MicroBio6 Lecture ppt Ch01 HP PDF

CHAPTER 1 Lecture Slides Microbial Life: Origin and Discovery Copyright © 2024 by W. W. Norton & Company, Inc.  CHAPTER OVERVIEW 1.1 FROM GERM TO GENOME: WHAT IS A MICROBE? 1.2 MICROBES SHAPE HUMAN HISTORY 1.3 MEDICAL MICROBIOLOGY 1.4 ENVIRONMENT AND ECOLOGY 1.5 THE MICROB...

CHAPTER 1 Lecture Slides Microbial Life: Origin and Discovery Copyright © 2024 by W. W. Norton & Company, Inc.  CHAPTER OVERVIEW 1.1 FROM GERM TO GENOME: WHAT IS A MICROBE? 1.2 MICROBES SHAPE HUMAN HISTORY 1.3 MEDICAL MICROBIOLOGY 1.4 ENVIRONMENT AND ECOLOGY 1.5 THE MICROBIAL FAMILY TREE 1.6 CELL BIOLOGY AND THE DNA REVOLUTION  1.1 FROM GERM TO GENOME: WHAT IS A MICROBE?  A microbe is a living organism that requires a microscope to be seen.  Most microbes consist of a single cell, but some are multicellular. However, this does not mean that they can function as individual entities. Microbes range in size from 0.2 micrometers (mm) to just a few millimeters (mm). Viruses may be ten times smaller than the smallest cells.  Each microbe contains in its genome the capacity to reproduce its own kind. A Microbe Is a Microscopic Organism A Microbe Is a Microscopic Organism A Microbe Is a Microscopic Organism A Microbe Is a Microscopic Organism TABLE 1.1 Sizes of Some Microbes Microbe Description Approximate size Varicella-zoster Virus that causes chickenpox and shingles 100 nanometers (nm) = 10-7 meter (m) virus I Prochlorococcus Photosynthetic marine bacterium 500 nm = 5 x 10 -7 m Escherichia coli Bacterium growing within human intestine 2 micrometers (um) = 2 x 10 -6 m Spirogyra Aquatic alga that forms long filaments of cells 5 millimeters (mm) = 5 x 10 -3 m Ameba (a protist) that consumes bacteria in Pelomyxa 5 millimeters (mm) = 5 x 10 -3 m soil or water  A microbe is a Microscopic Organism  Microbes include many different types of organisms. Prokaryotes (cells lacking a nucleus): bacteria, archaea Some eukaryotes (cells with a nucleus): algae, fungi, protists Viruses and prions (acellular entities)  The bacteria, archaea, and eukaryotes—known as the three “domains”— “evolved” from a common ancestral cell. A Microbe Is a Microscopic Organism  Microbial Genomes Are Sequenced  A genome comprises the total genetic information of an organism.  The first method of DNA sequencing that was fast enough to sequence large genomes was developed by Fred Sanger. He shared the 1980 Nobel Prize in chemistry.  In 1995, scientists completed the first genome sequence of a cellular microbe, the bacterium Haemophilus influenzae.  Today’s sequencing efforts generate metagenomes, collections of sequences from diverse populations of microbes taken directly from the environment. Microbial Genomes Are Sequenced 1.2 MICROBES SHAPE HUMAN HISTORY  Microbes have shaped human cultures since our earliest civilizations. Yeasts and bacteria yielded fermented foods and beverages and spoiled meat and wine. “Rock-eating” bacteria (lithotrophs) aided metal mining and deteriorated ancient stone monuments. Microbes of all types caused diseases and famines. Microbial Disease Devastates Human Populations  Microbial Disease Devastates Human Populations  Microbial diseases have profoundly affected human demographics and cultural practices. Fourteenth century: bubonic plague caused by Yersinia pestis Nineteenth century: tuberculosis caused by Mycobacterium tuberculosis Today: acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) Microbial Disease Devastates Human Populations  Microbial Disease Devastates Human Populations  More soldiers have died of microbial infections than of wounds in battle.  The significance of disease in warfare was first recognized by the British nurse Florence Nightingale (1820–1910). She founded the science of medical statistics and professional nursing. To show the deaths of soldiers due to various causes, she devised the “polar area chart.” Medical Statistics and Health Disparities Medical Statistics and Health Disparities Microscopes Reveal the Microbial World  Robert Hooke (1635–1703) Built the first compound microscope Used it to observe mold Published Micrographia, the first manuscript that illustrated objects observed with a microscope Coined the term “cell” Microscopes Reveal the Microbial World Microscopes Reveal the Microbial World  Antonie van Leeuwenhoek (1632–1723) Dutch cloth draper and tailor Built single-lens magnifiers, complete with sample holder and focus adjustment First to observe single-celled microbes – He called them “small animals (animalcules).” Microscopes Reveal the Microbial World  Spontaneous Generation: Do Microbes Have Parents?  The theory of spontaneous generation suggested that living creatures could arise without parents.  Francesco Redi (1660s) showed that maggots in decaying meat were the offspring of flies.  Lazzaro Spallanzani (1760s) showed that a sealed flask of meat broth sterilized by boiling failed to grow microbes. Spontaneous Generation: Do Microbes Have Parents?  