Fundamentals of Microbiology Chapter 1 Lecture Notes PDF

Welcome to MCB2610 Fundamentals of Microbiology Dr. Patricia Pelczar Rossi Copyright © 2013 John Wiley & Sons, Inc. All rights reserved. Chapter 1: The Microbial World Chapter ObjecEves 1) What is microbio...

Welcome to MCB2610 Fundamentals of Microbiology Dr. Patricia Pelczar Rossi Copyright © 2013 John Wiley & Sons, Inc. All rights reserved. Chapter 1: The Microbial World Chapter ObjecEves 1) What is microbiology? 2) EvoluIon of microbes 3) Microbial energy acquisiIon 4) How microbes interact with world 5) How microbes are associated with disease Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  The microbes: What is microbiology? – Microbiology is the study of microbes. – The Peld examines how microbes interact with humans, with food, and how they can be used BY humans (among other aspects). Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Types of Microbial Cells prokaryoEc cells lack a true membrane-delimited nucleus – This is not absolute eukaryoEc cells – have a membrane-enclosed nucleus – are more complex morphologically 4  ClassiJcaEon Schemes Two Group Five Kingdom-Monera, Pro7sta, Fungi, Animalia, Plantae Three domain system – developed due to advances in molecular techniques Carl Woese et al (1990 paper) based on a comparison of ribosomal RNA, divides microorganisms into: – Bacteria (true bacteria), – Archaea – Eukarya (eukaryotes) 5  Universal Phylogenetic Tree 6  Domain Bacteria Usually single-celled Majority have cell walls with pepIdoglycan Most lack a membrane-bound nucleus Ubiquitous and some live in extreme environments Some cause disease but most are benePcial 7  Domain Archaea disInguished from Bacteria by unique rRNA sequences lack pepIdoglycan in cell walls and have unique membrane lipids some have unusual metabolic characterisIcs many live in extreme environments Their role in causing diseases is unclear 8  Domain Eukarya - Eukaryotes generally larger than Bacteria and Archaea – Plants, Animals – Microorganisms classiPed as proIsts or fungi ProIsts-1) algae 2) protozoa Protozoa, water molds, slime mold, algae are all protists 3) slime molds 4) water molds – fungi – (e.g. yeasts – unicellular, molds – mulIcellular) Primarily decomposers, some cause disease 9  Acellular InfecEous Agents viruses – smallest of all microbes – Very simple – some consist of only proteins and nucleic acids – requires host cell to replicate – cause range of diseases, – some cancers viroids and virusoids – infecIous agents composed of RNA prions – infecIous proteins 10  How do we deJne life? – Metabolism – Growth – ReproducIon – GeneIc variaIon/evoluIon – Response/adaptaIon to the external environment – Homeostasis (maintaining internal organizaIon and order, usually by expending energy) Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  What are the macromolecules (major building blocks) needed for life? Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  PolypepEdes PolypepEdes have many roles -One of the most important is as enzyme as catalysts of chemical reacIons Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Nucleic Acids Nucleic acids (DNA/RNA) are also criIcal as storehouses of geneIc informaIon. Comparisons of DNA sequences allow us to break life into three domains. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Lipids Lipids: form foundaIon of plasma membrane Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Polysaccharides Polymers of sugars -Important for energy producIon/storage -Important structural components MCB 2610 Chapter 1 Notes: Microbes encompass: viruses and microorganisms. Viruses living, or not? Debated by some. 3 lbs of bacteria in gut, escherichia, lactic bacillus, and others which help with digestion. So much ‘good’ bacteria to take up space which blocks bad pathogens from taking hold and using up gut resources. antibiotics reduce bene cial bacteria of gut microbiome, which is of course why doctors ask to monitor symptoms. Prokaryotic Lack true membrane delimited nucleus. Not absolute. Eukaryotic Have membrane bound nucleus. Membrane bound organelles for higher order complexity morphologically. Two group Five kingdom - Monera, Protista, Fungi, Animalia, Plantae And Three Domain system: developed after more advanced molecular techniques were developed Aristotle, BC established the Two group system (organized macroscopic organisms by looking at them), only animal and plant were delineating characters 1969 ve kingdom came in to play by Robert Whittaker O ered more groups to de ne certain combinations of characteristics, did not take anything in the molecular level into consideration. Carl Woese in the 1990 paper, helped establish the Three Domain System based on the genes that encode Ribosomal RNA, dividing microorganisms into: Bacteria (true bacteria) Archaea Eukarya If you want to