Prokaryotes: Bacteria and Archaea

• Chapter 11 covers prokaryotes, specifically domains Bacteria and Archaea.
• The content is copyrighted by Pearson Education, Inc. in 2024.

Classification of Prokaryotes

• Prokaryotes are classified into Bacteria and Archaea.
• Bacteria are further divided into phyla, including Pseudomonadota, Cyanobacteria, Chlorobiota, Chloroflexota, Chlamydiota, Planctomycetota, Bacteroidota, Fusobacteriota, and Spirochaetota.
• Archaea includes the phyla Thermoproteota and Euryarchaeota.

Bacteria (Gram-Negative)

• Pseudomonadota are also known as Proteobacteria.
• Alphaproteobacteria includes Ehrlichia and Rickettsia.
• Betaproteobacteria includes Bordetella and Burkholderia.
• Gammaproteobacteria includes Vibrio, Salmonella, Helicobacter, Escherichia, and Pseudomonas.
• Deltaproteobacteria includes Bdellovibrio.
• Epsilonproteobacteria includes Campylobacter and Helicobacter.
• Cyanobacteria are oxygenic photosynthetic bacteria.
• Chlorobia are photosynthetic, anoxygenic, and green sulfur bacteria.
• Chloroflexi are anoxygenic, photosynthetic, filamentous green nonsulfur bacteria.
• Chlamydiota grow only in eukaryotic host cells.
• Planctomycetota are aquatic bacteria, some stalked.
• Bacteroidota include opportunistic pathogens.
• Fusobacteriota are anaerobic and can cause tissue necrosis and septicemia in humans.
• Spirochaetota cause syphilis and Lyme disease.

Bacteria (Gram-Positive)

• Bacillota (Firmicutes) include Bacilli (low G + C gram-positive rods and cocci) and Clostridia (low G + C wall-less bacteria).
• Mycoplasmatota include Mollicutes.
• Actinomycetota include Actinobacteria (cause tissue necrosis and septicemia in humans).
• Deinococcota include Deinococci (radiation- and heat-resistant genera).

Archaea

• Thermoproteota includes Thermoprotei, which are thermophiles and hyperthermophiles.
• Euryarchaeota includes Methanobacteria (important sources of methane) and Halobacteria (require high salt concentrations).

Pseudomonadota (Proteobacteria) Characteristics

• Most are gram-negative.
• They are the largest taxonomic group of bacteria.
• There are five classes within this group.
• They can be phototrophic, autotrophic, chemotrophic, and heterotrophic.
• Metabolism can be anaerobic, facultative anaerobic and obligate aerobic.

Alphaproteobacteria

• Most can grow in low-nutrient environments.
• They have stalks or buds (prosthecae) for adhering to surfaces.
• They include agriculturally important nitrogen-fixing bacteria with symbiotic relationships with plants.
• Some are plant and human pathogens.
• Key genera include Caulobacter, Hyphomicrobium, Pelagibacter, Azospirillium, Acetobacter, Gluconobacter, Rhizobium, Bradyrhizobium, Agrobacterium, Nitrobacter, Nitrosomonas, Rickettsia, Ehrlichia, Brucella, Bartonella, and Wolbachia.
• Caulobacter and Hyphomicrobium are found in low-nutrient aquatic environments and reproduce via budding instead of binary fission.
• Pelagibacter is one of the most abundant microorganisms in oceans, is extremely small, has an advantage in low-nutrient environments, and plays an important role in the Earth's carbon cycle.
• Azospirillium grows in the soil, uses nutrients excreted by plants, forms associations with roots, fixes nitrogen, and converts N2 to NH4 absorbed by plants to make amino acids and proteins.
• Acetobacteraceae (Acetobacter and Gluconobacter) converts ethanol into acetic acid.
• Rhizobium and Bradyrhizobium fix nitrogen in roots of leguminous plants and are also know as rhizobia.
• Agrobacterium is a plant pathogen causing crown gall by inserting a plasmid into plant cells, which induces a tumor.
• Nitrobacter and Nitrosomonas are chemoautotrophic, use inorganic chemicals for energy, and use CO2 as a carbon source; Nitrosomonas converts NH4+ to NO2- and Nitrobacter converts NO2- to NO3-.
• Rickettsia are obligate intracellular parasites that cause spotted fevers, including epidemic typhus (R. prowazekii), endemic murine typhus (R. typhi), and Rocky Mountain spotted fever (R. rickettsii), and are transmitted by insects and tick bites.
• Ehrlichia is transmitted by ticks and causes ehrlichiosis.
• Brucella is an obligate parasite of mammals, survives phagocytosis, and causes brucellosis.
• Bartonella is a human pathogen, B. henselae, which causes cat-scratch disease.
• Wolbachia is a bug found in 60% of insects naturally and eliminates viruses in Aedes aegypti mosquitos.

