Microbial Genomes and Metabolic Diversity

Phylogenetic Diversity of bacteria

• distinguished based on 16S ribosomal RNA

• 4 main phyla

  • Proteobacteria

  • Actinobacteria

  • firmicutes

  • bacteroidetes.

Proteobacteria

• largest and most metabolically diverse due to HGT

• ALL gram (-)

• relationships to oxygen:

  • anaerobic, microaerophilic, and facultatively aerobic

• Morphologically diverse:

  • rods, cocci, spirilla, filamentous, budding and appendage forms

• 6 classes

  1. Alpha

  2. beta

  3. delta

  4. gamma

  5. epsilon

  6. zeta

Class: Alphaproteobacteria

• 2nd largest

• most are obligate or facultative aerobes

• Main orders

  • Rickettsiales

    • Wolbachia, Ehrlichia, and Rickettsia

    • obligate intracellular parasites (require host) or mutualists of animals

    • transmitted through arthopods

    • cause human disease

  • Caulobacterales

    • Caulobacter

    • oligotrophic

    • aerobic chemoorganotroph

    • form stalks (extension of body)

    • aquatic

Class: Betaproteobacteria

• 3rd largest

• Main orders:

  • Neisseriales

    • Neisseria:

    • chemoorganotrophs

    • human diseases (pathogenic): meningitis and gonorrhea.

  • Nitrosomonadales

    • Nitrosomonas:

    • nitrogen cycle by oxidizing ammonia (bacteria) into nitrite

    • 1st step nitrification

Class: Gammaproteobacteria

• Largest and most diverse class

• well-known human pathogens

• Main orders:

  • Enterobacteriales (Enteric bacteria),

  • facultatively anaerobic

    • Escherichia:

    • Salmonella

    • Yersinia

    • Klebsiella:

    • Proteus:

    • serratia

    • enterobacter

  • Pseudomonadales:

    • pseudomonas

    • chemoorganotrophs, aerobic

    • grow as aerobes but can perform anaerobic respiration using nitrate

    • opportunistic pathogens

  • Legionellales (-)

    • Legionella:

    • pneumonia

    • can thrive in aquatic environments.

Deltaproteobacteria and Epsilonproteobacteria

• Deltaproteobacteria:

  • Includes sulfate-reducing bacteria

• Bdellovibrionales

  • Bdellovibrio

  • predatory species

• Myxococcales

  • myxococcus: spore forming

  • Life cycle:

    1. Vegetative: nutrient availability, cells feed bacteria, motility using slime trails

    2. starvation: nutrient depletion → swarming and aggregation

    3. Aggregation: form mounds

    4. fruiting body and myxospore formation: protects cells in unfavorable conditions

    5. Germination: triggered by nutrient availability, spores germinate back to vegetative cells

• Epsilonproteobacteria:

  • extreme environments, such as deep-sea vents and gastric systems of animals

• Campylobacterales

• both are pathogenic

• sulfur metabolism

  • campylobacter: causes gastroenteritis, produces enterotoxin

  • helicobacter: causes gastric and peptic ulcers

Gram (+) Bacteria and Relatives

• Actinobacteria

  • high G+C (Gram +)

  • Actinomycetales

    • Mycobacterium

    • Streptomyces: antibiotic producers, mold-like morphology

    • actinomyces

• Tenericutes

  • Lack cell wall

  • Mycoplasmatales

    • Mycoplasma (Gram +): phylogenetically related to Firmicutes

    • ribosomal RNA (16S rRNA) → gram +

    • Gram (-), stain pink

    • Gram (+) based on phylogeny (rRNA)

    • resistant to antibiotics targeting peptidoglycan

  Firmicutes

• low G+C (Gram +)

  • Bacillales

    • endospore (survival advantage) formers found in soil, adapted for survival in extreme conditions

    • Bacillus: produce antibitoics

    • Staphylococcus: form clusters and is associated with various infections

    • listeria

  • Lactobacillales: lactic acid bacteria

    • lactobacillus: dairy fermentation

    • streptococcus: strep throat and dental caries

  • Clostridiales

    • Clostridium:

      obligate anaerobes, ferment sugars or amino acids.

      generate ATP through Sub-level phosphorylation

  • Aerobic conditions: Bacillus species grow

  • anaerobic conditions: Clostridium species grow

  Mycobacterium

  • acid-fast staining for identification

  • mycolic acids: Long-chain fatty acids found in the cell wall→ thick, waxy, and hydrophobic.

  • cord factor: A glycolipid → serpentine "cord-like" patterns.

  • Mycobacterium tuberculosis: Causes tuberculosis

  • Mycobacterium leprae: Causes leprosy.

Orders of chlamydiae

• Chlamydiae

• Chlamydiales:

  • obligate intracellular parasites

  • Chlamydia

  • gram (-) but lack peptidoglycan

    Infection Cycle:

    1. Attachment and entry: elementary body (EB) attaches to host cell and is internalized through phagocytosis

    2. Conversion to Reticulate Body (RB): within host endosome, EB → RB = active = replication

    3. Reconversion to Elementary Bodies: RBs reorganize into EBs making them infectious again

    4. Cell Lysis: rupture and release of EBs that infect nearby cells

  • Elementary body (EB): infectious, extracellular, non-replicative

  • Reticulate Body (RB): intracytoplasmic, non-infectious, replicative

Hyperthermophilic Bacteria

• in geothermal aquatic systems e.g. hydrothermal vents

• produces ether-linked lipids like archaea → heat-resistant, providing stability in extreme environments.

• ether bonds (C-O-C)

• R- hydrophilic residue

Radiation Resistant Deinococcus Radiodurans

• highly efficient in repairing damaged DNA

• resistant to radiation and desiccation

• pink and red because of carotenoids

  • Deinococcus radiodurans: Radiation-resistant, superior DNA repair.

  • Thermus aquaticus: Source of Taq polymerase for PCR.