classify di erent microbes, the R RNA is highly variable (parts that do not interact with translational machinery which is where you will see variability) but conserved (areas that needed to interact to make protein), gives insight into the organisms transcriptomic di erences. Domain bacteria: Usually single celled Majority have cell wall made of peptidoglycan or murine Lack membrane bound nucleus Lack membrane bound organelles Some live in extreme environments Some cause disease but most are bene cial Domain Archaea: Distinguished from bacteria by unique rRNA sequences Lack peptidoglycan in their cell walls but have unique membrane lipids coined pseudomurine (like peptidoglycan) Some have unusual metabolic characteristics (methanogens for example, producing methane) Many live in extreme environment, super acidic, super alkaline, super hot or cold, etc. their role in causing diseases is unclear. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Microbial geneEcs: What can studying the gene7cs of microbes teach us about the evolu7on of life on Earth? – There was ligle oxygen in the atmosphere, and the surface of the planet was a soup of chemicals in liquid form. – This early atmosphere and environment led to the iniIal synthesis of the Prst forms of macromolecules (and their use in primiIve single-celled life). Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Origins of Life Through radioisotope analysis Earth is thought to be between 4.5 to 4.6 billion years old. microbial fossils – Swartkoppie chert – 3.5 billion years old fossil record sparse Early microfossils similar to modern Jlamentous cyanobacteria About 3.5 billion years old  Stromatolite – layers of cyanobacteria and minerals  How did the Jrst microbial life arise? – In the 1950s, a grad student named Stanley Miller formed organic molecules from a primordial soup. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  What were the earliest molecules? original molecule-single molecule that could 1) do cellular work 2) replicate itself ribozymes – Discovered by Thomas Cech in 1981 – RNA molecules that form pepIde bonds – perform cellular work and replicaIon  Microbial geneEcs: – Ribozymes- RNA molecules with ability to catalyze reacIons – RNA could serve the dual purpose of geneIc informaIon storage AND catalyzing reacIons! – Lipid membrane formed around RNA Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Microbial geneEcs: But what about separaIng interior from exterior? – A single lipid layer known as a micelle may have been an early form of plasma membrane. – This could have formed a crude way of separaIng interior contents from the external environment. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Microbial geneEcs: So then, the basic idea of how microbial life arose on Earth is: – Early condiIons formed RNA and micelles. – These came together into a primiIve cell using RNA for storing geneIc info and coding. – PrimiIve cells eventually changed from using RNA to DNA instead for storing their geneIc informaIon. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  So then when/how did eukaryotes appear? – EndosymbioIc theory: PrimiIve prokaryoIc microbes ingested other microbes, starIng a symbioIc relaIonship, forming the Prst basic eukaryotes. Ingested microbes that could use oxygen for a respiratory process to produce chemical energy became mitochondria. Ingested microbes that could Px carbon dioxide into organic molecules using light energy became chloroplasts. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Microbial Species Bacteria and Archaea do not reproduce sexually Strain-consists of descendants of a single, pure microbial culture – may be biovars, serovars, morphovars, pathovars A biovar is a variant prokaryotic strain that di ers physiologically or biochemically from other strains in a particular species. Morphovars are those strains that di er morphologically. Serovars are those strains that have antigenic properties that di er from other strains. binomial nomenclature – developed by Carolus Linnaeus (1750) – genus and species epithet – (e.g., Escherichia coli – italics or underline) genus speciel – Can abbreviate aler Prst use (e.g. E. coli)  History of Microbiology study of microorganisms tools used for the study – microscopes – culture techniques – molecular geneIcs – genomics  Discovery of Microorganisms Robert Hooke (1635-1703) Looking at a thin slice of cork with a crude microscope Life consisted of “ligle boxes” – cells Cell theory – all living things are composed of cells  Discovery of Microorganisms Antony van Leeuwenhoek (1632-1723) – Prst person to observe and describe microorganisms accurately with a microscope that could magnify 50 – 300 Imes – Called microbes animalcules 30  Leeuwenhoek (cont) “I weighed about 160 pounds…and I ordinarily a-morning have a well-formed stool, but now