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Microbial diversity (protist (Distribution (– grow in a wide …

- - - - Outer gelatinous ectoplasm just underneath plasma membrane
      - Inner fluid region termed endoplasm
  - - - Microaerophilic protist
        
        epidemic diarrhea from contaminated water
        
        members are flagellated and lack mitochondria
        
        Giardia have mitosomes
      - Most are harmless symbionts with the following exceptions :
        
        Giardia – causes diarrhea
        
        Hexamida salmonis – fish parasites
        
        H. meleagridis – turkey pathogen
    - - Most are flagellated endosymbionts of animals
        
        Lack a distinct cytosome, use phagocytosis to engulf food
      - Subgroups
        
        Trichonymphida
        
        • obligate mutuals of wood-eating insects such as termites
        
        • release cellulose for digesting
        
        • may account for 1/3 biomass in termite
        
        • ecdysone hormone produced by host triggers sexual reproduction
        
        Trichomonadida
        
        • do not required oxygen
        
        • possess hydrogenosomes
        
        • asexual reproduction only
        
        • symbionts of digestive, reproductive, and respiratory traits of many vertebrates, including humans
        
        some strains are human pathogens
    - - • Commonly found in fresh water
      - • 1/3 photoautotrophic, rest are chemoorganotrophs
      - • Euglena is the representative phototroph
        
        – pellicle - proteinaceous strips, microtubules
        
        – red eye spot (stigma) orients to light
        
        – chlorophylls a and b, carotenoids
        
        – contractile vacuole and flagella
  - - - Extremely diverse including
        
        diatoms
        
        golden and brown algae
        
        öomycetes and labyrinthulids
        
        haptophytes
        
        brown seaweeds and kelp
      - Diatoms
        
        • Chlorophylls and accessory pigments
        • Frustule – two-piece cell wall of silica
        
        • Asexual division
        
        • Important in global carbon cycling
    - - Apicomplexans
        
        • Distinguished by the unipolar apical complex
        • Parasitic with complex life cycles
        
        • Most important member is Plasmodium, the cause of malaria
      - Dinoflagellata dinoflagellates)
        
        • Large group found in marine plankton
        
        • Nutritionally complex
        
        • Trichocysts are defensive proteins
        
        • Symbiotic forms (zooxanthellae)
    - - • Chemoorganotrophic
      - • Found in both benthic and planktonic communities in water and soil systems
      - • Use many cilia as locomotory and feeding organelles
      - • Reproduction
        
        – asexual by transverse binary fission
        – sexual by conjugation
  - - - all higher plants and many algal species are included
- - - - Gram-negative rod
      - chemolithoautotroph
      - thermophile
      - microaerophilic
  - - - – have functional glycolytic pathway
      - – can grow anaerobically on carbohydrate/protein digest
      - – ~24% of coding sequences similar to archaeal genes
  - - - Aerobic-catalase positive
      - Extraordinarily resistant to desiccation and radiation
      - Isolated from ground meat, feces, air, freshwater and other sources but natural habitat is unknown
  - - - Chlorobi
        
        Green sulfur bacteria
        
        morphologically diverse, thrive in sulfide rich areas, have chlorosomes
        
        lack flagella, non-motile, some have gas vesicle
        
        obligate anaerobic photolithoautotrophs
        
        one class, Chlorobia
        
        one order Chlorobiales
        
        one family, Chlorobiaceae
        
        genera
        
        Chlorobium
        
        Pelodictyon
        
        Prosthecochloris
      - Chloroflexi
        
        Green nonsulfur bacteria
        
        Has both photosynthetic and non-photosynthetic members
        
        genus Chloroflexus (photosynthetic)
        
        genus Herpetosiphon (non-photosynthetic)
      - Cyanobacteria
        
        Largest, most diverse group of photosynthetic bacteria
        
        Chlorophyceae – blue green algae common term
        
        Gram-negative
        
        Many are obligate photolithoautotrophs but some can grow slowly in dark such as chemoheterotrophs
        
        Cyanobacteria I structures and arrangements
        
        Some storage structures have
        
        carboxysomes (enzymes for Calvin cycle)
        
        cyanophycin (arginine, aspartic acid)
        
        Range in diameter from ~1 to 10 µm
        
        May be unicellular, colonial, or filaments called trichomes (row of cells in close contact)
        
