Microbiology Textbook Chapter 1 PDF

Microbiology USTH Dr. Suh-Der Tsen May, 2023 1 1 The Evolution of Microorganisms and Microbiology 2 Copyright © McGraw-Hill...

Microbiology USTH Dr. Suh-Der Tsen May, 2023 1 1 The Evolution of Microorganisms and Microbiology 2 Copyright © McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or display. 1.1 Members of the Microbial World 1. Differentiate the biological entities studied by microbiologists from those studied by other biologists 2. Explain Carl Woese’s contributions in establishing the three domain system for classifying cellular life 3. Provide an example of the importance to humans of each of the major types of microbes 4. Determine the type of microbe (e.g., bacterium, fungus, etc.) when given a description of a newly discovered microbe 3 The Importance of Microorganisms Most populous and diverse group of organisms Found everywhere on the planet Play a major role in recycling essential elements Source of nutrients and some carry out photosynthesis Benefit society by their production of food, beverages, antibiotics, and vitamins Some cause disease in plants and animals 4 Members of the Microbial World Organisms and acellular entities too small to be clearly seen by the unaided eye – some < 1 mm, some macroscopic These organisms are relatively simple in their construction and lack highly differentiated cells and distinct tissues 5 6 Type of Microbial Cells Prokaryotic cells lack a true membrane-delimited nucleus – this is not absolute! Eukaryotic cells have a membrane-enclosed nucleus, are more complex morphologically, and are usually larger than prokaryotic cells 7  Classification Schemes Three domain system, based on a comparison of ribosomal RNA genes, divides microorganisms into – Bacteria (true bacteria), – Archaea – Eukarya (eukaryotes) 8 Domain Bacteria Usually single-celled Majority have cell wall with peptidoglycan Most lack a membrane-bound nucleus Ubiquitous and some live in extreme environments Cyanobacteria produce significant amounts of oxygen 9 Domain Archaea Distinguished from Bacteria by unique rRNA gene sequences Lack peptidoglycan in cell walls Have unique membrane lipids Some have unusual metabolic characteristics Many live in extreme environments 10 Domain Eukarya - Eukaryotic Protists – generally larger than Bacteria and Archaea – algae – photosynthetic – protozoa – may be motile, “hunters, grazers” – slime molds – two life cycle stages – water molds – devastating disease in plants Fungi – yeast - unicellular – mold - multicellular 11 Acellular Infectious Agents Viruses – smallest of all microbes – requires host cell to replicate – cause range of diseases, some cancers Viroids and virusoids – infectious agents composed of RNA Prions – infectious proteins 12 1.2 Microbial Evolution 1. Propose a timeline of the origin and history of microbial life and integrate supporting evidence into it 2. Design a set of experiments that could be used to place a newly discovered cellular microbe on a phylogenetic tree based on small subunit (SSU) rRNA sequences 3. Compare and contrast the definitions of plant and animal species, microbial species, and microbial strains 13 Microbial Evolution Definition of life – cells and organization – response to environmental changes – growth and development – biological evolution – energy use and metabolism – regulation and homeostasis – reproduction 14 Origins of Life Microbial fossils – Swartkoppie chert – granular silica – 3.5 billion years old Fossil record sparse Indirect evidence and scientific method are used to study origins of life 15 16 17 Earliest Molecules - RNA Original molecule must have fulfilled protein and hereditary function Ribozymes – RNA molecules that form peptide bonds – perform cellular work and replication Earliest cells may have been RNA surrounded by liposomes 18 Earliest Molecules – RNA - 2 Cellular pool of RNA in modern day cells exists in and is associated with the ribosome (rRNA, tRNA, mRNA) – RNA catalytic in protein synthesis – RNA may be precursor to double stranded DNA Adenosine 5’ triphosphate (ATP) is the energy currency and is a ribonucleotide RNA can regulate gene expression 19  Earliest Metabolism Early energy sources under harsh conditions – inorganics, e.g., FeS Photosynthesis – cyanobacteria evolved 2.5 billion years ago – stromatolites – mineralized layers of microorganisms 20  Evolution of 3 Domains of Life Universal phylogenetic tree – based on comparisons of small subunit rRNA (SSU rRNA) – aligned rRNA sequences from diverse organisms are compared and differences counted to derive a value of evolutionary distance – relatedness, but not time of divergence, is determined this way 21 Last Universal Common Ancestor (LUCA) The root or origin of modern life is on bacterial branch but nature still controversial Archaea and Eukarya evolved independently of Bacteria Archaea and Eukarya diverged from common ancestry 22 Endosymbiotic Hypothesis Origin of mitochondria, chloroplasts, and hydrogenosomes from endosymbiont Mitochondria and chloroplasts – SSU rRNA genes show bacterial lineage – genome sequences closely related to Rickettsia and Prochloron, respectively Hydrogenosomes – anaerobic endosymbiont 23 Evolution of Cellular Microbes Mutation of genetic material led to selected traits New genes and genotypes evolved Bacteria and Archaea increase genetic pool by horizontal gene transfer within the same generation 24 Microbial Species Eukaryotic microbes fit definition of reproducing isolated populations Bacteria and Archaea do not reproduce sexually and are referred to as strains – a strain consists of descendents of a single, pure microbial culture – may be biovars, serovars, morphovars, pathovars binomial nomenclature – genus and species epithet 25 1.3 Microbiology and Its Origins 1. Evaluate the importance of the contributions to microbiology made by Hooke, Leeuwenhoek, Pasteur, Koch, Cohn, Beijerinck, von Behring, Kitasato, Metchnikoff , and Winogradsky 2. Outline a set of experiments that might be used to decide if a particular microbe is the causative agent of a disease 3. Predict the difficulties that might arise when using Koch’s postulates to determine if a microbe causes a disease unique to humans 26 Microbiology - Origins Study of microorganisms Tools used for the study – microscopes – culture techniques – molecular genetics – genomics 27 28 29  Discovery of Microorganisms Antony van Leeuwenhoek (1632-1723) – first person to observe and describe microorganisms accurately 30 The Conflict over Spontaneous Generation Spontaneous generation – Idea that living organisms can develop from nonliving or decomposing matter Francesco Redi (1626-1697) – discredited spontaneous generation – showed that maggots on decaying meat came from fly eggs 31 But Could Spontaneous Generation Be True for Microorganisms? John Needham (1713-1781) – his experiment: mutton broth in flasks → boiled →sealed – results: broth became cloudy and contained microorganisms Lazzaro Spallanzani (1729-1799) – his experiment: broth in flasks →sealed → boiled – results: no growth of microorganisms 32 Louis Pasteur (1822-1895) ‘Swan-neck flask’ experiments – placed nutrient solution in flasks – created flasks with long, curved necks – boiled the solutions – left flasks exposed to air results: no growth of microorganisms 33 34  Final Blow to Theory of Spontaneous Generation 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 exceptionally heat-resistant forms of bacteria Ferdinand Cohn (1828-1898) – heat-resistant bacteria could produce endospores 35 The Role of Microorganisms in Disease Was not immediately obvious Infectious disease believed to be due to supernatural forces or imbalances of 4 bodily-fluid ‘humors’ Establishing connection depended on development of techniques for studying microbes 36 Evidence for the Relationship between Microorganisms and Disease Agostini 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 37  More Evidence… Louis Pasteur – demonstrated microorganisms carried out fermentations, helping French wine industry – developed pasteurization to avoid wine spoilage by microbes – showed that the pébrine disease of silkworms was caused by a protozoan 38  Other Evidence… Joseph Lister – provided indirect evidence that microorganisms were the causal agents of disease – developed a system of surgery designed to prevent microorganisms from entering wounds as well as methods for treating instruments and surgical dressings – his patients had fewer postoperative infections 39 Final Proof… Robert Koch (1843-1910) – established the relationship between Bacillus anthracis and anthrax – used criteria developed by his teacher Jacob Henle (1809-1895) – these criteria now known as Koch’s postulates still used today to establish the link between a particular microorganism and a particular disease 40 41 Limitations of Koch’s Postulates Some organisms cannot be grown in pure culture Using humans in completing the postulates is unethical Molecular and genetic evidence may replace and overcome these limits 42 The Development of Techniques for Studying Microbial Pathogens Koch’s work led to discovery or development of: – agar – Petri dishes – nutrient broth and nutrient agar – methods for isolating microorganisms 43 Other Developments… Charles Chamberland (1851-1908) – developed porcelain bacterial filters used by Ivanoski and Beijerinck to study tobacco mosaic disease determined that extracts from diseased plants had infectious agents present which were smaller than bacteria and passed through the filters infectious agents were eventually shown to be viruses 44 Other Developments… Pasteur and Roux – discovered that incubation of cultures for long intervals between transfers caused pathogens to lose their ability to cause disease (termed ‘attenuation’) Pasteur and his coworkers – developed vaccines for chicken cholera, anthrax, and rabies 45 Immunological Studies once established, led to study of host defenses - immunology Edward Jenner (ca. 1798) – used a vaccination procedure to protect individuals from smallpox NOTE: this preceded the work establishing the role of microorganisms in disease! 46 More Developments… Emil von Behring (1854-1917) and Shibasaburo Kitasato (1852-1931) – developed antitoxins for diphtheria and tetanus – evidence for humoral (antibody-based) immunity Elie Metchnikoff (1845-1916) – discovered bacteria-engulfing, phagocytic cells in the blood – evidence for cellular immunity 47 The Development of Industrial Microbiology and Microbial Ecology Louis Pasteur – demonstrated that alcohol fermentations and other fermentations were the result of microbial activity – developed the process of pasteurization to preserve wine during storage 48 Developments in Microbial Ecology Sergei Winogradsky (1856-1953) and Martinus Beijerinck (1851-1931) – studied soil microorganisms and discovered numerous interesting metabolic processes (e.g., nitrogen fixation) – pioneered the use of enrichment cultures and selective media 49 1.4 Microbiology Today 1. Construct a concept map, table, or drawing that illustrates the diverse nature of microbiology and how it has improved human conditions 2. Support the belief held by many microbiologists that microbiology is experiencing its second golden age 50 Microbiology Has Basic and Applied Aspects Basic aspects are concerned with individual groups of microbes, microbial physiology, genetics, molecular biology and taxonomy Applied aspects are concerned with practical problems – disease, water, food and industrial microbiology 51 Molecular and Genomic Methods Led to a second golden age of microbiology (rapid expansion of knowledge) Discoveries – restriction endonucleases (Arber and Smith) – first novel recombinant molecule (Jackson, Symons, Berg) – DNA sequencing methods (Woese, Sanger) – bioinformatics and genomic sequencing and analysis 52 Major Fields in Microbiology Medical microbiology – diseases of humans and animals Public health microbiology – control and spread of communicable diseases Immunology – how the immune system protects a host from pathogens 53 More Fields… Microbial ecology is concerned with the relationship of organisms with their environment – less than 1% of earth’s microbial population has been cultured Agricultural microbiology is concerned with the impact of microorganisms on agriculture – food safety microbiology – animal and plant pathogens 54 More Fields…. Industrial microbiology began in the 1800s – fermentation – antibiotic production – production of cheese, bread, etc. Microbial physiology studies metabolic pathways of microorganisms 55 More Fields…. Molecular biology, microbial genetics, and bioinformatics study the nature of genetic information and how it regulates the development and function of cells and organisms Microbes are a model system of genomics 56