Prokaryotic Microbial Diversity 1 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 2 3
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 Aspects of molecular biology Membrane lipid chemistry Cell wall chemistry Extreme environments www.steve.gb.com/science/transcription.html
4 Whats a Species? Eukaryotes: plants and animals Generally, 2 organisms are of same species if they can successfully interbreed Definition based on sexual reproduction Bacteria dont 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. 5
Viable, non-culturable bacteria Many bacteria present in environments: 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 dont know how to grow them? Pathogenic forms can resume growing in infection Others?
Detected and studied using molecular techniques 6 Metagenomics 7 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 Fatty acid composition (FAME)
DNA-DNA hybridization Ribotyping (specific rRNA sequences; uses PCR) Multilocus sequence typing (sequences from several conserved genes; uses PCR) 8 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 9 Major groups of Bacteria-2 Proteobacteria 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 10 Major groups of Bacteria-3 Gram Positive bacteria
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 11
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! 12
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