Microorganism Classification

• Chapter 2 discusses the characteristics and classification of microorganisms.
• There are two kinds of cells: prokaryotic and eukaryotic.
• All living things are made of cells, and contain similar macromolecules and cell structures.

Prokaryotes

• Prokaryotes are small and microscopic.
• They are genetically simple.
• Their genetic material is "naked" DNA, not protein-bound chromosomes, and they do not have a nucleus.
• They have no organelles
• The cell walls of prokaryotes are made of peptidoglycan.

Eukaryotes

• Eukaryotes are larger and can be single-celled or multicellular.
• They are genetically complex
• Their genetic material is DNA as a complex with proteins, which form chromosomes.
• The chromosomes of eukaryotes are contained in a nucleus.
• They have membrane-bound organelles.
• Some eukaryotes have cell walls made of cellulose or chitin.

Prokaryotic Cells

• They are characterized by having no nucleus, DNA in a nucleoid region, no membrane-bound organelles, and cytoplasm bound by the plasma membrane.

Eukaryotic Cells

• Eukaryotic cells are characterized by DNA in a nucleus bounded by a membranous nuclear envelope.
• They contain membrane-bound organelles and cytoplasm in the region between the plasma membrane and nucleus.
• Eukaryotic cells are generally much larger than prokaryotic cells.

Taxonomic Hierarchy

• The categories, from broadest to most specific, are: Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.
• A mnemonic device to remember this order is: "Dear King Philip Come Over For Good Soup".
• Example: Penicillium chrysogenum.
• It is in the Kingdom Fungi
• It is in the Division Ascomycota
• It is in the Class Eurotiomycetes
• It is in the Order Eurotiales
• It is in the Family Trichocomaceae
• It is in the Genus Penicillium
• The species is P. chrysogenum
• The binomial name is Penicillium chrysogenum Thom (1910)

Five Kingdoms Classification

• Animalia: multicellular
• Protista: simple eukaryote
• Monera (Prokaryotae): all bacteria
• Plantae: multicellular, photosynthesis
• Fungi: grow by spores or fermentation of hypae

Scientific Names

• All organisms have a scientific name that includes a genus name and a species name.
• The scientific name is always italicized or underlined.
• The genus name is capitalized at the beginning.
• The species name is not capitalized at the beginning.
• Scientific names can be abbreviated/ shortened by using the capital letter of the genus followed by a period, e.g., M. koenigii.

Scientific Names Can

• Describe an organism, such as Staphylococcus aureus.
• staphylo describes the clustered arrangement of the cells.
• coccus indicates that they are sphere-shaped.
• aureus is Latin for golden, the color of many colonies.
• Honour a researcher, e.g., Escherischia coli named after Theodor Escherich.
• Identify the habitat of a species, e.g., coli from E. coli indicates it lives in the colon or large intestines.
• To achieve formal taxonomic standing for a new genus or species, a detailed description of the isolate and proposed name is published.
• A viable culture of the organism is deposited into international culture collections like the ATCC or DSMZ.
• Taxonomy is the science of classifying organisms and provides universal names for organisms.

Prokaryotes

Domain Bacteria & Archaea

• Archaea are prokaryotic cells that may have cell walls lacking peptidoglycan.
• Archaea are often found in extreme environments and are not known to cause disease in humans.
• Archaea are divided into three main groups: Methanogens (produce methane as waste), Extreme halophiles (live in salty environments), and Extreme thermophiles (live in hot water).
• Bacteria are small and common microorganisms, prokaryotic and unicellular without a nucleus.
• Bacteria contains an enormous variety of prokaryotes and morphologies.

Bacteria is Identified By

• Shape
• Chemical nature of their cell walls
• The way they move
• The way they obtain energy
• Cell morphology

Bacterial Shapes

• Coccus
• Bacillus (Rod)
• Spirillum
• Spirochete
• Stalk
• Hypha
• Budding and appendaged
• Filamentous

Bacteria Arrangements

• Coccus
• Diplococcus
• Streptococcus
• Tetrad
• Sarcina
• Staphylococcus

Bacteria Sizes

• Prokaryotic cells are smaller than eukaryotic cells.
• Small size is important because it allows for better nutrient exchange and faster growth, due to a higher surface area relative to cell volume.