Betaproteobacteria

• Key genera are Spirillum, Sphaerotilus, Burkholderia, Bordetella, Neisseria, and Zooglea.
• Spirillum is found in freshwater and moves via polar flagella.
• Sphaerotilus is found in freshwater and sewage and forms sheaths for protection and nutrient gathering.
• Burkholderia includes B. cepacia that degrades more than 100 organic molecules, and B. pseudomallei that causes meliodosis.
• Bordetella contains nonmotile rods, and B. pertussis which causes whooping cough.
• Neisseria includes N. gonorrhoeae (cause of gonorrhoea) and N. meningitidis (cause of meningococcal meningitis).
• Zoogloea is important in the activity of the activated sludge system.

Gammaproteobacteria

• Key genera include Acidithiobacillus, Thiotrichales, Francisella, Pseudomonas, Azotobacter, Azomonas, Moraxella, Acinetobacter, Legionella, Coxiella, and Vibrionales.
• Acidithiobacillus oxidizes H2S or S0 into SO42−.
• Thiotrichales includes Beggiatoa which grows in aquatic sediments and oxidizes H2S to S0 for energy.
• Francisella includes F. tularensis, the cause of tularemia (aka Rabbit Fever).
• Pseudomonas live in the soil, are opportunistic pathogens, metabolically diverse, and have polar flagella; P. aeruginosa causes wound and urinary tract infections.
• Azotobacter and Azomonas are nitrogen-fixing.
• Moraxella includes M. lacunata which causes conjunctivitis, and M. catarrhalis which causes ear infections.
• Acinetobacter A. baumanii is a respiratory pathogen that is resistant to antibiotics.
• Legionella are found in streams, warm-water pipes, and cooling towers and cause legionellosis.
• Coxiella C. burnetii causes Q fever and transmitted by aerosols or milk, animal feces, and urine.
• Vibrionales are found in aquatic habitats; V. cholerae causes cholera, and V. parahaemolyticus causes gastroenteritis.
• Enterobacteriales, commonly called enterics, inhabit the intestinal tract and are non-spore forming, as well as ferment carbohydrates, are facultative anaerobes, produce bacteriocins, and have peritrichous flagella.
• Escherichia E. coli is an indicator of fecal contamination while some strains cause foodborne illness and urinary tract infections.
• Salmonella includes S. bongeri, predominantly associated with cold-blooded animals, but it can infect humans, as well as S. enterica which infects warm blooded animals, has 2500 serovars, and is the common cause of foodborne illness; S. typhi (a serovar) causes typhoid fever.
• S. typhi – a serovar not a species, the Cause of typhoid fever; has a 2-3 week incubation period, and about 20% fatality rate if left untreated, as well as it being spread by consuming food or drink that is contaminated and bacteria multiplies and spread in the bloodstream causing sepsis; chronic carriers have the bacteria in the gall bladder and asymptomatic super spreader Mary Mallon is known as Typhoid Mary.
• Shigella cause bacillary dysentery and Shigellosis.
• Klebsiella K. pneumoniae causes pneumonia.
• Serratia produces a red pigment and is a common cause of nosocomial infections.
• Yersinia includes Y. enterolitica, which causes yersiniosis and Y. pestis, which causes plague and is transmitted via fleas.
• Erwinia are Plant pathogens
• Proteus shows swarming motility, forms colonies of concentric rings, P. vulgaris and P. mirabilis, primarily cause UTI's especially in individuals with catheters.
• Enterobacter includes E. cloacae and E. aerogenes, that causes urinary tract infections and nosocomial infections.
• Cronobacter comprises C. sakazakii which is found in a variety of environments and foods and can cause sepsis, necrotizing enterocolitis, and meningitis in infants.
• Pasteurella has P. multocida that is transmitted to humans via animal bites.
• Haemophilus H. influenzae causes meningitis, ear infections, and epiglottitis.

