BIOL 2P98 Principles of Microbiology Fall 2023 Lecture Notes PDF

BIOL 2P98 Principles of Microbiology Fall 2023 Professor • Dr. M.J. Bidochka • [email protected] TEXTBOOK Brock Biology of Microorganisms 15th edition Madigan et al. TEXTBOOK Brock Biology of Microorganisms 14th edition Madigan et al. Course marking scheme • Please review the course syllab...

BIOL 2P98 Principles of Microbiology Fall 2023 Professor • Dr. M.J. Bidochka • [email protected] TEXTBOOK Brock Biology of Microorganisms 15th edition Madigan et al. TEXTBOOK Brock Biology of Microorganisms 14th edition Madigan et al. Course marking scheme • Please review the course syllabus, available on Brightspace Evaluation Component Grade Weight Due Date Test 1 15% Oct 6 Test 2 15% Nov 10 Laboratory component 35% Throughout Final Exam 35% TBD PowerPoint® Lecture Presentations CHAPTER 1 The Microbial World © 2018 Pearson Education, Inc. Chapter Outline • Introduction and major themes of microbiology • Microbiology in historical content Lecture #1- The mighty microbe Escherichia coli “It always has been, and always will be, the age of bacteria” Ciliate soil protozoan Microorganisms • Organisms too small to be seen clearly by the unaided eye • Microscopic • Generally 1 mm or less in diameter • Consists of a single cell or cell cluster, or a virus Microbiology • The study of microbes (microorganisms) and their interactions with other living organisms • Revolves around two interconnected themes: Streptococcus pneumoniae • Understanding the nature and functioning of the microbial world • A basic biological science • Uses microbial cells to understand fundamental processes of life • Applying our understanding of the microbial world for the benefit of humankind and planet Earth • An applied biological science • At the forefront of medicine, agriculture, and industry Streptococcus thermophilus Two patterns of internal structure Common elements of both cell types • A cytoplasmic membrane that separates the inside of the cell from the outside • Cytoplasm containing an aqueous mixture of macromolecules, small organic molecules and ions • Macromolecules – carbohydrates, proteins, lipids, nucleic acids • Ribosomes for protein synthesis • Most microorganisms contain a cell wall that provides structural strength Prokaryotes vs. Eukaryotes Prokaryotes • Bacteria and Archaea • Smaller in size (~0.4 – 10 µM) • No internal membranes • Genome is usually a single closed circular chromosome • Aggregates in the cell to form a mass called a nucleoid • May contain additional small circles of DNA called plasmids Eukaryotes • Microorganisms in Domain Eukarya include protists and fungi • Larger in size (~10 – 100 µM) • Contain membrane-bound organelles • Genome organized into linear chromosomes • Contained in a membrane- enclosed nucleus • Genome is typically larger than prokaryotes Genome • An organism’s complete genetic content • Many genomes have been sequenced • ~15,000 prokaryotic genomes and 1,000 eukaryotes • First sequenced genome was H. influenzae in 1995 • E. coli genome is a fairly “typical” prokaryotic genome • 4.6 million base pairs of DNA in a single circular chromosome • 4,288 genes • Human haploid genome contains: • 3,200 million base pairs in 23 linear chromosomes • ~20,000 genes Properties of all microbial cells • Metabolism: All biochemical reactions that occur within a cell • The cell’s catalytic machinery (enzymes) carries out reactions that supply energy and precursors needed for biosynthesis of all cell components • Growth: An increase in cell number over time • Evolution: Descent with modification in which genetic variants are selected based on reproductive fitness • Leads to new forms or species • Evolution in microbes can be very rapid when selective pressure is strong Evolution of Antibiotic Resistance Properties of some microbial cells • Differentiation to form modified cells specialized for growth, dispersal, or survival • Communication by responding to chemical signals released into the environment by other cells • Genetic exchange: Transfer of genes from one cell to another • Motility: Movement of cells in the environment Evolution and Diversity • Earth is 4.6 billion years old • First cells (microbes) appeared from nonliving materials 3.8 – 3.9 BYA • Atmosphere originally lacked O2 (anoxic) • Only anaerobes could survive • Cyanobacteria began oxygenating Earth ~3 BYA • Current O2 levels achieved ~500 – 800 MYA • For most of Earth’s history, life was exclusively microbial! Origin of Domains • All cells are descended from a common ancestral cell • = Last universal common ancestor (LUCA) • Cells have been evolving for nearly 4 billion years • Three major cell lineages (domains) can be distinguished: • Bacteria, Archaea, and Eukarya • Bacteria and Archaea are phylogenetically distinct • Archaea are more closely related to Eukarya than Bacteria Determining Phylogenies • Evolutionary relationships between organisms (phylogenies) can be determined by comparing DNA sequences • Ribosomal RNA (rRNA) genes are usually used Phylogenetic tree All microorganisms & microorganisms microorganisms Major groups studied by microbiologists Prokaryotes Eukaryotes Viruses • Bacteria • Protists • Algae • Protozoa • Slime molds • Fungi • DNA viruses • Archaea • Yeast • Mold • RNA viruses Microbial