Microbiology Lecture Presentation PDF

MICROBIOLOGY Prof. Dr. Tunç ÇATAL Üsküdar University Faculty of Engineering and Natural Sciences Department of Molecular Biology and Genetics...

MICROBIOLOGY Prof. Dr. Tunç ÇATAL Üsküdar University Faculty of Engineering and Natural Sciences Department of Molecular Biology and Genetics E-mail: [email protected] © 2019 Pearson Education Ltd.  Course Material Brock, Biology of Microorganisms Benjamin cummings, Microbiology: An Introduction Lectures: Monday 14.40 Lab. : Friday 09.40-17.30 © 2019 Pearson Education Ltd.  Term Project: Various topics Written report Oral presentation (A diagram (A) and a photograph (B) of an air-cathode and mediator-less MFC). © 2019 Pearson Education Ltd.  I. Exploring the Microbial World 1.1 Microorganisms, Tiny Titans of the Earth 1.2 Structure and Activities of Microbial Cells 1.3 Microorganisms and the Biosphere 1.4 The Impact of Microorganisms on Human Society © 2019 Pearson Education Ltd.  1.1 Microorganisms, Tiny Titans of the Earth Microorganisms (microbes) are life forms too small to be seen by the human eye diverse in form/function inhabit every environment that supports life many single-celled, some form complex structures, some multicellular live in microbial communities (Figure 1.1) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.1  1.1 Microorganisms, Tiny Titans of the Earth Oldest form of life Major fraction of Earth’s biomass Surround plants and animals Affect human life (infectious diseases, food and water, soils, animal health, fuel) © 2019 Pearson Education Ltd.  1.1 Microorganisms, Tiny Titans of the Earth Tools for study microscopy culture: cells grown in/on nutrient medium medium: liquid/solid mixture containing all required nutrients growth to form a visible colony (Figure 1.2) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.2  1.1 Microorganisms, Tiny Titans of the Earth Studying fundamental life processes molecular biology and biochemistry genomics and molecular genetics © 2019 Pearson Education Ltd.  1.2 Structure and Activities of Microbial Cells The cell: A living compartment that interacts with the environment and other cells Elements of microbial structure All cells have the following in common (Figure 1.3): cytoplasmic (cell) membrane: barrier that separates the inside of the cell from the outside environment cytoplasm: aqueous mixture of macromolecules, small organics, ions, and ribosomes inside cell ribosomes: protein-synthesizing structures cell wall: present in some microbes; confers structural strength © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.3  1.2 Structure and Activities of Microbial Cells Prokaryotic versus eukaryotic cells prokaryotes (Figure 1.3a) Bacteria and Archaea no membrane-enclosed organelles (membrane-enclosed structures), no nucleus eukaryotes (Figure 1.3b) plants, animals, algae, protozoa, fungi contain organelles DNA enclosed in a membrane-bound nucleus © 2019 Pearson Education Ltd.  1.2 Structure and Activities of Microbial Cells Genes, genomes, nucleus, and nucleoid genome: a cell's full complement of genes eukaryotic DNA linear chromosomes within nucleus much larger/more DNA (up to billions of base pairs) prokaryotic DNA generally single circular chromosome that aggregates to form the nucleoid region (Figure 1.3a) may also have plasmids (extrachromosomal DNA) that confer special properties (e.g., antibiotic resistance) small, compact (0.5–10 million base pairs) © 2019 Pearson Education Ltd.  1.2 Structure and Activities of Microbial Cells Activities of microbial cells (Figure 1.4) In nature, cells typically live in microbial communities. metabolism: chemical transformation of nutrients enzymes: protein catalysts transcription: DNA information converted to RNA translation: RNA used by ribosome protein © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.4  1.2 Structure and Activities of Microbial Cells Activities of microbial cells (Figure 1.4) Motility: Many cells move through self-propulsion. Differentiation: Some microbes modify structures to form specialized cell. Intercellular communication: Some microbes respond to other microbes. Evolution: Genetic changes transfer to offspring. © 2019 Pearson Education Ltd.  1.3 Microorganisms and the Biosphere History of Life on Earth (Figure 1.5) Earth is 4.6 billion years old. First cells appeared between 3.8 and 4.3 billion years ago. The atmosphere was anoxic (no O2) until ~2.6 billion years ago. only anaerobic metabolisms first anoxygenic phototrophs ~3.6 billion years ago (Figure 1.6) plants and animals ~0.5 billion years ago © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.5 © 2019 Pearson Education Ltd. Figure 1.6  1.3 Microorganisms and the Biosphere Domains: three distinct lineages of microbial cells (Figure 1.5b) Bacteria (prokaryotic) Archaea (prokaryotic) Eukarya (eukaryotic) Descended from last universal common ancestor (LUCA) © 2019 Pearson Education Ltd.  1.3 Microorganisms and the Biosphere ~2 x 1030 microbial cells on Earth