Prokaryotes Classification: Bacteria

Classification of Selected Prokaryotes

• Table 11-1 summarizes the classification of selected prokaryotes, divided into Domains: Bacteria and Archaea.

Domain Bacteria - Gram Negative

• This group includes bacteria with an outer membrane, staining pink/red with Gram stain.
• Features Pseudomonadota phyla, formerly known as Proteobacteria, which is the largest taxonomic group of bacteria.
• Alphaproteobacteria class includes Ehrlichia and Rickettsia.
• Betaproteobacteria class includes Bordetella and Burkholderia.
• Gammaproteobacteria class includes Vibrio, Salmonella, Helicobacter, and Escherichia, Pseudomonas.
• Deltaproteobacteria class includes Bdellovibrio.
• Epsilonproteobacteria class includes Campylobacter and Helicobacter.
• Cyanobacteria are oxygenic photosynthetic bacteria.
• Chlorobia are photosynthetic utilizing anoxygenic processes; green sulfur bacteria.
• Chlorobiota including Chloroflexi: Anoxygenic, photosynthetic, filamentous green nonsulfur bacteria
• Include Chlamydiae which grow only in eukaryotic host cells.
• Planctomycetota include Planctomycetia which aquatic bacteria, some are stalked.
• Bacteroidota include Bacteroidetes and are aquatic bacteria; some are stalked
• Fusobacteriota include Fusobacteria which are anaerobic and cause tissue necrosis and septicemia in humans.
• Spirochaetota include Spirochaetia which are pathogens that cause syphilis and Lyme disease.

Domain Bacteria - Gram Positive

• This group includes bacteria with thick peptidoglycan layer, retaining crystal violet stain in Gram stain.
• Bacillota (Firmicutes) that include Bacilli which are low G + C gram-positive rods and cocci
• Bacillota (Firmicutes) also include Clostridia that are low G + C wall-less bacteria
• Mycoplasmatota include Mollicutes which are anaerobic with some causing tissue necrosis and septicemia in humans
• Actinomycetota include Actinobacteria
• Deinococcota include Deinococci which radiation- and heat-resistant

Domain Archaea

• This domain includes prokaryotes that often live in extreme environments.
• Thermoproteota include Thermoprotei are thermophiles and hyperthermophiles.
• Euryarchaeota include Methanobacteria, important sources of methane.
• Euryarchaeota also include Halobacteria which require high salt concentrations.

Pseudomonadota

• These are Gram-negative and the largest taxonomic group of bacteria.
• It encompasses five classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria.
• Metabolic diversity includes phototrophs, autotrophs, chemotrophs, and heterotrophs.
• They can be anaerobes, facultative anaerobes, and obligate aerobes.

Alphaproteobacteria

• Many can grow in environments with very low nutrient levels.
• Some possess structures called prosthecae, which are stalks or buds used for surface attachment.
• Includes agriculturally important bacteria capable of nitrogen fixation along with symbiotic relationships with plants.
• Some members are plant and human pathogens.
• Taxonomic groups include Caulobacter and Hyphomicrobium
• Also include Pelagibacter
• There is also Azospirillium
• Another group is Acetobacteraceae
• Includes Rhizobium and Bradyrhizobium
• Can also find Agrobacterium in this family
• Can also find Nitrobacter and Nitrosomonas
• Other species include Rickettsia
• Some more bacteria include Ehrlichia
• Others are Brucella
• Other bacterial species are Bartonella
• There are also Wolbachia species

Alphaproteobacteria: Caulobacter and Hyphomicrobium

• Found in aquatic environments with low nutrients.
• They form stalks and prosthecae to enhance nutrient uptake.
• Budding, not binary fission, is their mode of reproduction.

Alphaproteobacteria: Pelagibacter

• Abundant in oceans.
• They are extremely small.
• They thrive in low-nutrient conditions.
• Important for the Earth's carbon cycle.

Alphaproteobacteria: Azospirillum

• Grows in soil and utilizes nutrients excreted by plants.
• Forms associations with plant roots, specifically with tropical grasses and sugarcane.
• Plays a crucial role in nitrogen fixation.
• Converts N₂ (inert gas) into NH₄, which is absorbed by the host plant to synthesize amino acids and proteins.

