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Chapter 1 Lecture Notes Microbial Life: Origin and Discovery Chapter 1 Welcome to General Microbiology, Biol 3444 https://play.kahoot.it/#/k/93b47b07-a986-47bf-8690-42ea16b9afe7 https://www.youtube.com/watch?v=fU0XO1X1tAE https://www.youtube.com/watch?v=fU0XO1X1tAE https://www.youtube.com/watch?v=fU0XO1X1tAE Overview • What is a microbe? • How have microbes shaped human history? • What is the development of medical microbiology? Microbial ecology? • What is the microbial family tree? • What is the advent of cell biology and DNA revolution? Quick Intro • Microorganisms are every where • Life began early in the history of the earth with microbes • First two billion years, all life was microbial Antarctic “Dry Valleys” 1.1 From Germ to Genome: What is a Microbe? • Microbe: • A living organism that cannot be seen without a microscope • Cells range in size from millimeters to 0.2 micrometer (viruses are much smaller) • Some consist of a singe cell • Contains in its genome the capacity to reproduce its own kind Exceptions: • Supersize microbial cells • Thiomargarita namibiensis • Microbial communities • Biofilms • Viruses • Mimivirus /aPB5O5Q/theres-an-exception-to-every-rule-except-this-onehttps://9gag.com/gag Let’s Not Argue About It… • We will consider microbes to include: • Prokaryotes • Bacteria and Archaea • Eukaryotes • Algae, Fungi, and Protists • Bacteria, archaea, and eukaryotes evolved from a common ancestral cell Microbial Genomes Are Sequenced • Genome: Total genetic information contained in an organism’s chromosomal DNA • Fred Sanger developed the first methods of DNA sequencing that was fast enough to sequence large genomes • Haemophilus influenzae: first sequenced genome of a circular microbe (1995) • Metagenome: The collection of sequences taken directly from the environment 1.2 Microbes Shape Human History • Microbes have shaped and influenced human culture for a very long time • Yeasts and bacteria for foods and beverages • Lithotrophs, “rock-eating” bacteria, leached copper and other metals from ores exposed by mining • Enabled ancient human miners to obtain the metals • Unfortunately, these bacteria also consume stones of ancient monuments 1.2 Microbes Shape Human History • Microbes have shaped and influenced human culture for a very long time • Yeasts and bacteria for foods and beverages • Lithotrophs, “rock-eating” bacteria, leached copper and other metals from ores exposed by mining • Enabled ancient human miners to obtain the metals • Unfortunately, these bacteria also consume stones of ancient monuments Microbial Disease Devastates Human Populations • Microbial disease have vastly affected human demographics & cultural practices • 14th century: bubonic plaque caused by Yersinia pestis • 19th century: tuberculosis caused by Mycobacterium tuberculosis • Today: acquired immunodeficiency syndrome (AIDS) caused by human immunodeficiency virus (HIV) Microbial Disease Devastates Human Populations • Fun fact: more soldiers have died of microbial infections than of battle wounds • The significance of disease in warfare was 1st recognized by the British nurse, Florence Nightingale • Founded the science of medical statistics • Devised the “polar chart” to display the deaths of soldiers due to various causes Microscopes Reveal the Microbial World • Robert Hooke (1635 – 1703) • Constructed the 1st compound microscope • Limitation 30X at best • Utilized it to observe mold • Published Micrographia, the first manuscript that illustrated objects under the microscope • Coined the term ”cell” • Never observed single-celled bacteria Microscopes Reveal the Microbial World • Antonie van Leeuwenhoek (1632 – 1723) • A cloth draper (introduced him to magnifying glass) • Build single-lens magnifiers, complete with sample holder and focus adjustment • First to observe single-celled microbes • “small animals” Spontaneous Generation: Do Microbes Have Parents? • Spontaneous generation: The theory that living creatures could arise without parents • Francesco Redi, an Italian priest (1660s) • Demonstrated that maggots in decaying meat were the offspring of flies • https://www.youtube.com/watch?v=-9FZE4aHCuw • Lazzaro Spallanzani, and Italian priest (1760s) • Demonstrated that a sealed flask of meat broth sterilized by boiling failed to grow microbes https://www.youtube.com/watch?v=-9FZE4aHCuw Spontaneous Generation: Do Microbes Have Parents? • Louis Pasteur, a French microbiologist (1822 – 1895) • Started his scientific career as an organic chemist • Discovered the microbial basis of fermentation • Microbes gain energy by converting sugars into alcohol • Devised “swan-neck” flasks • Demonstrated that, after boiling, the contents remain free of microbial growth, despite access to air https://www.youtube.com/watch?v=Z7oLUWDeq7w https://www.youtube.com/watch?v=Z7oLUWDeq7w 