) ribosomal RNA from Thermus thermophilus  Proteins in blue  Single strand rRNA in orange Small subunit ribosomal RNA 28
  24. 24. Early (wrong) Trees of Life #1 Carl Linnaeus Woesian ToL has 3 Domains 30
  25. 25. Early (wrong) Trees of Life #1 Carl Linnaeus Woesian ToL: Pace NR, Science 199731
  26. 26. Early (wrong) Trees of Life #2 Ernst Haeckl 33
  27. 27. Early (wrong) Trees of Life #3 Robert Whittaker 35
  28. 28. Modern Tree of Life remains (mostly) true to the Woesian tree • Woesian tree was based on amplicon sequencing of SSU rRNA aka 16S rRNA • Modern methods “Omics” – Genomics – Transcriptomics – Proteomics – Metabolomics – Phylogenetics – Meta-omics Bacteria Archaea Eukaryotes 37
  29. 29. Activity for Review of Unit 01.2 Measures of Diversity Draw a picture of the Woesian Tree of Life, and annotate it with labels including a. The contribution of Carl Woese b. The contribution of Ernst Haeckl c. The contribution of Carl Linnaeus When you are satisfied with your sketch, you may (optionally) take a picture and email it to me with the subject line 480: ToL 39
  30. 30. Unit 1. How to measure diversity LECTURE LEARNING GOALS 1. Identify the important historical founders of modern microbiology and describe their contributions to our science. 2. For common measures of microbial diversity, explain how diversity is measured. 3. Recognize the abundance and diversity of organisms we cannot see, microbes, in all natural and manufactured environments. 40
  31. 31. The microbial world is vast • Are there more microbes on Earth or stars in the known universe? http://www.skyandtelescope.com/astronomy-resources/how-many-stars-are-there/ 41
  32. 32. http://www.skyandtelescope.com/astronomy-resources/how-many-stars-are-there/ 42
  33. 33. 106 per mL109 per g 101-3 per m3 How many microbes are there? 106 per mL109 per g 101-3 per m3 43
  34. 34. How many microbes are there? 1013 bacteria vs 1013 human cells 1-3% body mass 44
  35. 35. How many species are there? …but what is a species? HMS Beagle being hailed by native Fuegians during the survey of Tierra del Fuego, by Conrad Martens. 45
  36. 36. How can we expand known diversity? • Cultivation and enrichment • Molecular techniques 47
  37. 37. How can there be so much diversity? 48
  38. 38. What is diversity?  Diversity = Richness + evenness 50
  39. 39. Rarefaction analysis a way to estimate total richness Also sometimes called a “collector’s curve”  Most organisms exist at very low relative abundance  A potentially bottomless well of diversity: rare biosphere 52
  40. 40. Why is diversity important?  Direct link between plant and microbial diversity and  stress resistance  Net N mineralization  Microbial biomass  Microbial activity Zak et al., 2003; 53
  41. 41. Why is diversity important?  Human health  Clean soil, air  Resistance to disturbance Lozupone et al., Science 2012 54
  42. 42. Activity for Review of Unit 01.3 Extent of Diversity For each set of pairs, which environment has the most microbes? Which has the most diversity? Why? Discuss in groups, then we will review answers together 1. Open ocean (top) or salt marsh (bottom)? 2. Top, surface soil (top) or deep soil (bottom)? 3. Skin (top) or gut (bottom)? 56
  43. 43. Unit 1. How to measure diversity LECTURE LEARNING GOALS 1. Identify the important historical founders of modern microbiology and describe their contributions to our science. 2. For common measures of microbial diversity, explain how diversity is measured. 3. Recognize the abundance and diversity of organisms we cannot see, microbes, in all natural and manufactured environments. Next class is Unit 2: Phylogeny Reading for next class: Brown Ch. 4, 5 & 6 57

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