Deltaproteobacteria

• Bdellovibrio attacks other gram-negative bacteria.
• Desulfovibrionales use S0 or SO42− instead of O2 as final electron acceptors including Desulfovibrio found in anaerobic sediments and intestinal tracts.

Epsilonproteobacteria

• Slender gram-negative rods that are helical or curved and microaerophilic.
• Campylobacter are microaerophilic vibrios with one polar flagellum; C. jejuni causes foodborne intestinal disease and C. fetus causes spontaneous abortions in domestic animals.
• Helicobacter consist of microaerophilic curved rods, multiple flagella that cause peptic ulcers and stomach cancer.

Nonproteobacteria Gram-Negative Bacteria

• It includes Chlamydia, Spirochetes, the CFB group containing Cytophaga, Fusobacterium, and Bacteroides and Plantomycetes.
• Chlamydiae are small, non-motile obligate intracellular parasites and the elementary body is infective; Chlamydia trachomatis causes trachoma and urethritis, Chlamydophila psittaci causes respiratory psittacosis, and Chlamydophila pneumoniae causes a mild form of pneumonia prevalent in young adults.
• Planctomycetes are gam-negative, budding bacteria; DNA analysis place them among bacteria, however, cell walls resemble those of archaea, and an organelle resembles a eukaryotic nucleus. Gemmata obscuriglobus has a membrane around DNA, resembling an eukaryotic nucleus.
• CFB Group consists of Cytophaga, Fusobacteria and Bacteroides which are anaerobic, gram negative rods, fermenters and are responsible for their digestion of complex organic materials and that may be part of the normal flora of people and animals.
• Cytophaga are soil organisms able to breakdown cellulose and are found in the gut of ruminants
• Fusobacterium comprises the normal flora of mouth, upper respiratory, and gastrointestinal tract of people and animals, are seems to be opportunistic and are associated with dental abcesses, ulcerative colitits and colorectal cancer
• Bacteroides represents the largest group of the CFB phylum, part of the normal gut flora of people and animals making about 30% of the human gut microbiome and are species are mutualistic as well as can be opportunistic, causing infections like peitonitis or infections with perforated bowel.
• Spirochaetes are Coiled and move via axial filaments that create a rotating corkscrew as well as Treponema and cause T. pallidum causes syphilis, as well, Borrelia includes B. burgdorferi causing relapsing fever and Lyme disease, and Leptospira are Excreted in animal urine.

Phototrophic bacteria

• Contains both Proteobacteria and Nonproteobacteria
• Photosynthetic bacteria can be subdivided into two groups, namely oxygenic and anoxygenic phototrophs, depending on their type of photosynthesis.
• Traditionally, these bacteria are classified into sulfur and nonsulfur bacteria and they are further differentiated by color.
• The purple sulfur bacteria
• The green sulfur bacteria
• Purple nonsulfur
• The green nonsulfur bacteria

Cyanobacteria

• Carry out oxygenic photosynthesis
• Have Huge O2 output
• Many contain heterocysts that fix nitrogen
• They provide buoyancy via Gas vesicles
• Exsist as Unicellular, colonial, and filamentous forms

Anoxygenic Photosynthetic Bacteria

• The Phyla Chlorobi and Chloroflexi carry out anoxygenic photosynthesis
• Included is Green sulfur bacteria, Chlorobi phylum
• With Green nonsulfur bacteria; Chloroflexi phylum.
• As well as, Purple sulfur and purple non-sulfur included in the proteobacterias.