Alphaproteobacteria: Acetobacteraceae

• Includes Acetobacter and Gluconobacter.
• Converts ethanol into acetic acid.

Alphaproteobacteria: Rhizobium and Bradyrhizobium

• Fix nitrogen in the roots of leguminous plants.
• They are commonly known as rhizobia.

Alphaproteobacteria: Agrobacterium

• Considered plant pathogens that cause crown gall.
• This bacteria species inserts a plasmid into plant cells, and induces a tumor.

Alphaproteobacteria: Nitrobacter and Nitrosomonas

• Chemoautotrophic, using inorganic chemicals as a source of energy and CO₂ as a carbon source.
• Nitrosomonas converts NH₄⁺ to NO₂⁻.
• Nitrobacter converts NO₂⁻ to NO₃⁻.

Alphaproteobacteria: Rickettsia

• Obligate intracellular parasites.
• Cause spotted fevers.
• R. prowazekii causes epidemic typhus.
• R. typhi causes endemic murine typhus.
• R. rickettsii causes Rocky Mountain spotted fever.
• Transmitted via insect and tick bites.

Alphaproteobacteria: Ehrlichia

• Transmitted by ticks.
• Causes ehrlichiosis.

Alphaproteobacteria: Brucella

• Obligate parasite of mammals that survives phagocytosis.
• Causes brucellosis

Alphaproteobacteria: Bartonella

• Human pathogen
• One species, B. henselae is known to cause cat-scratch disease

Betaproteobacteria

• Taxonomic groups include Spirillum
• There is also Sphaerotilus
• Include species of Burkholderia
• There are species of Bordetella
• Another species if Neisseria
• also contains Zooglea

Betaproteobacteria: Spirillum

• Found in freshwater environments.
• They move by polar flagella.

Betaproteobacteria: Sphaerotilus

• They are found both in fresh water and sewage.
• They form protective sheaths to aid in protection and nutrient gathering.

Betaproteobacteria: Burkholderia

• B. cepacia is noted for its ability to degrade over 100 organic molecules.
• B. pseudomallei is known as the cause of melioidosis.

Betaproteobacteria: Bordetella

• These are nonmotile rods.
• B. pertussis causes whooping cough.

Betaproteobacteria: Neisseria

• N. gonorrhoeae is the causative bacteria of gonorrhea.
• N. meningitidis causes meningococcal meningitis.

Betaproteobacteria: Zoogloea

• Important in the activity of the activated sludge system.

Gammaproteobacteria

• Taxonomic groups include Acidithiobacillus
• There is also bacteria called Thiotrichales
• Anothe bacteria in this group are Francisella
• Includes species of Pseudomonas
• can also find Azotobacter and Azomonas here
• Another species is Moraxella
• Another species if Acinetobacter
• It includes Legionella in this group
• There are also species of Coxiella in this group
• can find Vibrionales in this group as well

Gammaproteobacteria: Acidithiobacillus

• Oxidizes H₂S or S⁰ into SO₄²⁻.

Gammaproteobacteria: Thiotrichales

• Beggiatoa are in this group.
• These bacteria grow in aquatic sediments.
• They oxidize H₂S to S⁰ for energy.

Gammaproteobacteria: Francisella

• F. tularensis causes tularemia, also known as Rabbit Fever.

Gammaproteobacteria: Pseudomonas

• Part of the Pseudomonadales order
• Commonly found in soil and other natural environments.
• Considered opportunistic pathogens, causing nosocomial infections.
• Characterized by metabolic diversity and polar flagella.
• P. aeruginosa causes wound and urinary tract infections.

Gammaproteobacteria: Azotobacter and Azomonas

• They are nitrogen-fixing.

Gammaproteobacteria: Moraxella

• M. lacunata causes conjunctivitis.
• M. catarrhalis causes ear infection.

Gammaproteobacteria: Acinetobacter

• A. baumanii, is a respiratory pathogen that is commonly resistant to antibiotics.

Gammaproteobacteria: Legionellales

• Legionella are found in streams, warm-water pipes, and cooling towers.
• Legionella is the bacteria that causes legionellosis.
• Coxiella
• C. burnetii is the cause of Q fever.
• The bacteria transmits via aerosols or milk, animal feces, and urine
• This bacteria naturally infects animals, such as goats, sheep, and cows.