1.3 Medical Microbiology • Germ Theory of Disease: many diseases are caused by microbes • Robert Koch (1943) • German physician • Founder of the scientific method of microbiology • Applied his methods to numerous lethal diseases around the world Growth of Microbes in Pure Culture • While working with anthrax, Koch demonstrated an important principle of epidemiology: the chain of infection • Transmission of a disease • To prove a particular bacterium caused a specific disease, pure culture of microorganisms were needed • Angelina & Walther Hesse • Solid medium using agar • Julius Petri • Double – dish container Koch’s Postulates Criteria for establishing a causative link between an infectious agent and a disease: 1. Microbe is always present in diseased host (absent in healthy) 2. Microbe is grown in pure culture (no other microbes present) 3. Pure microbe is introduced into healthy host (Individual becomes sick). 4. Same microbe is re-isolated from now-sick individual. Koch’s Postulates Immunization Prevents Disease • In the 18th 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 matter from cowpox lesions • Practice of cowpox inoculation was called vaccination • Louis Pasteur developed the 1st vaccines based on attenuated strains • Immunization: the stimulation of an immune response by deliberate inoculation with an attenuated pathogen Antiseptics • Ignaz Semmelweis, in 1847, 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 20th century, aseptic surgery was developed • Environments completely microbe-free Antibiotics • In 1929, Alexander Fleming discovered Penicillium mold generated a substance that kills bacteria • In 1941, Howard Florey and Ernst Chain purified penicillin • The 1st commercial antibiotic to save human lives The Discovery of Viruses • In 1892, Dmitri Ivanovsky studied tobacco mosaic disease (TMD) • Agent of transmission could pass through a porcelain filter that blocked all known microbes • Martinus Beijerinck: The agent of TMD is not a bacterium • The filterable agent was purified and crystallized by Wendell Stanley • Tobacco mosaic virus (TMV) 1.4 Microbial Ecology • Microbes cycle the many minerals essential for all life, including all global N2 and much of the O2. • Yet less than 0.1% of all microbial species can be cultured in the laboratory. • The remainder make up the majority of Earth’s entire biosphere. • Only the outer skin of Earth supports complex multicellular life. Microbes Support Natural Ecosystems • Sergei Winogradsky (1856–1953) • A Russian scientist who was among the first to study microbes in natural habitats • Discovered lithotrophs • Developed enrichment cultures • Built the Winogradsky column • A wetland model ecosystem containing regions of enrichment for microbes of diverse metabolism Microbes Support Natural Ecosystems Winogradsky and others showed the importance of bacteria in geochemical cycling Bacterial Endosymbiosis with Plants & Animals • Endosymbionts are microbes living symbiotically inside a larger 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 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 biofilms. 1.5 The Microbial Family Tree • 19th century microbiologists had the wonderful yet almost impossible task of classification • So little was known about life under the lens • 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. • This was overcome via advances in biochemistry and microscopy • 2. • However, microbiologists have devised working definitions of microbial species • 95% similarity of DNA sequence Microbes Include Eukaryotes and Prokaryotes • Ernst Haeckel (1834–1919): determined microbes are neither plant nor animal • A third kind of life called Monera • Herbert Copeland (1902–1968): divided Monera into two groups • Eukaryotic protists (protozoa and algae) • Prokaryotic bacteria • Robert Whittaker (1920–1980): added Fungi as a fifth kingdom of eukaryotic microbes Lynn Margulis & The Serial Endosymbiosis Theory • 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. Archaea Differ from Bacteria & Eukaryotes • In 1977, Carl Woese studied recently discovered prokaryotes that lived in hot springs and produced methane • Analysis of the 16S rRNA revealed that these prokaryotes were a distinct form of life • Carl Woese called them archaea. Archaea Differ from Bacteria & Eukaryotes • Woese’s discovery replaced the classification scheme of five kingdoms with three equally distinct groups. • Now called the three domains: Bacteria, Archaea, and Eukarya • In the three-domain model, the bacterial ancestor of mitochondria derives from ancient proteobacteria, whereas chloroplasts derive from ancient cyanobacteria. 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. • Developed by Ernst Ruska • 2. • Developed by Theodor Svedberg Microbial Genetics • In 1928, Frederick Griffith discovered transformation in bacteria. •