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• Phylogenetic classification of bacteria remains complex and while there have been over 40 phyla proposed (and other 1500 projected) for bacteria, there remain less than 20 that are accepted and used regularly

  
• Deep-branching Bacterial Taxa


  • Diverged early or before the well-characterised phyla
  • Mostly thermophilic
  • Extremely diverse compared to other bacterial taxa
  • Exhibit archael-like traits including ether-linked membrane lipids and similar genes

  
• Phylum Aquificota


  • Some of the earliest "deepest" branches of the Domain Bacteria which thrive in harsh thermophilic environments
  • Aquifex spp. are hydrogenotrophs and able to produce water by oxidizing hydrogen gas
  • Obligate autotrophs fixing CO2 using the reverse TCA cycle

  
• Phylum Thermotogota


  • Some of the earliest "deepest" branches of the Domain Bacteria which thrive in harsh thermophilic environments
  • Show mosaic-type genomes with up to a quarter derived from Archaea

  
• Phylum Chloroflexota


  • Filamentous photoheterotrophs informally called "Green Nonsulfur Bacteria"
  • Do anoxygenic photoheterotrophy and supplement with aerobic respiration
  • Use chlorosomes to drive efficient photosynthesis
• Phylum Deinococcota


  • Highly resistant to environmental hazards and are extremophiles
  • Substitute L-ornithine for diaminopimelic acid (DAP) in peptidoglycan cross-bridges
  • Have thick cell walls and test positive like Gram-positives, but have a second membrane and more closely resemble Gram-negative bacteria
  • Important for molecular biology applications due to hardy, resilient enzymes

  
• Firmicutes


  • Gram-positive bacteria with low G+C genomes
  • Cocci or bacilli with thick peptidoglycan walls reinforced by teichoic acids

  
• Clostridia


  Obligate anaerobic, many are saprophytes, many produce severe toxins, sporulating
• Bacilli


  Obligate aerobes or facultative anaerobes, nearly all are sporulating
• Lactobacillales


  • Lactic Acid Bacteria (LAB) and Streptococcus
  • Aerotolerant, non-sporulating
  • Found in decomposing plants and milk products
• Actinobacteria


  • Gram-positive bacteria with high G+C content and variable morphology
  • Mostly aerobes and secondary metabolite producers
  • Play central role in decomposition of organic materials in soil
• Cyanobacteria


  • Large, morphologically and ecologically diverse group of oxygenic photoautotrophic Gram-negative bacteria
  • Responsible for oxygen in atmosphere and gave rise to modern chloroplasts
  • Can be unicellular or filamentous
  • Perform both carbon and nitrogen fixation
  • Can use molecules other than CO2 in photoheterotrophy

  
• Cyanobacteria are the only known oxygenic photosynthetic bacteria and perform photosynthesis on flattened sacs of membrane folds called thylakoids

  
• Cyanobacteria employ photoactive molecules including bacteriochlorophyll and phycocyanin for their light reactions, and use phycobilisomes as light harvesting complex antennae
• Cyanobacteria


  • Can be either unicellular or form filamentous structures
• Metabolic Activity of Cyanobacteria


  • Only bacteria to have both photosystems
  • Many can undergo both carbon and nitrogen fixation
  • Under anoxic conditions, many are able to use molecules other than CO2 (when less is present) in a process called photoheterotrophy

  
• Cyanobacteria are the only known oxygenic photosynthetic bacteria (originally misidentified as "blue-green algae") and perform photosynthesis on flattened sacs of membrane folds called thylakoids, which resemble their eukaryotic counterparts

  
• Photosynthesis in Cyanobacteria


  • Employ photoactive molecules including bacteriochlorophyll (green) and phycocyanin (blue) for their light reactions
  • Light harvesting complex antennae (phycobilisomes) capture light to drive the photosystems found on the thylakoid membranes
• Carboxysomes in Cyanobacteria


