Introduction to Microbiology Chapter 1 - Spring 2025 PDF

Chapter 1 What is Microbiology? How microbes affect our lives. Members of microbial world History of Microbiology 1  What is Microbiology? Microbiology - the study of life forms too small to be seen with the naked eye. The science of Microbiology includes many...

Chapter 1 What is Microbiology? How microbes affect our lives. Members of microbial world History of Microbiology 1  What is Microbiology? Microbiology - the study of life forms too small to be seen with the naked eye. The science of Microbiology includes many subfields. 2 Key Terms Microorganism (Microbe): A microscopic organism consisting of a single cell or cell cluster, also including the viruses, which are not cellular. (Brock 13th ed.) Iwencludes: Bacteria, Archaea, Microbial Eukaryotes, viruses, prions Microscopic = too small to see with the naked eye (~0.5 mm). Microorganisms are microscopic 3  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Microscopes are necessary to see Microbes 4 Microbes are Ubiquitous Microbes = ~ 50% of earth’s total biomass Plants= ~35% Animals= ~15% 5 Microbes Occupy every ecological niche…… 6 …..including some very “extreme” environments Boiling Mudpot: Home for Extremophiles http://www.taos-telecommunity.org/epow/EPOW-Archive/archive_2003/ EPOW-031027.htm 7 Figure 1.14 Some archaea live in extreme environments, such as the Morning Glory pool, a hot spring in Yellowstone National Park. The color differences in the pool result from the different communities of microbes that are able to thrive at various water temperatures. -Microbes are ubiquitous Antarctic sea ice - Many species thrive in environments inhospitable for eukaryotes Old Faithful geyser Yellowstone National Park Antarctic dry valley soil Salt pond 9 Microbiology includes many encompasses many fields of science 1. Bacteriology 2. Mycology 3. Parasitology 4. Virology 5. Protozoology - study of protozoa 6. Study of algae (Phycology 10  Bacteriology Bacterial colonies on an agar plate Staphylococcus epidermidis Salmonella enteriditis Stained bacterial cells viewed with light microscopy 11 Mycology 12 Figure 1.17 - Fungi Candida albicans is a unicellular fungus, or yeast. It is the causative agent of vaginal yeast infections as well as oral thrush, a yeast infection of the mouth that commonly afflicts infants. C. albicans has a morphology similar to that of coccus bacteria; however, yeast is a eukaryotic organism (note the nuclei) and is much larger. (credit: modification of work by Centers for Disease Control and Prevention)  Parasitology Leishmaniasis Trypanosomes 14 Virology SARS-CoV- 2 15  Figure 1.20 - Viruses (a) Members of the Coronavirus family can cause respiratory infections like the common cold, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Here they are viewed under a transmission electron microscope (TEM). (b) Ebolavirus, a member of the Filovirus family, as visualized using a TEM. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Thomas W. Geisbert) Algae 17  Protozoa Acanthamoeba Naegleria Giardia 18 Microbiology Includes many fields of study Microbes affect our lives in numerous ways 19  Environmental microbiology Microbes - recycle C, N, P, S (biogeochemical cycles, which are essential for life on earth). are used in sewage treatment. degrade pesticides and herbicides. bioremediation (eg. cleaning up toxic waste sites. 20 Food Microbiology Microbes are used in food production Microbes cause food spoilage Crop damage Microbes and Crop protection (ex. Bacillus thuringiensis) 21 Figure 1.3 A microscopic view of Saccharomyces cerevisiae, the yeast responsible for making bread rise (left). Yeast is a microorganism. Its cells metabolize the carbohydrates in flour (middle) and produce carbon dioxide, which causes the bread to rise (right). (credit middle: modification of work by Janus Sandsgaard; credit right: modification of work by “MDreibelbis”/Flickr) Microbes are used in production of medical, agricultural and industrial products Antibiotics (penicillin and streptomycin, etc., etc Steroids Organic solvents and acids (butanol, ethanol, etc.) Enzymes Animal protein products produced by genetically engineered microbes 23 Microbes and Genetic Engineering and Biotechnology Agricultural applications Recombinant protein production Gene therapy 24  Microorganisms cause infectious diseases. Infectious diseases historically Infectious diseases today Emerging infectious diseases Host-Microbe Interactions Immunology Microbes as experimental models e.g. E. coli, Yeast 25 Emerging infectious diseases 26 Microbiology subfields Medical microbiology and infectious diseases Environmental microbiology and microbial ecology Bioremediation Food microbiology Water and waste water microbiology Soil microbiology Industrial microbiology Biotechnology and genetic engineering, Immunology, Molecular biology, etc., etc. 27 History of Microbiology….. 