BIOL371: Microbiology Lecture 01 v2 PDF

BIOL371: Microbiology Dr. Adrian Tsang [email protected] 1 General information Office: GE 120.11 Office hours: Monday 12:00-14:00 or by appointment Student Evaluation 25% Midterm exam I, October 4, 2023 (lectures 1-7) 25% Midterm exam II, November 8, 2023 (lectures 8-14) 50% Final exam (c...

BIOL371: Microbiology Dr. Adrian Tsang [email protected] 1 General information Office: GE 120.11 Office hours: Monday 12:00-14:00 or by appointment Student Evaluation 25% Midterm exam I, October 4, 2023 (lectures 1-7) 25% Midterm exam II, November 8, 2023 (lectures 8-14) 50% Final exam (cumulative) date to be announced 2 Topics 1. Course outline and course examinations 2. The importance of microorganisms 3. Origins and early developments of microbiology 3 Course outline Lecture Date Topic Relevant chapters in text 01 02 03 04 05 06 07 08 Introduction to microbiology Microbial cell structure and function Microbial metabolism overview Culturing microbes and growth dynamics Environmental effects on microbial growth Molecular biology of growth Bacterial genetics Viruses and their multiplication Midterm exam I (lectures 1-7) Microbial evolution Metabolic diversity Fermentation and hydrocarbon metabolism Environmental microbiology Microbial ecosystems Nutrient cycles Microbiology of the built environment Midterm exam II (lectures 8-14) Microbial symbioses Microbial symbioses with humans Microbial infection and pathogenesis Innate immunity Adaptive immunity Antimicrobial therapy Infectious diseases Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 4 Chapter 8 Chapter 9 Chapter 5 09 10 11 12 13 14 15 16 17 18 19 20 21 22 Sep 06 Sep 11 Sep 13 Sep 18 Sep 20 Sep 25 Sep 27 Oct 02 Oct 04 Oct 16 Oct 18 Oct 23 Oct 25 Oct 30 Nov 01 Nov 06 Nov 08 Nov 13 Nov 15 Nov 20 Nov 22 Nov 27 Nov 29 Dec 04 Chapter 13 Chapter 14 Chapter 14 Chapter 19 Chapter 20 Chapter 21 Chapter 22 Chapter 23 Chapter 24 Chapter 25 Chapter 26 Chapter 27 Chapter 28 Chapter 29 4 Text Textbook and course material: Brock Biology of Microorganisms 16th edition by MT Madigan, et al. published by Pearson 2020 The course will follow the textbook, but is also partly developed from the primary scientific literature. Lecture material (i.e. power point slides) will be made available at the Moodle site prior to each lecture. 5 Topics of today 1. The importance of microorganisms 2. Origins and early developments of microbiology Materials covered:  Chapter 1.1-1.7, 1.11-1.15  Figures 1.1, 1.4, 1.5, 1.8-1.10, 1.12-1.19, 1.31, 1.33, 1.37, 1.39-1.42 6 Microorganisms – also called microbes • 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 • typically live in communities 7 Structural features of 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: • cytoplasmic (cell) membrane: barrier that separates the inside of the cell (cytoplasm) 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 8 Structural differences of prokaryotic and eukaryotic cells Prokaryotes • Bacteria and Archaea • no organelles (membrane-enclosed structures), no nucleus Eukaryotes • Plants and animals as well as microbes such as algae, protozoa, fungi • contain organelles • D N A enclosed in a membrane-bound nucleus • mitochondria and chloroplasts 9 Properties of microbial cells 10 Cell size • 1 micrometre (µm or micron) = one-millionth of a metre • Human eye can resolve objects >100 µm in diameter • Most prokaryotic cells range from 0.5 µm to 10 µm in length • Can be as small as 0.2 µm and as large as 600 µm • Eukaryotic cells typically range from 5 µm to 100 µm 11 Morphology (size and shape) of prokaryotes Major morphologies of prokaryotic cells • • • • • • • coccus (plural, cocci): spherical or ovoid rod/bacillus (plural, bacilli): cylindrical spirillum: flexible spiral spirochete: rigid spiral appendaged bacteria, irregular/asymmetrical (e.g., budding) some stay grouped/clustered after cell division in distinctive shapes (e.g., diplococci, streptococci, cubes, grapelike clusters, filamentous bacteria) 12 Domains of life Three major cell lineages: • Bacteria • Archaea • Eukarya Life forms visible with the human eye 13 Microorganisms vary greatly in size and shape 14 Bacteria  Prokaryotic cell structure  Diverse in size and shape  Most are undifferentiated single cells of 0.5 µm to 10 µm in length  Based on DNA sequence analysis of bacteria that can be cultured, 30 phyla (singular, phylum), or phylogenetic lineages, are classified  Sequencing of environmental samples provides evidence of >80 phyla 15 Archaea  Prokaryotes  Five well-described phyla  Sequencing of environmental samples provides evidence of >12 phyla  Historically associated with extreme environments (e.g., volcanic systems and slat flats); but not all archaea are extremophiles  Lack known parasites or pathogens of plants and animals 16 Eukarya  Includes plants and animals  Eukaryotic microbes:  Fungi, protists, algae, protozoans  Vary tremendously in size, shape and physiology – plasmodial slime moulds with a single