The Microbial World PDF

Chapter 1 – The Microbial World © 2012 Pearson Education, Inc.  I. Exploring the Microbial World 1.1 Microorganisms, Tiny Titans of the Earth © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc.  90 mm 0.01 m...

Chapter 1 – The Microbial World © 2012 Pearson Education, Inc.  I. Exploring the Microbial World 1.1 Microorganisms, Tiny Titans of the Earth © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc.  90 mm 0.01 mm (10 µm) 2 mm © 2012 Pearson Education, Inc.  1.2 Structure and Activities of Microbial Cells Elements of microbial structure: – Cytoplasmic membrane – Cytoplasm – Ribosomes – Cell wall – Genetic material © 2012 Pearson Education, Inc.  Two major structural classes of cells: – Prokaryotic cells – Eukaryotic cells (Compare and contrast prokaryotic and eukaryotic cells) © 2012 Pearson Education, Inc. Fig. 1.4 Prokaryotic cell © 2012 Pearson Education, Inc.  Eukaryotic cell Fig. 1.4 (Yeast (Saccharomyces cerevisiae) cell shown here) © 2012 Pearson Education, Inc.  Activities of microbial cells © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc.  1.3 Cell Size and Morphology © 2012 Pearson Education, Inc.  Table 1.1 Cell Size and Volume of Some Cells of Bacteria, From the Largest to the Smallest © 2012 Pearson Education, Inc.  Cell size and the significance of being small 0.2 to >700 µm Most are on the smaller end of the scale Epulopiscium fishelsoni Shown here - 600µm long Some of the smallest prokaryotes are Thiomargarita namibiensis Mycoplasmas (0.2 µm) Largest known prokaryote 400-750 µm long © 2012 Pearson Education, Inc.  Cells generally remain small – Maintain a high surface/volume ratio – Growth rate depends on many factors including how fast a cell can exchange nutrients with its surrounding. © 2012 Pearson Education, Inc. Figure 1.7 © 2012 Pearson Education, Inc.  Small cells in general grow faster than larger cells – Can this affect evolution? © 2012 Pearson Education, Inc.  Cell Morphology In microbiology, the term morphology means cell shape. © 2012 Pearson Education, Inc. Coccus (Sphere) Sarcina Streptococcus Staphylococcus © 2012 Pearson Education, Inc. Figure 2.1 (Part 2 of 6) Bacillus (Rod) © 2012 Pearson Education, Inc. Figure 2.1 (Part 3 of 6) Spirillum © 2012 Pearson Education, Inc. Figure 2.1 (Part 4 of 6) Spirochete © 2012 Pearson Education, Inc. Figure 2.1 (Part 5 of 6) Stalk Hypha Budding and appendaged bacteria © 2012 Pearson Education, Inc. Figure 2.1 (Part 6 of 6) Filamentous bacteria © 2012 Pearson Education, Inc.  1.5 Microorganisms and the Biosphere - A Brief History of Life on Earth Figure 1.10 A Summary of Life on Earth © 2012 Pearson Education, Inc. Figure 1.11 Examples of Phototrophic microorganisms (derive energy from sunlight) © 2012 Pearson Education, Inc. Figure 1.10b Three domains of cellular organisms © 2012 Pearson Education, Inc.  Microbial abundance and activity in the biosphere Major fraction of global biomass Key reservoirs of nutrients essential for life © 2012 Pearson Education, Inc.  Microbial habitats © 2012 Pearson Education, Inc.  “The role of the infinitely small in nature is infinitely large” - Louis Pasteur © 2012 Pearson Education, Inc.  1.6 Impact of Microorganisms on Human Society - Microbial Applications © 2012 Pearson Education, Inc.  I. Microorganisms as agents of disease Fig 1.13 Death rates for the leading causes of death in the United States © 2012 Pearson Education, Inc. II. Microorganisms, Agriculture and Human Nutrition © 2012 Pearson Education, Inc.  III. Microorganisms and Food spoilage, safety and production © 2012 Pearson Education, Inc. IV. Microorganisms and Industry – Biofilms – Commercially valuable prod. – antibiotics, enzymes, chemicals – Biotechnology - genetically engineered microorganisms – Biofuels – Bioremediation – Wastewater treatment Figure 1.17 Industrial Microbiology © 2012 Pearson Education, Inc.  II. Microscopy and the Origins of Microbiology Microbiology and microscopy advanced hand- in-hand. © 2012 Pearson Education, Inc.  1.7 Light Microscopy and the Discovery of Microorganisms Robert Hooke’s microscope (1665) Dead cork cells of Oak Robert Hooke – English mathematician and natural historian © 2012 Pearson Education, Inc.  