Louis Pasteur (1822–1895) Began his scientific career as an organic chemist Discovered the microbial basis of fermentation Produced data that refuted spontaneous generation – Invented the “swan-neck” flask – Showed that a broth boiled in a swan-neck flask remained free of microbial growth, despite being exposed to air Spontaneous Generation: Do Microbes Have Parents? Q: John Tyndall’s experiment ????  1.3 MEDICAL MICROBIOLOGY  The germ theory of disease suggests that many diseases are caused by microbes.  Robert Koch (1843–1910) German physician Developed principles and methods crucial to microbial investigation Applied his methods to the study of several lethal diseases around the world Growth of Microbes in Pure Culture  Growth of Microbes in Pure Culture  Working with anthrax, Koch demonstrated an important principle of epidemiology: the chain of infection, or transmission of a disease.  To prove that Mycobacterium caused tuberculosis, Koch needed to establish a pure culture of the microbes being studied.  Koch’s colleagues contributed important tools for the generation of pure cultures. Angelina and Walther Hesse were the first to use the gelling agent agar to solidify liquid culture medium. Julius Petri developed the double-sided Petri dish container that bears his name. Growth of Microbes in Pure Culture  Koch’s Postulates  Koch’s postulates are an ordered set of criteria for establishing a causative link between an infectious agent and a disease. 1. Suspected microbe is always present in diseased hosts. – absent in healthy hosts 2. Suspected microbe is grown in pure culture outside hosts. – no other microbes present in culture 3. Cultured microbe is introduced into healthy hosts. – Individuals become sick with same disease as original hosts. 4. Same microbial suspect is re-isolated from sick individuals. Koch’s Postulates  Immunization Prevents Disease  In the eighteenth century, smallpox infected a large fraction of the European population.  Lady Mary Montagu introduced the practice of smallpox inoculation to Europe in 1717.  Edward Jenner (1749–1823) deliberately infected patients with material he collected from cowpox lesions. The practice of cowpox inoculation was called vaccination (from Latin vacca for “cow”). Immunization Prevents Disease Immunization Prevents Disease  Louis Pasteur developed the first vaccines based on attenuated (weakened) strains of microbes. Fowl cholera Rabies  Immunization is the stimulation of an immune response by deliberate inoculation with an attenuated pathogen. Antiseptics and Antibiotics  In 1847, Ignaz Semmelweis ordered doctors to wash their hands with chlorine, an antiseptic agent. Mortality rates fell.  In 1865, Joseph Lister developed carbolic acid to treat wounds and clean surgical instruments.  In the twentieth century, aseptic surgery was developed. Environments completely microbe-free  Antiseptics and Antibiotics  In 1929, Alexander Fleming discovered that Penicillium mold generated a substance that kills bacteria.  In 1941, Howard Florey and Ernst Chain purified penicillin. Penicillin quickly became the first commercial antibiotic used to save human lives.  The Discovery of Viruses  In 1892, Dmitri Ivanovsky studied tobacco mosaic disease. He discovered that the agent of transmission could pass through a 0.1 μm porcelain filter that blocked all known microbes. Martinus Beijerinck proposed that the causative agent of tobacco mosaic disease is not a bacterium because it passes through a filter that retains bacteria. Wendell Stanley purified and crystallized the filterable causative agent we now call tobacco mosaic virus (TMV). The Discovery of Viruses  1.4 ENVIRONMENT AND ECOLOGY  Microbes cycle the many nutrients essential for life, including all global N2 and most of the O2 in Earth’s atmosphere. Less than 0.1% of all microbial species can be cultured in the laboratory. The remainder make up the majority of Earth’s biosphere.  Only the outer skin of Earth supports complex multicellular life. Environmental Microbes Support Ecosystems  Sergei Winogradsky (1856–1953) Russian scientist who was among the first to study microbes in natural habitats Discovered lithotrophs using enrichment cultures Built the Winogradsky column, a model of a wetland ecosystem containing regions of enrichment for microbes utilizing diverse metabolisms Bacteria that he isolated can grow only on inorganic minerals Environmental Microbes Support Ecosystems Environmental Microbes Support Ecosystems The Global Nitrogen cycle Environmental Microbes Support Ecosystems Microbial Endosymbiosis with Plants and Animals  Endosymbionts are microbes that live inside a larger host organism. Endosymbiotic bacteria known as rhizobia induce the roots of legumes to form special nodules to facilitate bacterial nitrogen fixation. Endosymbiotic microbes make essential nutritional contributions to certain host animals. – Ruminant animals such as cattle, as well as insects such as termites, require digestive bacteria to break down cellulose and other plant polymers. – Human intestinal bacteria such as Escherichia coli and Bacteroides species grow as complex communities, or biofilms, that contribute positively to human health. Microbial Endosymbiosis with Plants and Animals Microbial Life on Other Planets  1.5 THE MICROBIAL FAMILY TREE  The bewildering diversity of microbial life forms presented nineteenth-century microbiologists with a seemingly impossible task of classification.  