1674 - Antony van Leeuwenhoek “discovered” microorganisms. (http://www.ucmp.berkeley.edu/history/leeuwenhoek.html) 28 Leeuwenhoek’s Microscope Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 29 Figure 1.6 (a) Louis Pasteur (1822–1895) is credited with numerous innovations that advanced the fields of microbiology and immunology. (b) Robert Koch (1843–1910) identified the specific microbes that cause anthrax, cholera, and tuberculosis. History of Microbiology….. Spontaneous generation was a widely held belief in the 1600’s 1800’s – Louis Pasteur (and others) disprove Spontaneous generation. Pasteur’s “Swan-necked flasks” experiment 31  Spontaneous Generation Spontaneous generation was the widely held belief that life could arise from nonliving matter  by the 17th century, scientists at that time were working to disprove this notion Francesco Redi, in 1668, attempted to disprove this idea through experimtation Flies only appeared on the meat when it was exposed to open air Explanation – flies laid eggs on the meat when they had direct contact with it; resulting in maggots (fly larvae) and eventually flies Redi’s results were not accepted by everyone at the time; Several other scientists performed inconclusive experiments; the debate continued Figure 3.2; Openstax 32 Swan-necked flask experiment In the 1800’s, Louis Pasteur set about to disprove spontaneous generation He showed that microorganisms could be filtered out of the air Swan-necked flask experiment irrefutably disproved spontaneous generation  Pasteur also invented pasteurization, and developed vaccines (e.g. for rabies) If the flask remains upright, no microbial growth occurs. If the flask is tipped, the microorganisms trapped in the neck reach the sterile broth and grow. Figure 3.4; Openstax 33 Koch’s work and others led to the “Golden Age of Microbiology” Causes of many diseases were determined  Improved culture methods  Improved staining techniques Pure Culture Concept pure culture = 1 type of organism grown in culture, once this was accomplished, microbes could be studied individually. 34  Robert Koch in the “Golden Age of Microbiology” Germ Theory of Disease - proved role of microorganisms in causing disease. 1870’s Robert Koch - demonstrated 6 different infections in mice caused by 6 different bacteria; demonstrated anthrax was caused by bacteria First demonstration of a single isolated microorganism causing a known human disease Robert Koch (1843–1910) identified the specific microbes that cause anthrax, cholera, and tuberculosis. 35 Germ Theory of Disease (in chapter 3) In 1546, Fracastoro may have been the first to suggest that some “unseen” something could be transferred from person to person (early idea of Germ Theory of Disease) In 1847, Semmelweis observed a higher mortality rate from puerperal fever among women giving birth in hospitals (10 – 20%) compared to birth via midwives (1%). The difference – interns and physicans performed autopsies, and then did not wash their hands afterwards, but assisted with childbirth Semmelweis suspected that the causative agent was being transferred between patients He implemented handwashing with chlorinated lime water before and after examining a patient Maternal mortality declined (to 1%), thus demonstrating that handwashing prevented the transfer (still, handwashing was slow to be adopted) 1848 - John Snow showed Cholera was transmitted through contaminated water In 1867 Joseph Lister insisted on handwashing and using carbolic acid (phenol) spray disinfectant/antiseptic during surgery (prior to that, 50% of surgical patients were dying of infection 36 1884 - 4 postulates (Koch’s Postulates) 1) microorganism present in disease cases, absent in healthy animals  2) microorganism can be isolated from diseased animal and grown in pure culture  3) disease can be reproduced by inoculation of healthy animal with cultured organism  4) organism can be re-isolated from experimentally infected animal and returned to culture (pure) 37 Key points – Dependent on microscopes an culturing techniques! 38 Classification of Microbes 39  Taxonomy Classification/description, Identification and Nomenclature Based on shared characteristics Establishes phylogenetic or evolutionary relationships. Provides identification schemes. Continually evolving field.  