Cell wall of bacteria

• Phospholipid layer of cytoplasmic membrane
• A rigid peptidoglycan cell wall
• Gram-positive bacteria have 90% peptidoglycan, teichoic acid embedded within the wall
• Gram-negative bacteria contain an outer membrane called LPS (Lipopolysaccharide)

Gram Staining Technique

• Application of crystal violet (purple dye)
• Application of iodine (mordant)
• Alcohol wash (decolorization)
• Application of Safranine

Cell wall of Gram +ve bacteria

• Thick layer of peptidoglycan, attached to the outer surface of the membrane.
• 60-90% of the cell wall is peptidoglycan and only contain little protein.
• If peptidoglycan is digested, Gram +ve bacteria become protoplasts (cells with a cell membrane but without a cell wall)
• Protoplasts will shrivel or burst unless they're kept in an isotonic solution.
• Lack both an outer membrane & periplasmic space.

Cell wall of Gram -ve bacteria

• Thinner but more complex than Gram +ve bacteria.
• Only 10-20% is peptidoglycan, the remainder consists of various polysaccharides, proteins, & lipids.
• Contains an outer membrane.
• The inner surface of the cell wall is separated from the cell membrane by a wide periplasmic space.
• Toxins & enzymes remain in the periplasmic space to help destroy substance that might harm the bacterium, but they don't harm the organism that produce them.
• If the cell wall is digested away, Gram -ve bacteria become spheroplasts (cells that have both a cell membrane & most of the outer membrane).

Cell wall of bacteria - Lipopolysaccharide (LPS)

• Also called endotoxin.
• Important part of the outer membrane used to identify Gram negative bacteria.
• It An integral part of the cell wall that is not released until the cell walls of dead bacteria break down.
• LPS consists of polysaccharides and lipid A
• Lipid A is often toxic and makes any Gram negative infections a potentially serious medical issue

Relation between Lipid A / endotoxin and antibiotics

• Lipid A causes fever & dilates blood vessels, so the blood pressure drops precipitously.
• Bacteria release endotoxin mainly when dying. Killing them will increase the concentration of this toxic substance.
• Antibiotics given late in an infection may worsen symptoms or cause death.

Cell wall of Acid-Fast Bacteria (the Mycobacteria)

• The cell wall can be thick like Gram +ve bacteria. 60% of it is lipid & contain less peptidoglycan.
• Lipids make acid-fast organisms impermeable to most stains & protect them from acids & alkalis.
• Organisms grow slowly because the lipids impede/block entry of nutrients into cells, & the cells expend/use large quantities of energy to synthesize lipids.
• Acid-fast cells can be stained by the Ziehl-Neelsen Stain
• Can also be stained via the Gram stain method: they stain as gram-positive
• Acid-fast bacteria include Mycobacterium tuberculosis and Mycobacterium leprae.

Endospores

• Many bacteria form spores in unfavorable conditions.
• An endospore forms when a bacterium produces a thick internal wall that encloses its DNA and some of its cytoplasm.
• Spores remain dormant for months or years, allowing bacteria to survive harsh conditions.
• Certain species of bacteria produce structures called endospores during sporulation
• Endospores are extremely resistance to heat, harsh chemicals, and radiation.
• Endospores Function as survival structures and enable the organism to endure unfavorable growth conditions
• Life cycle: vegetative cell – endospore-vegetative cell cycle
• Commonly found in soil, and species of Bacillus are the best-studied representatives.

Bacterial Flagella

• Long, thin appendages free at one end and attached to the cell at the other end
• The filament of a bacterial flagellum is composed of many copies of flagellin protein
• Motility is by rotation, much like a propeller of a boat motor. Gliding allows a cell to exploit new resources and to interact with other cells.

Growth and Reproduction

• Most prokaryotes reproduce by binary fission.
• The process of which an organism replicates its DNA and divides in half, producing two identical daughter cells.
• Some prokaryotes take part in conjugation.
• Other prokaryotes produce spores.