Gammaproteobacteria: Vibrionales

• These bacteria are commonly found in aquatic habitats.
• V. cholerae causes cholera.
• V. parahaemolyticus causes gastroenteritis.

Gammaproteobacteria: Enterobacteriales

• These are commonly called enterics because they inhabit the intestinal tract,
• They are non-spore forming and ferment carbohydrates
• They are described as facultative anaerobes that produce bacteriocins.
• They display peritrichous flagella.
• Escherichia
  • E. coli is an indicator of fecal contamination.
  • Some strains cause foodborne disease and urinary tract infections.
• Salmonella
  • S. bongeri is predominantly associated with cold-blooded animals, but it can infect humans.
  • S. enterica infects warm-blooded animals.
  • There are 2500 serovars (serological varieties).
  • They are a common form of foodborne illness.
  • A serovar of this bacteria, S. typhi can cause typhoid fever.
• Salmonella enterica serovar typhimurium
  • S. typhi is a serovar and not a species.
  • Causes typhoid fever
  • Incubation period lasts 2-3 weeks with a 20% fatality rate if untreated.
• Bacteria spreads by contamination Chronic carriers have bacteria in the gall bladder.
• Asymptomatic super spreader Mary Mallon transmitted without knowing

Gammaproteobacteria: Shigella, Klebsiella, Serratia

• Shigella
• Causes bacillary dysentery Causes shigellosis -Klebsiella -K. pneumoniae causes pneumonia. -Serratia -Produce red pigment. -Common cause of nosocomial infections.

Gammaproteobacteria: Yersinia, Erwinia

• Yersinia
• Y. enterolitica causes yersiniosis
• Y. pestis causes the plague
• Transmitted via fleas. Erwinia
• Are plant pathogens.
• Proteus
• Undergoes swarming motility where colonies form concentric rings,
• P. vulgaris and P. mirabilis that cause UTIs especially if catheters are used.

Gammaproteobacteria: Enterobacter and Cronobacter

• Enterobacter
• E. cloacae and E. aerogenes cause urinary tract infections and nosocomial infections. Cronobacter
• C. sakazakii
• Found in variety of environments and foods
• Can cause sepsis, necrotizing enterocolitis and meningitis in infants.
• More outbreaks are associated with dry foods

Gammaproteobacteria: Pasteurellales

• Pasteurella
• Pathogen of domestic animals
• P. multocida is transmitted to humans via animal bites.

Gammaproteobacteria: Haemophilus

• H. influenzae causes meningitis, ear infections, and epiglottitis
• This bacteria does not cuase influenza.

Deltaproteobacteria

• Includes Bdellovibrio and Desulfovibrionales
• Bdellovibrio attacks other gram-negative bacteria
• Desulfovibrionales uses S⁰ or SO₄²⁻ instead O₂ as a final electron acceptor.
• Desulfovibrio is found in anaerobic sediments and intestinal tracts.

Epsilonproteobacteria

• Are slender 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 is known to cause spontaneous abortions in domestic animals. Helicobacter
• Microaerophilic curved rods that has multiple flagella

Nonproteobacteria Gram-Negative Bacteria

• Chlamydia
• Spirochetes
• CFB group
  • Cytophaga, Fusobacterium, and Bacteroides
• Plantomycetes

Chlamydiae

• Small, non-motile obligate intracellular parasites.
• Have an elementary body that is infective
• Chlamydia trachomatis causes trachoma and urethritis.
• Chlamydophila psittaci causes respiratory psittacosis. Chlamydophila pneumoniae causes a mild form of pneumonia prevalent in young adults

Planctomycetes

• Gram-negative, budding bacteria
• Have cells walls that resemble archaea.
• Show that DNA analysis places them within the bacteria domain but the cell walls are similar to archaea.
• The Gemmata obscuriglobus is a bacteria in this group that has a nucleus

Other Gram-Negative Bacteria: CFB Group

• Refers to Cytophaga, Fusobacteria and Bacteroides, They are anaerobic, gram neg. rods Known for fermentation and break down of organic materials Can be normal flora in animals

Other Gram-Negative Bacteria: Cytophaga

• It is a soil organism.
• Able to breakdown cellulose.
• Found in the gut of ruminants.

