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Microbial Diversity (Archaea (Physiological groups (Extremely thermophilic…

- - - - Group I archaea
      - Originally known as crenarchaeol
      - Widespread in nature
      - Unique membrane lipid (thaumarchaeol)
      - capable of nitrification
        
        Ammonia -> Nitrate
    - - 5 major groups
        
        Thermoplasms
        
        3 genera
        
        Thermoplasmataceae
        
        Picrophilaceae
        
        Ferroplasmataceae
        
        Thermoacidophiles
        
        Lack cell walls
        
        Extremely Thermophilic Sulfur-Reducers
        
        3 genera (one family)
        
        Thermococcus
        
        Paleococcus
        
        Pyrococcus
        
        Motile by flagella
        
        Optimum growth temperatures 88–100°C
        
        Strictly anaerobic
        
        Reduces Sulfur --> Sulfide
        
        Halobacteria
        
        17 genera (one family)
        
        Extreme halophiles
        
        growth optima near 3–4 M NaCl
        
        require at least 1.5 M NaCl
        (disintegrate)
        
        Aerobic
        
        Chemoheterotrophs with complex nutritional requirements
        
        Sulfate-Reducing
        
        3 genera (one family)
        
        irregular coccoid cells
        
        cell walls = glycoprotein subunits
        
        extremely thermophilic (optimum 83°C)
        
        isolated from marine hydrothermal vents
        
        metabolism
        
        possess some methanogen coenzymes
        
        e- acceptor: sulfate / sulfite / thiosulfite
        
        Lithotrophic / organotrophic
        
        Methanogens
        
        Characteristics
        
        26 genera (largest group)
        
        Differ in morphology
        
        Importance
        
        Produce methane
        
        Used as clean burning fuel & energy source
        
        Contribute to global warming (greenhouse gas)
        
        Important in wastewater treatment
        
        Can oxidize iron
        
        Contribute to pipe corrosion
        
        Can form symbiotic relationships with certain bacteria
        (assist carbon / sulfur cycling)
    - - Most are extremely
        thermophilic
        
        hyperthermophiles (hydrothermal vents)
      - Most are strict anaerobes
      - Some are acidophiles
      - Many are sulfur-dependent
        
        used as e- source
        
        used as e- acceptor in anaerobic respiration
      - Include organotrophs and lithotrophs
      - Contains 25 genera
        
        Best studied
        
        Sulfolobus
        
        Thermoproteus
  - - - Rod / cocci / irregular-shaped cells
      - Most: bright-red colonies, Some: unpigmented
      - Mesophilic
    - - Pleomorphic cells
      - Thermoacidophilic & chemoorgnotrophic
      - Facultative anaerobe
    - - Regular and irregular cocci
      - Thiosulfate + Sulfate = Hydrogen Sulfide
      - Extremely thermophilic & strictly anaerobic
    - - Rods / filaments / cocci
      - Obligate thermophile
      - Strict anaerobe (may be aerobic / facultative)
      - Acidophilic / Neutrophilic
    - - Methane = end product
      - Strict anaerobes
    - - Marine and soil environment
      - Chemolithoautothropic
      - e- donor: ammonia, e- acceptor: oxygen
- - - - Aquifex & Hydrogenobacter (most studied genera)
      - Aquifex
        
        Gram -ve; rod-shaped
        
        thermophile
        
        microaerophilic
        
        chemolithoautotroph
      - thermophiles
    - - alpha (α)
        
        Rickettsiales (short, non-motile rod; aerobic; obligate intracellular parasite) & Holosporales
      - beta (β)
        
        chemoheterotroph & chemolithotroph
        
        use decomposed organic matter anoxically
        
        some use hydrogen, methane, ammonia volatile fatty acids
      - gamma (γ)
        
        chemoorganotroph, photolithotroph, chemolithotroph, methylotroph; aerobic & anaerobic
      - delta (δ)
        
        aerobic, chemoorganotroph, predator
        
        anaerobic, chemoorganotroph, sulfur- & sulfate-reducer
      - epsilon (ε)
        