and then hitherto I have had a looseness, at intervals of 2, 3 or 4 weeks, when I went to stool some 2, 3 or 4 Imes a day… My excrement being so thin, I was at diverse Imes persuaded to examine it…I will only say that I have generally seen, in my excrement, many irregular parIcles of sundry size. All parIcles aforemenIoned lay in a clean and transparent medium wherein I have someImes also seen animalcules a-moving very preply. Their bodies were somewhat longer than broad, and their belly, which was qagened was furnished with sundry ligle paws, wherewith they made such a sIr in the medium and among the globules.” (describing Giardia)  Archaezoa No mitochondria MulIple qagella Giardia lamblia Figure 12.17b-d  Leeuwenhoek’s Microscope 33 The ConZict over Spontaneous GeneraEon idea that living thing just appear spontaneous generaIon – living organisms can develop from nonliving or decomposing mager Francesco Redi (1626-1697) – discredited spontaneous generaIon – showed that maggots on decaying meat came from qy eggs – His experiment – 3 containers with meat, one covered with paper, one covered with gauze, one open 34  But Could Spontaneous GeneraEon Be True for Microorganisms? John Needham (1713-1781) – his experiment: mugon broth in qasks → boiled →sealed – results: broth became cloudy and contained microorganisms Lazzaro Spallanzani (1729-1799) – his experiment: broth in qasks →sealed → boiled broth remained clear – results: no growth of microorganisms sealed before boiling to heat everything died inside due the They initially thought oxygen was needed for 35 micro-organisms to grow Louis Pasteur (1822-1895) 36 Louis Pasteur (1822-1895) He wanted to know if micro-orgs spontaneously generate and they need oxygen to do so Segled the mager of spontaneous generaIon his experiments – placed nutrient soluIon in qasks – created qasks with long, curved necks – boiled the soluIons He used a ask that you could leave open, but couldn’t let anything in owing air to enter in. (Curved neck ask). – lel qasks exposed to air results: no growth of microorganisms Biogenesis – Life comes from life 37  Louis Pasteur performed a simple yet elegant experiment to disprove spontaneous generaIon theory in the late 1800s. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Final Blow to Theory of Spontaneous GeneraEon John Tyndall (1820-1893) – demonstrated that dust carries microorganisms – showed that if dust was absent, nutrient broths remained sterile, even if directly exposed to air – also provided evidence for the existence of excepIonally heat-resistant forms of bacteria Ferdinand Cohn (1828-1898) – heat resistant bacteria could produce endospores heat resistant b c of the Tospores 39 Evidence for the RelaEonship between Microorganisms and Disease AgosIni Bassi (1773-1856) – showed that a disease of silkworms was caused by a fungus M. J. Berkeley (ca. 1845) – demonstrated that the great Potato Blight of Ireland was caused by a water mold Heinrich de Bary (1853) – showed that smut and rust fungi caused cereal crop diseases 40  Indirect Evidence… Louis Pasteur (1822-1895) – demonstrated that microorganisms carried out fermentaIons – developed pasteurizaIon – low temperature heaIng to destroy unwanted microbes in wine and milk – used to reduce spoilage bacteria and kill harmful bacteria – heated to 145F(63C) for 30 min. then cooled, now 161F (72C) for 15 sec When he got rid of the bacteria the quality of the alcohol increased 41  Indirect Evidence… Ignaz Semmelweis (1840’s) high incidence of purpural fever in obstetrical paIents could be reduced by washing hands (autopsy source) Joseph Lister (1827-1912) – provided indirect evidence that microorganisms were the causal agents of disease – developed a system of anIsepIc surgery – his paIents had fewer postoperaIve infecIons first person to dress wounds wentsurgical instruments post op infections went down 42 correlation I ws ca s John Snow – 1st Epidemiologist 1854 Choleara outbreak Soho neighborhood of London 500 died in 10 days Mapped atected areas Centered on Broad Street well – sewer pipe __ was leaking into well Convinced oucials to remove pump handle outbreak went away asser InteresIngly people who worked at a local brewery were unatected. a foundoutbreak is associated w the wells H2O system  First Direct Evidence Robert Koch (1843-1910) – established the relaIonship between Bacillus anthracis Spore forming and anthrax – used criteria developed by his teacher Jacob Henle (1809-1895) – these criteria now known as Koch’s postulates sIll used today to establish the link between a parIcular microorganism and a parIcular disease 44  Microbes and disease: Robert Koch determined Bacillus anthracis and Mycobacterium tuberculosis were the causes of anthrax and tuberculosis (respecIvely). His work with anthrax helped sheep herders and cagle ranchers avoid costly animal losses. