Week 1 Lecture 1 Introduction to Microbiology-part 1 PDF

Introduction to Microbiology Linfeng Huang Associate Professor of Biology BIOL 212 Microbiology Why is microbiology so important? Covid Test at Kunshan My first of work  Covid-19 2019-nCoV SARS-CoV-2 Coronavirus...

Introduction to Microbiology Linfeng Huang Associate Professor of Biology BIOL 212 Microbiology Why is microbiology so important? Covid Test at Kunshan My first of work  Covid-19 2019-nCoV SARS-CoV-2 Coronavirus 29,903 nt Double-stranded RNA virus  Covid-19 vaccines made of another virus Chinese adenovirus vaccine Russian adenovirus vaccine Approved by Russia government without a Phase 3 clinical trial ?! Oxford adenovirus vaccine Launch of Sputnik-1 satellite in 1957  Tulip, environment, fungicide and human health https://www.insider.com/dutch-farmers-protecting-tulip-fields-from-instagram-users-2019-4  Fungal pathogen transportation that might be related to the tulip industry “… research showing that the inter- country transfer of bulbs of Holland's Triazole class fungicide iconic flowers may inadvertently have Difenoconazol opened up a new transport route for a particularly nasty fungal pathogen For plants called Aspergillus fumigatus.” In Netherlands, there is a widespread use of Triazole antifungal drugs as fungicides in agriculture and Selection floriculture which may be selecting fungicide-resistant fungus out in the Aspergillus fumigatus environment. The samples taken from five out of six sciencephoto.com Resistant imported tulip-bulb packages cultured A. fumigatus resistant to Voriconazole - the leading antifungal For human therapy in Aspergillosis - while some isolates showed cross-resistance to other Triazole antifungals. Voriconazole M. Renz via the Public Health Image Library of the Centers https://www.sciencedaily.com/releases/2017/05/170518104017.htm for Disease Control and  Microbes and food Soy sauce 酱油 Fermented soybean 豆豉 古法酿造酱油 https://haokan.baidu.com/v?vid=550166089283 0430261&pd=bjh&fr=bjhauthor&type=video Shaoxing Anchang  Liquor company is the most valuable company in Chinese stock market The most valuable Market cap: 300 billion USD company in the USA Market cap: 1.97 trillion USD http://biz.ifeng.com/huanan/focus/deta il_2012_12/13/480753_22.shtml Textbook  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) Phase-contrast Fluorescent microscopy microscopy Scanning electron micrograph Figure 1.1  Microorganisms, Tiny Titans of the Earth Oldest form of life Major fraction of Earth’s biomass Surround plants and animals Inside the bodies and tissues Affect human life (infectious diseases, food and water, soils, animal health, fuel)  Tools for studying microorganisms Grow and visualization: microscopy culture: cells grown in/on nutrient medium medium: liquid/solid mixture containing all required nutrients for example, bacteria can grow to form a visible colony on a culture plate (Figure 1.2) Molecular, genomic and immunological techniques PCR sequencing antibody-based tests …  Macroscale: Microscale: A single colony can contain A bacterial cell in this colony is more than 10 million (107) about 10 µM in length individual cells. Figure 1.2  Historical perspective of microbiology Infusoria under microscope Antonie van Leeuwenhoek Otto Friedrich Müller 1632-1723 Danish naturalist Invented microscope. http://ikanrainbowfish.blogspot. hk/2013/07/kultur-infusoria.html 1730 -1784 Organized bacteria into genera and species according to the classification methods Wikipedia of Carolus Linnaeus.  “Germ theory” – diseases are caused by microbes Wikipedia Friedrich Henle Louis Pasteur Robert Koch In 1840, the German pathologist Friedrich Henle proposed criteria for proving that microorganisms were responsible for causing human disease (the “germ theory” of disease). Robert Koch and Louis Pasteur confirmed this theory in the 1870s and 1880s with a series of elegant experiments proving that microorganisms were responsible for causing anthrax, rabies, plague, cholera, and tuberculosis.  Pasteur disproved spontaneous generation theory 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 Swan-necked Pasteur flask Figure 1.26 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 Used until today to prove the causative agent of an infection disease for e.g. Covid-19 Figure 1.29 A hand-colored photograph taken by Walther Hesse of colonies formed on agar. The colonies include those of molds and bacteria obtained during Hesse’s studies of the microbial content of air in Berlin, Germany, in 1882. From Hesse, W. 1884. “Ueber quantitative Bestimmung der in der Luft enthaltenen Mikroorganismen.” Mittheilungen aus dem Kaiserlichen Gesundheitsamte. 