Microbiology

• Microorganisms

  Organisms that are only visible using a microscope
• Types of microorganisms

  • Cellular (living) microbes: bacteria, archaea, protists, fungi
  • Acellular (non-living) microbes: viruses, viroids, satellites, prions
• Cellular microbes

  • Size range, genome structures, cell shapes and structures, metabolism, replication strategies
• Viruses

  Considered non-living, provide an overview of the general virus replication cycle
• Niche

  Set of environmental conditions in which a species of microbe can replicate
• Factors that determine a microbe's niche

  • Nutrient availability
  • Oxygen concentration
  • Temperature
  • pH
  • Light intensity
  • Radiation
  • Solute concentration (osmolarity) & water activity
• Microbe lifestyles

  • Free-living
  • Symbiotic: Pathogenic, Mutualistic, Commensal
• Bacteria

  • Single-celled prokaryotes, asexual reproduction by binary fission, lifestyles: free-living, commensals, mutualists, pathogens, 1 circular chromosome (dsDNA), no nucleus, may have plasmids, cell morphologies: spherical (cocci), rods (bacilli), spirals, peptidoglycan in cell wall, gram stain identifies 2 main groups
• Gram positive bacterium

  • Peptidoglycan layer traps crystal violet-iodine stain, appears purple
• Gram negative bacterium

  • Crystal violet-iodine stain rinsed away, cells stained red/pink with safranin
• Bacterial cell structures

  • Cell wall, capsule, fimbriae, flagellum
• Biofilm formation

  Attachment, multiplication, microcolony formation, maturation, detachment & dissemination
• Sex pilus

  Thread-like appendage bacteria use to exchange plasmids
• Photorhabdus luminescens

  • Bacterium that forms mutualistic relationship with nematodes, infect insect larvae causing lethal septicaemia, dead larvae glow in the dark
• Archaea

  • Single-celled prokaryotes, asexual reproduction, lack peptidoglycan in cell wall, unique cell membrane lipids, 1 circular chromosome, no nucleus, may have plasmids, forms: spherical, rods, spirals, rectangles/squares, lemon-shaped, lifestyles: free-living (many are extremophiles), commensals, mutualists
• Methanosarcina

  • Commensal of ruminants that produces methane gas
• Haloquadratum walsbyi

  • Ultra thin square-shaped cells
• Halococcus salifodinae

  • Lives in water with high concentrations of salt
• Methanococcoides

  • Survives at -2.5°C
• Pyrococcus furiosus

  • Species of archaea that lives in deep sea hydrothermal vents, swims at 90°C using "archaella" at 110 μm/s
• Fungi

  • Single-celled & multicellular eukaryotes, asexual & sexual reproduction, chitin in cell wall, multiple linear chromosomes within nucleus, forms: yeasts, moulds (or both), lifestyles: decomposers, mutualists, pathogens
• Rhizopus nigricans

  • Mould growing on stale bread
• Candida albicans

  • Yeast pathogen
• Saccharomyces cerevisiae

  • Yeast used in fermentation (brewing/baking)
• Penicillium

  • Mould commonly encountered as a decomposer of food
• Protists

  • Single-celled & multicellular eukaryotes, slime molds, algae, amoebae, asexual or sexual reproduction, multiple linear chromosomes within nucleus, most unicellular, some multicellular, lifestyles: free-living, pathogenic, mutualistic
• Protist groups

  • Diplomonads
  • Parabasalids
  • Euglenozoans
  • Excavata
  • Diatoms
  • Golden algae
  • Brown algae
  • Dinoflagellates
  • Apicomplexans
  • Ciliates
  • Forams
  • Cercozoans
  • Radiolarians
• Classification of cellular microbes is distinct from that of acellular microbes
• Acellular microorganisms

  Viruses, viroids, satellites, prions
• Viruses

  Composed of protein and nucleic acid, lack metabolism and replicate only in host cells
• Viroids

  Non-translated ssRNAs, lack protein (infect plants)
• Satellites

  Subviral infectious agents composed of nucleic acid and sometimes protein
• Prions

  Infectious proteins
• Cellular microorganisms

  • Slime molds
  • Algae
  • Amoebae
• Reproduction

  Asexual or sexual
• Cellular microorganisms

  • Multiple linear chromosomes within the nucleus
  • Most unicellular, some multicellular
  • Free-living, Pathogenic, Mutualistic
• Acellular microbes

  • Viruses
  • Viroids
  • Satellites
  • Prions
• Satellites

  Subviral infectious agents composed of nucleic acid and protein that require a helper virus to replicate
• Prions

  Infectious proteins, cause spongiform encephalopathies (mad cow disease, scrapie, CJD)
• Viruses

  • Particles (virions): genome (DNA or RNA) in a protein coat
  • May have an envelope
  • Multiply only in living cells and often cause disease
  • Are not living - no metabolism
  • Do not grow - they are assembled from constituent parts
  • Virus-specified proteins are synthesized using host ribosomes