Communities • A group of microbial organisms of the same species forms a population • The immediate environment in which a population exists is a habitat • Different habitats favour different organisms • Two or more populations coexisting and interacting in a habitat form a microbial community • Interactions can be beneficial or harmful • Abundance and diversity within a community is determined by resources (food) and conditions (temperature, pH, oxygen, etc.) Microbial community from a small Michigan lake Microbial community in a sewage sample Microbial community scraped from a human tongue Microbial Ecosystems • An ecosystem includes all living organisms, plus physical and chemical components of their environment • Major microbial ecosystems: • Aquatic • Terrestrial • Higher organisms • Metabolic processes of microbial organisms can alter their ecosystems • Resources and conditions may change, altering the microbial community and redefining the ecosystem • Microbial ecology is the study of microorganisms in their natural environments Microbes & their environments • Microbes are present everywhere on Earth that will support life • Soil, water, animals, plants, man- made structures • Some Archaea and Bacteria are extremophiles • Grow optimally under various chemical or physical extremes Methanopyrus kandleri (Archaea) Habitat: Deep see hydrothermal vents Growth at 90 – 122°C Optimal growth at 106°C Microbes & their environments • Microbes constitute the major fraction of biomass on earth • Total number of microbial cells = ~2.5 x 1030 • Key reservoirs of carbon, nitrogen, phosphorus • Most reside in marine subsurfaces, at depths up to 10 km • The human body has 10X more microbial cells than human cells! Microorganisms & Disease • Some bacteria & viruses are pathogens • Cause disease • Control of infectious disease has come from a variety of advances • Increased understanding • Improved sanitary & public health practices • Vaccines • Antimicrobial agents (e.g. antibiotics) • Infectious diseases are still a threat • In developing countries • Rapidly emerging diseases • Most microbes cause no harm or are beneficial to humans! Microorganisms & Agriculture • The cycling of nutrients by microorganisms is important for agriculture • e.g. Legumes (a major crop plant) live in close association with nitrogen-fixing bacteria that form nodules on their roots • Convert atmospheric nitrogen (N2) into ammonia (NH3) • Nitrogen is a key component of proteins • Legumes are a rich-source of plant protein! • Eliminates need for nitrogen fertilizers • Other bacteria cycle sulfur • Convert toxic hydrogen sulfide (H2S) into sulfate (SO42-), a nontoxic essential plant nutrient Microorganisms & Agriculture • Ruminant animals, such as cattle, sheep, and goats, have a specialized digestive chamber called a rumen • The rumen is a microbial ecosystem containing microorganisms that digest and ferment cellulose • = Major component of plant cell walls • Glucose units linked by β linkages, which cannot be broken by animals • Produces fatty acids that the animal uses for energy Microorganisms & Agriculture • Microorganisms can also negatively impact agriculture by causing diseases in plants and animals • Huge economic loss • Contaminated food products can cause serious human disease • Pathogenic E. coli or Salmonella transmitted from infected meat • Contaminated fruits and vegetables 2013 – 2014 outbreak of multidrug resistant Salmonella Heidelberg  Initial outbreak linked to Foster Farms chicken products at California Costco  ~100,000 pounds of chicken recalled  634 infected persons, 38% hospitalized, 15% blood infections Microorganisms & Human GI Tract • Humans lack a rumen and do not have cellulose-degrading microorganisms • Microbes live throughout GI tract • Most in the large intestine • GI microbes: • Synthesize vitamins and other essential nutrients • Compete with pathogens for space and resources Microorganisms & Food Industry • Food spoilage • Most fresh foods have short shelf lives because contamination is impossible to prevent • Leads to economic losses • Food safety • Constant monitoring to ensure products are pathogen-free • Tracking of disease outbreaks • Canada Food Inspection Agency spent $364 million on food-safetyrelated activities in 2013/2014 Basic biological research: Applicable to higher organisms Physiology Biochemistry Genetics Ecology Xanthomonas campestris Microorganisms & Food Industry • Food production • Fermentation by microorganisms yields products that preserve food & give it flavour • Fermentation of dairy produces cheese, yogurt, buttermilk, sour cream, etc. • Other fermented foods include sauerkraut, pickles and soy sauce • Fermentation by yeast generates carbon dioxide and alcohol that raises dough and produces alcoholic beverages (beer, wine, rum, etc.) Microorganisms & Energy • Production of biofuels • Yeast can be used to produce ethanol from sugarcane, corn, or grasses • Fuel or fuel supplement • Methanogens (Archaea) produce methane by anaerobic metabolism • Major component of natural gas Microorganisms & Bioremediation • Microorganisms can be used to consume spilled oil, solvents, pesticides and other toxic pollutants • = Bioremediation • Microbes are introduced to a polluted environment, or nutrients are added to stimulate