2: 182–207. Figure 1.30  Microbial diversity: focuses on nonmedical aspects of microbiology in soil and water Enrichment culture 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) Figure 1.9  Discovery of chemolithotrophy 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) (see 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  The start of modern antibiotics Penicillium in culture Antibiotic susceptibility test Sir Alexander Fleming Fleming discovered, by “accident”, antibiotic substance benzylpenicillin (Penicillin G) from the mold (fungus) Penicillium notatum in 1928. β-Lactam ring β-Lactam antibiotics inhibit the formation Wikipedia of peptidoglycan cross-links in the bacterial cell wall.  Microorganisms and the biosphere History of Life on Earth 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 plants and animals ~0.5 billion years ago LUCA : the last universal common ancestor Figure 1.5  Microbial ecology Notable umbers: – ~2 x 1030 microbial cells on Earth – in humans, 1–10 microbial cells per human cell Ecosystem refers to all living organisms plus physical and chemical constituents of their environment. Metabolic activities can change habitats and affect other organisms. Structures and colors formed by microbes in the environment Halobacteria http://www.biochem.mpg.de/522218/Org_Hasal http://halo.umbc.edu/haloed/motility Lake Hillier of Australia’s Recherche Archipelago; Pink color possibly caused pink bacteria halobacteria living in high salinity lake water. https://www.tumblr.com/search/halobacteria Extremophiles live in habitats too harsh for other life forms. examples: hot springs, glaciers, high salt, high acidity/alkalinity, high pressure (Table 1.1) Table 1.1 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 For plant: nitrogen-fixing bacteria For animal: cellulose-degrading microbes in rumen  Microorganisms as disease agents Bacterial, fungal, parasitic, and viral pathogens Figure 1.8  Most microorganisms are with us and beneficial Figure 1.10 Gut microbiome: digests complex carbohydrates in humans: synthesize vitamins and other nutrients Commensal microorganisms and human Commensal population of microbes plays a critical role in human survival by participating in the metabolism of food products, provides essential growth factors, protects against infections with highly virulent microorganisms, and stimulates the immune response.  Microorganisms and food negative impacts can cause food spoilage and foodborne disease harvest, storage, safety, prevention of spoilage influenced by microbes positive impacts improving food safety, preservation dairy products (e.g., cheeses, yogurt, buttermilk) other food products (e.g., sauerkraut, kimchi, pickles, chocolate, coffee, leavened breads, beer) Figure 1.11  Microorganisms and industry Biofilms: growth on submerged surfaces (e.g., pipes, storage tanks, implanted medical devices) - Bad Industrial microbiology: massive growth of naturally-occurring microbes to make low-cost products (e.g., antibiotics, enzymes, some chemicals) – good Biotechnology and synthetic biology: genetically engineered microbes making high-value products in small amounts – great and the future!  Production of biofuels examples: methane, ethanol (Figure 1.12) Wastewater treatment Bioremediation: cleaning up pollutants Figure 1.12 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  Prokaryotic versus eukaryotic cells Prokaryotes (Figure 1.3a) Bacteria and Archaea no membrane-enclosed organelles (membrane-enclosed structures), no nucleus 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) Eukaryotes (Figure 1.3b) plants, animals, algae, protozoa, fungi contain organelles DNA enclosed in a membrane-bound nucleus Linear and much larger/more DNA (up to billions of base pairs) Figure 1.3  Activities of microbial ells 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 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. Figure 1.4  Microbial life Viruses Very small: Diameter from 18 to 600 nanometers (most viruses are less than 200 nm and cannot be seen with a light microscope); Minimal content: usually only protein with DNA or RNA, or even proteins without DNA/RNA (prions); Parasitic: Requiring host cells for replication. Influenza Ebola H1N1 SARS www.huffingtonpost.com CDC CDC  Bacteria Prokaryotic organisms: simple unicellular organisms with no nuclear membrane, mitochondria, Golgi bodies, or endoplasmic reticulum—that reproduce by asexual division; Various