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Chapter 4: PROKARYOTIC DIVERSITY

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Chapter 4: PROKARYOTIC DIVERSITY Chapter 4: PROKARYOTIC DIVERSITY 1. Prokaryote Habitats, Relationships & Biomes 2. Proteobacteria 3. Gram-negative and Phototropic Non-Proteobacteria 4. Gram-Positive Bacteria 5. Deeply Branching Bacteria 6. Archaea 1. Prokaryote Habitats, Relationships & Biomes Important Metabolic Terminology Oxygen tolerance/usage: aerobic – requires or can use oxygen (O2) anaerobic – does not require or cannot tolerate O2 Energy usage: phototroph – uses light as an energy source • all photosynthetic organisms chemotroph – acquires energy from organic or inorganic molecules • organotrophs – get energy from organic molecules • lithotrophs – get energy from inorganic molecules …more Important Terminology Carbon Source: autotroph – uses CO2 as a carbon source • e.g., photoautotrophs or chemoautotrophs heterotroph – requires an organic carbon source • e.g., chemoheterotroph – gets energy & carbon from organic molecules Oligotrophs require few nutrients, the opposite of eutrophs or copiotrophs Facultative vs Obligate (or Strict): facultative – “able to, but not requiring” • e.g., facultative anaerobes can survive w/ or w/o O2 obligate – “absolutely requires” • e.g., obligate anaerobes cannot survive in O2 Symbiotic Relationships Symbiotic relationships (close, direct interactions) between different organisms in nature are of several types: • e.g., humans have beneficial bacteria in their digestive tracts that also benefit from the food we eat (mutualism) Microbiomes All the microorganisms that inhabit a particular organism or environment (e.g., human or soil microbiome): Classification in the Bacterial Domain We will look at important genera from a variety of bacterial groups classified largely on staining & rRNA sequences (ribotyping): Gram-negative Bacteria • Proteobacteria • Nonproteobacteria & Phototrophic Bacteria Gram-positive Bacteria • High G+C (Actinobacteria) • Low G+C (Firmicutes) Deeply Branching Bacteria 2. Proteobacteria Alphaproteobacteria Betaproteobacteria Gammaproteobacteria Deltaproteobacteria Epsilonproteobacteria Alphaproteobacteria Most are oligotrophs: Rhizobium Rhizobium • nitrogen fixation in soil Pathogenic genera: Rickettsia • intracellular pathogens • typhus, Rocky Mountain spotted fever Chlamydia R. rickettsii • C. trachomatis – most common STD Betaproteobacteria Most are eutrophs: Thiobacillus • oxidize H S to sulfate is soil 2 Pathogenic genera: • important in sulfur cycle Neisseria • gonorrhea (N. gonorrheae) • meningococcal meningitis (N. meningitidis) Bordetella • whooping cough (B. pertussis) N. meningitidis Gammaproteobacteria Largest & most diverse class of Proteobacteria, including many enteric bacteria and human pathogens: Escherichia Vibrio • E. coli • cholera (V. cholerae) Legionella • legionnaires disease (L. pneumophila) Pseudomonas • opportunistic pathogens Salmonella • typhoid fever, foodborne L. pneumophila salmonellosis Deltaproteobacteria Small class of Proteobacteria containing soil bacteria that reduce sulfate (Desulfovibrio) and the Myxobacteria that form unusual “fruiting bodies”: Myxobacteria Epsilonproteobacteria Smallest class of Proteobacteria containing microaerophilic species that are typical helical or vibrioid in shape : Pathogenic genera: Helicobacter • H. pylori – peptic ulcers Campylobacter • various species cause blood poisoning, intestinal illness (e.g., C. jejuni) H. pylori 3. Gram-Negative & Phototropic Non-Proteobacteria Spirochetes Very thin, highly coiled bacteria that are hard to see under the microscope and harder to culture: Treponema • T. pallidum – syphilis Borrelia • B. burgdorferi – Lyme disease The CFB Group Grouped based on DNA