Microbial diversity

Microbial diversity

1. Fungi

   • Fungal Distribution and Importance -Industrial and Research Use
   • Ascomycota
     • Aspergillus
       • A. fumigatus
         • – ubiquitous environmental – allergies and significant pathogen
       • A.spergillus
         • – 37 Mb genome, model system
       • A. oryzae
         • production of fermented foods – important in biotechnology
     • • Ascomycetes or sac fungi – 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
     • More Pathogenic Ascomycota
       • • Claviceps purpura – parasite on higher plants – ergotism • toxic condition from eating infected grain • due to lysergic acid diethylamide (LSD) • Candida, Blastomyces, Histoplasma – human pathogens • Stachybotrys – “sick building syndrome” • Aspergillus – aflatoxins and cancer
   • Basidiomycota
     • Urediniomycetes
       • Some urediniomycetes are also human pathogens
     • Ustilaginomycetes
       • Plant pathogens causing “rusts” and “smuts’ – dimorphic • yeasts are infectious form • mold - teliospores form tumors
     • • Basidiomycetes (club fungi) – examples include rusts, shelf fungi, puffballs, toadstools, mushrooms – sexual reproduction form basidium • basidiospores are released at maturity
     • Basidiomycota Impact on Human Beings
       • • Decomposers • Edible and non-edible mushrooms – toxins are poisons and hallucinogenic • Pathogens of humans, other animals, and plants – e.g. Cryptococcus neoformans – cryptococcosis • systemic infection, primarily of lungs and central nervous system 34
   • Glomeromycota
     • • Aseptate flat hyphae (appressoria) to penetrate host plants; produce large, multinucleate spores and only reproduce asexually • 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
   • Zygomycota
     • Genus Rhizopus• Zygomycetes • Most are saprophytes – a few are plant and animal parasites • Form coenocytic hyphae containing numerous haploid nuclei • Some of industrial importance – foods, antibiotics and other drugs, meat tenderizer, and food coloring • 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
     • 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
   • Chytridiomycota
     • • Simplest fungi, also called chytrids – 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 • 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
   • Microsporodia
     • • Obligate intracellular fungal parasites that infect insects, fish, and humans – Aquatic birds are common hosts and contribute to large numbers of spores in environment • Transitional form is a spore structure capable of surviving outside the host • 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 • diarrhea • Pneumonia – Encephalitozoon cuniculi • encephalitis • Nephritis – severe in HIV/AIDS patients
   • • Eukaryotic, spore-bearing • Chemoorganoheterotrophs with absorptive metabolism • Saprophytes – absorb nutrients from dead organic material by releasing degradative enzymes – osmotrophy - absorb soluble products • Lack chlorophyll • Reproduce sexually and asexually
   • Tricky Taxonomy of Fungi • Basidiomycota and Ascomycota are dikarya – two parental nuclei are initially paired – nuclei fuse, undergo meiosis, produce haploid progeny • Zygomycota and Chytridiomycota are paraphyletic – taxonomic group includes some descendents of a single common
   • Fungal Distribution and mportance
     • • Primarily terrestrial, few aquatic – global from polar to tropical • Primarily terrestrial – few aquatic species • Many are pathogenic in plants or animals • Some form associations – mycorrhizae – associations with plant roots – lichens • associations with algae or cyanobacteria • Decomposers – 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
     • • Industrial importance – 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 • Research use – geneticists, cytologists, biochemists, biophysicists, and microbiologists – Saccharomyces cerevisiae • yeast model system for cell biology, genetics, and cancer 28

