Taxonomy

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VOCABULARY Microorganisms: organisms that are too small to be seen with the unaided eye. Germs: a rapidly growing cell. Normal microbiota: microorganisms that are normally found on or in the body and do not cause disease. Pathogen: a microorganism that causes disease

VOCABULARY Bacteriology: a study of bacteria. Mycology: a study of fungi. Parasitology: the study of protozoa, parasites, and worms (helminthes). Immunology: a study of immunity. Virology: the scientific study of viruses.

Aseptic adjective a: preventing infection b: free or freed from pathogenic microorganisms  Things cleaned specifically in a way that prevents infection were first described as "aseptic" in the late 19th century. The word combines the prefix "a-," meaning "not," and "septic," from Greek "sēptikos," meaning "putrifying." "Aseptic" was preceded by more than a century by "antiseptic" (from "anti-," meaning "opposing,").  

Appertization Term of French origin for the process of destroying all the micro-organisms of significance in food, i.e. ‘commercial sterility’; a few organisms remain alive but quiescent. Named after Nicholas Appert (1752–1841), a Paris confectioner who invented the process of canning; he opened the first vacuum-bottling factory in 1804.

Fomite A fomite is an inanimate object, such as a keyboard, that might have microorganisms on it that can be picked up by someone. "Fomite" is a Latin word for “tinder”. Much like tinder is a catalyst of fire, a fomite can kindle disease.

BENEFITS OF MICROORGANISMS Decompose organic wastes Are producers in the ecosystem by photosynthesis (algae, cyanobacteria, etc) Produce industrial chemicals such as ethanol and acetone Produce fermented foods such as vinegar, cheese, bread, beer, wine. Fermentation also produces useful products such as solvents to dissolve substances. To be “probiotic” means to add microbes to your diet. Produce products used in manufacturing (e.g. cellulose) and treatment of diseases (e.g. E coli can make insulin). Genetic Engineering (recombinant DNA technology)

WHY STUDY MICROORGANISMS? Allows humans to prevent food spoilage Prevent disease occurrence and transmission Understanding of aseptic techniques

Number of Bacteria You have more bacterial cells living in and on your body than you have human cells! If you judge based on cell count or DNA diversity your physical being is more bacteria than human.  (If you go based on weight, human cells still predominate.)

LINNAEUS Established the system of scientific nomenclature: Genus and species.

NAMING AND CLASSIFYING MICROORGANISMS The first letter of the genus name is always capitalized, but never the first letter of the species name. The genus may be abbreviated with the first letter, and the species is written out. The genus and species of an organism is always either underlined OR italicized: E. coli or E. coli are both acceptable.

NAMING AND CLASSIFYING MICROORGANISMS Escherichia coli is the name of a common bacterium normally found in the large intestine of all humans and animals. If E. coli gets out of that location and into the small intestine or elsewhere, it can cause disease. Staphylococcus aureus is the name of a common bacterium that is found on human skin. If S. aureus gets inside of an open wound, it can cause disease.

HOW NAMES ARE CHOSEN FOR MICROORGANISMS Named by location of organism: Enterococcus faecalis (located in feces) Named by the shape of organism: Bacillus megaterium (large rod shape) Named by the arrangement of organism: Staphylococcus aureus (clusters of circles)

CLASSIFICATION OF MICROORGANISMS Taxonomy: the science of the classification of organisms. SUPERKINGDOMS PROKARYA: Prokaryotes have no nucleus EUKARYA: Eukaryotes have a nucleus

KINGDOMS: Monera MONERA BACTERIA VIRUSES ARCHAEBACTERIA

Bacteria Prokaryotes (no nucleus) Peptidoglycan cell walls Reproduce by binary fission For energy, use organic chemicals, inorganic chemicals, or photosynthesis Normal microbiota are non-pathogenic Figure 1.1a

BACTERIA Three main types Gram positive Gram negative Acid fast

Main shapes cocci (ball shaped) vibrio (comma shaped) bacillus (rod shaped) spirochetes (spiral shape)

Arrangements of the cocci staphylococcus (clusters like grapes) Example: Staphylococcus aureus diplococcus (pairs of two) tetrads (groups of four) streptococcus (chains like bead necklace) Example: Streptococcus pyogenes (“strep throat”)

Viruses Acellular Consist of DNA or RNA core Core is surrounded by a protein coat Coat may be enclosed in a lipid envelope Viruses are replicated only when they are in a living host cell (obligate intracellular parasites) Figure 1.1e

VIRUSES HIV Common cold virus Hepatitis A

VIRUSES Vaccines can prevent some viral infections, but antibiotics are ineffective for treatment after infection. Antibiotics work by interfering with cell wall synthesis or metabolism; since viruses don’t have these things, they are not effective. There are medicines that treat but don’t cure viruses, such as acyclovir for Herpes Simplex 1.

