Microbiology 1

SANITARY ENGINEERING

MICROBIOLOGY

• Microbiology is the study of microorganisms.

• It's a specialized area of biology focused on living things too small to be seen without magnification.

• Microorganisms are microscopic organisms.

• Microbes or germs are terms used for microorganisms, particularly when discussing their role in infection and disease.

MICROBIOLOGY & PARASITOLOGY

• Microbiology: Study of microorganisms.

  • Originates from Greek words: Mikros (small) and logos (science/study).

• Microorganisms:

  • Microscopic organisms.

  • Referred to as microbes or germs in the context of infection and disease, also known as pathogens.

• Includes a diverse group of microscopic organisms existing as single cells or cell clusters, and viruses (microscopic but not cellular).

• Major Divisions of Microorganisms:

  • Prokaryotes: Bacteria & Archaea.

  • Eukaryotes: Algae, Fungi & Protozoa.

• Three Domains of Life:

  • Domain Eucarya.

  • Domain Bacteria.

  • Domain Archaea.

• Major groups of microorganisms:

• Cellular:

  • Bacteria

  • Fungi

  • Algae

  • Protozoa

• Acellular:

  • Viruses (dependent on a living host, i.e., parasites)

  • Helminths (parasitic worms)

Examples of Microorganisms and Related Information:

• Fungi: Penicillin mold.

• Algae.

• Protists.

• Viruses:

  • DNA Virus.

  • Enveloped Viruses.

• Helminths:

  • Ascaris

  • Pinworm

  • Liver Fluke

  • Trichuris Trichiura.

  • Giardia (cysts).

• Yeast (dependent on host).

• Acyclovir is a medicine for viruses.

• John Snow: pioneer of epidemiology.

• Etiological agent: use of chemicals for therapy (e.g., cancer treatment).

• Focuses on environment (e.g., activated sludge).

• Application of microbiology for the protection of public health and to maximize yield.

• Earth is habitable because it is an oxygenated planet and a supplier of oxygen (e.g., algae).

• Algae manufacture their own food and produce oxygen.

• Aerobic organisms are dependent on oxygen.

• Nitrogen fixing bacteria degrade complex substances to simpler substances.

Biomes and Human Use of Microorganisms:

• Biomes: habitat/sanctuary to microorganisms (e.g., human body, stomach chamber for cellulosic fiber).

• Create/manufacture Queen of drugs - Penicillin (made of fungi, molds).

• Hormonal treatment: gain weight through hormones (medical intervention).

• Human use of microorganisms: National Oceanic Atmospheric Agency (NOAA), removal of 63,000 tons of crude oil though fungi (oil eating species).

• Decay: absence of dissolved oxygen.

• Accidental discovery [incubation period 30 years (father of epidemiology) ~ Syphilis (STD) disease (component arsenic)].

Taxonomy:

• Consists of three interrelated areas:

  • Classification: Arrangement of organisms into taxonomic groups (taxa) based on similarities or relationships.

  • Nomenclature: Assignment of names to taxa according to international rules.

  • Identification: Determining if an isolate belongs to an established taxa or represents a previously unidentified species.

Levels of Classification:

• From most generic to most specific:

  • Domain: Giant, all-inclusive category based on a unique cell type.

  • Kingdom.

  • Phylum (for protozoa, animals, and bacteria) or Division (for algae, plants, and fungi).

  • Class.

  • Order.

  • Family.

  • Genus.

  • Species: Smallest and most specific taxon.

• Mnemonic: Did King Philip Come Over For Good Spaghetti

Assigning Specific Names:

• Binomial system of nomenclature: Method of assigning the scientific or specific name.

• Scientific name: Combination of the genus name followed by the species name.

• Capitalize the first letter of the genus name only, and use lowercase for the species name; underline or italicize the entire species name (e.g., Homo sapiens).

• Examples:

  • Staphylococcus aureus: Describes clustered arrangement of cells and golden-yellow color of colonies.