2. Protists

   • Super-Group Excavata
     • Fornicata
       • Microaerophilic protist – epidemic diarrhea from contaminated water – members are flagellated and lack mitochondria – Giardia have mitosomes (mitochondria-like doublemembrane bounded organelles)
       • Most are harmless symbionts with the following exceptions – Giardia – causes diarrhea – Hexamida salmonis – fish parasite – H. meleagridis – turkey pathogen
     • Parabasilia
       • Most are flagellated endosymbionts of animals
       • Lack a distinct cytosome, use phagocytosis to engulf food
       • 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
     • Euglenozoa
       • 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 10
     • Includes Fornicata, Parabasilia, and Euglenozoa
     • Includes some of most primitive, or deeply branching eukaryotes – most have a cytostome • characterized by a suspension-feeding groove • plays role in capturing particles from a feeding current
   • Super-Group Amoebozoa
     • Amoeboid motility - use of pseudopodia for locomotion and feeding
       • terms for shape of pseudopods • lobopodia – rounded • filopodia – long and narrow • reticulopodia – form a netlike mesh
     • Naked amoebae are surrounded only by a plasma membrane
     • Testate amoebae
       • plasma membrane covered by material made by amoeba or obtained from the environment
     • Reproduce by binary or multiple fission
   • Super-Group Rhizaria
     • Stramenophila
       • Diatom
         • found in marine plankton – produce 40% to 50% of organic carbon in ocean
           • Important in global carbon cycling
         • Chlorophylls and accessory pigments
         • Frustule – two-piece cell wall of silica – unique, beautiful patterns
         • Asexual division – hypotheca emplate forming epitheca
       • golden and brown algae
       • öomycetes and labyrinthulids • previously thought to be fungi
       • haptophytes
       • brown seaweeds and kelp
       • Unifying feature is heterokont flagella
     • Alveolata
       • Apicomplexa (Apicmplexans)
         • 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
         • many cilia as locomotory and feeding organelles
         • Reproduction – asexual by transverse binary fission – sexual by conjugation
     • Includes Stramenopila, Alveolata
     • Amoeboid in morphology – distinguished by fine pseudopodia (filopodia) - branched, simple, connected
     • axopodia • filopodia supported by microtubules • protrude from the axoplast • primarily used in feeding
   • Super-Group Archaeplastida
     • Includes organisms containing a photosynthetic plastid that arose through an ancient endosymbiosis with a cyanobacterium – all higher plants and many algal species are included 19
       • Chloroplastida
         • Chiorella
         • Volvox
         • Spirogyra
         • Acetabularia
       • Chlamydomonas
   • Lack the level of tissue organization present in higher eukaryotes
   • Most are unicellular
   • Distribution
     • grow in a wide variety of moist habitats
     • most are free living
     • chemoorganotrophic forms play role in recycling nitrogen and phosphorus
     • terrestrial and planktonic forms
     • parasitic forms cause disease in humans and domesticated animals

3. Archaea

   • Phylum Crenarchaeota: Metabolically Diverse Thermophile
     • -Hyperthermophilic (hydrothermal vents)
     • Strict anaerobes
     • Some are acidophiles
     • Many are sulfur dependent
     • Include organotroph and lithotroph (sulfur oxidizing and hydrogen oxidizing)
     • Contain 25 genera
       • Sulfolobus
       • Thermoproteus
   • Phylum Thaumarchaeota: Mesophilic Ammonia Oxidizers)
     • GROUP 1 ARCHAEA :The discovery of an archeal-specific lipid called crenarchaeol
       • Now known as thaumarcheol
         • rice paddies
         • soil
         • freshwater
         • marine waters
     • Recent cultured growth of mesophilic archaea
       • Capable of nitrification (ammonia to nitrate)
       • Metabolic feature of this phylum
       • Nitrification of microbes in marine ienvironment (ECOLOGICALLY IMPORTANT)
   • Euryachaeota
     • Methanogen
       • Methanogens : produce methane
       • Methanogenesis: last organic compound degradation step
         • Occur in anaerobic env.
       • Importance
         • Wastewater treatment
         • Can produce enough amounts of methane
     • Halobacteria
       • Extreme halophiles
         • Require at least 1.5 NaCl
         • Aerobic, respiratory, chemoheterotrophs with complex nutrional requirements
     • Thermoplasms
       • Thermoacidophiles
       • Lack cell walls
     • Extremely thermophilic Sulfur-metabolizers
       • Thermococcus, Paleococcus, Pyrococcus
       • Motile by flagella
       • Optimum growth temperatures 88-100 C
       • Strictly anaerobic
       • Reduce sulfur to sulfide
     • Sulfur reducer
       • Archaeoglobus
       • Irregular coccoid cells
       • Metabolism
         • Lithotrophic or organotrophic
         • Use sulfate, sulfite or thiosulfaite as e acceptor
         • Possess some methanogen coenzymes
       • Extremely thermophilic (optimum 83 C)