Extremophiles live in habitats too harsh for other life forms. examples: hot springs, glaciers, high salt, high acidity/alkalinity, high pressure (Table 1.1) Ecosystem refers to all living organisms plus physical and chemical constituents of their environment. Metabolic activities can change habitats and affect other organisms. Microbial ecology is the study of microbes in their natural environment. in humans, 1–10 microbial cells per human cell © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Table 1.1  1.4 The Impact of Microorganisms on Human Society Microorganisms can be both beneficial and harmful to humans. agents of disease food and agriculture valuable human products, energy generation, environmental clean-up © 2019 Pearson Education Ltd.  1.4 The Impact of Microorganisms on Human Society Microorganisms as disease agents (Figure 1.8) control of infectious disease during last century bacterial and viral pathogens Most microorganisms beneficial © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.8  1.4 The Impact of Microorganisms on Human Society Microorganisms, agriculture, and human nutrition Many aspects of agriculture depend on microbial activities. (Figure 1.9) nitrogen-fixing bacteria cellulose-degrading microbes in rumen gut microbiome: digests complex carbohydrates in humans (Figure 1.10) synthesize vitamins and other nutrients © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.9 © 2019 Pearson Education Ltd. Figure 1.10  1.4 The Impact of Microorganisms on Human Society Microorganisms and food negative impacts can cause food spoilage and foodborne disease harvest, storage, safety, prevention of spoilage influenced by microbes positive impacts (Figure 1.11) improving food safety, preservation dairy products (e.g., cheeses, yogurt, buttermilk) other food products (e.g., sauerkraut, kimchi, pickles, © 2019 Pearson Education Ltd. chocolate, coffee, leavened breads, beer) © 2019 Pearson Education Ltd. Figure 1.11  1.4 The Impact of Microorganisms on Human Society Microorganisms and industry biofilms: growth on submerged surfaces (e.g., pipes, storage tanks, implanted medical devices) industrial microbiology: massive growth of naturally- occurring microbes to make low-cost products (e.g., antibiotics, enzymes, some chemicals) biotechnology: genetically engineered microbes making high-value products in small amounts © 2019 Pearson Education Ltd.  1.4 The Impact of Microorganisms on Human Society Microorganisms and industry production of biofuels examples: methane, ethanol (Figure 1.12) wastewater treatment bioremediation: cleaning up pollutants © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.12  II. Microscopy and the Origins of Microbiology 1.5 Light Microscopy and the Discovery of Microorganisms 1.6 Improving Contrast in Light Microscopy 1.7 Imaging Cells in Three Dimensions 1.8 Probing Cell Structure: Electron Microscopy © 2019 Pearson Education Ltd.  1.5 Light Microscopy and the Discovery of Microorganisms Microbiology began with the microscope. Robert Hooke (1635–1703): first to describe microbes (Micrographia in 1665) illustrated the fruiting structures of molds (Figure 1.13) Antoni van Leeuwenhoek (1632–1723): first to describe bacteria (Figure 1.14) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.13 © 2019 Pearson Education Ltd. Figure 1.14  1.5 Light Microscopy and the Discovery of Microorganisms Van Leeuwenhoek’s microscope was a light microscope (illuminating sample with visible light). magnification: the ability to make an object larger resolution: the ability to distinguish two adjacent objects as distinct and separate Limit of resolution for light microscope is about 0.2 μm. © 2019 Pearson Education Ltd.  1.5 Light Microscopy and the Discovery of Microorganisms Several types bright-field phase-contrast differential interference contrast dark-field fluorescence © 2019 Pearson Education Ltd.  1.5 Light Microscopy and the Discovery of Microorganisms © 2019 Pearson Education Ltd.  1.5 Light Microscopy and the Discovery of Microorganisms Compound light microscope uses visible light to illuminate cells. (Figure 1.15) Two sets of lenses form the image objective lens (magnifies 10–100x) and ocular lens (magnifies 10–30x) total magnification = objective magnification x ocular magnification magnification of 1,000x needed for 0.2 μm diameter resolution (limit for most light microscopes) Bright-field scope specimens visualized because of differences in contrast (density) between specimen and surroundings pigmented microbes (Figure 1.16) add contrast © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.15 © 2019 Pearson Education Ltd. Figure 1.16  1.6 Improving Contrast in Light Microscopy Staining improves contrast Dyes are organic compounds that bind to specific cellular materials. basic dyes: positively charged, bind strongly to negatively-charged cell components (e.g., nucleic acids, acidic polysaccharides, cell surfaces) examples: methylene blue, crystal violet, and safranin Simple stain uses dried cells. (Figure 1.17) © 2019 Pearson Education Ltd.  