Bacteria and archaea

  1. Why do microbiologists classify organisms?

  • Helps organize

  • Helps understand relationships

  • Helps understand evolution

  1. Definition of taxonomy and phylogeny

Taxonomy: The science of classification Eg. Pigeons, finches, bacteria under microscope, etc. Kingdom system

Phylogeny: Interrelatedness of things to one another Eg. Phylogenetic trees, including common ancestors that gave rise to all organisms that are included in a branch.

  1. Thoroughly understand the diversity of the microbial world and know the major, general classes of organisms -      

-Domains based on Ribosomal RNA genes: Archaea, Bacteria, Eukarya

- 5 Kingdom system: Animalia, Plantae, Mycetae, Protista, Monera

- Domain, Kingdom, phylum, class, order, family, genus, species

“Do Kings put class over family”

 Genus species name. Eg. Bacillus anthracis

  1. Classification – Domains – be able to place an organism into each – what is the basis for each classification system (Domain vs Kingdom – what has driven classification in each of these systems? / genotypic vs. phenotypic) – How, specifically, was the Domain system of classification constructed?

Genotypic classification is categorized by RNA. The domain system is built from tracing RNA from the earliest forms of cells. The branches of the domain system split first into bacteria and another common ancestor (not bacteria). Then that common ancestor split into eukarya and archaea. Phenotypic categorization is based on characteristics of organisms. This is included in the kingdom system. For example, while both protozoans and humans fit in the domain eukarya, humans would be part of the animalia kingdom and protozoans would be placed into the kingdom protista. 

Classify bacteria phenotypically based on cell wall: Gram-positive vs. Gram-negative

Colony form, cell shape and arrangement, oxygen requirements, endospore formation, biochemical reactions

  1. Be able to place the organisms listed here into the correct domain

  • The microbe that causes influenza: None

  • Streptococcus sp.: Bacteria

  • Bacillus anthracis: Bacteria

  • The protozoan that causes Malaria: Eukarya 

  • Lice: Eukarya

  • Planaria(flatworm): Eukarya 

  • Cyanobacteria: Bacteria

  • Spirochetes: bacteria

  • Euglena: Eukarya

  • Penicillium mold: Eukarya

  • E. coli: Bacteria

  • The Microbe that causes AIDS: none 

  • Thermophiles: Archaea

  • Ebola: None

  • Methanogens: Archeae

  • Yeast: Eukarya 

  • Psilocybin mushrooms: Eukarya 

  • Tapeworms: Eukarya 

  • Staphylococcus aureus: Bacteria

  • The microbe that causes rabies: None

  • High-salt loving microbes: Archaea

  • Spirillum volutans: Bacteria

  • Vibrio cholerae: Bacteria

  • 6. Be able to interpret a phylogenetic tree

Relatedness can be proximity of two organisms on one branch of the tree, however it can also relate to how far down they are on each branch. 

Example: Aquifex is closer related to Pyrodictium than it is to Spirochetes because they are closer to the base of the tree.

Coccus/Cocci: Spherical/ball shaped

  • Monococci = 1

  • Diplococci = 2

  • Tetrads = 4

  • Staphylococci / Micrococci = Irregular clusters 

  • Streptococci = Chains of cocci

  • Sarcina = Cubical packet of 8, 16, or more cells

Rod/Bacillus: Long narrow straight, can be more rectangular or curved edges.

  • Bacilli = 1

  • Diplobacilli = 2 

  • Streptobacilli = 3+

Curved:

  • vibrio: Gently curved

  • spirillum: long rigid cylindrical curled or spiral

  •  spirochete: flexible resembling a spring

  • Spirilla occasionally found in short chains

  • Spirochetes rarely remain attached after division

  • 8. What defines a species in bacteria?  What is a ‘strain’?

The species bacteria is defined by genetics and phenotypic characteristics such as cell wall differences. Different strains of bacteria are the same species but have different factors that can have different effects. Eg. E-coli B which can exist normally inside the body and E. Coli 057:H7 which causes disease in humans.

