Taxonomy

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.

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

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

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

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) Staphylococcus aureus – diplococcus (pairs of two) – tetrads (groups of four) – streptococcus (chains like bead necklace) Streptococcus pyogenes (“strep throat”)

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 Viruses 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.

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

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

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

Eukaryotes Absorb or ingest organic chemicals May be motile (can move) by pseudopods (false foot), cilia (hairs) or flagella (tail). Diseases caused by protozoa include malaria (carried by mosquitoes) and ameobiasis (food and water poisoning). Protozoa Figure 1.1c

FUNGI – Eukaryotes: have a nucleus in the cell – Chitin cell walls 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. Fungi Figure 1.1b

KINGDOM: Plantae PLANTAE (plants) – Plants are phototrophic and photosynthetic (use sunlight for food). – They are autotrophs (make their own food) – They do not cause many microbiological diseases; not covered in this course. – There is some cross-over in taxonomy from one Kingdom to another; algae can be considered Protists and plants.

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

Eukaryote Multicellular animals Parasitic flatworms an2d tapeworms are called Helminthes. Roundworms are called Nematodes. Microscopic stages in life cycles. Multicellular Animal Parasites Figure 12.28

TAXONOMY Kingdom Phylum Class Order Family Genus Species

Microorganisms: Figure 1.1

MICROBES COMPARISON CHART BACTERIAProkaryotic Peptidoglycan cell walls Reproduced by binary fission Uses organic and inorganic chemicals or photosynthesis for energy Shapes are rod, coccus, spiral ARCHAEAProkaryotic Lack peptidoglycan Live in extreme environments Include methanogens, extreme Halophiles (love salt), extreme thermophiles (love heat and cold) FUNGIEukaryotes Cell walls have chitin Heterotrophes: use only organic chemicals for energy Molds and mushrooms are multicellular; consist of masses of mycelia, which are composed of filaments hyphae. Yeasts are unicellular

PROTOZOAEukaryotes Absorb or ingests organic compounds May be motile via pseudopods, cilia, or flagella ALGAEEukaryotes Cell wall contain cellulose Uses photosynthesis for energy Produces oxygen and organic food for other species VIRUSESNon-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 Eukaryotes Helminthes: parasitic flat worms and tapeworms Nematodes: parasitic roundworms Endoparasites: animals that live inside other animals through fecal contamination Microscopic stages of life cycle Parasite is in the bite of mosquito or bug; spreads infection in body MICROBES COMPARISON CHART

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; originated from Beijerinck and Windogradskyi. 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 your diet. 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, nutientss, 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.

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

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: adding bacteria to our diet that are found in milk, yogart, etc. 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 in bacteria cut the DNA strands of any organism at precise points. 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. Other 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