So little was known about life under the lens that natural scientists despaired of ever learning how to distinguish microbial species.  The famous classifier of species, Swedish botanist Carolus Linnaeus (1707–1778), called the microbial world “chaos.” Microbes Are a Challenge to Classify  Early taxonomists faced two challenges as they attempted to classify microbes: 1. Resolution of the light microscope was too low. – This challenge was overcome via advances in biochemistry and microscopy. 2. Microbial species are hard to define. – Nevertheless, microbiologists have devised working definitions of microbial species. o 95% similarity of DNA sequence Microbes Include Eukaryotes and Prokaryotes  Ernst Haeckel (1834–1919) Determined microbes are neither plant nor animal Devised a third category of life, the Monera, for microbes  Herbert Copeland (1902–1968) Divided Haeckel’s Monera into two groups: eukaryotic protists (protozoa and algae) and prokaryotic bacteria  Robert Whittaker (1920–1980) Added Fungi as a fifth kingdom of eukaryotic microbes Eukaryotes Evolved through Endosymbiosis  The five-kingdom system was modified dramatically by Lynn Margulis (1938–2011). She proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes.  The endosymbiosis theory was highly controversial. It implied a polyphyletic ancestry of living species, instead of the long-held assumption that species evolve only by divergence from a common ancestor (monophyletic ancestry). Eukaryotes Evolved through Endosymbiosis Archaea Differ from Bacteria and Eukaryotes  In 1977, Carl Woese studied recently discovered prokaryotes that live in hot springs and produce methane.  Analysis of their 16S rRNA revealed that these prokaryotes were a distinct form of life.  Woese called these new prokaryotes the archaea.  Woese’s discovery replaced the classification scheme of five kingdoms with three equally distinct groups called domains. Bacteria Archaea Eukarya  In the three-domain model, the bacterial ancestor of mitochondria derives from ancient proteobacteria, whereas chloroplasts derive from ancient cyanobacteria. Archaea Differ from Bacteria and Eukaryotes Archaea Differ from Bacteria and Eukaryotes  1.6 CELL BIOLOGY AND THE DNA REVOLUTION  More than 99% of what we know about microbes today was discovered after 1900. Advances in biochemistry and microscopy revealed the fundamental structure and function of cell membranes and proteins. The revelation of the DNA and RNA structures led to the discovery of the genetic programs of model organisms. Beyond microbiology, these advances produced “genetic engineering” and more. Cell Membranes and Macromolecules  Two instruments had exceptional impact on the study of cell structure: 1. The electron microscope – Developed by Ernst Ruska – Revealed internal structure of cells 2. The ultracentrifuge – Developed by Theodor Svedberg – Enabled separation of subcellular parts Cell Membranes and Macromolecules Cell Membranes and Macromolecules Microbial Genetics Leads the DNA Revolution  In 1928, Frederick Griffith discovered transformation in bacteria.  In 1944, Oswald Avery and colleagues showed that the transforming substance is DNA.  In 1953, Rosalind Franklin used X-ray crystallography to determine that DNA is a double helix.  Later that year, James Watson and Francis Crick discovered the complementary bases and antiparallel nature of DNA. Microbial Genetics Leads the DNA Revolution Microbial Genetics Leads the DNA Revolution  Modern X-ray crystallography reveals with atomic precision the structure of DNA, including its complementary base pairs. The complementary pairing of DNA bases led to the development of techniques for DNA sequencing, the reading of a sequence of DNA base pairs. Microbial Genetics Leads the DNA Revolution Microbial Genetics Leads the DNA Revolution  Reading the genomes enabled microbiologists to see the history of microbial evolution, reaching back to a time even before the advent of DNA.  This hypothetical world without DNA is called the RNA world.  How did life function in the RNA world? We hypothesize that cells used RNA for all the functions of DNA and protein, including information storage and replication and biochemical catalysis. Ribozymes (Ribonucleic acids + enzymes) Microbial Genetics Leads the DNA Revolution Microbial Genetics Leads the DNA Revolution  The promise of DNA was first fulfilled in bacteria and bacteriophages. Bacteria readily recombine DNA from unrelated organisms. – Recombinant DNA ultimately enabled us to transfer genes. A heat-stable bacterial DNA polymerase such as Taq (from thermophilic bacteria, Thermus aquaticus) DNA polymerase was used for amplifying DNA via the polymerase chain reaction (PCR). Gene regulation discovered in bacteria provided Microbial Discoveries Transform Medicine and Industry Special Topic 1 An mRNA Vaccine for COVID-19