ARCHAEBACTERIA Prokaryotic Lack peptidoglycan Live in extreme environments Include: Methanogens Extreme halophiles Extreme thermophiles Figure 4.5b

KINGDOMS: Protista PROTISTA ALGAE PROTOZOA FUNGI Molds (multicellular) Yeasts (single-celled)

Algae Eukaryotes Cellulose cell walls Use photosynthesis for energy Produce molecular oxygen and organic compounds Figure 1.1d

Protozoa Eukaryotes Absorb or ingest organic chemicals Classified according to their motility (movement) by pseudopods (false foot), cilia (hairs) or flagella (tail). Diseases caused by protozoa include malaria (carried by mosquitoes) and ameobiasis (food and water poisoning). Figure 1.1c

Fungi FUNGI Eukaryotes: have a nucleus in the cell Cell walls made of chitin or cellulose Although mushrooms look like plants, they are not because they do not use photosynthesis for food. Fungi are not phototrophic. They are heterotrophic: Use organic chemicals for energy, not photosynthethesis. Not as diverse as bacteria Two types: Yeasts: unicellular, no mycelia Saccharomyces (Baker’s and Brewer’s yeast) Candida albicans (vaginal yeast infections) Molds and mushrooms: multicellular, consisting of masses of mycelia which are composed of filaments called hyphae. Figure 1.1b

KINGDOM: Plantae PLANTAE (plants) Plants are photosynthetic (use sunlight to make food). That means they are autotrophs (make their own food) They have roots, stems, and leaves (unlike algae) They do not cause many microbiological diseases; not covered in this course.

Kingdom: Animalia ANIMALIA (animals): We will just cover multicellular animal parasites. HELMINTHES Flat worms Tapeworms NEMATODES Roundworms

Multicellular Animal Parasites Eukaryote Multicellular animals Parasitic flatworms and tapeworms are called Helminthes. Roundworms are called Nematodes. Microscopic stages in life cycles. Figure 12.28

TAXONOMY Domain Kingdom Phylum Class Order Family Genus               Species 

TAXONOMY Dashing King Phillip Came Over From Greece               Singing 

Microorganisms: Figure 1.1

MICROBES COMPARISON CHART BACTERIA Prokaryotic Peptidoglycan cell walls Reproduced by binary fission Uses organic (heterotrophs) and inorganic chemicals (chemoheterotrophs) or photosynthesis (autotrophs) for energy Shapes are rod, coccus, spiral ARCHAEA Prokaryotic; these are bacteria that: Lack peptidoglycan Live in extreme environments Include methanogens (love methane gas), extreme Halophiles (love salt), extreme thermophiles (love heat and cold) FUNGI Eukaryotes Cell walls have chitin Heterotrophs: use only organic chemicals for energy Molds are multicellular; Yeasts are unicellular

MICROBES COMPARISON CHART PROTOZOA Eukaryotes Heterotrophs: use only organic chemicals for energyMay be motile via pseudopods, cilia, or flagella ALGAE Cell wall contain cellulose Uses photosynthesis for energy (autotrophs); Produces oxygen and organic food for other species. They are like plants except they don’t have roots, stems, leaves and can be unicellular. VIRUSES Non-cellular intracellular parasites; lives at the expense of host Contain either DNA or RNA surrounded by a protein coat May have an envelope Smallest of all microbes Replicates in living host cell Antibiotics do not work; requires antiviral agents HELMINTHES AND NEMATODES (parasitic worms) Helminthes: parasitic flat worms and tapeworms Nematodes: parasitic roundworms They are endoparasites: animals that live inside other animals through fecal contamination

VOCABULARY Biotechnology: the industrial application of microorganisms, cells, or cell components to make a useful product. Microbial ecology: the study of the relationship between microorganisms and their environment Microbial genetics: study of the mechanisms by which microorganisms inherit traits. Microbial physiology: the study of the metabolism of microbes. Molecular biology: the science of dealing with DNA and protein synthesis of living organisms.

