What are microbes? helminths yeast viruses cyanobacteria protozoa Intro helminths yeast viruses cyanobacteria small organisms, usually smaller than human eye can detect bacteria - among most abundant organisms on Earth (prokaryote) cyanobacteria - (a.k.a blue-green algae) Photosynthetic bacteria! both freshwater and marine (prokaryote) protozoa - single-celled eukaryotes [classified into groups accd. to how they move] amoebas, ciliates, flagellates, sporozoa a.k.a. apicomplexans marine amoeba “Radiolarians” in picture above fungi - used to be considered plants because they have cell wall (eukaryote) have chitin in cell wall (plants don’t) so not classified as plants anymore two groups: yeasts & molds unicellular algae (eukaryotes) - anything plantlike that’s structurally different than typical land plants diatoms - cell walls have silicon dioxide - leave behind diatomaceous earth when die dinoflagellates - amoebas that have a hard shell viruses* - not prokaryotic or eukaryotic… noncellular! Are they alive? helminths - parasitic worms, microscopic stage of life cycle protozoa bacteria algae mold Foothil Bio 41

Taxonomy Taxonomy = science of classification Intro Taxonomy http://www.linnean.org/html/history/linnaeus_biography.htm Taxonomy = science of classification some important taxonomists Aristotle - 4th century B.C.! plants & animals into categories accd. to appearance & habits Linnaeus - 1700’s, Swedish botanist Systema Naturae classified plants & animals into kingdoms Plantae & Animalia used binomial nomenclature - standardized classified microbes under Vermes (vermin) heading in Chaos category Another of Linnaeus's contributions to science was the recognition that plants reproduce sexually. The notion wasn't exactly popular when he introduced it. "Who would have thought that bluebells, lilies and onions could be up to such immorality?" sniffed academician Johann Siegesbeck. But Linnaeus had the last laugh; he named an ugly little weed Siegesbeckia orientalis http://www.nhm.ac.uk/library/linn/ Foothil Bio 41

Taxonomy Taxonomy = science of classification Intro Taxonomy www.amazon.com Taxonomy = science of classification some important taxonomists Bergey - 1923 chairperson of editorial board for first edition published by ASM Bergey’s Manual of Systematic Bacteriology: first edition has four volumes working on second edition, major overhaul, five volumes bacteria now in kingdom Procaryotae Determinative Bacteriology: aimed at identification of bacteria, not systematics (classification) Foothil Bio 41

Five kingdom system Plantae Animalia Fungi Protista Monera Intro Plantae Animalia Fungi Monera Protista Five Kingdom System 1969 - Robert Whittaker categorized all organisms accd. to cellular organization then by mode of nutrition organization - unicellular vs. multicellular +/- nucleus mode of nutrition method of energy production (autotroph vs. heterotroph) method by which energy enters organism next page -> Foothil Bio 41

Three Domain System EUBACTERIA EUKARYA ARCHAEA Intro Three Domain System Animals Plants Marine group 1 EUKARYA EUBACTERIA ARCHAEA Fungi Paramecium Porphyra Dictylostelium Entamoeba Naegleria Euglena Trypanosoma Physarum Encephalitozoan Valrimorpha Hexamita Giardia Trichomonas Chromatium Riftia E. coli Organisms visible to human eye Chlorobium Agrobacterium Thermus Thermomicrobium Aquifex Thermotoga Bacillus Cytophaga Epulopiscium Synechococcus Methanococcus Methanobacterium Methanopyros Thermococcus Haloferax Methanospirillum Methanosarcina Sulfolobus Thermoproteus Thermofilum pSL50 pSL4 pSL22 pSL12 pJP27 pJP78 proposed by Carl Woese (“Woes”) in 1970s domains ~ superkingdoms came about when new info about archaebacteria - don’t really fit into prokaryotes or eukaryotes placement into domains dependent upon evolutionary relationships as determined by nucleic acid sequencing (ribosomal RNA sequences) 3 domains Eubacteria Archaebacteria Protista Multicellulars go in this group Black, J.G. (2002) Fig. 9.13 Foothil Bio 41

Taxonomical “ranks” Human Being Kingdom Animalia Phylum Chordata Class Intro Human Being Kingdom Animalia Phylum Chordata Class Mammalia Order Primata Family Homindae Genus Homo Species H. sapiens Kingdom - two or more phyla Phylum - a.k.a. division (bacteriology, botany) groups of classes Class - groups of orders Order - groups of families Family - groups of genera Genus- two or more species Species for bacteria must have 70% biochemical similarity AND differ significantly from other species for plants & animals = groups that can breed with one another subspecies in bacteriology useful in practice for ID’ing bacteria share a characteristic(s) e.g. biotype, serotype, strain, morphotype, variety after Alcamo Fig. 3.4 Foothil Bio 41