Microscopy & Staining Overview © 2019 Pearson Education Ltd.  Staining © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.17  1.6 Improving Contrast in Light Microscopy Differential stains: Different kinds of cells are different colors. example: gram stain (Figure 1.18) differences because of cell wall structure Bacteria can be divided into two major groups: gram-positive and gram-negative. Gram-positive bacteria appear purple-violet, and gram-negative bacteria appear pink. (Figure 1.18b) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.18  1.6 Improving Contrast in Light Microscopy Phase-contrast microscopy (Figure 1.19) improves image contrast of unstained, live cells Phase ring amplifies differences in the refractive index of cell and surroundings. Resulting image—dark cells on a light background (Figure 1.19b) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.19  1.6 Improving Contrast in Light Microscopy Dark-field microscopy Light reaches the specimen from the sides. Only light reaching the lens has been scattered by specimen. Image appears light on a dark background. (Figure 1.19c) better resolution than light microscopy excellent for observing motility (flagella) © 2019 Pearson Education Ltd.  1.6 Improving Contrast in Light Microscopy Fluorescence microscopy used to visualize specimens that fluoresce (emit light after illumination with different wavelength) (Figure 1.20) Cells appear to glow on black background due to filters. fluoresce naturally (autofluorescence) or after they have been stained with a fluorescent dye such as DAPI widely used in microbial ecology for enumerating bacteria in natural samples © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.20  1.7 Imaging Cells in Three Dimensions Differential interference contrast (DIC) microscopy uses a polarizer to create two distinct beams of polarized light (light in single plane) gives structures such as nuclei, endospores, vacuoles, and inclusions a three-dimensional appearance (Figure 1.21) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.21  1.7 Imaging Cells in Three Dimensions Confocal scanning laser microscopy (CSLM) uses a computerized microscope coupled with a laser source to generate a three-dimensional image (Figure 1.22) Computer can focus the laser on single layers of the specimen. Different layers can then be compiled for a three- dimensional image. © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.22  1.8 Probing Cell Structure: Electron Microscopy Electron microscopes use electrons instead of visible light (photons) to image cells and structures (Figure 1.23) electromagnets function as lenses operates in a vacuum camera takes a picture = electron micrograph Two types: transmission electron microscopes (TEM) scanning electron microscopes (SEM) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.23  1.8 Probing Cell Structure: Electron Microscopy Transmission electron microscopy (TEM) (Figure 1.24) much greater resolving power (0.2 nm) than light microscope enables visualization of structures at the molecular level Specimen must be very thin (20–60 nm) and stained with high atomic weight substances that scatter electrons well and improve contrast. Negative staining allows direct observation of intact cells/components. (Figure 1.24b) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.24  Electron Microscopy © 2019 Pearson Education Ltd.  1.8 Probing Cell Structure: Electron Microscopy Scanning electron microscopy (SEM) Specimen is coated with a thin film of heavy metal (e.g., gold). An electron beam scans the object. Scattered electrons are collected and projected to produce an image. (Figure 1.24c) Even very large specimens can be observed. magnification range of 15–100,000x only surface visualized © 2019 Pearson Education Ltd.  III. Microbial Cultivation Expands the Horizon of Microbiology 1.9 Pasteur and Spontaneous Generation 1.10 Koch, Infectious Diseases, and Pure Cultures 1.11 Discovery of Microbial Diversity © 2019 Pearson Education Ltd.  III. Microbial Cultivation Expands the Horizon of Microbiology Aseptic technique: collection of practices that allow preparation and maintenance of sterile (no living organisms) chemicals Pure cultures: cells from only a single type of microorganism Enrichment culture techniques: isolate microbes having particular metabolic characteristics from nature Answer two questions: (1) Does spontaneous generation occur? (2) What is the nature of infectious disease? © 2019 Pearson Education Ltd.  1.9 Pasteur and Spontaneous Generation Louis Pasteur: chemist and microscopist discovered that living organisms discriminate between optical isomers (Figure 1.25) discovered that alcoholic fermentation was a biologically (not just chemically) mediated process Using the swan-necked Pasteur flask, he disproved theory of spontaneous generation (Figure 1.26): Life arose spontaneously from nonliving material. led to sterilization methods and food preservation