similarity and includes the following genera: Cytophaga Fusobacterium Bacteroides • most are anaerobic rods • Some are potentially pathogenic (Cytophaga, Fusobacterium), others are beneficial (Bacteroides) Bacteroides Cyanobacteria Gram-negative, oxygenic photoautotrophs + • produce vast amounts of oxygen gas via photosynthesis, fix nitrogen (N2 NH4 ) Anabaena • carry out nitrogen fixation in non-photosynthetic heterocysts Vegetative cell Sheath Heterocyst Akinete Anabaena Oscillatora Purple & Green Bacteria Obligately anaerobic, anoxygenic photoautotrophs Green and Purple non-sulfur bacteria • use organic molecules as a source of electrons (not H2O) Green and Purple sulfur bacteria • use H2S as a source of electrons • elemental sulfur is then released (green sulfur bacteria) or forms inclusions (purple sulfur bacteria) 4. Gram-Positive Bacteria Classification of Gram-Positive Bacteria Gram-positive bacteria are grouped based on DNA similarity: Low G+C Gram-positive bacteria (Firmicutes) • contains many serious pathogens High G+C Gram-positive bacteria (Actinomycetes) • characterized by branching filaments • includes some pathogens Actinobacteria (High G+C) Streptomyces • important soil bacteria, recycle nutrients • many produce antibiotics (erythromycin, tetracycline) Corynebacterium C. diphtheria • diphtheria (C. diphtheria) Mycobacterium • contain mycolic acids in cell wall (stain acid-fast) • tuberculosis (M. tuberculosis), leprosy (M. leprae) Streptomyces Bifidobacterium • significant member of beneficial gut microbiota Firmicutes (Low G+C)… Streptococcus S. pyogenes • strep throat (S. pyogenes) Staphylococcus • MRSA (S. aureus) S. aureus C. difficile *Bacillus • anthrax (B. anthracis) *Clostridium *produce • tetanus (C. tetani) endospores • botulism (C. botulinum) • colitis (C. difficile) …more Firmicutes Lactobacillus • species used in fermented food products (e.g., yogurt, buttermilk, pickles) • part of normal, healthy microbiota in human mouth, digestive tract, vagina colonies Mycoplasma • very small (less than 1 mm) • no cell wall (stain Gram-negative) • obligate intracellular pathogens Mycoplasma 5. Deeply Branching Bacteria What Are “Deeply Branching Bacteria”? Bacteria very close to the base of the phylogenetic tree: • members of the domain Bacteria that diverged very early, ~3.5 billion years ago Last Common Universal Ancestor Genera of “Deeply Branching Bacteria” Acetothermus • deepest branching bacteria known to date D. radiodurans • thermophiles and hyperthermophiles Aquifex • adapted to harshest conditions on planet (e.g., thermal oceanic vents that reach 138oC!) Deinococcus • D. radiodurans known as “Conan the Bacterium” for the extremes of heat, UV, radioactivity, etc, it can survive 6. Archaea The Domain Archaea Highly diverse group of prokaryotes first classified in 1977 by Carl Woese and George Fox: • have metabolic processes, rRNA sequences and other features more closely resembling eukaryotes • e.g., initiate translation with methionine (as do eukaryotes) rather than N-formyl methionine as do the Bacteria • cell walls made of material other than peptidoglycan • have unusual membrane lipids • much larger genomes that bacteria Two Main Phyla Sulfolobus Crenarchaeota • most are hyperthermophiles, some acidophiles Euryarchaeota • includes the methanogens, halophiles, a few thermophiles Other Phyla • Korarchaeota, Nanoarchaeota, Thaumarchaeota • based on environmental RNA **NO known archaeon causes disease in humans or animals!** Key Terms for Chapter 4 • aerobic vs anaerobic • facultative vs obligate • phototroph, chemotroph, organotroph, lithotroph • autotroph, heterotroph, oligotroph, eutroph • symbiosis: mutualism, amensalism, commensalism, neutralism, parasitism • thermophile, halophile.
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