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MICROBIAL DIVERSITY (THE FUNGI (EUMYCOTA) (Fungal Distribution and…

- - - - obtain electron for their respiration process
    - - produces organic compounds
    - - use energy from light to carry out cellular metabolism
  - - - some use electron acceptor in anaerobic respiration
      - some use as electron source
    - - organotrophs
      - lithotrophs
        
        sulfur-oxidising
        
        hydrogen-oxidising
      - 25 Genera
        
        most studies
        
        Sulfobolus
        
        Thermoproteus
  - - - have unique membrane lipid known as crenarchaeol (now known as thaumarchaeol)
    - - capable of nitrification (ammonia to nitrate)
  - - - produce methane
      - Methanogenesis
        
        occurs in anaerobic environments
        
        last organic compound degradation step
      - 26 genera, largest cultured groupsof archaea
        
        differ in morphology
        
        16S rRNA
        
        cell walls
        
        membrane lipids
      - Ecological and Practical Importance of Methanogens
        
        wastewater treatment
        
        produce significance amount of methane
        
        used as clean burning fuel and energy source
        
        greenhouse gas and may contribute to global warming
        
        oxidized iron
        
        corrosion of pipes
        
        form symbiotic relationships with certain bacteria, assisting carbon/sulfur cycling
    - - Order Halobacteriales;17 genera in one family, Halobacteriaceae
      - extreme halophiles
        
        require at least 1.5 M NaCl•cell wall disintegrates if [NaCl] < 1.5 M
        
        growth optima near 3–4 M NaCl
      - aerobic
      - respiratory
      - chemoheterotrophs with complex nutritional requirements
    - - Class Thermoplasmata
      - Three different genera
        
        Thermoplasmataceae
        
        Picrophilaceae
        
        Ferroplasmataceae
      - thermoacidophiles
      - lack cell walls
    - - Class Thermococci; one order, Thermococcales
      - motile by flagella
      - Optimum growth temperatures 88–100°C
      - strictly anaerobe
      - reduce sulfur to sulfide
    - - class Archaeoglobi; order Archaeoglobales :; one family with three genera, Archaeoglobus being one
      - irregular coccoid cells
        
        cell walls consists of glycoproteins 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
- - - - two best studied genera
        
        Aquifex
        
        G(-) rod
        
        thermophiles
        
        growth optimum 85°C - maximum 95°C
        
        microaerophilic
        
        chemolithoautotroph
        
        ses hydrogen, thiosulfite, and sulfur as electron donor
        
        uses oxygen as electron acceptor
        
        genome ~1/3 size of E. coli
        
        Hydrogenobacter
  - - - best studied genus
        
        Thermotoga
        
        G(-) rod
        
        outer sheathlike envelope balloons from ends of cell
        
        thermophiles
        
        grow in active geothermal areas
        
        optimum 80°C; maximum 90°C
        
        Chemoheterotrophs
        
        have functional glycolytic pathway
        
        can grow anaerobically on carbohydrate/protein digests
        
        ~24% of coding sequences similar to archaeal genes
        
        may be due to horizontal gene transfer
    - - Spherical or rod-shaped; in pairs or tetrads
        
        G(+) but, lack cell walls
        
        layered outer membrane similar to Gram-negatives
        
        L-ornithine in peptidoglycan
        
        lacks teichoic acid
        
        plasma membrane has large amounts of palmitoleic acid rather than phosphatidylglycerol phospholipids
      - Metabolism and Sources
        
        aerobic
        
        catalase (+)
        
        Extraordinarily resistant to desiccation and radiation
        
        Isolated from ground meat, feces, air, fresh water, and other sources, but natural habitat unknown
    - - Phylum Cyanobacteria
        
        carry out oxygenic photosynthesis
        
        have two photosystems
        
        water as electron donor
        
        generate oxygen during photosynthesis
        
        purple and green bacteria
        
        anoxygenic photosynthesis
        
        Largest, most diverse group of photosynthetic bacteria
        
        Chlorophyceae – blue green algae common term
        
        Gram-negative
        
        Many are obligate photolithoautotrophs; some can grow slowly in dark as chemoheterotrophs
        
        Cyanobacterial Structures and Arrangements
        
        Some storage structures have carboxysomes (enzymes for Calvin cycle) and cyanophycin (arginine, aspartic acid)
        
        Range in diameter from ~1 to 10 μm
        
        May be unicellular, colonial, or filaments called trichomes (a 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 - modulation of pigment concentrations in different light
        
        Phototaxis by use of gas vacuoles
        
        Ecology of Cyanobacteria
        
        Tolerant of environmental extremes
        
        Thermophilic species can grow at temperatures up to 75°C
        
        often are primary colonizers
        
        Can cause blooms in nutrient-rich ponds and lakes
        
        Some produce toxins
      - Phylum Chlorobi
        
        Green sulfur bacteria
        
        Morphologically diverse
        
        Thrive in sulfide rich areas
        
        Have chlorosomes
        
        ellipsoidal vesicles attached to plasma membrane
        
        contain accessory photosynthetic pigments
        
        very efficient light harvesting complexes
        
        Lack flagella; nonmotile
        
        Some have gas vesicles
        
        adjust depth of cell for light/H2S
        
        Obligate anaerobic photolithoautotrophs
        
        bacteriochlorophyll reaction center in plasma membrane
        
        use H2S, elemental sulfur, and H2 as electron sources
        
        elemental sulfur deposited outside cell
        
        Representative genera are Chlorobium, Prosthecochloris, and Pelodictyon
      - Phylum Chloroflexi
        