phenotypic and genotypic properties: the size (1 to 20 µm or larger), shape (spheres, rods, spirals), and spacial arrangement (single cells, chains, clusters), cell wall components (two basic forms: gram-positive and gram-negative). Thousands of species co-exist with human. Staphylococcus aureus Bacillus cereus Streptococcus pneumoniae  Parasites Complex eukaryotic microbes: unicellular Plasmodium falciparum and or multicellular, range in size from tiny (1 to 2 µm similar to many bacteria) to up to 10 meters (tapeworms) and arthropods (bugs); Life cycles involve a complex relationship with animal hosts. Fungi Eukaryotic organisms that contain a well- Candida albicans defined nucleus, mitochondria, Golgi bodies, and endoplasmic reticulum; Unicellular form (yeast) or filamentous form (mold); Replicate asexually or sexually.  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 Basic characters of bacteria Surface structures Pili, appendages involved in “conjugation” – transfer of genetic materials. Fimbriae, structures concerned with the adhesion of bacteria to various surfaces. Glycocalyx, polysaccharide and protein film that surround bacterial cells. Two types: capsules (well- defined outer layers) and S- layers (loosely organized network of materials). Bacterial cell walls Gram-negative Has an extra outer membrane containing lipopolysaccharide (LPS) - endotoxins that can cause diseases and are activators of immune response. Gram-positive Thick and compact peptidoglycan layer which helps to retain crystal violet dye.  Lipopolysaccharide (LPS) LPS (endotoxin) consists of three structural sections: Lipid A, core polysaccharide (rough core), and O antigen. Lipid A is a basic component of LPS and is essential for bacterial viability. Lipid A is responsible for the endotoxin activity of LPS. LPS structure is used to classify bacteria. The basic structure of lipid A is identical for related bacteria and is similar for all gram-negative Enterobacteriaceae. The core region is the same for a species of bacteria. The O antigen distinguishes serotypes (strains) of a bacterial species. For example, the O157:H7 (O antigen:flagellin) serotype identifies the E. coli agent of hemolytic-uremic syndrome. Inner structures of bacterial cells Cytoplasmic membrane Nucleoid, the site in the bacterial cytoplasm that contains DNA. Cytoplasmic inclusion bodies, storage places of various compounds e.g. carbohydrate, phosphate, nucleic acid, protein and lipid etc. Arrows: nucleoid in E. coli  Bacterial spores Under harsh environmental conditions, such as the loss of a nutritional requirement, bacteria can convert from a vegetative state to a dormant state, or spore. Some gram-positive, but never gram-negative, bacteria, such as members of the genera Bacillus and Clostridium (soil bacteria), are spore formers. The spore is a dehydrated, multishelled structure that protects and allows the bacteria to exist in “suspended animation”.  Biofilm Aggregation of growing bacterial cells occurs on a surface, forming a highly hydrated polysaccharide matrix in which the cells become enmeshed. The biofilm is a sturdy colony which is difficult to dislodge and provides the bacteria with protection against many environmental factors and also against antibiotics. TEM of biofilm formed by Prevotella intermedia. The gel matrix of the biofilm appears as a network of fine fibres interspersed between the cells. Biofilm of Staphylococcus aureus  Bacterial pathogenesis Bacterial Disease Production 1.Disease is caused by damage produced by the bacteria plus the consequences of innate and immune responses to the infection. 2.The signs and symptoms of a disease are determined by the function and importance of the affected tissue. 3.The length of the incubation period is the time required for the bacteria and/or the host response to cause sufficient damage to initiate discomfort or interfere with essential functions. Examples of bacterial diseases and disease symptoms Vibrio cholerae causing watery diarrhea and vomiting Pseudomonas infection of burn wound Concepts of sterilization, disinfection, and antisepsis Antisepsis: Use of chemical agents on skin or other living tissue to inhibit or eliminate microbes; no sporicidal action is implied. Disinfection: Use of physical procedures or chemical agents to destroy most microbial forms; bacterial spores and other relatively resistant organisms (e.g., mycobacteria, viruses, fungi) may remain viable. Sterilization: Use of physical procedures or chemical agents to destroy all microbial forms, including bacterial spores