Prokaryotes: Bacteria and Archaea

• Summarized notes on prokaryotes, including Bacteria and Archaea

Classification of Prokaryotes

• Prokaryotes are classified into domains and phyla, which are further divided into classes.
• Table 11-1 classifies selected prokaryotes by domain, phylum, selected classes, and provides notes.

Bacteria (Gram-Negative)

• The Pseudomonadota phylum encompasses the largest taxonomic group of bacteria and are Gram-negative.
• Includes 5 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria
• They exhibit diverse metabolic lifestyles, including phototrophy, autotrophy, chemotrophy, and heterotrophy.
• Can be anaerobes, facultative anaerobes, and obligate aerobes.
• Selected gram-negative bacteria:
  • Ehrlichia and Rickettsia belong to Alphaproteobacteria.
  • Bordetella and Burkholderia belong to Betaproteobacteria.
  • Vibrio, Salmonella, Helicobacter, and Escherichia belong to Gammaproteobacteria.
  • Deltaproteobacteria includes Bdellovibrio.
  • The Campylobacter and Helicobacter are from Epsilonproteobacteria.
• Cyanobacteria employ oxygenic photosynthesis.
• Chlorobiota includes photosynthetic bacteria that are anoxygenic and produce green sulfur.
• Filamentous green nonsulfur bacteria are found in Chloroflexota and utilize anoxygenic photosynthesis.
• Chlamydiota require a eukaryotic host to grow.
• Planctomycetota are aquatic, with some stalked species.
• Bacteroidota encompasses opportunistic pathogens.
• Fusobacteriota are anaerobic bacteria responsible for tissue necrosis.
• Spirochaetota contains pathogens that cause syphilis and Lyme disease.

Alphaproteobacteria

• These bacteria can grow in low-nutrient conditions.
• Prosthecae may be used for surface adhesion.
• Capable of nitrogen fixation and establishing symbiotic relationships with plants.
• Includes plant and human pathogens.
• Includes:
  • Caulobacter and Hyphomicrobium are found in low-nutrient aquatic environments
  • Pelagibacter are abundant marine microorganisms and play a role in Earth's carbon cycle
  • Azospirillum grows in soil and associates with plant roots and fixes nitrogen
  • Acetobacteraceae (Acetobacter and Gluconobacter) converts ethanol into acetic acid
  • Rhizobium and Bradyrhizobium fix nitrogen in the roots of leguminous plants
  • Agrobacterium are plant pathogens, that cause crown gall
  • Nitrobacter and Nitrosomonas are chemoautotrophic, derive energy from inorganic chemicals
  • Rickettsia are obligate intracellular parasites transmitted by insects and ticks
    • _R. prowazekii: epidemic typhus
    • _R. typhi: endemic murine typhus
    • _R. rickettsii: Rocky Mountain spotted fever
  • Ehrlichia is transmitted by ticks and causes ehrlichiosis.
  • Brucella are obligate parasites of mammals, survive phagocytosis and cause brucellosis
  • Bartonella are human pathogens; B. henselae causes cat-scratch disease
  • Wolbachia can eliminate viruses of dengue, Zika and chikungunya in mosquitoes

Betaproteobacteria

• The group includes: Spirillum, Sphaerotilus, Burkholderia, Bordetella, Neisseria, Zoogloea:
  • Spirillum are found in freshwater and move via polar flagella.
  • Sphaerotilus are found in freshwater and sewage and form sheaths for protection and nutrient gathering.
  • The Burkholderia includes:
    • B. cepacia: degrades more than 100 organic molecules.
    • B. pseudomallei: causes meliodosis.
  • Bordetella:
    • Nonmotile rods.
    • B. pertussis: causes whooping cough.
  • Neisseria:
    • N. gonorrhoeae: cause of gonorrhea.
    • N. meningitidis: cause of meningococcal meningitis.
  • Zoogloea: are important in activated sludge systems.

Gammaproteobacteria

• This group includes organisms such as Escherichia, Salmonella, Shigella, Klebsiella, Serratia:
  • Acidithiobacillus oxidizes hydrogen sulfide or sulfur into sulfate.
  • Beggiatoa grows in aquatic sediments and oxidizes hydrogen sulfide.
  • F. tularensis causes tularemia (Rabbit Fever).
• Pseudomonas:
  • Common in soil.
  • Metabolically diverse with polar flagella
  • Cause wound and urinary tract infections
  • Acinetobacter includes A. baumanii which is a respiratory pathogen.
• Legionella:
  • Found in streams and warm water pipes and cause legionellosis.
• Coxiella:
  • C. burnetii causes Q fever and is transmitted via aerosols.
• Vibrio:
  • V. cholerae causes cholera.
  • V. parahaemolyticus causes gastroenteritis.
• The “Enterics” (Enterobacteriales):
  • Commonly inhabits the intestinal tract and ferment carbohydrates.
  • They are facultative anaerobes that produces bacteriocins.
  • Peritrichous flagella provides motility.
    • Escherichia (E. coli) can indicate fecal contamination.
    • Salmonella includes S. typhi, a serovar that causes typhoid fever.
    • Shigella causes bacillary dysentery and shigellosis.
    • Klebsiella ( K. pneumoniae) causes pneumonia.
    • Serratia produces a red pigment and is a common cause of nosocomial infections.
    • Yersinia includes zoonotic disease causing species like Y.enterolitica and bubonic plague causing species like Y. pestis.
    • Erwinia are plant pathogens.
    • Proteus exhibits swarming motility and primarily causes UTIs.
    • Enterobacter includes E. cloacae and E. aerogenes cause urinary tract infections.
    • Cronobacter (C. sakazakii), can cause sepsis, necrotizing enterocolitis and meningitis in infants.
• Pasteurella are pathogens of domestic animals; can be transmitted through animal bites.
  • Haemophilus (H. influenzae) can cause meningitis and ear infections.