        Camphylobacteriales & Nautiliales
        
        slender, Gram -ve, rod-shaped
        
        pathogens -> deep sea bacteria
        
        thermophilic; chemolithotroph
    - - Thermotoga
        
        Gram -ve; rod-shaped
        
        has outer sheath-like envelope
        
        thermophiles
        
        chemoheterotroph
    - - Gram +ve; (lack typical Gram +ve cell wall - thick)
        
        outer membrane layer similar to Gram -ve
        
        has L-ornithine in peptidoglycan
        
        lacks teichoic acid
      - spherical / rod-shaped; pairs / tetrads
      - plasma membrane has palmitoleic acid rather than phosphatidylglycerol phospholipids
      - aerobic; catalase +ve
      - resistant to desiccation and radiation
      - isolated from ground meat, feces, air, fresh water and other; natural habitat is unknown
      - extremophiles
    - - Actinobacteria
        
        high G+C content
        
        Gram +ve, aerobic
        
        produce filamentous cells (hyphae); differentiate into asexual spore
        
        adapt to climate (similar like fungi)
        
        source of most currently used antibiotics
        
        produce anti-cancer, anti-helminthic & immunosuppressive metabolites
        
        most non-motile due to flagellated spores
        
        mostly in soil; play roles in organic matter mineralization
        
        most free living; some pathogens
      - Firmicutes
        
        low G+C content
        
        3 classes : Clostridia, Bacilli & Negativicutes
    - - Planctomycetes
        
        has compartmentalized cells (annamoxosome); carry out anammox reaction (anaerobic ammonia oxidation)
        
        cell wall lacks peptidoglycan; not a Gram -ve / Gram +ve
        
        attach through stalk & holdfast (Planctomyces), others genera lack stalk; most have sessile cells bud (produce motile swarmer cells) in life cycle
      - Chlamydiae
        
        Gram -ve
        
        obligate intracellular parasite (need host to grow & reproduce)
    - - chemoheterotroph
      - contribute to digestion of cellulose, agar, chitin
      - terrestrial & marine environment; sewage treatment plant
      - Bacteroides
        
        Gram -ve rods: shape vary
        
        do not form endospores
        
        motile / non-motile
        
        chemoheterotroph - fermentative
        
        in oral cavity & intestinal tract
    - - slender, long with flexible helical shape
      - Gram -ve
      - chemoheterotroph
      - creeping / crawling motility - due to axial filament
      - ecologically diverse
        
        free living
        
        symbiotic -> hindguts of termites, digestive tracts of mollusks & mammals, oral cavities of animals
        
        disease -> Lyme disease & syphilis
    - - Chlorobi
        
        genera
        
        Chlorobium
        
        Prosthecochloris
        
        Pelodictyon
        
        green sulfur bacteria
        
        have chlorosomes
        
        ellipsoidal vesicles; attached to plasma membrane
        
        contain accessory photosynthetic pigments
        
        efficient light harvesting complexes
        
        thrive in sulfide rich area
        
        non-motile; lack flagella
        
        gas vesicles (some); adjust cell depth for light / hydrogen sulfide
        
        obligate anaerobic photolithoautotrophs
        
        bacteriochlorophyll reaction in plasma membrane
        
        hydrogen sulfide, elemental sulfur and hydrogen -> electron sources
        
        elemental sulfur deposited outside cell
      - Gram -ve thermophilic - Acidobacteria
      - Firmicutes (heliobacteria)
      - Cyanobacteria
        
        oxygenic photosynthesis (produce oxygen)
        
        2 photosystems
        
        water as electron donor
        
        purple & green -> anoxygenic photosynthesis
        
        purple sulfur
        
        γ-proteobacteria family ( Chromatiaceae & Ectothiorhodospiraceae)
        
        purple non-sulfur
        
        α- and β-proteobacteria
        
        storage structure (some) contains
        
        carboxysomes; enzymes for Calvin cycle (Calvin cycle to fix carbon dioxide)
        
        cyanophycin; arginine, aspartic acid
        
        Chlorophyceae -> blue-green algae
        
        Gram -ve
        
        most obligate photolithoautotroph; some can grow slowly in dark as chemoheterotroph
        
        may be unicellular, colonial or filaments (trichomes -> row of cells in close contact)
        
        cause bloom in nutrient-rich ponds & lakes; some produce toxin
        
        form symbiotic relationship
        
        phototrophic partner in lichens
        
        symbionts with protozoa & fungi
        
        nitrogen-fixing species form plant association
        
        phycobiliproteins - accessory pigments
        
        phycobilisomes - line thylakoid membranes, contain phycocyanin (blue-green) & phycoerythrin (red / brown)
        
        prochlorophytes - lack phycobilins
      - Chloroflexi
        
        green non-sulfur bacteria
        
        photosynthetic -> Chloroflexus; use unusual 3-hydroxypropionate bi-cycle to fix carbon dioxide
        
        filamentous; gliding motility
        
        thermophilic
        
        anoxygenic photosynthesis; doesn't use water as electron donor, photoheterotroph
        
        can grow aerobically as chemoheterotroph
        
        non-photosynthetic -> Herpetosiphon
        
        filamentous; gliding motility
        
        rod-shaped
        
        aerobic; chemoheterotroph with respiratory metaboilsm
        
        isolated from fresh water and soil habitats