  • The Archaea - section 4. 5

  • How related to the Bacteria and the Eukarya? Where, in the environment, do you find them?

Archaea are more related to eukarya based on RNA than bacteria. However, both archaea and bacteria are prokaryotic meaning they share the fact that they lack a true nucleus and double membrane bound organelles that are present in eukaryotic cells. Archaea extremophiles can be found in environments like the bottom of lakes and ocean, in deep sea heat vents, or very salty places like salt lakes. Archaea can also exist in common places such as methanogens in the digestive tracts of humans and animals. Another example is Halophiles because of the red color of the Red Sea. Hyperthermophiles thrive in volcanic waters and soils and submarine vents.

  • What sort of unusual things do they do? Know examples of Archaeal types mentioned in class and on the classification list

    • Methanogens: Convert CO2 + H2 → CH4 (Methane) through unusual and complex pathways. Can be used as a source of fuel or contribute to greenhouse effect in global warming.

    • Hyperthermophiles: Live in volcanic waters, soils, and submarine vents. (Often salt and acid tolerant also). Can live in waste piles of coal mines with a pH 1 and temp nearly 60 degrees celsius. 

    • Extreme Halophiles: Require salt to grow, some have such high salt tolerance that they can multiply in 36% NaCl solutions that would destroy most cells. Many use a red pigment to synthesize ATP in the presence of light. These pigments are responsible for the color of the Red Sea and Red color of salt ponds.

Additional Notes

  • Planktonic: Single-cell form (rare)

  • Biofilms: Where microbes live in cooperative association that can include other organisms of the same species. Microbial habitats with access to food,water, atmosphere, and other environmental factors that are beneficial. (common)

  • Peptidoglycan (Unique to bacterial cells)

    • Structure: Compound composed of a repeating framework of long glycan (sugar) chains cross-linked by short peptide (protein fragments) and enzymes. CROSS-LINKS give peptidoglycan STRENGTH

    • Function: Provide a strong but flexible support framework. Prevent rupture from internal pressure

    • Found: Mostly contained in bacterial cells walls

      • Gram-negative: 1-3nm thin layer between outer cell membrane layer and cytoplasmic membrane

      • Gram-positive: 20-80 nm thick layer on top of cytoplasmic membrane (no outer cell membrane present)

  • Lipopolysaccharide

    • Structure: Lipid A, Core, and O-antigens. A molecular complex of lipid and carbohydrate. Polysaccharide chains extending off the cell surface. Contain porins and proteins.

    • Function: Function as cell markers and receptors. Allows only relatively small molecules to penetrate. Porin size adjusted by the cell to block the entrance of harmful chemicals. LPS of gram-negative bacteria is an endotoxin with generalized pathologic effects such as fever. 

    • Found: In the bacterial cell wall of gram-negative bacteria (Contrast, gram-positive bacteria produce exotoxins.)

    • Eg. Meningitis, typhoid fever

  • Periplasmic Space

    • Structure: Contains peptidoglycan layer and proteins like binding proteins. Gel-like matrix in the space between the inner cytoplasmic membrane and outer membrane.

    • Function: Helps protect cells from harmful chemicals, detoxify and degenerate compounds from the cell.

    • Found: In gram-negative bacteria, below the outer and above the inner membrane (including thin peptidoglycan layer.

  • Teichoic Acids

    • Structure: Tightly bound acidic polysaccharide. Anionic polymer of ribitol or glycerol (alcohols) and phosphate.

    • Function: Cell wall maintenance and enlargement during cell division, also contribute to acidic charge on the cell surface.

    • Found: Appear in the walls of gram-positive bacteria. Embedded in peptidoglycan sheath. 

  • Phospholipid Bi-layer (cell membrane)

    • Structure: 5-10 nm thick flexible sheet. Contains 2 fatty acids attached to glycerol, and the third glycerol binding site holds a phosphate group. Phosphate is bonded to alcohol which varies from one phospholipid to another. Lipids have a hydrophilic region from the charge on the phosphoric acid-alcohol “head” of the molecule (facing outward and towards cytoplasm), and a hydrophobic region that corresponds to the long, uncharges “tail of the molecule” (facing towards the center of the phospholipid bilayer. Has proteins embedded.

