The Evolution of Microorganisms and Microbiology

Chapter 01 The Evolution of Microorganisms and Microbiology Members of the Microbial World Microorganisms – Organisms too small to be clearly seen by the unaided eye. • Generally <1 mm, but some macroscopic (that is bread mold). These organisms are simple in their construction. • Lack differentiated tissues. 2 Divisions and Types of Microbes 3 Diversity of Microorganisms More microbes on Earth than stars in the known universe. • 1030 microbial cells Different environments • Gut • Sediments deep beneath the seafloor 4 Classification Schemes Research based on a comparison of ribosomal R N A genes generated a three domain system for microorganisms: • Bacteria (true bacteria). • Archaea. • Eukarya (eukaryotes). Prokaryotic cells Eukaryotic cells • Have a membrane-enclosed nucleus. • Larger and more morphologically complex 5 Domain Bacteria Usually single-celled. Most have cell wall with peptidoglycan. Most lack a membrane-bound nucleus. Live in many environments (including our bodies). • Microbiome Both disease causing and non-disease causing exist. 6 Domain Archaea • Distinguished from Bacteria by unique rRNA sequences. • Have unique membrane lipids. • Some have unusual metabolic characteristics. • Many live in extreme environments. • Do not directly cause disease in humans. 7 Domain Eukarya 1 Protists • Unicellular, but generally larger than Bacteria and Archaea. • Protozoa—animal-like metabolism. • Algae—photosynthetic. Fungi • Unicellular or multicellular. • Yeast—unicellular. • Molds and mushrooms— multicellular. 8 Microbial Evolution Definition of life. • Orderly structure. • Ability to obtain and use energy (that is, metabolism). • Ability to reproduce. Life was present on Earth 3.5-3.8 billion years ago. • Determined through many different pieces of evidence. • Fossils • Molecular fossils • Hopanes 9 Relationships of DNA/RNA/Protein in Cells Proteins • Catalytic (enzymes) • Structural DNA • Stores hereditary information that is replicated passed on to next generation. RNA • Molecule that acts as a messenger, taking information from DNA to then synthesizing proteins. 10 Which Came First? • Proteins require RNA and other proteins to be made. • DNA cannot do cellular work (just storage). • RNA requires both DNA as a template and proteins as catalysts. • Appear to rely on one another, but one molecule was first. 11 Earliest Molecules—RNA Original molecule must be able to store, copy, and express genetic information. Ribozymes • Catalytic RNA molecules • RNA molecules that form peptide bonds. Earliest cells may have been RNA surrounded by liposomes. 12 RNA World Precellular state in the evolution of life. • Lipid membrane formed around RNA. • Lipids spontaneously form vesicles. • Evidence of RNA World Hypothesis: Most cellular RNA in modern cells exists in and is associated with the ribosome (rRNA, tRNA, mRNA) to construct proteins. 13 Earliest Metabolism Early Earth was hot and lacked oxygen. • Cells that were made must be able to use energy sources under harsh conditions. • Inorganic molecules (that is, FeS) Photosynthesis • Stromatolites • Mineralized layers of cyanobacteria Horst Mahr/imagebroker/age fotostock 14 Endosymbiotic Hypothesis Origin of mitochondria, chloroplasts, and hydrogenosomes • Endosymbiosis–interaction between two organisms in which one lives inside of the other. Mitochondria and chloroplasts • DNA and ribosomes have similar sequences to bacteria. • Mitochondria - proteobacteria • Chloroplast - Prochloron Hydrogenosomes • Anaerobic endosymbiont that makes ATP via fermentation. 15 The Endosymbiotic Theory 16 Evolution of Cellular Microbes • Mutation of genetic material led to selected traits. • New genes and genotypes evolved—producing mosaic of genetic information. • Bacteria and Archaea increase gene pool by horizontal gene transfer. • Eukaryotes increase diversity through sexual reproduction. 17 Phyletic Classification Systems 1 Compare organisms on basis of evolutionary relationships. Microbial phylogeny • Comparison of cell wall structure, biomolecules, and nucleotide sequences. Phylogenetic tree • Display evolutionary relationship between organisms. 18 Phyletic Classification Systems 2 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, determined this way. 19 Building a Phylogenetic Tree – Distance Distance-based approach • Differences in sequences made into a statistic that is used to determine evolutionary distance. • More sequence differences = Greater evolutionary distance. • Algorithm generates tree. Access the text alternative for these images 20 Building a Phylogenetic Tree – Character Character-based approach • More complicated but makes more robust tree. • Use assumptions about the pathway of evolution to infer ancestors at each node. • Requires check for accuracy. 21 Microbial Taxonomy Taxonomy Science of classifying living things. • Classification • Nomenclature - Binomial nomenclature (Genus species) • Identification Strain – descendants of a pure microbial culture. • Can differ biochemically, morphologically and pathogenically. • Recent research uses metagenomic analysis to define hierarchy. 