  • Polyhedral bodies rich in RuBisCO enzymes and carbonic anhydrase
  • Concentrate and sequester CO2, bicarbonate (HCO3-), or carbonic acid (H2CO3) for use in Calvin cycle
  • Located near the thylakoid structures for efficient coupling

  
• Proteobacteria (also now called Pseudomonadota) are essential to life on Earth and live in nearly every environment on Earth. They are all Gram-negative
• Proteobacteria is the largest and most metabolically diverse taxonomic phylum that are Gram-negative. The majority of bacteria of known medical, industrial, and agricultural significance are classified in this phylum

  
• Classes within the Proteobacteria phylum

  • Alphaproteobacteria
  • Betaproteobacteria
  • Gammaproteobacteria
• Alphaproteobacteria


  • Generally grow under low nutrient conditions (oligotrophic)
  • Include nitrogen-fixing bacteria, and several plant and human pathogens
  • Most are obligate aerobes or facultative anaerobes
• Key Orders of Alphaproteobacteria

  • Rhizobiales
  • Rickettsiales
• Rhizobiales


  • Contains metabolically diverse bacteria including phototrophs and nitrogen-fixing bacteria
  • Mostly obligate aerobes
  • Named after rhizobia (a polyphyletic collection of genera that form root nodules)

  
• Rickettsiales


  • Obligate intracellular parasites or mutualists of animals
  • Most are associated with arthropods or insects
• Betaproteobacteria


  • Includes a metabolically diverse group of bacteria
  • Many are pathogenic and/or utilize nutrient wastes produced by anaerobes
  • Collectively most are classified as heterotrophs
• Key Orders of Betaproteobacteria


  • Rhodocyclales
  • Neisseriales
• Rhodocyclales


  • Contains two important genera: rhodocyclus (containing purple nonsulfur bacteria) and zoogloea (aerobic chemoorganotrophs which forms thick gelatinous matrices in sewage plants)

  
• Neisseriales


  • All are cocci, which often inhabit the mucous membranes of animals
  • Contains many human pathogens
• Gammaproteobacteria


  • Largest class of proteobacteria
  • Vary greatly in their physiological niches (environments) containing phototrophs, chemoorganotrophs, chemolithotrophs, and many different types of fermenters
• Key Orders of Gammaproteobacteria

  • Enterobacteriales
  • Vibrionales
  • Pseudomonadales
• Enterobacteriales


  • Order of facultative anaerobes that inhabit the intestinal tracts of animals
  • Many are pathogenic
  • Most are motile
  • Commonly called Enterics
• Vibrionales


  • Order of facultative aerobes with most having a vibrio shape
  • Many are aquatic and several are major human pathogens
• Pseudomonadales


  • Order containing bacteria that are all chemoorganotrophs and are commonly found in soil
  • Some are human pathogens

  
• Bacteroidota


  • Gram-negative, non-sporulating aerobic or anaerobic rod shaped bacteria
  • Found everywhere including soil, sediment, water, and are a normal part of the human microbiome (being the primary bacterial component of feces)
• Bacteroidia


  • Most well studied class in the Bacteroidota phylum
  • Contains the genus Bacteroides, which contains common human colonic bacteria

  
• Bacteroides


  • Non-motile opportunistic pathogens found in gingival crevices and large intestine
  • Frequently recovered from deep tissue infections
  • Infections usually caused by puncture wounds or surgery
• Chlorobiota


  • Phylum which contains primarily Gram-negative green sulfur bacteria
  • Anoxygenic obligate anaerobes which undergo anoxygenic photoautotrophy, but use sulfide ions, hydrogen, or ferrous (Fe2+) ions as a final electron donor
  • Elemental sulfur may be deposited as a waste product (rather than oxygen) outside of the cell

  
• Spirochaetota


  • Characterized by flexible, helical (spirochete) cells with a modified outer membrane (the outer sheath) and modified flagella (axial filaments) located within the outer sheath
  • Important pathogenic genera include Treponema, Borrelia, and Leptospira