cytoplasm can reach diameter of 30 cm 17 The largest living organism on Earth is a “microorganism”  Mushrooms are fungi, classified as microbial eukaryotes, that are visible to the unaided human eye  The fungus Armillaria ostoyae (pictured) can grow into enormous size, mostly underground  A specimen of A. ostoyae found in Oregon’s Blue Mountains covers 9.6 square kilometres and is estimated to weigh 31,500 tonnes, making it the largest living organism on Earth This image of Armillaria ostoyae is Image Number 8037 at Mushroom Observer 18 Viruses and bacteriophages  Viruses are NOT living organisms and are not included in the tree of life  Viruses of bacteria are called bacteriophages  Obligate parasites that can only replicate their DNA within a host cell  No metabolic machinery  Small genomes or double-stranded or single-stranded DNA or RNA  Classified based on structure, genome composition, and host specificity 19 Life on Earth through time  Earth is ~4.6 billion years old  First cells appeared ~3.8 billion years ago  The atmosphere is anoxic (no oxygen) until ~2.6 billion years ago  Only anaerobic metabolism  Cyanobacteria (oxygenic phototrophs appeared ~2.6 billion years ago and Earth was slowly oxygenated  Plants and animals appeared ~500 million years ago 20 Microorganisms and the biosphere >1,000,000,000,000,000,000,000,000,000,000 prokaryotic cells (that is 1030 cells) And there’s an order of magnitude more viruses than prokaryotes! 21 Contribution of microbial cells to global biomass Note: Animal biomass is a minor fraction (0.1%) of total global biomass, not shown 22 Classes of extremophiles Descriptive term Habitat Minimum Optimum Maximum Undersea hydrothermal vents 90 °C 106 °C 122 °C Sea ice -12 °C 5 °C 10 °C Acidophile Acidic hot springs pH -0.06 pH 0.7 pH 4 Alkaliphile Soda lakes pH 8.5 pH 10 pH 12 Barophile (piezophile) Deep ocean sediments 500 atmospheres 700 atmospheres >1000 atmospheres Salterns 15% NaCl 25% NaCl 32% NaCl Hyperthermophile Psychrophile Halophile 23 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 24 Microorganisms as disease-causing agents and prevention   Microorganisms as disease agents  Control of infectious disease over past 120 years (see next figure)  Bacterial and viral pathogens Most microorganisms beneficial  Vaccination and antibiotic therapy  Water and wastewater treatment  Food safety (e.g., pasteurization) 25 Leading causes of death in the United States 1900 2016 2020/2021 Source: U.S. National Center for Health Statistics Antibiotic resistance is becoming a major health crisis 26 Examples of microorganisms in modern agriculture 27 Gut microbiome  Digests complex carbohydrates  Synthesize vitamins and other nutrients 28 Examples of foods fermented by microorganisms 29 Industrial microbiology Wastewater treatment Biotechnology – production of enzymes and pharmaceuticals Bioremediation Biofilms can foul pipes Fermentation to produce chemicals, solvents and materials (e.g., plastics) Biofuels production: bioethanol and 30 biodiesel Topics of today 1. The importance of microorganisms 2. Origins and early developments of microbiology 31 Robert Hooke and early microscope  Microbiology began with the invention of microscope  Robert Hooke (1635-1703) first to describe microbes by illustrating the fruiting bodies of moulds (Micrographia in 1665) In 1665-1666, the Great Plague of London killed 100,000 people, or 20% of the population. No one knew the causative agent was a microbe. 32 Antoni van Leeuwenhoek (1632-1723) first to see bacteria  Antonie van Leeuwenhoek’s microscope was a light microscope (illuminating sample with visible light) with a lens to magnify the image  He was first to describe bacteria 33 Types of microscopes    Light microscopes  Bright-field  Phase-contrast  Differential interference contrast  Dark field  Fluorescence Confocal scanning laser microscopy – three-dimension reconstruction Electron microscopy – high resolution to probe cell structure 34 Two major biological questions of the mid-19th century 1. Does spontaneous generation occur? (i.e., the emergence of life from sources other than living matter) 2. What is the nature of infectious disease? From miasma (first described in the 1600s as the source of vaporous disease-causing substance) to germ (pathogenic microorganism) theory 35 Microbial cultivation expands the horizon of microbiology  Aseptic technique: collection of practices that allow preparation and maintenance of sterile (no living organisms) media and solutions  Pure cultures: cells from only a single type of microorganism  Enrichment culture techniques: isolate microbes having particular metabolic characteristics from nature 36 Louis Pasteur (1822-1895)  Chemist and microbiologist  One of the two giants of microbiology in the 19th century  Discovered that fermentation of alcohol and organic acid was mediated by microorganisms  Refuted the concept of spontaneous generation  Developed methods of controlling growth of microorganisms  Developed vaccines