22 Microbiology—Origins Study of microorganisms. Tools used for the study • Microscopes • Culture techniques • Pure culture – isolated strain • Molecular genetics • Genomics 23 Discovery of Microorganisms Earliest microscopic observations. • Francesco Stelluti: observed bees and weevils between 1625 to 1630. • Robert Hooke: published drawings of the fungus Mucor in his book, Micrographia, in 1665. • Antony van Leeuwenhoek (1632 to1723): first person to observe microorganisms accurately. (a, 1) Kathy Park Talaro/Pasadena City College; (a, 2) Pasadena City College/Kathy Park Talaro; (b) Dr. Jeremy Byrgess/SPL/Getty Images 24 The Conflict Over Spontaneous Generation Spontaneous generation • Idea that living organisms can develop from nonliving or decomposing matter. • Discredited by Francesco Redi (1626 to 1697). • Showed maggots on decaying meat came from fly eggs. John Needham (1713 to 1781) • Based on observation that boiled hay gave rise to microorganisms he stated that some extracts have have what it takes to confer life from non-living material. Lazzaro Spallanzani (1729 to 1799) • Proved that the Hay itself didn’t make microorganisms if in sealed environment. 25 Louis Pasteur (1822 to 1895) ‘Swan-neck flask’ experiments. • Created flasks with long, curved necks. • Boiled the solutions. • Left flasks exposed to air. Results: no growth of microorganisms in swan-neck flasks. Pixtal/age fotostock 26 Swan-Necked Flask Experiments of Pasteur 27 Final Blow to Theory of Spontaneous Generation John Tyndall (1820 to 1893) • Demonstrated that dust carries microorganisms. • No dust  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 to 1898) • Heat-resistant bacteria could produce endospores. 28 Early Evidence for the Relationship Between Microorganisms and Disease Establishing a connection between microorganisms and disease depended on development of techniques for studying microbes. Agostino Bassi (1773 to 1856) • Showed a disease of silkworms was caused by a fungus. M. J. Berkeley (1803 to 1889) • Demonstrated the potato blight of Ireland was caused by a protozoan. Heinrich de Bary (1831 to 1888) • Showed fungi caused crop diseases. 29 Louis Pasteur (1822 to 1895) • Demonstrated microorganisms carried out fermentation. • Helped French wine industry by developing pasteurization to avoid wine spoilage by microbes. Joseph Lister (1827 to 1912) • Provided indirect evidence that microorganisms were the causal agents of disease. • Developed an antiseptic surgery system to prevent microorganisms from entering wounds. • His patients had fewer postoperative infections. 30 Final Proof Robert Koch (1843 to 1910) • Established the relationship between Bacillus anthracis and anthrax. • Demonstrated that Mycobacterium tuberculosis causes tuberculosis (TB). • “Koch’s postulates” Bettmann/Getty Images • Criteria still used today to establish the link between a microorganism and a disease. 31 Koch’s Postulates and Tuberculosis 32 Limitations of Koch’s Postulates Some organisms cannot be grown in pure culture because they rely on host cells. Lack animal model • Using humans in completing the postulates is unethical. Molecular and genetic evidence may replace and overcome these limits. 33 The Development of Techniques for Studying Microbial Pathogens Koch’s work led to discovery or development of • Nutrient broth and nutrient agar. • Methods for isolating microorganisms. Charles Chamberland (1851 to 1908) • Developed porcelain bacterial filters used by Ivanoski and Beijerinck to study tobacco mosaic disease. • Extracts from diseased plants were passed through this filter. • Extracts still infectious; therefore, must have something smaller than bacterium (viruses). 34 Development of Vaccines Pasteur and Roux • Discovered that incubation of cultures for long intervals between transfers caused pathogens to lose their ability to cause disease. • These attenuated cultures could be used to developed vaccines for chicken cholera, anthrax, and rabies. 35 Immunological Studies Led to study of host defenses—immunology. Edward Jenner (1749 to 1823) • Used vaccination procedure to protect against smallpox. Emil von Behring (1854 to 1917) and Shibasaburo Kitasato (1852 to 1931) • Developed antitoxins (antibodies) for diphtheria. Elie Metchnikoff (1845 to 1916) • Discovered first immune system cells. • Phagocytic cells in blood engulf bacteria. 36 Microbial Ecology Sergei Winogradsky (1856 to 1953) • Studied soil microorganisms and discovered numerous interesting metabolic processes (for example, nitrogen fixation). Martinus Beijerinck (1851 to 1931) • Pioneered the use of enrichment cultures and selective media. 37 Basic and Applied Aspects of Microbiology Basic aspects • Concerned with individual groups of microbes, microbial physiology, genetics, molecular biology, and taxonomy. Applied aspects • Concerned with practical problems—disease, water, food, and industrial microbiology. 38 Major Fields in Microbiology • Medical microbiology—diseases of humans and animals (that is, COVID-19). • Public health microbiology—control and spread of communicable diseases. • Immunology—how the immune system protects a host from pathogens. • Microbial ecology—the relationship of organisms with their environment. • Agricultural microbiology—the impact of microorganisms on food production. • Food microbiology—microbes used to make food and beverages as well as spoilage microbes. 39 More Microbiology Fields Industrial microbiology—uses microbes to make products useful to humans. • Antibiotics, vaccines, steroids, alcohols and other solvents, vitamins, amino acids, enzymes, and biofuels. Microbial physiology—studies metabolic pathways of microorganisms. Microbial genetics, molecular biology, and bioinformatics— studies the nature of genetic information and how it regulates the development and function of cells and organisms. 40