Fungi

• Mycology is the study of fungi.
• They are chemoheterotrophs.
• They decompose organic matter.
• Fungi are either aerobic or facultative anaerobic.
• They obtain nutrients through absorptive heterotrophy.
• Cell walls are made of chitin.
• Fungi also grow better at pH of 5; grow in high sugar and salt concentration, resistant to osmotic pressure; can grow in low moisture content; and can metabolize complex carbohydrates.
• Cells organized in Hyphae (thread of cells/ one cell thick), high surface area to volume ratio that allows them to absorb water, ions, and nutrients. Also participates in gas exchange and waste disposal.
• Some fungi are eukaryotic, while bacteria are prokaryotic.
• The cell membranes of fungi contain sterols, while bacteria lack sterols (except Mycoplasma).
• The cell walls of fungi contain glucans, mannans, and chitin, but lack peptidoglycan.
• Fungi are limited to heterotrophic metabolism, are aerobic or facultatively anaerobic.

Fungal Body

• Mycelium.
• Loosely woven mat of hyphae.
• Feeding structure.

Spore-Producing Fungi

• Used for reproduction.
• Either by mitosis or meiosis.
• Referred to as "fruiting bodies".

Yeasts

• Eukaryotic.
• Classified as members of the fungus kingdom.
• Single-celled budding organisms.
• Often isolated from sugar-rich materials.
• Do not produce mycelia.
• Colonies are visible on agar plate in 24 hours.
• Yeast species such as Saccharomyces cerevisiae converts carbohydrates to carbon dioxide and alcohol by fermentation.

Economic Importance of Fungi

• Saccharomyces cerevisiae (YEAST) produces bread, wine, and hepatitis B vaccine.
• Trichoderma produces cellulase.
• Taxomyces produces taxol.
• Entomophaga is used for biocontrol.
• Coniothyrium minitans kills fungi on crops.
• Paecilomyces kills termites.

Viruses

• Nucleic acid particles, proteins, and sometimes lipids
• Can reproduce only by infecting living cells
• A typical virus is composed of a protein coat and a core of DNA or RNA.
• Viruses are minuscule and must be viewed via an electron microscope

Capsid

• A virus's protein coat; capsid proteins bind to receptors on a cell's surface and "trick" the cell into allowing it inside.
• Viral genes are expressed.
• Viral genes make copies of the virus.
• Then the host cell is destroyed.
• Most viruses must bind to proteins precisely on the cell surface.
• Viruses are highly specific to the cells they infect.

Viral Infection

• Once the virus is inside the host cell, two different processes may occur: lytic infection or lysogenic infection.

Lytic Infection

• A virus enters a cell.
• Copies are made of itself.
• The cell eventually bursts.

Lysogenic Infection

• A virus integrates its DNA into the DNA of the host cell.
• Viral genetic information replicates with the host's.
• Lysogenic viruses do not lyse the host cell right away.
• A lysogenic virus remains inactive.
• One of a number of factors activates the DNA of a prophage to remove itself from the host cell DNA and direct the synthesis of new viruses particles.
• Virus is considered a parasite and it must infect a living thing in order to grow and reproduce, as well as take advantage of the host's functions.

Viral Disease in Humans

• Like bacteria, viruses produce disease.
• Unlike bacterial diseases, viruses can't be treated with antibiotics.
• Prevention through vaccinations is the best defense.
• COVID-19.

Types of Parasites

• Microparasite -> Small, unicellular & multiplies within its vertebrate host, example like protozoa, fungi, bacteria
• Macroparasite -> Large, multicellular and has no direct reproduction within its vertebrate host
• Ectoparasites -> Organisms that live on the surface of the body (ex: mites)
• Endoparasites -> Organisms that live within the body

Protozoa

• Unicellular eukaryotes that inhabit both water and soil.
• Reproduce asexually and sexually.

Test your knowledge of microorganism classification based on reproduction, cellular structure, and cell wall composition. This quiz covers bacteria, yeasts, viruses, and other single-celled organisms. Questions focus on identifying characteristics and classifying organisms into appropriate groups.