Genomics: the study of an organisms genes; used to classify a microorganisms. Bio remediation: bacteria degrade organic matter in sewage. Bacteria also degrade or detoxify pollutants such as oil and mercury. Genetic engineering: a new technique for biotechnology. Bacteria and fungi can produce a variety of proteins including vaccines and enzymes. Probiotic: adding microbes to food to cause a benefit. Nosocomial diseases: acquired in hospitals; an infection that develops during the course of a hospital stay and was not present at the time the patient was admitted. Neonate: newborn Immunocompromised: vulnerable to disease caused by normal microbiota.

MICROBES AND HUMAN WELFARE

ECOLOGY Bacteria recycle carbon, nutients, sulfates, and phosphates that can be used by plants and animals.

BIOREMEDIATION This is any process that uses microorganisms to return the environment altered by contaminants to its original condition. Used to clean up oil spills. Used to clean up industrial toxic wastes.

Bioremediation Bacteria degrade organic matter in sewage. Bacteria degrade or detoxify pollutants such as oil and mercury

Oil Spills

INSECTICIDES Bacteria can be used in the place of pesticides. Environmentally friendly Little or no effect on humans, wildlife, pollinators and most other beneficial insects.

PHARMACOLOGY Production of pure chemicals for use as pharmaceuticals. Insulin Growth factors Antibodies

FOOD Lactobacillus: fermented foods Cheese Pickles Soy sauce Sauerkraut Vinegar Wine Yogart

FOOD Probiotics: Live microorganisms which when administered in adequate amounts confer a health benefit on the host. These are bacteria added to milk, yogurt, and other foods. Lactic acid bacteria (LAB) as the most common microbes used. provides the characteristic sour taste of fermented dairy foods acts as a preservative, by lowering the pH and creating fewer opportunities for spoilage organisms to grow.

BIOTECHNOLOGY The manipulation of biological organisms to make products that benefit human beings. Food production Waste disposal Mining Medicine

BIOTECHNOLOGY: Genetic Engineering Restriction enzymes cut the DNA strands of any organism at precise points. This is how the sequence of a person’s DNA can be determined. A specific gene can be removed from one bacterium and inserted it into another using restriction enzymes.

BIOTECHNOLOGY: Recombinant DNA Technology Transgenic bacteria (bacteria to which a gene from a different species has been transferred) Example: A human gene which codes for a hormone is transferred to Escherichia coli bacteria. Escherichia coli produces this human hormone along with their own normal chemical compounds.

RECOMBINANT DNA TECHNOLOGY Recombinant DNA is a form of artificial DNA which is engineered through the combination or insertion of one or more DNA strands, thereby combining DNA sequences which would not normally occur together. It is produced through the addition of DNA into an existing organism’s genes to alter traits for a specific purpose, such as immunity. Bacteria can also be used to produce large quantities of human insulin.

NORMAL MICROBIOTA There are approximately 10 times as many bacterial cells as human cells in the human body. Three pounds of E. coli live in our intestines, helping to digest food that we cannot digest. These microbes produce folic acid, biotin, and vitamin K, substances we need to survive but cannot make ourselves. Useful microbes compete for nutrients in our body, keeping out harmful bacteria.

WHY WE HAVE MICROBIAL DISEASES Mutation leads to evolution of bacteria Antibiotic use causes resistance and evolution of bacteria Travel exposes us to microbes we are not used to Deforestation (removal of trees, especially in the tropics, Africa, Central America) destroys the ecosystem and disturbs natural balance of microbes

Lab Soil Project This Thursday, bring a soil sample to lab. Don’t use really fertile soil…dry is better, but not in an area where no plants are growing. It is best to get soil close to roots of nearby plants, and dig down about 2 inches first. Fill a 15 ml test tube all the way up with soil. Record the place of collection, temperature, and any of the below data you can collect LOCATION Location  Latitude Longitude

Lab Soil Project Date and Time Collected * Date Time Sample Site Descriptors * SOIL SAMPLE Air Temperature (°C) Humidity (%) Depth (In.) Type of Soil Soil Temperature (°C) pH of Soil Water Content (%)