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Koch’s Postulates 1) the microorganism must be present in every case of the disease but absent from healthy individuals 2) the suspected microorganism must be isolated and grown in a pure culture 3) the same disease must result when the isolated microorganism is inoculated into a healthy host 4) the same microorganism must be isolated again from the diseased host healthy carriers affects postulates I 46 remain healthy but make others sick you  LimitaEons of Koch’s Postulates some organisms cannot be grown in pure A ects postulate 2 culture (e.g. Mycobacterium leprae) using humans in compleIng the postulates is unethical (e.g. Ebola hemorrhagic fever) Postulate 3 and 4 molecular and geneIc evidence may be used instead Koch’s Postulates applied to tuberculosis  The Development of Techniques for Studying Microbial Pathogens Koch’s work led to discovery or development of: – Agar (Fanny Hess) – Petri dish (Richard Petri) – nutrient broth and nutrient agar – methods for isolaIng microorganisms – AsepIc technique 49 Advantages of using Agar over gelaEn as a solidifying agent Not broken down by most organisms Doesn’t melt unIl it reaches 100C Doesn’t solidify unIl it reaches 50C Produces a clear product broken down microorganisms gelatin will be by also used to andgrow steralized potatoes was if try microorganisms on  g Other Developments…methods for studying viruses Interested in protecting against bacteria Charles Chamberland (1851-1908) – developed porcelain bacterial Plters used by Ivanoski and Beijerinck to study tobacco mosaic disease determined that extracts from diseased plants had infecIous agents present which were smaller than bacteria and passed through the Plters infecIous agents were eventually shown to be viruses Called “Plterable parIcles” disease on the tobacco plant was not bacteriabut filters viruses b c bacteria was too large to passthroughthe 51  Early Immunology… Pasteur and Roux -discovered that incubaIon of cultures for long intervals between transfers caused strain agenuaIon -Pasteur and his coworkers developed vaccines for chicken cholera, anthrax, and rabies 52  Edward Jenner Edward Jenner (ca. 1798) – used a vaccinaIon procedure to protect individuals from small pox Milkmaid with cowpox was immune Tested on 8 year old “volunteer” NOTE: this preceded the work establishing the role of microorganisms in disease 53  Drug Treatment Paul Ehrlich (1910) – German Physician found dyes to distinguish Concept of “magic bullet” – Dyes as drugs magic bullet find drug a to attack the bad cells and not the good Trypan red dye was able to target (trypanosome)  The Birth of Modern Chemotherapy 1928: Alexander Fleming discovered the Prst anIbioIc. He observed that Penicillium fungus made an anIbioIc, penicillin, that killed S. aureus. 1940s: Penicillin was tested clinically and mass produced. Penicilium mold he originally found could not produce high quantities of penicillin, but they sought to nd strains that produced higher concentration of penicillin (discovered at Yale). What was going on in 1940s (WW2 of course, so soldiers were experiencing secondary infections from battle wounds. Figure 1.5  Microbes and disease: Some microbial diseases have had a profound impact on humanity—e.g., plague. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Microbes and disease: Urban plague or rural plague. During Black Death it was urban plague carried by eas directly to humans. We do see some incidence of Plague rural plague, usually in the southwest (cats, or eas carrriers). Yersinia pestis (black plague) Copyright © 2013 John Wiley & Sons, Inc. All rights reserved. Microbes and disease: influenza Spanish In the twenIeth century, we have seen a dramaIc drop in U.S. deaths from infecIous A ftp.he diseases, however… Antibiotic resistance. Antibiotics target speci c structures but of course mutations of bacteria occur. Antibiotics are the ‘selection pressure’ for biotic organisms. Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Microbes and disease: Where has this reducIon in deaths come from? – PrevenIon of infecIon through Use of anIsepIcs (Joseph Lister) SanitaIon improvements (sewage treatment) Food/water safety (pasteurizaIon) Personal hygiene improvements VaccinaIon – Treatment of infecIons (anIbioIcs!) Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Microbes and disease: Humanity’s interacIon with infecIous diseases is always changing. SomeImes cultural/economic diterences can mean diterences in disease rates (lack of malaria in the United States versus Africa). Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.  Conclusion: Microbiology is a very diverse Peld Of all the microbes we can grow in the lab, it’s esImated there are many more that can’t be grown Copyright © 2013 John Wiley & Sons, Inc. All rights reserved.