        Green nonsulfur bacteria
        
        Has both photosynthetic and non photosynthetic members
        
        Genus Chloroflexus – photosynthetic, use an unusual 3-hydroxypropionate bi-cycle to fix CO2
        
        Filamentous - gliding motility
        
        Thermophilic - often isolated from neutral to alkaline hot springs; grow in orange-reddish mats
        
        Metabolism
        
        Anoxygenic photosynthesis
        
        Does not use water as electron donor
        
        Photoheterotroph
        
        Can grow aerobically as a chemoheterotroph
        
        Genus Herpetosiphon - non photosynthetic
        
        Non-photosynthetic, gliding, rod-shaped, or filamentous
        
        Aerobic chemoorganotrophs with respiratory metabolism
        
        Isolated from fresh water and soil habitats
  - - - Morphologically unique in having compartmentalized cells – anammoxosome compartment
        
        Anammox reaction - localized anaerobic ammonia oxidation
        
        May contribute 70% of nitrogen cycling in oceans
      - Cell wall lacks peptidoglycan
      - Genus Planctomyces–attaches to surfaces through stalk and holdfast
      - Other genera lack stalk –most have life cycles in which sessile cells bud to produce motile swarmer cells
        
        Cells ultimately settle down, attach, and reproduce
    - - Gram-negative
      - Obligate intracellular parasites
        
        Must grow and reproduce inside host cells
        
        Although known for ability to cause disease, many grow within hosts such as protists, and animal cells without adverse effects
      - One class, one order, four families, six genera –genus Chlamydia is best studied
  - - - Slender, long with flexible helical shape
      - Creeping (crawling) motility due to a structure called an axial filament
    - - Ecologically diverse
        
        Free living
        
        Symbiotic
        
        Hindguts of termites
        
        Digestive tracts of mollusks and mammals
        
        Oral cavities of animals
        
        Disease
        
        Lyme disease and syphilis are spirochete diseases
  - - - Many contribute to digestion of cellulose, agar, chitin, etc.
    - - Anaerobic, Gram-negative rods, various shapes
        
        Do not form endospores
        
        Motile or nonmotile
      - 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
  - - - The largest phylogenetically coherent bacterial group with more than 500 genera
      - Remarkable diverse morphologically, physiologically, and other ways
    - - Proteobacteria may have arose from a single photosynthetic ancestor
      - 16S rRNA shows five distinct lineages
        
        Alphaproteobacterium
        
        Betaproteobacterium
        
        Includes Chemoheterotrophs and Chemolithotrophs
        
        Considerable metabolic diversity
        
        Overlap α-proteobacteriametabolically but generally use decomposed organic matter anoxically
        
        Some use hydrogen, methane, ammonia, volatile fatty acids
        
        Gammaproteobacterium
        
        Largest subgroup of proteobacteria–contains 14 orders and 28 families
        
        Very diverse physiological types
        
        Chemoorganotrophs, photolithotrophs, chemolithotrophs, methylotrophs
        
        Aerobic and anaerobic
        
        Many deeply branching
        
        Deltaproteobacterium
        
        Contains eight orders and 20 families - include Chemoheterotrophic, Anaerobes and Predators
        
        Divided into two general groups
        
        Aerobic, chemoorganotrophic predators
        
        Anaerobic, chemoorganotrophic sulfur- and sulfate-reducers
        
        Epsilonproteobacterium
        
        Smallest of proteobacterial classes
        
        Probably two orders, Campylobacteriales and Nautiliales; three families
        
        Slender Gram-negative rods
        
        Ranges from Pathogens to Deep-Sea Bacteria
        
        Newly discovered; are thermophilic, chemo- lithoautotrophic, and others
        
        Found in marine hydrothermal vents, terrestrial springs, ground water, oil-field brines, limestone caves, sulphidic springs
        
        Found in filamentous microbial mats in anoxic, sulfide-rich cave springs
  - - - Grouped based on shape (rods, cocci, or irregular) and ability to form endospores
      - Low G + C Gram positive bacteria Bergey's Manual
        
        Placed in phylum Firmicutes
        
        Divided into 3 classes
        
        Clostridia
        
        Bacilli
        
        Negativicutes
      - High G + C
        
        Actinomycetes
        
        Gram-positive, aerobic bacteria that produce filamentous cells called hyphae and differentiate into asexual spores
        
        Adapt to climates similar to fungi
        
        General Properties of the Actinomycetes
        
        Source of most currently used antibiotics
        
        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
- - - - Microaerophilic protist
        