    • Function: Provides sites for functions such as energy reactions, nutrient processing, and synthesis. Uses embedded proteins and enzymes to perform these functions. Regulate transport, the passage of nutrients into the cell and discharge of wastes out of the cell. Selectively permeable.

    • Found: Beneath the cell wall (if present) and in direct contact wrapped directly around the cytoplasm.  Found in both gram-negative and gram-positive bacteria.

  • Types of stains and their functions

Chapter 4.1-4.3 Bacteria and archaea

Learning Objectives

Be able to provide similarities between Prok and Euk microbes (other than they are both living cells). 

Both prokaryotes and Eukaryotes contain cytoplasm, a cell membrane, ribosomes, and genetic material in some form.

PROKARYOTIC external cell structures – know the structure and function of each item below  – (**contrast these structures w/ what we see in eukaryotic)

  • Cell Envelope (Contains both cell membrane and cell wall)

  • Cell membrane –   Provides sites for functions such as energy reactions, nutrient processing, and synthesis. Uses embedded proteins and enzymes to perform these functions. Regulate transport, the passage of nutrients into the cell and discharge of wastes out of the cell. Selectively permeable. Energy production (ATP production) across membrane

  • Cell Wall 

    • Protection, shape, withstand internal pressure

    • Peptidoglycan structure:  Compound composed of a repeating framework of long glycan (sugar) chains cross-linked by short peptide (protein fragments) and enzymes

    • Difference between gram + and gram – cell wall (be able to describe the cell wall structure in detail): Gram+ bacteria lack Lipopolysaccharide layer present in Gram- bacteria. Also, Gram- bacteria lack Teichoic acids present in Gram+ bacteria.

    • What are teichoic acids? (See Chapter 4 additional notes)

    • What is Lipopolysaccharide?  What is the periplasmic space? (See chapter 4 additional notes)

  • Understand principles behind how the Gram stain works and why it works the way it does (make sure to read the 'insight' box that talks about this- important for lab also!)

(See Chapter 4 additional notes)

  • Fimbriae, Pili (pilus), Capsule and S-layer – structure and function –Also be able to talk about what advantage this structure would give to the bacterial cell that has it. 

    • Fimbriae: Fine, hairlike bristles extending from the cell surface that help in adhesion to other cells and surfaces.

    • Pili: Long, rigid, tubular structure made of protein pilin. Function is to connect two different cells in a process called conjugation, which involves partial transfer of DNA from one cell to another. A pilus from the donor cell unites with a recipient cell, bringing it close enough for DNA transfer. Conjugation takes place only between compatible gram-negative cells. 

    • Capsule: Outermost coating of bacterial cell, layer of molecules external to the cell wall. Serves protective, adhesive, and receptor functions. It may fit tightly or be very loose and diffuse. Also, called slime layer and glycocalyx. Cloak of invisibility.

    • S-layer: Single layer of protein used for protection and/or attachment.

  • Bacterial Flagella (see below)- 

    • Primary function to provide mobility, or self-propulsion. 

    • This structure allows the filament to rotate 360 degrees!

    • Generally all spirilla, half of rods, and a small number of cocci have flagella. 

    • Flagella vary in number and arrangement according to two arrangements

      • Polar arrangement, with flagella attached at one or both ends of the cell. Eg. Monotrichous, lophotrichous, and amphitrichous

      • Peritrichous arrangement, flagella are disperse randomly over the surface of the cell

      • Identification of motility is important in the identification/diagnosis of a pathogen. 

      • Chemotaxis: Flagellated bacteria can detect and move in response to chemical signals

        • Positive chemotaxis- movement towards a favorable chemical (nutrient)

        • Negative chemotaxis- movement away from a repellent (potentially harmful)

        • Move via a series of runs (smooth linear direction towards the stimulus) and tumbles (flagellum reverse direction and cause the cell to stop and change direction.)

  • Less peptidoglycan, alcohol dissolves lipoproteins and outer membrane during decolorization.