developed vaccines for anthrax, fowl cholera, and rabies © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.25  1.10 Koch, Infectious Disease, and Pure Cultures Robert Koch (1843–1910): physician and microbiologist (Figure 1.28) experimentally demonstrated the link between microbes and infectious diseases (germ theory of infectious disease) identified causative agents of anthrax, tuberculosis, and cholera Koch's postulates (Figure 1.29) developed solid media for obtaining pure cultures of microbes (Figure 1.30) observed that masses of cells (called colonies) have different shapes, colors, and sizes awarded Nobel Prize for Physiology and Medicine in 1905 © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.28 © 2019 Pearson Education Ltd. Figure 1.29 © 2019 Pearson Education Ltd. Figure 1.30  1.11 Discovery of Microbial Diversity Microbial diversity: focuses on nonmedical aspects of microbiology in soil and water Martinus Beijerinck (1851–1931) Developed enrichment culture technique Microbes can be isolated from natural samples in a highly selective fashion by manipulating nutrient and incubation conditions. example: nitrogen-fixing rhizobia (Figure 1.9) © 2019 Pearson Education Ltd.  1.11 Discovery of Microbial Diversity Sergei Winogradsky (1856–1953) and the concept of chemolithotrophy demonstrated that specific bacteria are linked to specific biogeochemical transformations (e.g., N and S cycles) (Figure 1.32) proposed concept of chemolithotrophy oxidation of inorganic compounds to yield energy demonstrated chemolithotrophs use carbon from CO2 (autotrophy) first to demonstrate nitrogen fixation (Clostridium pasteurianum) and nitrification © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.32  IV. Molecular Biology and the Unity and Diversity of Life 1.12 Molecular Basis of Life 1.13 Woese and the Tree of Life 1.14 An Introduction to Microbial Life © 2019 Pearson Education Ltd.  1.12 Molecular Basis of Life Ability to grow bacteria rapidly under controlled conditions makes them excellent models for fundamental nature of life. Led to foundations of molecular biology, genetics, and biochemistry Metabolic model chemistry: Certain macromolecules and reactions are universal. © 2019 Pearson Education Ltd.  1.12 Molecular Basis of Life Cracking the Code of Life Genetic transfer in bacteria and DNA is genetic material. Frederick Griffith, Streptococcus pneumoniae (Figure 1.34), and transformation Avery-MacLeod-McCarty experiment Frederick Griffith, Streptococcus pneumoniae (Figure 1.34), and transformation James Watson, Francis Crick, Rosalind Franklin: structure of DNA Emile Zuckerkandl and Linus Pauling: molecular sequences and evolutionary relationships © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.34  1.13 Woese and the Tree of Life Ribosomal RNA (rRNA) present in all cells made it possible to build the first tree of life. Carl Woese (1928-2012) realized rRNA sequences could be used to infer evolutionary relationships. (Figure 1.36b) discovered rRNA from methanogens distinct from Bacteria and Eukarya named new group Archaea found relationships can be deduced by comparing genetic information in the different specimens (Figure 1.36a) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.36  1.13 Woese and the Tree of Life Phylogenetic tree: depicts phylogeny (evolutionary history) of all cells clearly shows three domains Root is LUCA. evolution along two paths to form Bacteria and Archaea Archaea diverged to distinguish Eukarya. Cultivation-independent methods show most microbes have not been cultured yet. (Figure 1.37) © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.37  1.14 An Introduction to Microbial Life Bacteria (Figure 1.38) prokaryotes usually undifferentiated single cells 1–10 μm long but vary widely 30 major phylogenetic lineages, mostly diverse species with diverse physiologies and ecological strategies © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. Figure 1.38  1.14 An Introduction to Microbial Life Archaea prokaryotes less morphological diversity than Bacteria mostly undifferentiated cells 1–10 μm long five well-described phyla historically associated with extreme environments, but not all extremophiles lack known parasites or pathogens of plants and animals © 2019 Pearson Education Ltd.  1.14 An Introduction to Microbial Life Eukarya plants, animals, fungi first were unicellular, may have appeared two billion years ago at least six kingdoms vary dramatically in size, shape, physiology (Figure 1.38) © 2019 Pearson Education Ltd.  1.14 An Introduction to Microbial Life Viruses obligate parasites that only replicate within host cell not cells do not carry out metabolism; take over other metabolic systems to replicate have small genomes of double-stranded or single- stranded DNA or RNA very diverse classified based on structure, genome composition, and host specificity © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. © 2019 Pearson Education Ltd. REFERENCE: BROCK BIOLOGY OF MICROORGANISMS