Microbial Diversity and Prokaryotes

Microbial Diversity

• Microbiologists study a wide array of organisms and biological entities, including animals, plants, and acellular entities.
• Animals and plants are both cellular, while acellular entities are not.
• Fungi, protists, bacteria, and archaea are examples of cellular organisms.
• Viruses, viroids, and virusoids are examples of acellular entities.
• Prions are also acellular entities.
• Fungi include yeasts and molds, and some other entities.
• Protists include algae, protozoa, and slime molds ( among others).
• Bacteria and archaea are prokaryotes, while fungi, protists, and plants are eukaryotes.
• Prokaryotes are unicellular and lack internal membrane systems.
• Eukaryotes are either unicellular or multicellular but contain internal membrane systems

Prokaryotes (Unicellular)

• Prokaryotes are divided into two taxa: Bacteria and Archaea.
• Key differences in size and simplicity compared to eukaryotes.
• Most prokaryotes lack internal membrane systems.

Bacterial Morphology

• Cocci (spheres) and rods are common shapes.
• Other shapes include coccobacilli (very short rods), vibrios (comma-shaped), spirilla (rigid helices), and spirochetes (flexible helices).
• Arrangement varies according to the plane of bacterial division, and whether they separate or not.
• Size can vary considerably.
• Mycelium is a network of long, multinucleate filaments.
• Many prokaryotes are pleomorphic (meaning they are variable in shape).
• Archaea are also pleomorphic, exhibiting branched, flat, square, or other unique shapes.

Prokaryotic Cell Structure

• Glycocalyx: A covering external to the cell wall with protective, adhesive, and receptor functions.
• Bacterial chromosome (nucleoid): Concentrated DNA packet directing genetics and heredity.
• Pilus: Elongate, hollow appendages used in DNA transfer to other cells and adhesion.
• Pilus & Fimbriae assist in attachment to surfaces.
• Inclusion/Granules: Stored nutrients (fat, phosphate, or glycogen) deposited for later use.
• Cell wall: A semirigid protective layer offering structural support and shaping.
• Mesosome: Infolding of the cell membrane increasing surface area.
• Flagellum: Specialized appendage with a basal body and rotating filament providing motility.
• Cell membrane: Lipid and protein sheet surrounding the cytoplasm to control material flow.
• Ribosomes: Protein-RNA particles acting as sites of protein synthesis.

Differences Between Archaea and Bacteria

• Archaea and bacteria both lack internal membrane systems, but archaea have a more unique makeup and organization than that of bacteria.

Bacterial and Archaeal Structure and Function (prokaryotes)

• Detailed information on the structure and function of bacteria and archaea.
• Archaea are quite different from bacteria in their lipid makeup (particularly ether bonds instead of ester bonds and isoprene units instead of fatty acids)
• Archaea also don't have peptidoglycan in their cell walls instead of pseudomurein which is similar in structure.

Shape and Arrangement

• Cocci, bacilli, coccobacilli, vibrios, and spirilla are the major shapes of bacterial cells.
• Variation in morphology (shape and arrangement) amongst all bacterial cells.
• Specific arrangement terms such as diplococci, streptococci, and staphylococci are used to categorize the shapes of bacteria.

Size

• Mycoplasma is the smallest bacterium (0.3 µm).
• E. coli is an average sized rod (1.1-1.5 x 2-6 µm).
• Others are much larger such as Epulopiscium fishelsoni (600 x 80 µm).

Comparison of Sizes of Biological Entities

• Size comparisons for various entities.
• Oscillatoria and red blood cells are much larger than e.g bacteria and even viruses.

Size-Shape Relationship

• Size and shape are key to nutrient uptake.
• Small cells have high surface-to-volume ratios maximizing nutrient uptake.
• Small size may be a protective mechanism as some bacterias are small for predator avoidance.

Bacterial Cell Envelope

• A three-layered structure (plasma membrane, cell wall, and layers outside the cell wall)
• The components of the bacterial envelope (plasma membrane and cell wall)

Bacterial Plasma Membrane

• Absolute requirement for all living organisms.
• Some bacteria also have internal membrane systems.

Plasma Membrane Functions

• Encompasses cytoplasm, acts as selectively permeable barrier.
• Interacts with external environment through receptors for detection and response to chemicals (transport systems) and metabolic processes.

Fluid Mosaic Model of Membrane Structure

• Lipid bilayers with floating proteins
• Amphipathic lipids (polar ends and non-polar tails).
• Membrane proteins embedded in the lipid bilayer.