  • Escherichia coli: Honors the discoverer, Theodor Escherich, and describes its habitat, the colon.

• After the first use, scientific names may be abbreviated with the first letter of the genus and full species epithet (e.g., E. coli).

• Special notations:

  • sp. - used to designate a single species.

  • spp. - used to designate more than one species.

  • ssp. - used to designate a subspecific epithet.

Phylogeny:

• The natural relatedness between groups of living things.

• Used by biologists to create a system of taxonomy.

• First phylogenetic trees of life included plants and animals.

• Later recognition of:

  • 3rd kingdom: protists

  • 4th kingdom: bacteria

  • 5th kingdom: fungi

Systems of Presenting a Universal Tree of Life:

• Traditional Whittaker system:

  • Robert Whittaker added a 5th kingdom for fungi (1959-1969).

  • 5 kingdoms:

    • Monerans (Prokaryotae): Bacteria and Archaea.

    • Fungi.

    • Protists: Algae and Protozoa.

    • Plantae.

    • Animalia.

Additional Notes:

• No true nucleus - abundant nucleus (true nucleus cell).

• Others self manufacture own food (inorganic, e.g., tar). (survive 30 years who food).

• Carbon dioxide (CO_2)

• Oxygen (O_2)

Environmental Conditions for Microorganisms:

• Acidophiles: Thrive in extremely acidic conditions (pH 2-5).

• Alkaliphiles: Thrive in extremely alkaline conditions (pH > 8.5).

• Thermophiles/Sternothermophiles: Thrive in extremely hot conditions.

• Psychrophiles/Cryophiles: Thrive in extremely cold conditions.

• Piezophiles/Barophiles: Thrive in extremely high pressure.

• Halophiles: Thrive in extremely salty conditions.

• Haloduric: Organisms that do not prefer salty environments but can survive in them (e.g., Staphylococcus aureus).

Methods for Studying Microorganisms: The Five "I"s

• Specimen Collection: Any object can be a source; common sources are body fluids/tissues, foods, water, and soil.

• Sampling devices: swabs, syringes, or special transport systems.

• The Five "I"s: How the sample is processed and profiled.

  • Inoculation: Introducing a tiny sample (inoculum) into a container of nutrient medium to produce a culture.

    • Sample is placed into a container of sterile medium with appropriate nutrients.

    • Involves spreading the sample on the surface of a solid medium or introducing it into a flask or tube.

    • Selection of media with specialized functions can improve later steps.

    • Some microbes may require a live organism (animal, egg) as the growth medium.

  • Incubation: Using an incubator to maintain appropriate growth temperature and other conditions to promote multiplication over time.

    • Produces a culture: visible growth of the microbe in or on the medium.

  • Isolation: Separating one species from another.

    • Isolated microbes form separated colonies (discrete mounds of cells) on solid media or turbidity (free-floating cells) in broths.

    • Subculturing: Taking growth from an isolated colony and inoculating a separate medium to make a pure culture.

  • Inspection: Macroscopic observation of colonies or broth cultures for growth characteristics (color, texture, size).

    • Microscopic details (cell shape, size, motility) are assessed using slides.

    • Staining techniques provide specific information on microscopic morphology.

  • Identification: Using information from initial inspection and additional tests to describe and differentiate microbes.

    • Specialized tests include biochemical tests, immunologic tests, and genetic analysis.

Serial Dilution and Colony Isolation:

*Serial dilution
*Pouring plate
*Isolated colonies

Prokaryotic vs. Eukaryotic Cells:

• Prokaryote (w/o nucleus):

  • Cell wall, Cytoplasmic membrane, Cytoplasm, Nucleoid, Ribosomes

• Eukaryote (w/ nucleus):

  • Cytoplasmic membrane, Endoplasmic reticulum, Ribosomes, Nucleus, Nucleolus, Nuclear membrane, Cytoplasm, Mitochondrion, Chloroplast

Additional Notes:

• (1 type of cell) (diff types of (ex humans)).

• can survive at high methane gas (protist).

• non living organism misfolded proteins