Introduction to Microbiology A Historical Perspective Bio3124 Lecture 1

Objectives and reading Reading: Ch.1 What is microbiology? History: How it came to be a field of study? Modern microbiology: day to day impact on society

The Scope and Relevance of Microbiology importance of microorganisms first living organisms on the planet How many bugs are out there? live everywhere life is possible more numerous than any other kind of organisms global ecosystem depends on their activities (possess 50% of earth’s carbon and 90% of nitrogen) influence human society in many ways

Microbes and Microbiology? Microbes are living organisms Except for viruses, which are noncellular Metabolize energy, grow, reproduce Visualized by a microscope Unicellular , potentially exist independently simple in their construction; lack differentiated cells and distinct tissues Microbiology: study of organisms too small to be seen by the unaided eye (i.e., microorganisms) How small?

Size of Microorganisms Naked eye ~10 nm to 100 μm different type of optical system needed to resolve Where the bugs stand in the universe? Click here

Thiomargarita namibiensis Exceptions to the size rule Thiomargarita namibiensis (Pearl of Namibia) Sulfur Pearl of Namibia was dicovered by Heide Schultz chemolitothrophic G- bacterium 1000X larger than bacteria (0.5-1 mm)

Exceptions to the size rule Mimivirus: DNA virus 1.2 Mbp genome, ds linear 400-800 nm in diameter Infects amoeba Unique genes Primitive life form? Mimivirus Click to read more

The Microbial Tree Difficult to classify Difficult to distinguish by shape Often reproduce asexually Pass DNA to each other horizontally Use biochemical properties to classify Gram stain (G- and G+) Ability to metabolize different substrates (Bergey’s manual determinative bacteriology) Use DNA sequence to classify Microbial genomes are sequenced (click to link to database) Bacterial genomes are relatively small Genome = organism’s total genetic content Complete gene sequence known for many species Over 3000 bacteria, over >100 archaea thousands of viruses Microbes have greatest diversity of genomes Important for understanding evolution

The Microbial Family Tree Carl Woese 16s rRNA gene conserved Divergence reflects relatedness Phylogenetic tree Microbial world in 3 domains Prokaryotes include 2 domains Domain of Eubacteria Domain of Archaea Eukaryotic domain Algea Fungi Protista

Microbes 6 major groups studied by microbiologists Cellular forms: Prokaryotes Bacteria Eukaryotes Algae Acellular: Viruses Archaea Protists Fungi

History of Microbiology

Old times… Humans knew how to deal with germs before even knowing about their existence Storing food in cooler temperatures Salting, drying, smoking Use of spices Cremation of dead concealing and burying dead beyond a nearest passing river or in a distant area traditional, mystical and superstitious explanations

Discovery of Microorganisms Antony van Leeuwenhoek (1632-1723), the father of microbiology a hobbyist microscopist Dutchman first to observe and describe microorganisms accurately

Leeuwenhoek’s microscope Composed of one lens Light shines objects at a 45˚ angle Worked like a dark field microscope Magnification: 50-300 fold bright microorganisms could be seen in a dark bkg

Leeuwenhoek’s Observations Spirillum as seen by Leeuwenhoek’s microscope Tripartite structure of a human sperm PMN RBC Original blood smear image by Leeuwenhoek Note the polymorphonuclear cell and RBC Reported to the Royal Society of London (1673) Accurate shape, detailed movement Subjects were most possibly bacteria and protozoa and called them “animalcules“ also reported spermatozoa, blood cells Check out a paper by Brian J. Ford about Leeuwenhoek

Where do microorganism originate from? Few days of being exposed to air. Where do microorganism originate from? Spontaneous generation??

The Conflict over Spontaneous Generation living organisms can develop from nonliving or decomposing matter publically a common sense vision with social and cultural roots (almost 2000 years ago) Examples: flies from rotten meat and animal carcasses Mice from fungus infested grain barns Scientific methodology was not established What was the proof?

Jan Baptista Van Helmont (1577-1644) A Flemish noble man, alchemist and physician discovered carbon dioxide, introduced the term gas in its present scientific sense believed in spontaneous generation Paper by Louis Rosenfeld about Van Helmont

Jan Baptista Van Helmont The Origin of life (17th Centuray) 1579-1644 Adult mice

Spontaneous Generation

Could spontaneous generation be true for microorganisms?

Francesco Redi (1626-1697) First blow to spontaneous generation Laying eggs is required for maggots and flies to come to existence Supporters of SG: Life is necessary in order to bring about life in certain cases!