Bacterial nomenclature Intro Bacterial nomenclature Genus + species e.g.: Escherichia (genus) coli (species) Bacillus subtilis Enterococcus faecalis Genus + species e.g. Escherichia coli, Bacillus subtilis, Enterococcus faecalis name may give a clue about a characteristic of the organism E. coli lives in intestinal tract, named after discoverer Theodor Escherich Enterococcus faecalis is a fecal organism, coccus shape ITALICIZE OR UNDERLINE!!! strains: subgroups of species characteristics that distinguish it from other subgroups of same species e.g. E. coli O157:H7 OR, underline if handwritten: Enterococcus faecalis strains? (subspecies) Foothil Bio 41

Where do bacteria come from? Intro Where do bacteria come from? Palaeolyngbya Earth formed ~ 4.5 billion years ago Fossil bacteria are found in oldest rocks (~3.8 billion years ago) Early Earth - anaerobic Earliest fossil eukaryotes ~ 1.5 billion years old (animals evolved 0.6 billion years ago) Cyanobacteria evolved the ability to use water as a raw material in photosynthesis, produced O2 as waste. Buildup of atmospheric O2 from 0% to ~20% by about 2 billion years ago Ancient Fossil Bacteria : Pictured above are two kinds cyanobacteria from the Bitter Springs chert of central Australia, a site dating to the Late Proterozoic, about 850 million years old. On the right is a colonial chroococcalean form, and on the left is the filamentous Palaeolyngbya chroococcalean form www.ucmp.berkeley.edu/ bacteria/cyanofr.html Foothil Bio 41

Where do bacteria live? EVERYWHERE! (almost) Intro Where do bacteria live? EVERYWHERE! (almost) humans host 1014 bacterial cells in 1013 human cells! NOT found inside tissues (of organisms) most abundant organisms on Earth! found everywhere! air, water, soil, rocks even found in rocks more than 1 mile below surface of Earth humans host 1014 bacterial cells in 1013 human cells about 10% of dry weight of humans is bacterial (mostly living in the large intestine) !! feces is 1/3 bacteria! NOT found inside tissues (of organisms) because of host defense mechanisms Major human problem: eliminating microbes or preventing their growth. problem for food, beverage, cosmetic, pharmaceutical, & other industries Foothil Bio 41

What do microbes do? Eat, grow, and divide!! How to accomplish? Intro What do microbes do? Eat, grow, and divide!! How to accomplish? modify metabolism make toxins structural modifications www.microbiologyonline.org.uk/ faq.html Eat, grow & divide! growth rates vary if divide every 20 minutes, could have 271 bacteria in 24 hours = 2.4 x 1021 cells. one bacterial cell weighs ~ 10-12 g SO in 24 hours these guys would weigh 2.4 x 1010 g = 2.4 x 107 kg = 26,400 tons usually NOT in optimal conditions, extreme conditions may include Antarctic ice, rocks, boiling sulfur springs, and others!! have many ways of dealing with absence of food some ways of handling food shortages secreting toxins (eliminate the competition), modification of intracellular metabolism, evolved lots of metabolic tricks- e.g., some bacteria can use up to 150 different chemicals as their ONLY carbon source producing modified structures for dormancy (spores, cysts, endospores) Foothil Bio 41

Why do we care? Disease Agriculture Food and beverages Chemicals Intro Why do we care? Disease Agriculture Food and beverages Chemicals Basic research Biotechnology Disease: since discovery of infectious microbes, most infectious diseases controlled by sanitation, preventive medicine, chemotherapy Agriculture: microbes are vital to process materials in soil, such as nitrogen, sulfur, etc Food and beverages: fermentation responsible for ALL alcoholic beverages, breads, pickles, cheeses, etc. Chemicals: Microbes use variety of metabolic tricks. May be used to produce acetone or other commercial solvents, pharmaceuticals, antibiotics, preservatives Basic research: Advantages to using include: they grow fast, produce enormous number of offspring. Thus, it’s easy to find events that occur rarely (1 in a billion) if have 100 billion bacteria in the test tube Biotechnology: a.k.a genetic engineering- requires ability to move genes freely from one organism to another, select genes of interest and amplify their expression- BACTERIA! Foothil Bio 41