        Photosynthesis in Cyanobacteria – Carbon Fixation
        
        Use phycobiliproteins as accessory pigments
        
        phycobilisomes, which line thylakoid membranes, contain phycocyanin and phycoerythrin
        
        prochlorophytes lack phycobilins
        
        Use Calvin cycle to fix CO2
        
        Cyanobacterial Pigmentation
        
        Pigmentation
        
        most appear blue-green due to presence of phycocyanin
        
        presence of phycoerythrin in many ocean isolates gives them red or brown coloration
        
        chromatic adaption
        
        Phototaxis by use of gas vacuoles
        
        Cyanobacterial Ecological Relationship
        
        Often form symbiotic relationships
        
        phototrophic partner in most lichens
        
        symbionts with protozoa and fungi
        
        nitrogen-fixing species form plant associations
        
        Profound effect on global carbon cycle
        
        Synechococcus, Prochlorococcus
        
        Prochlorococcus evolved into two non-competing ecotypes (high light and low light)
  - - - anammoxosome compartment
        
        anammox reaction - localized anaerobic ammonia oxidation
        
        may contribute 70% of nitrogen cycling in oceans
    - - attaches to surfaces through stalk and holdfast
  - - - must grow and reproduce inside host cells
      - grow within hosts without adverse effects
    - - genus Chlamydia is best studied
  - - - Ecologically diverse
        
        free living
        
        symbiotic
        
        • hindguts of termites
        
        • digestive tracts of mollusks and mammals
        
        • oral cavities of animals
        
        disease
        
        Lyme disease and syphilis
  - - - Anaerobic, Gram-negative rods, various shapes
      - Chemoheterotrophs – fermentative
      - Often found in oral cavity and intestinal tract of humans and other animals and the rumen of ruminants
        
        often benefit host by degrading complex carbohydrates, providing extra nutrition to host
        
        constitute up to 30% of bacteria from human feces
        
        some cause disease
  - - - Proteobacteria may havearose from a single photosynthetic ancestor
      - 16S rRNA shows five distinct lineages
        
        -Alphaproteobacterium
        
        – Gammaproteobacterium
        
        – Deltaproteobacterium
        
        – Epsilonproteobacterium
        
        – Betaproteobacterium
  - - - Placed in phylum Firmicutes
      - divided into 3 classes
        
        • Clostridia
        
        • Bacilli
        
        • Negativicutes
    - - Actinomycetes
        
        Gram-positive, aerobicbacteria that produce filamentous cells called hyphae and differentiateinto asexual spores
        
        adapt to climates similar to fungi
        
        General Properties of the
        Actinomycetes
        
        Source of most currently used antibiotics
        
        Also produce metabolites that are anticancer, antihelminthic, and immunosuppressive
        
        Complex life cycle
        
        Most are not motile
        
        motility is restricted to flagellated spores
        
        Ecological Significance of Actinomycetes
        
        • Widely distributed in soil
        
        • Play important role in mineralization of organic matter
        
        • Most are free living, but a few are pathogens
        
        • Characteristics used in Actinomycete taxonomy
        
        four major cell wall types based on peptidoglycan structure and sugar content other than N-acetylglucosamine and N-acetylmuramic acid
- - - - degrade complex organic material in the environment to simple organic compounds and inorganic molecules
      - carbon, nitrogen, phosphorus, and other critical constituents are recycled for other living organisms
    - - fermentation – yeast used in making bread, wine, beer, cheese, soy sauce
      - – organic acids – citric and gallic acid
      - – certain drugs – ergometrine, cortisone
      - – antibiotics – penicillin, griseofulvin
      - – immunosuppressive agents – cyclosporin
    - - geneticists, cytologists, biochemists, biophysicists, and microbiologist
      - Saccharomyces cerevisiae
        
        yeast model system for cell biology, genetics, and cancer
  - - - – found in freshwater, marine, and terrestrial habitats
      - – red, brown, and blue-green molds cause food spoilage
      - – some are human and plant pathogens
      - – some yeasts and truffles are edible
      - – some used as research tools
      - Ascomycetes or sac fungi
      - Genus Aspergillus
        
        A. fumigatus
        
        A. oryzae
      - Pathogenic Ascomycota
        
        Claviceps purpura
        
        Candida, Blastomyces, Histoplasma
        
        Stachybotrys-siick building syndrome
        
        Aspergillus – aflatoxins and cancer
    - - Basidiomycetes (club fungi)
      - examples include rusts, shelf fungi, puffballs, toadstools, mushroom
      - sexual reproduction form basidium
      - Impact on Human Beings
        
        Decomposers
        
        Edible and non-edible mushrooms
        
        Pathogens of humans, other animals, and plants
        
        Cryptococcus neoformans – cryptococcosis
      - Urediniomycetes and Ustilaginomycetes
        
        Plant pathogens causing “rusts” and "smuts"
        
        Some urediniomycetes are also human pathogens
    - - Aseptate flat hyphae (appressoria)
      - Major importance as mycorrhizal symbionts of vascular plants
        
        form intracellular associations within roots of almost all herbaceous plants and tropical trees
        
