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Bacterial diversity - Coggle Diagram
Bacterial diversity
Phylogenetic Diversity of Bacteria
80+ phyla based on 16S rRNA
30 phyla successfully cultured
90% of characterized species from 4 phyla:
Proteobacteria
Deltaproteobacteria: Sulfate-reducing bacteria
Alphaproteobacteria: Mostly aerobes, oligotrophic, includes Rhizobiales, Rickettsiales
Rickettsiales: Obligate intracellular parasites or mutualists (e.g., Rickettsia prowazekii, R. rickettsii)
Betaproteobacteria: Functional diversity, includes Neisseria (N. gonorrhoeae, N. meningitidis)
Neisseria: Commensals/pathogens in oral cavity, moist environments
Gammaproteobacteria: Includes Enterobacteriales (E. coli, Salmonella, Shigella), Pseudomonadales, Vibrionales
Enterobacteriaceae: Facultative anaerobes, fermenters, major pathogens
Vibrio cholerae causes cholera; Pseudomonas aeruginosa is an opportunistic pathogen
Epsilonproteobacteria: Includes Campylobacter, Helicobacter
Campylobacter jejuni: Gastroenteritis, Helicobacter pylori: Peptic ulcers
Largest, most metabolically diverse, all Gram-negative, Includes medically, agriculturally, industrially significant , 6 Classes: Alpha-, Beta-, Gamma-, Delta-, Epsilon-, Zeta-bacteria, Horizontal gene flow shapes metabolic diversity.
Actinobacteria
High G+C Gram-positive bacteria
Includes Mycobacterium (M. tuberculosis, M. leprae)
Rod-shaped, acid-fast, aerobic
Actinomycetes: filamentous soil bacteria
Actinomycetes: Filamentous soil bacteria, antibiotic producers (e.g., Streptomyces)
Firmicutes
Low G+C Gram-positive bacteria
Includes endospore formers (Bacillus, Clostridium)
Lactic acid bacteria: Lactobacillus, Streptococcus, Enterococcus
Staphylococcus (S. aureus, S. epidermidis)
Streptococcus mutans: Dental caries, S. pneumoniae: Pneumonia
Staphylococcus (S. aureus, S. epidermidis), antibiotic resistance (MRSA)
Bacteroidetes
Gram-negative, non-sporulating
Found in human gut microbiota
Found in human gut microbiota, aids digestion
Bacterial Classification
Shape, Gram stain, biochemical traits
16S rRNA gene sequencing
Domain → Phylum → Class → Order → Family → Genus → Species
Microbial Interdependence
Evolution within microbial communities
Gene deletions promote symbiotic relationships
Loss of biosynthetic pathways in host-associated bacteria (e.g., mitochondria, chloroplasts)
Microbial Evolution
Origins of Genetic Diversity
Mutations: random DNA changes over time
Recombination: homologous and nonhomologous
Genetic drift: random allele frequency changes
Mechanisms of Evolution
Mutation
Spontaneous (DNA polymerase errors) vs Induced (radiation, chemicals)
Point mutations: silent, missense, nonsense
Frameshift mutations: insertions, deletions
Reversions restore original phenotype
Reversions restore original phenotype
Selection
Natural selection favors beneficial mutations
Genetic drift impacts small populations
Bottleneck effect reduces diversity
Gene Duplication & Deletion
Duplication creates redundant copies, allowing mutations
Deletions eliminate non-essential genes (common in symbionts and pathogens)
Horizontal Gene Transfer (HGT)
Expands genetic diversity, transfers functional genes
Three Mechanisms:
Transformation: Uptake of naked DNA
Conjugation: Plasmid transfer via pili (e.g., F factor, Hfr conjugation)
Transduction: Bacteriophage-mediated DNA transfer (generalized, specialized)
HGT contributes to antibiotic resistance, virulence factor acquisition
Long-Term Evolution Experiments
E. coli LTEE: Evolution of citrate metabolism over 60,000 generations
Adaptation to environmental pressures over time
Experimental Approaches in Microbial Evolution
Replica Plating: Identifies bacterial mutants (e.g., auxotrophic mutants)
Ames Test: Assesses mutagenic potential of chemicals
DNA Repair Mechanisms, Proofreading by DNA polymerase, Mismatch repair fixes replication errors, Nucleotide excision repair for UV-induced thymine dimers