How did microbiology become a science? Intro How did microbiology become a science? Anthony van Leeuwenhoek (late 1600’s) microscope micrograph Anton van Leeuwenhoek (late 1600’s) made first careful descriptions of microbes NOTE: not necessarily first to OBSERVE them! draper, haberdasher amateur lens grinder, made a simple microscope initially used to inspect fabric quality drew bacteria, yeasts, etc., called them “animalcules” communication with Royal Society of London was essential to his fame when died (1723), interest waned secretive - didn’t show anyone how to make lens or microscopes didn’t know yet that microbes cause disease Foothil Bio 41

Spontaneous generation controversy Intro Spontaneous generation controversy Spontaneous generation controversy ancient belief was that life could spring from inert matter rats come from old rags & wheat bran maggots come from meat www.darwin.museum.ru/site_bac/ etap/etap2_A.htm Foothil Bio 41

Pasteur & Tyndall end spontaneous generation controversy Intro Pasteur & Tyndall end spontaneous generation controversy 1859: French Academy of Science sponsored competition to “throw new light on the question of spontaneous generation” Pasteur designed experiments to demonstrate that air carried contaminating microbes 1861: disproved spontaneous generation John Tyndall - English physicist demonstrated that dust carries germs broth remained sterile if no dust present (even if directly exposed to air) Foothil Bio 41

Disease transmission? miasma Intro Disease transmission? miasma importance of microbes in disease not immediately understood up until mid 1800’s thought disease caused by “miasma” poisonous entity in atmosphere especially arose from decaying/diseased bodies www.ghosthunting.org.uk/ cemetary3.htm Foothil Bio 41

Fracastoro “seeds” of contagion infection symptoms courses Intro Fracastoro “seeds” of contagion infection delpiano.com/millennium/html/ body_fracastoro.html symptoms courses http://cogsci.uwaterloo.ca/Articles/Pages/Concept.html Although some Hippocratics recognized that consumption (tuberculosis) is contagious, contagion played little role in medical explanations of disease until the work of Fracastoro, who was born in Verona about 1478. 1525 he published a long poem about the newly-recognized disease syphilis, and in 1546 he published his major treatise on contagion did not deny existence of bodily humors such as phlegm, but contended that there is a large class of diseases caused by contagion rather than humoral imbalance. Persons can contract infections even if their humors are normally balanced. Foothil Bio 41

Semmelweis accumulation of evidence that microbes cause human disease: Intro Semmelweis accumulation of evidence that microbes cause human disease: Ignaz Philipp Semmelweis (1818-1865) "Hungarian physician Assistant at First Obstetric Clinic of Vienna's great Allgemeines Krankenkhaus in 1847, discovered means of preventing puerperal (pyoo-er-per-al) fever: insisted that physicians and medical students wash their hands in chlorinated lime water before entering obstetric wards and again before examining each patient. rule was much resented and opposed - but hundreds of mothers' lives were saved. Though his doctrine was proved repeatedly, in hospitals in Vienna and in Budapest, most of his contemporaries opposed it; and both depressed from worry and broken-hearted from disappointment, Semmelweis died at age 47, of blood poisoning, the infection he had fought so valiantly to prevent in mothers under his care.” This painting by Robert A. Thom appeared in "Great Moments in Medicine" published by Parke Davis & Company, in 1966 www.personal.psu.edu/faculty/ j/e/jel5/micro/art.htm Foothil Bio 41

Intro John Snow John Snow In 1854,. In the London Soho district, nearly six hundred people died from cholera in just 10 days With no known cure, panic spread throughout city and residents began thinking that they were somehow being infected by the buried corpses of plague victims who died during the European pandemic a century before. Housing had been built on the cemetery where those plague victims were buried. As cholera deaths occurred in these homes, and in homes surrounding the area, the residents feared that they were being infected by vapours coming from the ground Snow, a London physician and anaesthesiologist, knew that to contain the disease, they would have to locate its source. Using maps showing the locations of water pumps and the homes of people who died of cholera, Snow was able to show that one pump, the public pump on Broad Street, was causing most of the disease. When water was brought into city from outside sources, incidence of cholera decreased. People could also see on this map that cholera deaths were not confined to the area around the cemetery and were therefore convinced that the infection was not due to vapours coming from it combined findings of Semmelweis and Snow indicated that a poison or unseen object in the environment was responsible for infectious disease.  However, indisputable proof of the exact nature of infectious disease was lacking. www.soi.city.ac.uk/ ~dk708/pg1_1.htm Foothil Bio 41

Germ Theory of Disease support for germ theory of disease growing Intro Germ Theory of Disease support for germ theory of disease growing first demonstrated in animals/plants Pasteur “Father of Microbiology” 1857 - showed that bacteria are cause of “souring” of wine (fermentation) - proposed germ theory of disease 1865 - demonstrated that “pebrine” disease of silkworms caused by a protozoan parasite Nosema bombycis helped silk industry! Foothil Bio 41