Taxonomy Field founded by Carolus Linnaeus in 1735 System to name and categorize organism, format standardized Provided consistent terminology for related organisms Linnaean taxonomy (1735) Three kingdoms – plants and animals three kingdoms; plant, animal, and mineral (later abandoned) Responsible for hierarchies (next slide) 41  Taxonomic Hierarchies Domain Kingdom Phylum (or division) Class Order Family Genus Species  Figure 1.8 Swedish botanist, zoologist, and physician Carolus Linnaeus developed a new system for categorizing plants and animals. In this 1853 portrait by Hendrik Hollander, Linnaeus is holding a twinflower, named Linnaea borealis in his honor.  Taxonomic Hierarchies More branches added as time went on. Whittaker ’s system was the standard for many years. Viruses not Figure 1.10  Classification Schemes Five kingdom system (1969) ◦ Whittaker ◦ plants, animals, fungi, protista, and prokaryotes (or monera – single cells lacking a nucleus) ◦ Based on physical characteristics Three domain system (1978) ◦ Woese and Fox genetics-based tree of life ◦ Domain level is above the kingdom level ◦ Reflects characteristics of cell types ◦ Three domains based on ribosomal RNA sequence data  Carl Woese – Three Domains Carl Woese -In 1977, he uncovered the 'third domain of life'. He achieved this by defining Archaea (a group of single-cell prokaryotic organisms) Did phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by him In 1990, based on the reconstruction of rRNA phylogenetic tree, he proposed a separate domain for Archaeabacteria and introduced the concept of three domains of life: Bacteria, Archaea and Eucarya. The small subunit (SSU) rRNA based tool of Woese revolutionized the world of microbial evolution and phylogeny and opened avenues for the study of complex microbial communities using metagenomics 46 Ribosomes Ribosomes – site of protein synthesis in all living cells. Ribosomes consist of two subunits and are made up of proteins and RNA. In bacteria, The 16S rRNA gene encodes the small subunit ribosomal RNA molecules of ribosomes. (18S rRNA in Eukaryotic cells) Bacterial Ribosomes - two subunits are 30S and 50S, which join together to form the 70S ribosome. ◦ 30S subunit: Made up of a single strand of RNA and 21 proteins ◦ 16S rRNA: In the small subunit ◦ 50S subunit: Made up of two strands of RNA and 34 proteins ◦ 23S rRNA: In the large subunit ◦ 5S rRNA: In the large subun Eukaryotic ribosomes - have 40S and 60S subunits joined 47 to form the 80S ribosome.  Three Domain Tree of Life Woese and Fox’s phylogenetic tree contains three domains: Bacteria, Archaea, and Eukarya. Domains Archaea and Bacteria contain all prokaryotic organisms, and Eukarya contains all eukaryotic organisms. (credit: modification of work by Figure 1.11 Eric Gaba) Phylogenetic trees – diagram that depicts relationships between organisms 3 Domains of Life Classifying all forms of life: Bacteria Archaea Eukarya Domain level accommodated discovery of archaea Based on rRNA sequencing (work by Carl Woese) Microorganisms are found in all three domains 49  Three Domain Tree of Life Domain - Largest taxonomic group Relatedness based on comparisons of DNA sequences for ribosomal RNA (rRNA) genes -archaea more closely related to eukarya - rRNA genes mutate slowly at constant, predictable rates - Closely related species have similar rRNA sequences - Distantly related have more differences 50 Three Domains Nomenclature of bacteria and other microorganisms Naming system for all living things developed by Carl Linnaeus in the 18th century Binomial system of Genus species names Naming is often shortened to First letter of Genus name and the species.  Nomenclature Species ◦ Basic unit of classification ◦ Includes a groups of related strains or isolates. ◦ Individual strains within a species vary in minor characteristics Species vs. Strains in microbiology A strain is a genetic variant; it is a subtype or culture of a biological species Strains vs. Species Escherichia coli (E. coli) Many different strains Vary in pathogenicity Some strains can cause food poisoning and traveler’s diarrhea. Example: E. coli O157:H7 - pathogenic (disease-causing) strain; causes abdominal cramps and diarrhea. May originate from contaminated water or food (raw vegetables and undercooked meat). Outbreak from undercooked hamburger in 1900’s. Most E. coli strains do not cause disease. Strains of E. coli in the gut help digest our food, provide helpful chemicals (vitamin K), and fight against pathogenic microbes. 