Antonie van Leeuwenhoek – Dutch draper and amateur microscope builder Antoni Van Leeuwenhoek’s microscope (1674) – He saw live Bacterial cells (Wee animalcules) © 2012 Pearson Education, Inc.  Microscopes: – Light microscopes Use visible light to illuminate objects Use glass lenses of different curvature Several types of light microscopy are now available – bright-field, dark-field, phase-contrast, differential interference contrast, fluorescence. – Electron microscopes – Use electrons to image cell structures Electromagnets serve as lenses, operates in a vacuum Two main types – Scanning electron microscopy, Transmission electron microscopy © 2012 Pearson Education, Inc.  Magnification- how large something appears – Light microscopes – up to 2000× – Electron microscopes – up to 100,000× © 2012 Pearson Education, Inc.  Resolution –ability to distinguish two adjacent objects as distinct and separate – Light microscopes – 0.2 µm (micrometer) – Electron microscopes – 0.2 nm (nanometer) © 2012 Pearson Education, Inc.  Figure 1.20 Light microscope (resolving power 0.2 micrometer) A compound light microscope © 2012 Pearson Education, Inc. Figure 1.21 Bright- field micrographs of pigmented organisms) © 2012 Pearson Education, Inc.  1.8 Improving Contrast in Light Microscopy Improving contrast between specimen and surrounding improves the image. – Use of stains (kills cells) – Other forms of light microscopy Phase-contrast microscopy Dark-field microscopy Do not kill cells © 2012 Pearson Education, Inc. Figure 1.23 Gram Step 1 stain- A differential Flood the heat-fixed smear with crystal Stain violet for 1 min Result: All cells purple Step 2 Add iodine solution for 1 min Result: All cells remain purple Step 3 Decolorize with alcohol briefly Result: — about 20 sec Gram-positive cells are purple; gram-negative cells are colorless Step 4 G- Counterstain with safranin for 1–2 min Result: Gram-positive (G+) cells are purple; G+ gram-negative (G-) cells are pink to red Molecular Porobes, Inc., Eugene, Leon J. Lebeau Oregon © 2012 Pearson Education, Inc. Figure 1.24 Cells visualized by different types of light microscopy Bright-field microscopy Phase-contrast microscopy Dark-field microscopy © 2012 Pearson Education, Inc. Figure 1.25 Fluorescence microscopy Bright-field microscopy Fluorescence microscopy Fluorescence micrograph of E.coli using fluorescent dye DAPI © 2012 Pearson Education, Inc.  1.9 Imaging Cells in Three Dimensions Confocal scanning laser microscopy Nucleus Differential interference microscopy Fig. 1.21 Fig. 1.22 © 2012 Pearson Education, Inc.  1.10 Probing Cell Structure: Electron microscopy (resolving power 0.2 nanometers) Transmission electron microscopy – – 2D images – eg. single bacterial cell cut into thin slices (20-60 nm thin) Scanning electron microscopy – – 3D images © 2012 Pearson Education, Inc.  Transmission electron microscopy – – 2D images – observe internal cell structures – Use stains of high atomic weight – OsO4, lead Scanning electron microscopy – – 3D images – observe surface of objects – Specimen coated with thin film of metal - gold © 2012 Pearson Education, Inc. Figure 1.28 Electron Microscope © 2012 Pearson Education, Inc.  III. Microbial Cultivation Expands the Horizon of Microbiology (1.11-1.13) © 2012 Pearson Education, Inc.  Mid 19th century- 2 major questions pervaded biology: – Does spontaneous generation occur – What is the nature of infectious disease Answers to these questions came from work by two major scientists – Louis Pasteur and Robert Koch © 2012 Pearson Education, Inc.  Louis Pasteur (French Chemist) – Microbial basis of fermentation – Experiment to disprove spontaneous generation – Process of pasteurization – Development of vaccines (anthrax, fowl cholera and rabies) © 2012 Pearson Education, Inc. Figure 1.31 © 2012 Pearson Education, Inc.  Figure 1.32 Louis Pasteur and some symbols of his contributions to microbiology A French 5-franc note The Pasteur Institute, Paris, France © 2012 Pearson Education, Inc.  