Membrane Proteins

• Peripheral proteins loosely connected to the membrane; easily removed.
• Integral proteins amphipathic; embedded within the membrane. They carry out important functions; may exist as microdomains.

Bacterial Lipids

• Saturation levels reflect environmental conditions (like temperature).
• Bacterial membranes lack sterols but have hopanoids (sterol-like molecules) which stabilize the membrane.
• Hopanoids are found in petroleum.

Bacterial Cell Wall

• Peptidoglycan (murein) forms a rigid structure just outside of the cell membrane.
• Two types based on Gram stain reaction: – Gram-positive: Stain purple; Thick peptidoglycan layer – Gram-negative: Stain pink/red; Thin peptidoglycan layer and outer membrane.

Cell Wall Functions

• Maintain bacterial shape and rigidity.
• Helps protect against osmotic lysis.
• Helps protect against toxic materials.
• May contribute to pathogenicity.

Peptidoglycan Structure

• Mesh-like polymer of identical subunits forming long strands.
• Two alternating sugars: N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).
• Alternating D- and L- amino acids form peptide cross-bridges.

Gram-Positive Cell Walls

• Primarily composed of peptidoglycan.
• May also contain large amounts of negatively charged teichoic acids.
• Helps maintain envelope stability and protect from environmental substances.

Periplasmic Space of Gram + Bacteria

• Lies between the plasma membrane and the cell wall.
• Smaller than that of gram-negative bacteria.
• Contains relatively few proteins.
• Secretion of exoenzymes aids in the degradation of large nutrients.

Gram-Negative Cell Walls

• More complex than Gram-positive walls.
• Consist of a thin peptidoglycan layer surrounded by an outer membrane.
• The outer membrane contains lipids, lipoproteins, and lipopolysaccharide (LPS).
• Lack teichoic acids.

Gram-Negative Outer Membrane Permeability

• More permeable than the plasma membrane due to the presence of numerous porins.

Lipopolysaccharides (LPS)

• Consists of three parts: Lipid A, core polysaccharide, and O side chain.
• Lipid A is embedded in the outer membrane.
• Core polysaccharide and O side chain extend out from the cell.

Importance of LPS

• Contributes to negative charge on cell surface.
• Helps stabilize the outer membrane structure.
• May contribute to attachment to surfaces and biofilm formation.
• Creates a permeability barrier.
• Offers protection against host defenses (O antigen).
• Can act as an endotoxin (lipid A).

Components Outside the Cell Wall

• Glycocalyx (capsules and slime layers): Outermost layer in cell envelope that aids in attachment to surfaces and protection.

Capsules

• Usually composed of polysaccharides.
• Well-organized and not easily removed from the cell.
• Visible under a light microscope.
• Protective advantages, such as resistance to phagocytosis, protection from desiccation, exclusion of viruses and detergents.

Slime Layers

• Similar to capsules but are diffuse, unorganized, and easily removed.
• May aid in motility.

S layers

• Regularly structured layers of proteins that self-assemble, adhering to the outer membrane in gram-negative bacteria or associating with the peptidoglycan surface in gram-positive bacteria.

S Layer Functions

• Protects bacteria from environmental factors (ion fluctuations, pH variations, osmotic stress, enzymes), predation.
• Maintains bacterial shape and rigidity.
• Promotes adhesion to surfaces and protects from host defenses. Potential use in nanotechnology.

Archaeal Cell Envelopes

• Differ from bacterial envelopes in molecular makeup and organization.
• May consist only of an S layer outside the plasma membrane.
• Some lack cell walls, and capsules and slime layers are rare.

Archaeal Membranes

• Composed of unique lipids.
• Contain isoprene units, ether linkages rather than ester linkages to glycerol.
• Some have a monolayer structure instead of a bilayer.

Archaeal Cell Walls

• Lack peptidoglycan.
• The most frequent cell wall is an S layer.
• May sometimes have a protein sheath external to the S layer.
• May have pseudomurein as the outermost layer (similar to gram-positive microorganisms).

Bacterial and Archaeal Cytoplasmic Structures

• Cytoskeleton
• Intracytoplasmic membranes
• Inclusions
• Ribosomes
• Nucleoid and plasmids

Protoplast and Cytoplasm

• Protoplast: the plasma membrane and all of the internal contents.
• Cytoplasm: The contents bounded by the plasma membrane in the protoplast

Cytoskeleton

• Homologs of all three eukaryotic cytoskeletal elements have been identified in bacteria and archaea.
• Functions in cell division, protein localization, and cell shape determination.