Non Proteobacteria Gram-Positive Bacteria

• Can be divided into groups, based on G+C ratios
• Have a High G + C ratios (formerly known as Actinomycetes) as well as Actinomycetota with Deincoccota.
• It is determined that they Have more than 50% G and C in their DNA nucleotides and they are Aerobes or facultative anaerobes and they resemble fungi or molds.
• Low G + C ratios (formerly known as firmicutes) contains Bacillota and Mycoplasmatota having less than 50% G and C in their DNA nucleotides and Many are spore forming.
• They are aerobes, facultative anaerobes and strict anaerobes and many are pathogens.

Actinomycetota (High G + C Gram-Positive Bacteria)

• Have a High G + C count
• Gram-positive
• Highly pleomorphic, also with branching filaments
• Common source of antibiotics and they are common inhabitants of soil with “Fresh dirt smell"

High G + C Gram-Positive Bacteria

• Mycobacterium Cell wall and an outermost layer of mycolic acids that is waxy and water-resistant making them slow-growing pathogens, M. tuberculosis causes tuberculosis and M. leprae causes leprosy.
• Nocardia Form fragmenting filaments that are and acid-fast is and N. asteroides causes pulmonary infections.
• Corynebacterium C. diphtheriae causes diphtheria.
• Propionibacterium that is forms propionic acid.
• Cutibacterium is commonly found on the skin while with C. acnes which may play a role in the development of acne.
• Gardnerella forms G. vaginalis and causes vaginitis, and Gram variable and highly pleomorphic.
• Streptomyces those that are Located from soil; produce many antibiotics and examples include:
• -S. aureofaciens - chlortetracycline
• -S. rimosis – tetracycline
• -S. griseus – streptomycin
• -S. erythraeus – erythromycin
• -S. venezuelae - chloramphenicol
• Actinomyces - Form filaments called hyphae and A. israelii Found in the mouth and throat.

Deinococcus radiodurans

• More resistant to radiation than endospores
• Unique arrangement of DNA facilitates rapid repair of radiation damage

Thermus aquaticus

• Found in a hot spring in Yellowstone National Park
• Source of Taq polymerase (thermotolerant enzyme used in the polymerase chain reaction)

Clostridiales

• Clostridium can Endospore-producing
• Can be obligate anaerobes
• includes diseases caused by C. tetani, C. botulinum,C. perfringens and C. difficile

Bacteria

• Bacillus are Endospore-producing rods and Common soil inhabitants
• Staphylococcus cluster in Grapelike form and S. aureus causes wound infections.
• Listeria L. monocytogenes contaminates food and causes wound infections.

Lactobacillales

• Aerotolerant anaerobes with lactic acid Lactobacillus colonize the body and are used commercially in food production and probiotic such as L. acidophilus.
• Enterococcus are Found in the intestinal tract and hospital contaminants while E. faecalis and E. faecium infect surgical wounds and the urinary tract.

Streptococcus

• Spherical cells in chains
• Produce enzymes that damage tissue
• Beta-hemolytic streptococci hemolyze blood agar and includes
• S. pyogenes (pharyngitis, scarlet fever,impetigo…) and S. agalactiae (neonatal sepsis and meningitis) and Alpha-hemolytic streptococci is responsible for S. pneumoniae causes pneumonia and to to the S. mutans causes dental caries.

(Low G + C Gram-Positive Bacteria)

• Lack a cell wall, pleomorphic
• Smallest self-replicating organisms capable of existing free