Deltaproteobacteria

• Bdellovibrio attacks other gram-negative bacteria.
• Desulfovibrionales uses sulfur or sulfate; Desulfovibrio is found in anaerobic environments.

Epsilonproteobacteria

• Gram-negative rods that are helical or curved and microaerophilic.
• Campylobacter:
  • Microaerophilic vibrios with one polar flagellum.
  • C. jejuni causes foodborne intestinal disease.
  • C. fetus causes spontaneous abortions in domestic animals.
• Helicobacter:
  • Microaerophilic curved rods with multiple flagella.

Nonproteobacteria - Gram-Negative Bacteria

• The group includes: Chlamydia, Spirochetes, CFB group
• Chlamydiae:
  • Small, non-motile obligate intracellular parasites.
    • Form an elementary body that is infective
    • Chlamydia trachomatis causes trachoma and urethritis.
    • Chlamydophila psittaci causes respiratory psittacosis.
• Planctomycetes:
  • Gram-negative budding bacteria.
  • Cell walls resemble those of archaea.
    • Gemmata obscuriglobus has a membrane around DNA, resembling a eukaryotic nucleus.
• CFB (Cytophaga, Fusobacteria and Bacteroides):
  • Anaerobic.
  • Fermenters
    • Cytophaga are soil organisms that can break down cellulose.
    • Fusobacterium are normal flora of the mouth but are opportunistic.
    • Bacteroides is the largest group and can be opportunistic.

Spirochaetes

• Coiled and move via axial filaments ( rotating corkscrew type of motility).
  • Treponema (T. pallidum) causes syphilis.
  • Borrelia ( B. burgdorferi) causes relapsing fever and Lyme disease.
  • Leptospira is excreted in animal urine.

Phototrophic Bacteria

• Includes both Proteobacteria and Nonproteobacteria.
• Can be oxygenic and anoxygenic phototroph.
• Includes: The purple sulfur, the green sulfur, purple nonsulfur, and the green nonsulfur bacteria.
  • Cyanobacteria (Oxygenic Photosynthetic Bacteria):
    • carry out oxygenic photosynthesis and produce oxygen.
    • gas vesicles that provide buoyancy

Non Proteobacteria - Gram-Positive Bacteria

• Divided into groups with high or low G+C ratios:
  • High G + C ratios (formerly known as Actinomycetes):
    • Many resemble fungi or molds
    • Actinomycetota (High G + C Gram-Positive Bacteria):
      • Common source of antibiotics with branching filaments.
        • Mycobacterium have mycolic acid within the cell wall.
          • M. tuberculosis causes tuberculosis; M. leprae causes leprosy.
        • Nocardia ( N. asteroides) causes pulmonary infections.
        • Gardnerella (G. vaginalis) causes vaginitis.
        • Streptomyces produces antibiotics.
    • Deinococcota
      • Thermus aquaticus, Source of Taq polymerase (used in the polymerase chain reaction).
  • Low G + C ratios (formerly known as firmicutes):
    • Bacillota
    • Mycoplasmatota (Have less than 50% G and C)
      • Many are spore forming, pathogens and are aerobes, facultative anaerobes, strict anaerobes.
        • Clostridiales:
          • Clostridium are endospore-producing and obligate anaerobes.
          • Bacillales:
            • Bacillus are endospore-producing rods.
            • Staphylococcus (S. aureus) causes wound infections
            • Listeria: (L. monocytogenes) contaminates food.
          • Lactobacillales:
            • Lactobacillus colonizes the body.
            • Streptococcus: S. pneumoniae causes pneumonia; S. mutans causes dental caries
            • Mycoplasma ( M. pneumoniae) causes pneumonia and M. hominis causes urogenital infections

Archaea

• Have distinct taxonomic grouping by nutritional needs. -The extremophiles proliferate under extreme environmental conditions.
  • Halophiles: require salt concentration >25%
• Thermophiles: require growth temperature > 80°C
• Acidophiles: can grow in pH values approaching 0.
• Methanogens:
  • Anaerobic.
  • Produce methane and are part of the human microbiota.