indigenous microorganisms • Goal is to accelerate the disappearance of the pollutant Alcanivorax borkumensis uses oil hydrocarbons as energy & carbon source Microorganisms & Industry • Industrial microbiology grows microorganisms on a massive scale to make large amounts of relatively low-value products • Antibiotics, enzymes, chemicals • Biotechnology employs genetically engineered microorganisms to synthesize products of high value • e.g. Insulin or other human proteins “The role of the infinitely small in nature is infinitely large” - Louis Pasteur The Discovery of Microorganisms • Light microscopes were first invented in the late 1590s • In 1665, Robert Hooke published Micrographia, a book devoted to microscopic observations • Included illustration of mold fruiting structure • In 1676, Antoni van Leeuwenhoek invented a single lens microscope that could magnify 270X • Observed bacteria (“wee animalcules”) Spontaneous Generation • Where do microorganisms come from? Two theories: • Organisms develop from “seeds or germs” that enter from air • Organisms originate spontaneously from nonliving materials • = Spontaneous generation • Louis Pasteur’s research had shown: • Living organisms discriminate between isomers • Alcoholic fermentation is caused by the growth of microorganisms (yeast) and is not a purely chemical process • Bacterial growth in “polluted containers” produces lactic acid that causes wine to sour – can be prevented with heating. • This led Pasteur to conduct a key experiment to disprove spontaneous generation Pasteur’s Experiment Led to the development of effective sterilization procedures in microbiological research, clinical medicine, and the food industry. Pasteur & Vaccines • In 1796, Edward Jenner discovered that cowpox could give cross-immunity to smallpox • In 1879, Pasteur found that a spoiled culture of cholera did not cause disease in chickens • Exposed chickens could not be infected later • Developed methods to artificially weaken disease organisms for use in vaccination • Developed a successful rabies vaccine in 1885 Infectious Disease • Robert Koch studied Anthrax • Infectious disease caused by Bacillus anthracis • Primarily infects cattle • Found that bacteria were always present in the blood of an animal with the disease, but wanted to confirm that the bacteria caused the disease • Formed set of four postulates used to definitively link cause and effect in an infectious disease Pure Culture • A culture containing a single kind of microorganism • Koch used a solid surface to culture bacteria • Potato slices, then liquid nutrient solidified with gelatin or agar • Found bacteria would form masses of cells with a characteristic shape and colour = colonies • Inferred each came from a single cell that grew into a mass of cells • Colonies bred true for shape, size & nutrient characteristics • Suggested different types of bacteria should be considered different species Tuberculosis • Koch also discovered the bacteria responsible for tuberculosis (Mycobacterium tuberculosis) • Caused 1 in 7 deaths at the time • Confirmed using his postulates and guinea pigs • Developed methods to diagnose infection with M. turberculosis • Tuberculin skin test • Later also discovered bacteria responsible for cholera (Vibrio Koch’s drawings of Mycobacterium tuberculosis cholerae) Microbial Diversity • In the 20th century, medical aspects of microbiology broadened to include studies of microorganisms in soil and water • Martinus Beijerinck developed the enrichment culture technique • Use of selective culture media and incubation conditions to isolate specific microbes from natural samples • E.g. Isolation of nitrogen-fixing bacteria using media without nitrogen • Sergei Winogradsky described chemolithotrophs, which use inorganic compounds for energy, and obtain carbon from CO2 • Widespread in nature Modern Microbiology • Many advances in microbiology are now fueled by genomics • Mapping, sequence and analysis of genomes • Pathogens often contain “signature” genes that can be used to positively identify them without laboratory culture • Improved speed & accuracy of disease diagnosis • Can also be applied to ancient medical questions Microorganisms & History The Black Death • Disease that swept through Europe in mid 14th century and killed 30 – 60% of the population • Believed to be caused by bacterium Yersinia pestis • Transmitted by rodent & flea bites • Causes bubonic plague • In 2011, researchers isolated DNA from graveyard specifically filled with Black Death victims • Sequenced full genome & compared with recent isolates of Y. pestis • Confirmed Black Death caused by Y. pestis • Current strains have changed very little Bubonic plague -Yersinia pestis- the bacterium responsible for Black Death -bubonic plague -began in 1347. -within 4 yrs killed 25 million people; one third of Europe. Effects of the Application of Microbiology on Human Life Expectancy Mortality rate (deaths/100,000) due to: 1920 Pneumonia and influenza 207 Tuberculosis 113 Syphilis 16 Diphtheria 15 Whooping cough 12 Measles 9 Other (nonmicrobial) 925 causes Life expectancy 54 1960 37 6 2 <1 <1 <1 909 1995 28 <1 <1 <1 <1 <1 790 70 76 Mainly due to: Development of vaccines, antibiotics and antiseptics Sanitary food handling Drinking water treatment Sewage treatment