Robert Koch (German Physician) – Early work with Anthrax – Found bacteria in all diseased animals – but mere association was not proof that the particular bacterium caused the disease. – Koch’s postulates - four criteria used to link a specific microorganism to a specific disease © 2012 Pearson Education, Inc. Figure 1.33 © 2012 Pearson Education, Inc.  Koch’s postulates today: © 2012 Pearson Education, Inc.  Robert Koch (German Physician) – Koch’s postulates (link organism to disease) – Developed methods for growing pure cultures of microorganisms © 2012 Pearson Education, Inc.  Robert Koch – Koch’s postulates (link organism to disease) – Developed methods for growing pure cultures of microorganisms – Discovered the causative agent of tuberculosis (Awarded Nobel Prize in 1905 for this discovery), causative agent of cholera and tuberculin test to diagnose exposure to bacterium that causes tuberculosis Figure 1.35 Robert Koch’s drawings of Mycobacterium tuberculosis © 2012 Pearson Education, Inc.  In the early 20th century interest grew in studying other microorganisms in soil, water, etc. Martinus Beijerinck (Dutch microbiologist/botanist) – many soil and aquatic bacteria studied – enrichment culture technique – founders of virology - concept for smaller disease causing agents (virus) – causing tobacco mosaic disease © 2012 Pearson Education, Inc.  Sergei Winogradsky – (Ukrainian-Russian Microbiologist) – Studied metabolic processes in microorganisms Chemolithotrophy (using inorganic compounds as a source of energy)– Beggiatoa (sulfur oxidizing bact.) Nitrogen fixation – Clostridium pasteurianum – (N2 fixing bacterium) © 2012 Pearson Education, Inc.  IV. Molecular Biology and the Unity and Diversity of Life © 2012 Pearson Education, Inc.  1.15 Carl Woese and the Tree of Life Depicting evolutionary history of all living organisms – Ernst Haeckel (1866) Single-celled organisms (monera) ancestral to other forms of life Did not resolve evolutionary relationships among microorganisms – Robert Whittaker’s Five- Kingdom classification system (1967) Fungi as a distinct lineage Little change in understanding evolutionary relationships among microorganisms © 2012 Pearson Education, Inc.  1.15 Carl Woese and the Tree of Life – Carl Woese (1970’s) Gene sequence that code for ribosomal RNA (rRNA) molecules can be used to infer evolutionary relationships between organisms © 2012 Pearson Education, Inc.  Woese compared sequences from many microorganisms and identified a third domain – Archaea, in addition to the previously recognized domains Bacteria and Eukarya Fig. 1.41 Evolutionary relationships and the tree of life Fig. 1.5 The Three Domains of Life © 2012 Pearson Education, Inc.  Norman Pace – Woese’s approach can be applied directly to rRNA molecules isolated directly from the environment without having to cultivate microorganisms. – Thus, most microorganisms on earth have yet to be brought into laboratory culture! © 2012 Pearson Education, Inc.  1.4 An Introduction to Microbial Life Bacteria Archaea Eukarya Viruses © 2012 Pearson Education, Inc.  Bacteria – Prokaryotic cell structure – Diverse in appearance and function – 30-80 Bacterial phyla – Some are pathogenic to humans, other animals, plants, etc. © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc.  Archaea – Prokaryotic cell structure – Quite diverse in physiology, less morphologically diverse than Bacteria – Some are extremophiles – Archaea distributed among 5 phyla – None discovered so far are pathogenic © 2012 Pearson Education, Inc.  Halophile Various Archaea Thermophile Methanogen © 2012 Pearson Education, Inc.  Eukarya – Eukaryotic cell structure – Group is relatively young (evolutionarily) compared to Bacteria and Archaea Microbial eukaryotes, Animals, Plants, Fungi © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc.  Fungi © 2012 Pearson Education, Inc.  Viruses – Not found on the tree of life – Are obligate parasites – infect organisms in all three domains of life – Not cellular, no cytoplasmic membrane, cytoplasm, ribosomes – Cannot conserve energy and do not carry out metabolic processes – Genomes often small, made of DNA or RNA which may be single or double stranded © 2012 Pearson Education, Inc.  SARS CoV 2 © 2012 Pearson Education, Inc.