Ribosomes

• Large complex structures (ribosome = 70S; made of protein and RNA).
• Involved in protein biosynthesis.

Nucleoid

• Irregularly shaped region of the cytoplasm that holds DNA.
• Usually not membrane-bound, but DNA is coiled and interacts with associated proteins.
• Usually contains a closed circular, double-stranded DNA molecule.
• Supercoiling (aided by nucleoid proteins) aids in the folding of the genome.

Plasmids

• Extrachromosomal DNA molecules (found in bacteria, archaea, and some fungi).
• Exist and replicate independently of the chromosome.
• May integrate into the chromosome (episomes).
• Contain few genes that are not essential, but can provide selective advantages to the host (example; drug resistance).
• Can exist in numerous copies in the cell.
• Stable transmission during cell division.

External Structures

• Extend beyond cell envelope in bacteria and archaea.
• Functions include protection, attachment, horizontal gene transfer, and cell movement.
• Pili and fimbriae.
• Flagella.

Pili and Fimbriae

• Fimbriae (short, thin appendages) and pili (longer, thicker appendages) aid in attachment and/or DNA uptake.
• Sex pili used for conjugation.

Flagella

• Threadlike appendages that extend outward from the plasma and cell wall for motility and swarming behavior.
• May provide attachment to surfaces; can be virulence factors.

Bacterial Flagella (Ultrastructure)

• Filament: hollow, rigid cylinder composed of the protein flagellin.
• Hook: Connects the filament to the basal body.
• Basal body: Series of rings that drive the flagellar motor.

Flagellar Synthesis

• A complex process involving many genes and gene products.
• New flagellin molecules are transported to the tip of the filament through a hollow, Type III-like secretion system.
• Filament subunits self-assemble at the tip of the filament.

Flagella Patterns

• Monotrichous: Single flagellum at the end
• Polar flagellum: Flagellum at one end
• Amphitrichous: Flagella at both cell ends
• Lophotrichous: Cluster of flagella at one or both ends
• Peritrichous: Flagella spread over entire cell surface

Spirochete Motility

• Multiple flagella form a tightly wound axial fibril within the periplasm inside an outer sheath for twisting/corkscrew-like movements.

Twitching and Gliding Motility

• Twitching motility: Involves Type IV pili at the ends of cells generating short, intermittent, jerky movements that occur when cells are in an contact on a surface.
• Gliding motility: Smooth movements aided by slime.

Myxococcus xanthus (Social Motility)

• Type IV pili from many cells work together in a large group.
• Slime released moves cells in a coordinated fashion.
• Adhesion complexes may move along paths created by the cytoskeleton.

Chemotaxis

• Movement toward a chemical attractant, or away from a repellent.
• Responses are regulated by changes in the concentration of chemicals.
• Chemoreceptors in the chemosensing system bind to attractants/repellents.

Endospores

• Complex, dormant structures formed by some bacteria when conditions are unfavorable.
• Resistant to various environmental conditions including heat, radiation, and chemicals.

Endospore Structure

• Spore surrounded by a covering, the exosporium.
• Thick layers of protein form the spore coat, beneath is a thick peptidoglycan cortex.
• Core contains nucleoid and ribosomes.

What Makes an Endospore So Resistant?

• Calcium ions complexed with dipicolinic acid.
• Small, acid-soluble, DNA-binding proteins (SASPs) that protect DNA from damage.
• Dehydrated core.
• Spore coat and exosporium offer protection

Sporulation (Endospore Formation)

• Complex, multistage process that occurs in about 8 to 10 hours.
• Usually begins when growth ceases due to lack of nutrients.

Germination (transformation of endospore into vegetative cell)

• Transformation of the endospore into a vegetative cell, a multi-stage process.
• Triggered by environmental stimuli like specific nutrients.
• Activation stage in which spores are prepared for germination (often triggered by heating)
• Germination stage in which spore swelling and absorption lead to loss of resistance and increased metabolic activity.
• Outgrowth: emergence of a vegetative cell.

Explore the fascinating world of microbial diversity, focusing on both cellular and acellular entities. Understand the differences between prokaryotes and eukaryotes, including the characteristics of bacteria, archaea, and various forms of fungi and protists.