        • Ectomycorrhizae do not penetrate root cells
        • Arbuscular mycorrhizae penetrate root cell wall
      - mutualistic relationship (both benefit)
        
        • fungus helps protect host from stress, delivers soil nutrients to the plant; plant provides carbohydrates to fungus
    - - • Zygomycetes
        • Most are saprophytes
      - • Form coenocytic hyphae containing numerous haploid nuclei
        • Some are industrial importance
      - • Usually reproduce asexually by spores that develop at the tips of aerial hyphae
      - • Sexual reproduction occurs when environmental conditions are not favorable
        
        – requires compatible opposite mating types
        
        – hormone production causes hyphae to produce gametes
        
        – gametes fuse, forming a zygote
        
        – zygote becomes zygospore
      - Genus Rhizopus
        
        R. stolonifer
        
        Importance
        
        Rhizopus-Burkholderia symbiosis
        
        Used to produce tempeh from soybeans
        
        Used with soybeans to make sufu curd
        
        Commercially
    - - Transitional form is a spore structure capable of surviving outside the host
      - Obligate intracellular fungal parasites that infect insects, fish, and humans
        
        Aquatic birds are common hosts and contribute to large numbers of spores in environment
      - Structurally similar to ‘classic’ fungi
        
        contain chitin, trehalose, and mitosomes
        
        however, lack mitochondria, peroxisomes and centrioles
        
        unique morphology is polar tube essential for host invasion
      - Microsporidia Pathogenesis
        
        Human infections
        
        Enterocystozoon bieneusi that causes diarrhea and pneumonia
        
        Encephalitozoon cuniculi that causes encephalitis and nephritis
        
        severe in HIV/AIDS patients
    - - Simplest fungi, also called chytrids
        
        – free living, saprophytic
        
        – parasitic forms infect aquatic plants, animals and insects
        
        – found in the anoxic rumen of herbivores
        
        – may be responsible for large-scale mortality of amphibians
      - Produce a zoospore with single, posterior, whiplash flagellum
        
        most primitive form of spore dispersal
        
        flagella lost in higher forms
      - Asexual and sexual reproduction
      - Many members degrade cellulose and keratin
- - - - group I archaea- archaeal unique membrane lipid, originally known as crenarchaeol (thaumarchaeol) is widespread in nature
      - Recent cultured growth of mesophilic archaea:
        
        capable of nitrification (ammonia to nitrate)
        
        this trait is the characteristic metabolic feature of this phylum
        
        nitrification by these microbes in marine environments may be very ecologically important
    - - Most are extremely thermophilic (hyperthermophiles)- hydrothermal vents
      - Most are strict anaerobes
      - Some are acidophiles but many are sulfur-dependent
      - General characteristics: include organotrophs and lithotrophs (sulfur-oxidizing and hydrogen-oxidizing)
      - Most studies are Sulfolobus and Thermoproteus
    - - Methanogens and methanogenesis
        
        produce methane
        
        Methanogenesis: last organic compound degradation step
        
        occurs in anaerobic environments (e.g. animal rumens, anaerobic sludge digesters, within anaerobic protozoa)
        
        26 genera, largest group of cultured archaea
        
        Ecological and Practical Importance
        
        Important in wastewater treatment
        
        Can produce significant amounts of
        methane
        
        Can oxidize iron
        
        can form symbiotic relationships with certain bacteria, assisting carbon/sulfur cycling
      - Halobacteria
        
        Order Halobacteriales; 17 genera in one family,
        Halobacteriaceae
        
        Extreme halophiles
        
        require at least 1.5 M NaCl
        
        growth optima near 3–4 M NaCl
        
        Aerobic, respiratory, chemoheterotrophs with
        complex nutritional requirements
      - Thermoplasms
        
        Class Thermoplasmata
        
        Genera
        
        – Thermoplasmataceae
        
        – Picrophilaceae
        
        – Ferroplasmataceae
        
        Thermoacidophiles nad lack cell walls
      - sulfate-reducing
        
        class Archaeoglobi; order Archaeoglobales
        
        irregular coccoid cells
        
        cell walls consist of glycoprotein subunits
        
        extremely thermophilic (optimum 83°C)
        
        isolated from marine hydrothermal vents
        
        metabolism
        
        lithotrophic (H2) or organotrophic (lactate/glucose)
        
        use sulfate, sulfite, or thiosulfite as electron acceptor
        
        possess some methanogen coenzymes
      - extremely thermophilic sulfur-metabolizers
        
        Class Thermococci; one order, Thermococcales
        
        Thermococcus, Paleococcus, Pyrococcus
        
        Motile by flagella
        
        Optimum growth temperatures 88–100°C
        
        Strictly anaerobic
        
        reduce sulfur to sulfite