54 Bergey's Manual of Systematic Bacteriology Classification of prokaryotic cells. First published in 1923 Now - Biochemical, serological, genetic relatedness Comprehensive information http:// on prokaryotes. www.cme.ms u.edu/ Five volumes bergeys/ Identifying Microorganisms Phenotypic Characteristics Genotypic Characteristics Identification/Naming Important to identify pathogens in order to appropriately treat patients Identify foodborne pathogens and sources Organisms must be identified and named consistently to study and communication The Microbial World 58 Bacteria and Archaea… Both are prokaryotes Morphologically similar Single-celled Single circular molecule of DNA Both are extremeley diverse Archaea are often extremophiles 59  Archaea Large, diverse group of prokaryotic microorganisms Archaea are a group of micro-organisms that are similar to, but evolutionarily distinct from bacteria. widely distributed in nature and are common in much less extreme habitats, such as soils and oceans. As such, they are significant contributors to the global carbon and nitrogen cycles. Many archaea have been found living in extreme environments, for example at high pressures, salt concentrations or temperatures. These types of organisms are called extremophiles. Small subunit rRNA gene sequence different from bacteria and eukaryotes 60 Figure 1.13 Common bacterial shapes. Note how coccobacillus is a combination of spherical (coccus) and rod-shaped (bacillus). (credit “Coccus”: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus”: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete”: Centers for Disease Control and Prevention)  Eukarya (Eukaryotes) Everything else is found in this domain! Single or multicellular. Cells have a true nucleus. Cells contain membrane-bound organelles (eg. mitochondria, chloroplasts) Cells contain a cytoskeleton. 62 Eukaryotic Microbes Protozoa Algae Fungi Some multicellular parasites 63  Protists Informal grouping includes protozoa and algae Very diverse groups of microbes Eukaryotic Most are free-living Some are parasitic Most are harmless to humans Many are non-pathogenic Some parasitic protozoa Giardia, malaria Assorted diatoms, a kind of algae, live in annual sea ice in Important ecological roles McMurdo Sound, Antarctica. Algae are photosynthetic Diatoms range in size from 2 μm to 200 μm and are visualized Useful products from algae here using light microscopy. (credit: modification of work by Agar, carageenan National Oceanic and Atmospheric Administration) 64  Fungi Very diverse groups of microbes Eukaryotic More that 1000 known species Single-celled or multicellular Microscopic or macroscopic Non-photosynthetic Different from plants Cells walls contain chitin (not cellulose) Many have useful roles Yeasts in food production Yeasts – single celled Some are disease causing Molds – multicellular; long filaments, form visible colonies Molds – sources of natural antibiotics 65 Non-living members of the microbial world Acellular agents Neither prokaryotic nor eukaryotic “Non-living” members Viruses Viroids Prions 66  Viruses Consist of Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. nucleic acid and protein (acellular) Infect plant, animal, bacteria, or archaea cells. 67 Viroids Infectious particles RNA only (no protein) obligate intracellular pathogens of plant cells (linked to ~16 plant diseases) Hepatitis D in humans 68 Prions Infectious proteins (no nucleic acid) Obligate intracellular pathogenic particles Example: Creutzfeldt-Jakob disease (CJD) is a rapidly progressive, invariably fatal neurodegenerative disorder believed to be caused by an abnormal isoform of a cellular glycoprotein known as the prion protein This tissue slide shows sponge-like lesions in the brain tissue of a classic CJD patient. 69  Clinical Focus – Case Study. Figure 1.2 (a) A lumbar puncture is used to take a sample of a patient’s cerebrospinal fluid (CSF) for testing. A needle is inserted between two vertebrae of the lower back, called the lumbar region. (b) CSF should be clear, as in this sample. Abnormally cloudy CSF may indicate an infection but must be tested further to confirm the presence of microorganisms. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by James Heilman)  Relative Sizes The relative sizes of various microscopic and nonmicroscopic objects. Note that a typical virus measures about 100 nm, 10 times smaller than a typical bacterium (~1 μm), which is at least 10 times smaller than a typical plant or animal cell (~10–100 μm). An object must measure about 100 μm to be visible without a microscope. Figure 1.12 Explore further the kinds of careers that are possible in Microbiology Click on the link below to watch the video: https://www.asm.org/Articles/2018/November/Careers-in- Microbiology-and-the-Microbial-Sciences What Is a Microbiologist? microbiologist \ ˌmī-​krō-​bī-​ˈä-​lə-​jist \ noun a scientist who studies living organisms and infectious particles, such as bacteria and viruses, that can only be seen with a microscope 72