Joseph Lister Lister Lister (late 1800’s) developed antiseptic surgery Intro Lister pw1.netcom.com/~aguldo/ agga/bt/txt/bt1899.htm www.umanitoba.ca/.../medicine/ history/lister/anessurg.html Joseph Lister Lister (late 1800’s) developed antiseptic surgery published findings in 1867 heat sterilizing instruments, swabbing surfaces with strong acids phenol Led to dramatic decrease in post-op infections Foothil Bio 41

Koch establishes causative link between B. anthracis & anthrax Intro Koch establishes causative link between B. anthracis & anthrax www.robert-koch-stiftung.de/ ziele.html Robert Koch http://www.vdem.state.va.us/prepare/terrorismtoolkit/anthraxoverview.htm Koch (late 1800’s) first to demonstrate causal link of a single microbe to a single disease Bacillus anthracus was responsible for Anthrax Foothil Bio 41

Intro Suspected microbe must be present in EVERY case of the disease Diseased subjects Microbe not typically found in healthy subjects Koch’s Postulates Must isolate & grow pure culture of microbe Microbe must be present in every case of disease, but absent from healthy individuals Suspected microbe must be isolated and grown in culture Same disease must result when the isolated microbe is introduced into a healthy host Same microbe must be isolated again from the diseased host Same microbe must be isolated from diseased experimental host Cultured microbe must cause disease when inoculated into a healthy, susceptible host Foothil Bio 41

Exceptions to Koch’s postulates Intro Exceptions to Koch’s postulates Organism can’t be cultured e.g. Mycobacterium leprae Combination of pathogens Ethical considerations Foothil Bio 41

“Golden Age” of Microbiology: Late 1800s Intro “Golden Age” of Microbiology: Late 1800s DISEASE Anthrax Gonorrhea Typhoid fever Malaria Tuberculosis Cholera Diphtheria Tetanus Diarrhea Pneumonia Meningitis Gas gangrene CAUSATIVE AGENT Bacillus anthracis Neisseria gonorrhea Salmonella typhi Plasmodium spp. Mycobacterium tuberculosis Vibrio cholera Corynebacterium diphtheriae Clostridium tetani Escherichia coli Streptococcus pneumoniae Neisseria meningitidis Clostridium perfringens YEAR 1867 1879 1884 1880 1882 1883 1883-84 1885-89 1885 1886 1887 1892 Golden Age of Microbiology from 1850’s to WWI (1917) Every year brought new evidence that particular diseases were caused by particular microbes microbiologists began to study how body defends itself against microbes: immunology born End of Golden Age = WWI Paris under siege - Pasteur Institute closed Foothil Bio 41

What’s included in “microbiology”? Intro What’s included in “microbiology”? Microbiology Basic research microbiology Applied microbiology In relation to disease After Black (2002) Microbiology: Principles & Explorations, 5th Ed. Table 1.2 By kind of organism By process Bacteriology Phycology Mycology Protozoology Parasitology Virology Microbial metabolism Microbial genetics Microbial ecology Immunology Epidemiology Etiology Fields of Microbiology - Basic Research Micro According to organisms studied Microbial taxonomy - Classification of microbes Bacteriology - bacteria Phycology - Algae Mycology - Fungi Protozoology - protozoa Parasitology - Parasites Virology - Viruses According to Processes or Functions studied Microbial metabolism - chemical reactions that occur in microbes Microbial genetics - transmission of genetic info in microbes Microbial ecology - relationships of microbes with each other & environment Health-related Immunology - host defense against microbes Epidemiology - frequency & distribution of disease Etiology - causes of disease Microbial taxonomy Foothil Bio 41

What’s included in “microbiology”? Intro What’s included in “microbiology”? Microbiology Basic research microbiology Applied microbiology After Black (2002) Microbiology: Principles & Explorations, 5th Ed. Table 1.2 Disease-related Environmental Industrial Infection control Chemotherapy Environmental microbiology Food/Beverage technology Pharmaceutical microbiology Genetic engineering Fields of Microbiology - Applied Micro Health-related Infection control - control of nosocomial infection Chemotherapy - development/use of chemical substances to treat disease Environmental Environmental microbiology - maintainence of safe drinnking water, waste disposal, control of environmental pollution Industrial Food & beverage technology - prevent disease from organisms in foods Pharmaceutical microbiology - manufacture antibiotics, vaccines, other health products Genetic engineering - use microbes to synthesize useful products Foothil Bio 41