Other Gram-Negative Bacteria: Fusobacterium

• Normal flora of mouth, upper respiratory, and gastrointestinal
• Seems to be opportunistic
• Associated with dental abcesses, ulcerative colitits and colorectal cancer

Other Gram-Negative Bacteria: Bacteroides

• The largest group of the CFB phylum
• Part of the normal gut flora of people and animals
• About 30% of a human gut microbiome They benefit from nutrients in the gut while preventing pathogens from colonizing the large intestine.
• Can be opportunistic.

Spirochaetes

• Undergo motility called axial filaments and create a corkscrew pattern
• Treponema
• T. pallidum can cause syphilis
• Borrelia
• B. burgdorferi can cause relapsing fever and Lyme disease
• Leptospira
• Are excreted in animal urine

Phototrophic Bacteria

• Includes both Proteobacteria and Nonproteobacteria Photosynthetic bacteria can be oxygenic and anoxygenic, depending.
• Traditionally classified into nonsulfur:
• There are purple and green nonsulfur bacteria based on color

Cyanobacteria

• O2 is huge and contains heterocysts that fixes
• They have gas to produce buoyancy. -Unicellular, colonial, etc.

Chlorobi and Chloroflexi

• Anoxygenic photosynthesis
• Green sulfur bacteria: phylum Chlorobi Green nonsulfur bacteria: phylum Chloroflexi Purple sulfur and purple Both included in theproteobacterias.

Non Proteobacteria Gram-Positive Bacteria

• Can be divided into groups, based on G+C ratios:
• High G + C ratios - Actinomycetota and Deincoccota
• Low G + C ratios - Bacillota and Mycoplasmatota

Actinomycetota

• High G + C Gram-Positive Bacteria-
• High G + C, Gram-positive and highly pleomorphic
• Common source of antibiotics
• Often common inhabitants of soil – “Fresh dirt smell”

Mycobacterium

• Cell wall has a thick peptidoglycan along with mycolic acid layer that causes them to be waxy and resistant

Nocardia

• Nocardia Form fragmenting filaments, is acid-Fast, and is often caused by N. asteroides.

Corynebacterium

• C. diphtheriae can cause diphtheria
• Gram-Positive
• Propionibacterium propionic acid.

Cutibacterium

• Found on the skin
• C. acnes can cause acne

Low G + C Gram-Positive Bacteria: Gardnerella

• G. vaginalis causes vaginitis. Gram causes variable and highly pleomorphic Streptomyces which are isolated from the soil
• Isolated from soil and produce antibiotics Can be S. aureofaciens which produce chlortetracycline , S. griseus which produce streptomycin Is from S. erythraeus that produce erythromycin, S. venezuelae that produces chloramphenicol Actinomyces
• Forms filaments called hyphae.

Deninococcus radiodurans

• More resistant to radiation with repair DNA
• Thermus aquaticus
• Found in hot springs
• Taq polymerase in polymerase chain reaction

Clostridiales

• Gram-Positive Bacteria-
• Clostridium:
• Endospore-producing.
• Obligate anaerobes.
• Disease-causing of tetaniC., botulinumC., perfringensC., difficileC.

Bacillales

• Bacillus: Endospore-producing rods in the soil
• B. anthracis causes anthrax B. anthracis - insect pathogen,
• B. cereus causes food poisoning Staphylococcus Grapelike clusters of cocci
• aureus causes and can undergo wound infections; is produce enterotoxin Listeria : L. monocytogenes contaminates the food.

Lactobacillales

• Aerotolerant anaerobes, lactic acid
• Lactobacillus-commerically food production
• L. acidophilus- probiotic Enterococcus
• hospitals ,E. faecalis and E. faecium the surgical and the the tract

Streptococcus

• Spherical chain cells that damage -hemolytic blood:
• pyogenesS.
• alpha causes pneumococcal pneumonias

Mycoplasma

• Cell that of a self-replicating
• Is a pneumonia organism

Extremophiles

• Found in Archaea
• Halophiles: salt>percent
• Thermophiles: have growth>Celsius,
• Acidophiles: growth,
• Methanogens: Anaerobic methane.