for anthrax, fowl cholera, and rabies 37 Pasteur and the microbial basis of fermentation  Production of alcohols and organic acids was thought to be solely a chemical process  Juice intended for alcohol production could turn into acid  Pasteur observed that vats producing ethanol were teeming with yeasts while those containing lactic acid were full of rod-shaped bacteria  Pasteur heat-sterilized culture broth  Left alone – no growth, no acid and no alcohol  Inoculated with yeasts – alcohol production  Inoculated with acid-producing bacteria – lactic acid production  Conclusions: 1) heat killed microorganisms; 2) microorganisms were responsible for fermentation; and 3) different microbes performed different fermentation processes 38 Pasteur vanquished the concept of spontaneous generation     Perishable turns putrid with time Putrefied materials are covered with microorganisms Spontaneous generation – a concept popularized up to the late 19th century. It posited that life arose spontaneously from nonliving matter Pasteur designed the swan-necked flask experiment to settle the spontaneous generation controversy 39 Robert Koch (1843-1910)  Physician and microbiologist  The other giant of microbiology of the 19th century  Experimentally demonstrated the germ theory of infectious disease  Identified causative agents of anthrax, tuberculosis, and cholera  Koch’s postulates: cause and effect in infectious disease  Developed solid media for obtaining pure cultures of microbes  Awarded Nobel Prize for Physiology and Medicine in 1905 40 Koch’s postulates: linking cause and effect in infectious diseases 41 Solid media – pure culture microbiology  The evolution of solid culture media used by Koch: 1. Potato slices (easily contaminated) 2. Gelatin (liquefies at 37oC) 3. Agar (superior, not degraded by most bacteria)  Colonies differing in size and colour bred true  Cells from different colonies typically differed in size, shape, and nutrient requirements 42 Scientific evidence and the myth of “scientific proof” Scientific evidence  Science relies on experimental evidence to support or counter theory or hypothesis  It bases on: 1. Statistical strength – reproducibility 2. Strength of controls – both positive and negative controls  Evidence is not Proof despite the repeated use of the word “proof” in the textbook  Strictly defined, there is no proof in science 43 Microbial diversity and the rise of general microbiology  Microbial diversity: focuses on nonmedical aspects and metabolic processes of microbes in soil and water  Early clues for microbial biochemistry occurring in the environment:  Soils would oxidize hydrogen, ability would disappear with heating or acidification  Ammonium changes to nitrate in sewage 44 Martinus Beijerinck – enrichment cultures Martinus Beijerinck (1851-1931)  Dutch microbiologist and botanist  Developed enrichment culture technique – isolate microorganisms from a natural sample in a selective fashion by manipulating nutrient availability and incubation conditions  Isolated Azotobacter chroococcum, the first aerobic nitrogen-fixing bacterium 45 Sergei Winogradsky - chemolithotrophy Sergei Winogradsky (1856-1953)  Ukrainian microbiologist and soil scientist  Invented the Winogradsky column – a column of pond mud, water, and various nutrients for culturing a diversity of microorganisms  Proposed concept of chemolithotrophy – oxidation of only inorganic compounds to yield energy 46 First tree (evolutionary history) of life  “On the origin of species” was published in 1859  Influenced by the concept of evolution, Ernest Haeckel (18341919) proposed in 1866 an universal tree of life  Single-celled organisms (which he called Monera / Moneres) formed the root of the tree as they were ancestors to other life forms  In this depiction, protists, plants and animals formed the three main branches 47 Early portrayal of the tree of life with five kingdoms  Robert Whittaker (1920-1980) proposed a five-kingdom classification scheme in 1969  Animals  Plants  Fungi  Protists (protozoan and algae  Monera (bacteria)  Classification based on special characteristics:  Do the organisms possess a true nucleus (eukaryotic) or not ( prokaryotic)?  Are the organisms unicellular or multicellular?  What is their mode of nutrition? 48 Use of ribosomal nucleic acid sequences to infer evolutionary relationships     Carl Woese (1928–2012) realized rRNA gene (rDNA) sequences could be used to infer evolutionary relationships  Present in all cells  Highly conserved  Functionally constant – rRNAs are components of ribosomes Discovered rDNA from methanogens distinct from Bacteria and Eukarya Named new group Archaea Found evolutionary relationships between all cells could be revealed by rDNA analysis 49 The tree-domain tree of life based on rRNA genes LUCA = Last universal common ancestor 50 Analysis of rRNA genes of environmental samples leads to discovery of new microbial species Cultivation-independent analysis of rRNA genes Microbial diversity 51