        Epidemic diarrhea from contaminated water
        
        Members are flagellated and lack mitochondria
        
        Giardia have mitosomes(mitochondria-like double-membrane bounded organelles)
      - Most are harmless symbionts with the following exceptions
        
        Giardia – causes diarrhea
        
        Hexamidasalmonis – fish parasite
        
        H. meleagridis – turkey pathogen
    - - Most are flagellated endosymbionts of animals
      - Lack a distinct cytosome, use phagocytosis to engulf food
      - Two 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
    - - Most have a cytostome
        
        Characterized by a suspension-feeding groove
        
        Plays role in capturing particles from a feeding current
  - - - Terms for shape of pseudopods
        
        Lobopodia – rounded
        
        Filopodia – long and narrow
        
        Reticulopodia – form a netlike mesh
    - - Plasma membrane covered by material made by amoeba or obtained from the environment
  - - - Distinguished by fine pseudopodia (filopodia) - branched, simple, connected
      - Axopodia
        
        Filopodia supported by microtubules
        
        Protrude from the axoplast
        
        Primarily used in feeding
    - - Extremely diverse
        
        Diatoms
        
        Found in marine plankton
        
        Chlorophylls and accessory pigments
        
        Frustule – two-piece cell wall of silica
        
        Unique, beautiful patterns
        
        Asexual division – hypotheca template forming epitheca
        
        Important in global carbon cycling
        
        Produce 40% to 50% of organic carbon in ocean
        
        Golden and brown algae
        
        öomycetes and labyrinthulids: previously thought to be fungi
        
        Haptophytes
        
        Brown seaweeds and kelp
      - Unifying feature is heterokont flagella
    - - Large group
        
        Apicomplexa
        
        Distinguished by the unipolar apical complex
        
        Parasitic with complex life cycles
        
        Life cycle has both sexual and asexual phases
        
        Clonal and sexual stages are haploid, except for zygotes
        
        Sporozoite is the motile, infective stage
        
        Most important member is Plasmodium, the cause of malaria
        
        Dinoflagellata (dinoflagellates)
        
        Large group found in marine plankton - cause phosphorescence/toxic blooms in seawater
        
        Nutritionally complex
        
        Trichocysts are defensive proteins
        
        Symbiotic forms (zooxanthellae) – live in association with reef building corals
        
        Ciliophora
        
        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
- - - - Absorb nutrients from dead organic material by releasing degradative enzymes
      - Osmotrophy - absorb soluble products
  - - - Mycorrhizae – associations with plant roots
      - Lichens - associations with algae or cyanobacteria
    - - 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 microbiologists
      - Saccharomyces cerevisiae: yeast model system for cell biology, genetics, and cancer
  - - - A. fumigatus –ubiquitous environmental which causes allergies and significant pathogen
      - A. oryzae–production of fermented foods and also important in biotechnology
      - Aspergillus –37 Mb genome, model system
    - - Claviceps purpura
        
        Ergotism-toxic condition from eating infected grain due to lysergic acid diethylamide (LSD)
        
        Parasite on higher plants
      - Candida, Blastomyces, Histoplasma –human pathogens
      - Stachybotrys – “sick building syndrome”
      - Aspergillus – aflatoxins and cancer
  - - - Decomposers
      - Edible and non-edible mushrooms –toxins are poisons and hallucinogenic
      - Pathogens of humans, other animals, and plants
        
        Cryptococcus neoformans – cryptococcosis: systemic infection, primarily of lungs and central nervous system
  - - - Yeasts are infectious form
      - Mold - teliosporesform tumors
  - - - 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
  - - - Requires compatible opposite mating types
      - Hormone production causes hyphae to produce gametes
      - Gametes fuse, forming a zygote –zygote becomes zygospore
    - - R. stolonifer
        
        Grows on surface of moist carbohydrate rich foods such as bread
        
        Hyphae quickly cover surface as rhizoids, absorb nutrients
        
        Stolon hyphae become form new rhizoids
      - Importance of Genus Rhizopus
        
        Rhizopus-Burkholderia symbiosis –seedling blight in rice bacterium Burkholderia growing within Rhizopus produces toxin
        
        Used to produce tempeh from soybeans
        
        Used with soybeans to make sufu curd
        
        Commercially –used to produce anesthetics, birth control, alcohols, meat tenderizers, yellow coloring in margarine
  - - - Free living, saprophytic
      - Parasitic forms infect aquatic plants and animals, insects
      - Found in the anoxic rumen of herbivores
      - May be responsible for large-scale mortality of amphibians
    - - Most primitive form of spore dispersal
      - Flagella lost in higher forms
  - - - Aquatic birds are common hosts and contribute to large numbers of spores in environment
    - - Contain chitin, trehalose, and mitosomes
      - Lack mitochondria, peroxisomes and centrioles
      - Unique morphology is polar tube essential for host invasion
    - - Human infections
        
        Enterocystozoon bieneusi - Diarrhea, Pneumonia
        
        Encephalitozoon cuniculi - Encephalitis, Nephritis
        
        Severe in HIV/AIDS patients