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1. Prokaryote Habitats, Relationships & Biomes Important Metabolic

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1. Prokaryote Habitats, Relationships & Biomes Important Metabolic 3/9/2020 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 1. Prokaryote Habitats, Relationships & Biomes 2 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 3 1 3/9/2020 …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 4 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) 5 Microbiomes All the microorganisms that inhabit a particular organism or environment (e.g., human or soil microbiome): 6 2 3/9/2020 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 7 2. Proteobacteria Alphaproteobacteria Betaproteobacteria Gammaproteobacteria Deltaproteobacteria Epsilonproteobacteria 8 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 9 3 3/9/2020 Betaproteobacteria Most are eutrophs: Thiobacillus • oxidize H2S to sulfate is soil Pathogenic genera: • important in sulfur cycle Neisseria • gonorrhea (N. gonorrheae) • meningococcal meningitis (N. meningitidis) Bordetella • whooping cough (B. pertussis) N. meningitidis 10 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 11 Deltaproteobacteria Small class of Proteobacteria containing soil bacteria that reduce sulfate (Desulfovibrio) and the Myxobacteria that form unusual “fruiting bodies”: Myxobacteria 12 4 3/9/2020 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 13 3. Gram-Negative & Phototropic Non-Proteobacteria 14 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 15 5 3/9/2020 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 16 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 17 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) 18 6 3/9/2020 4. Gram-Positive Bacteria 19 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 20 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 21 7 3/9/2020 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) 22 …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 23 5. Deeply Branching Bacteria 24 8 3/9/2020 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 25 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 26 6. Archaea 27 9 3/9/2020 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 28 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!** 29 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 30 10.
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