John Needham (1713-1781) Conclusion: Organic matter had vital force that confers properties of life to non-living matter BUT: he had left the flasks unsealed after bioling

Lazzaro Spallanzani (1729-1799) Air carries germs to broth and boiling kills the existing ones Supporters of SG: Compounds essential for generation of life were destroyed by heating!! sealing prevents air that is necessary for spontaneous generation

Louis Pasteur (1822-1895) Observations: John Tyndall: Organisms retained on cotton filters resemble microorganisms in contaminated foods Microorganisms are found in the air Microorganism in air settle on the surfaces

Pateur’s Swan neck flasks could supply air but could also trap ambient germs from entering broth

Pasteur Refutes the Spontaneous Generation

Pasteur Refutes the Spontaneous Generation ambient germs are necessary for promoting growth principle of sterility and aseptic work is important

Germ theory: Microorganisms Cause Disease For over 17 centuries the Galenism (Greek physician 129-199 B.C.) was predominant view for diseases according to which, Diseases are due to imbalances in 4 humors: blood, phlegm, yellow bile and black bile

Relationship between Microorganisms and Disease Agostino Bassi (1773-1856) showed that a disease of silkworms was caused by a fungus M. J. Berkeley (~1845-1852) demonstrated that the great Potato Blight of Ireland was caused by a water mold Louis Pasteur (1822-1895) showed that the pébrine disease of silkworms was caused by a protozoan Nosema bombycis

Other evidence… Joseph Lister (1827-1912) provided indirect evidence used diluted carbolic acid (phenol) to wash surgical devices and wash wounds developed the principles of aseptic surgery his patients had fewer postoperative infections Disease frequency dropped in his hospital

Final proof… Robert Koch (1843-1910) established the relationship between Bacillus anthracis and anthrax used criteria developed by his mentor Jacob Henle (1809-1895) these criteria now known as Koch’s postulates Read more about R. Koch. Check literature section

Microorganisms and Diseases Robert Koch Observations : The microorganism (Bacillus anthracis) is found only in the infected animals and not in healthy animals. Infected animals pass the disease to healthy ones The microorganism found outside of the animal could infect healthy animals

Germ theory: Koch’s postulates

Questions: Can Koch’s Postulates be applied to all microorganisms that cause disease? How can you apply Koch’s postulates to viruses and viral diseases? How can one apply Koch’s postulates to non-cultivable microorganisms?

The Development of Techniques for Studying Microbial Pathogens Koch’s work led to discovery or development of: agar Petri dish nutrient broth and nutrient agar methods for isolating microorganisms in pure culture

The Pure Cultures and Isolation of Single Colonies Koch : Observation: Slices of potato when exposed to air, will generate large number of bacteria (colonies) of different sizes, colours and forms Colonies

Problem: Not all bacteria could grow on potatoes! Solution : Koch used gelatin as a means for solidification of rich culture media. He formulated various culture media

Disadvantages of Gelatin Gelatin liquefaction: It is digested by various microorganisms eg. gelatinase positive enterococci and streptomyces Low melting temperature: It is in the liquid state above the temperature of 28oC.

Agar Gracilaria (red seaweeds) Polysaccharide derived from the cell walls of a red algae (Rhodophyta) A polysaccharide polymer that contains 3,6-anhydrogalactose, 2-O-methyl-α-l-galactopyranose and 6-O-methyl agarobiose Solid at >37oC. Melts at 100oC. Not digested by most bacteria

Corollary to Germ Theory Stop germ transmission, stop disease spread Kill germ, prevent disease Antiseptics 1865: Aseptic surgery Joseph Lister Antibiotics 1929–1941: Penicillin Alexander Fleming Many newer antibiotics Bacteria become resistant

Corollary to Germ Theory Stop germ transmission, stop disease spread Stop spread of germs Epidemiology, public health measures Resistant individuals prevent spread of germs 1798: Vaccination with cowpox prevents smallpox Turkish physicians, Lady Montagu, Edward Jenner

Other developments… Pasteur and Roux Pasteur and his coworkers discovered that incubation of cultures for long intervals between transfers caused pathogens to lose their ability to cause disease (attenuation) Pasteur and his coworkers developed vaccines for chicken cholera, anthrax, and rabies

Modern microbiology: day to day impact on society

Microbes Shape Human History Food & Pharmaceuticals Bread, wine, cheese, Chocolate Can also destroy crops Hormones, antibiotics etc Microbial diseases change history 14th century: Bubonic plague (Black death) caused by Yersinia pestis in Europe 19th century: Tuberculosis caused by Mycobacterium tuberculosis today: AIDS by the human immunodeficiency virus (HIV)

The golden age of microbiology (1857-1914) Many pathogens discovered Microbial metabolism studies undertaken Microbiological techniques refined A better understanding of the role of immunity and ways to control and prevent infection by microbes

Genetics and DNA Revolution Molecular genetics depends on bacteria Concept of “gene” proposed for bacteria DNA structure Genetic code Transcription, translation Restriction enzymes Recombinant DNA Cloning PCR reaction (watch the interview with Kery Mullis) E. coli has best understood genome

The Future of Microbiology Challenges and opportunities for future microbiologists infectious disease new and improved industrial processes microbial diversity and microbial ecology less than 1% of earth’s microbial population has been cultured

More challenges and opportunities… biofilms genome analysis microbes as model systems assessment of implications of new discoveries and technologies Stephen Jay Gould (1941-2002): “This is truly the "age of bacteria" - as it was in the beginning, is now and ever shall be.”