4. Bacteria

   • Deinococcus-Thermus
     • Two orders
       • Deinococcales
       • Thermales
     • Spherical or rod-shaped; in pairs or tetrads
       • Gram +ve, lack typical gram-positive cell wall)
         • Layered outer membrane similar to Gram -ve
         • L-ornithine in peptidoglycan
         • Lack techoic acid
       • plasma membrane has large amount of palmitoleic aacid rather than phosphatidylglycerol phospholipis
     • Metabolism
       • Aerobic
         • Catalase +ve
       • Extraordinarily resistant to desiccation and radiation
       • Isolated from ground meat, feces, air, fresh water and other sources but natural habitat unknown
   • Photosynthetic Bacteria
     • Chlorobi(Green sulfur bacteria)
       • Chlorobium
       • Prosthecochloris
       • Pelodictyon
       • Morphologically diverse
       • Thrive in sulfide rich areas
       • Have chlorosomes
       • Lack flagella; nonmotile
       • Some have gas vesicles
       • Obligate anaerobic photolithoautotrophs
     • Chloroflexi (Green nonsulfur bacteria)
       • 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
         • nonphotosynthetic
         • non-photosynthetic, gliding, rod-shaped, or filamentous
         • aerobic chemoorganotrophs with respiratory metabolism
         • isolated from fresh water and soil habitats
     • Firmicutes
     • Cyanobacteria
       • 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
       • Classification of Cyanobacteria
         • morphology and reproductive patterns
         • ultrastructure
         • genetics
         • habitat, ecology
         • physiology and biochemistry
       • Cyanobacteria l 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 (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
       • Cyanobacterial Ecological Relationships
         • Often form symbiotic relationships – e.g. are phototrophic partner in most lichens – e.g. symbionts with protozoa and fungi – e.g. nitrogen-fixing species form plant associations
         • Profound effect on global carbon cycle
         • Synechococcus, Prochlorococcus – two marine genera; ~1/3 of global CO2 fixation – less than 1% of ocean mass
   • Phylum Chlamydiae
     • 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 51
   • Phylum Spirochaetes
     • Gram-negative, chemoheterotrophic bacteria with distinctive structure and motility *slender, long with flexible helical shape * creeping (crawling) motility due to a structure called an axial filament
     • Oxygen requirements vary
     • Symbiotic Associations between Spirochetes and Other Organisms
       • 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
   • Proteobacteria
     • Class Alphaproteobacteria
     • Class Betaproteobacteria
       • Seven orders, 12 families
       • Includes Chemoheterotrophs and Chemolithotrophs
       • Considerable metabolic diversity – overlap α-proteobacteria metabolically but generally use decomposed organic matter anoxically – some use hydrogen, methane, ammonia, volatile fatty acids
     • Class Gammaproteobacteria
       • Largest subgroup of proteobacteria – contains 14 orders and 28 families
       • Very diverse physiological types – chemoorganotrophs, photolithotrophs, chemolithotrophs, methylotrophs – aerobic and anaerobic
       • Many deeply branching groups
     • Class Deltaproteobacteria
       • Contains eight orders and 20 families - includse Chemoheterotrophic Anaerobes and Predators – divided into two general groups
         • aerobic, chemoorganotrophic predators
         • anaerobic, chemoorganotrophic sulfur- and sulfate-reducers
     • Class Epsilonproteobacteria
       • Smallest of proteobacterial classes
       • Probably two orders, Campylobacteriales and Nautiliales; three families
       • Slender Gram-negative rods
       • Ranges from Pathogens to Deep-Sea Bacteria
       • 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
       • Newly discovered; are thermophilic, chemolithoautotrophic, and others
     • The largest phylogenetically coherent bacterial group with more than 500 genera
     • Remarkable diverse morphologically, physiologically, and other ways
   • Gram-Positive Bacteria
     • Firmicutes
       • Low G + C
       • divided into 3 classes • Clostridia • Bacilli • Negativicutes
     • Actinobacteria
       • High G + C
       • Gram-positive, aerobic bacteria that produce filamentous cells called hyphae and differentiate into asexual spores
       • adapt to climates similar to fungi
       • General Properties
         • 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
   • Aquificae
     • Genus Aquifex
       • Gram -ve rod
       • Thermophile
       • Microaerophilic
       • Chemolithoautotroph
     • The deepest (oldest) branch of Bacteria
     • Bacterial thermophiles
   • Thermotogae
     • Second deepest branch of Bacteria
     • Genus Thermotoga
       • Chemoheterotrophs
         • have functional glycolytic pathway
         • can grow anaerobically on carbohydrate/ protein digests
         • 24% of coding sequences similar to archeal genes
           • may be due to horizontal gene transfer
       • Gram -ve rods
         • Outer sheathlike envelope ballons from ends of cell
       • Thermophiles
         • Grow active in geothermal areas
           • Marine hydrothermal vents/ terrestrial solfataric springs
   • Phylum Planctomycetes
     • 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
   • Phylum Bacteriodetes
     • Very diverse – all known members are chemoheterotrophs – Many contribute to digestion of cellulose, agar, chitin, etc.
     • Common in variety of terrestrial and marine environments, and in sewage treatment plants
     • Includes important gut microbiota
     • Genus Bacteroides
       • 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