Download Prokaryotic Microbial Diversity

Prokaryotic Microbial Diversity
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• Early attempts at taxonomy: all plants and animals
• Whitaker scheme (late 20th century): Five kingdoms
– Animalia, Plantae, Fungi, Protista, and Monera
– Monera comprised of prokaryotes
• Classification of bacteria difficult
– Plants, animals can be distinguished from each other by
physical characteristics; backed up by DNA
– Bacteria look very similar
– Convergent evolution a problem
• Unrelated bacteria develop similar physical and
biochemical traits
Goal: Evolutionary classification
• In order to understand relatedness, organisms must
be viewed at the DNA level
– Similar sequences, mutations should give clues
– Which genes? Bacteria readily swap genes around.
• Carl Woese and 16S RNA
– Ribosomal RNA genes cannot afford to mutate much
• Changes would interfere with protein synthesis
– Change in rRNA genes over time very gradual
• Useful for looking at large differences among
organisms
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Domains
• Sequencing rRNA genes reveal differences
– Bacteria, Archaea, Eukarya all different from each other
• Despite Bacteria, Archaea both being prokaryotes
• Differences in Bacteria, Archaea backed up
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Aspects of molecular biology
Membrane lipid chemistry
Cell wall chemistry
Extreme environments
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What’s a Species?
• Eukaryotes: plants and animals
– Generally, 2 organisms are of same species if they can
successfully interbreed
– Definition based on sexual reproduction
– Bacteria don’t reproduce sexually
• Bacterial species: a group of strains that are more
closely related to each other than to another group.
– Members of a species have DNA that can hybridize
– Because of gene exchange, mutation, phase variation,
there are no sharp boundaries between species.
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Viable, non-culturable bacteria
• Many bacteria present in environments:
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Do not grow when placed in conventional media
include known pathogenic bacteria
Include bacteria previously unknown
Do not appear to multiply, but many can be shown to be
metabolically active
• We just don’t know how to grow them?
– Pathogenic forms can resume growing in infection
– Others…?
– Detected and studied using molecular techniques
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Metagenomics
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• Mixed population studies
– Using molecular techniques (PCR, sequencing) we find
various unique DNA sequences
– Most of these bacteria have not/ cannot be cultured
– Using molecular techniques to classify unculturable
bacteria is called metagenomics
• Identification techniques can be molecular or
traditional
– Traditional techniques require isolation into pure culture,
biochemical tests, sometimes serological tests.
Classical and MolecularTaxonomy
• Identification by phenotypic analysis
– Shape, size, Gram stain
– Basic metabolism (aerobic, fermentative, autotrophic)
– Motility, pigments, metabolic products, usable carbon
sources, temperature range
• ID by examining chemical features
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Fatty acid composition (FAME)
DNA-DNA hybridization
Ribotyping (specific rRNA sequences; uses PCR)
Multilocus sequence typing (sequences from several
conserved genes; uses PCR)
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Major groups of Bacteria-1
• Hyperthermophilic Gram negatives
– Grow at >70 degrees
• Green Sulfur and Green Non-sulfur bacteria
– Photosynthetic, anoxygenic
– Sulfur bacteria use H2S as electron donor
• Deinococcus and relatives
– Highly radiation resistant; great DNA repair
– Gram negative or positive? Odd mixture of traits
• Cyanobacteria
– “blue-green algae”; oxygenic photosynthesis
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Major groups of Bacteria-2
• Proteobacteria
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Largest group of Gram negative bacteria
Enteric bacteria (E.coli, Salmonella, Shigella)
Vibrio (related to enterics; V. cholerae; curved rods)
Pseudomonads (strictly respiratory)
Various groups affecting N and sulfur cycles
Purple sulfur and Purple non-sulfur anoxygenic
phototrophs
– Rickettsia: obligate intracellular parasites
• Bacteroides and Cytophaga
– First is strict anaerobic; 2nd aerobic and gliding
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Major groups of Bacteria-3
• Gram Positive bacteria
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Endospore formers (Bacillus, Clostridium)
Cocci (Staph, Strep, Micrococcus)
Other rods (Mycobacteria, Listeria, etc.)
Actinomycetes (filamentous, antibiotic producers)
Mycoplasma (DNA says G+, but no cell wall)
• Spirochetes
– Tight spirals, internal flagella, G-
• Chlamydia
– Obligate intracellular parasites; 2 stage life cycle
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Archaea
• Methanogens and Halophiles
– Methanogens strict anaerobes, make methane
– Halophiles need at least 1.5 M salt
• Mostly hyperthermophiles
– Growth from 80 upwards to 120 degrees C
• Third major group has one species!
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