Bios 312 Notes from 4/8 and 4/11
Bios 312 Notes from 4/8 and 4/11 Bios 312
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Date Created: 04/12/16
4/8: Microbial Diversity Readings: 14.114.19 I: Functional Diversity 14.1 Making Sense of Microbial Diversity Functional diversity diversity in form and function as it relates to microbial physiology and ecology Functional trait shared between divergent organisms due to: o Gene loss trait present is lost in some lineages and retained in others o Convergent evolution trait evolved independently in 2 or more lineages, not encoded on homologs o Horizontal gene transfer II: Diversity of Phototrophic Bacteria 14.2 Phototrophic Bacteria 1 anoxygenic phototrophs, used H as2electron donor All use pigments to harvest light energy, membrane reaction enters to drive electron transfer 14.3 Cyanobacteria Cyanobacteria oxygenic phototrophic Bacteria, first oxygen evolving organisms oxygenated atmosphere All use Calvin cycle, some fix N ,2and some can synthesize their own vitamins 14.4 Purple Sulfur Bacteria Anoxygenic phototrophs, use H S a2 electron donor, found in lakes, color from accessory carotenoid o H S oxidized to S further oxidized to SO 2 2 4 o Chromatiaceae store S in granules inside the cell o Ectothiorhodospiraceae deposit S outside of the cell 14.5 Purple Nonsulfur Bacteria Not all purple, conserve energy via photoautotrophy, aerobic respiration, and fermentation Aerobic anoxygenic phototrophs obligate anaerobic heterotrophs, strict heterotrophs (diff. than purple nonS) 14.6 Green Sulfur Bacteria Anoxygenic phototrophs, oxidize H S fo2 autotrophic growth (see 14.4), deposits S only outside the cell Have chlorosomes (funnel energy into the photosystem), live in anoxic sulfidic aquatic environments Form consortium (2 membered association with chemoorganotrophic bacterium) 14.7 Green Nonsulfur Bacteria Anoxygenic phototrophs Chloroflexi, capable of gliding motility. Grow best via photoheterotrophy, but also capable of growth via photoautotrophy 14.8 Other Phototrophic Bacteria Heliobacter gram +, anoxygenic, in phylum Firmicutes, rod shaped, strict anaerobes, form endospores. Found in soil (able to fix N) III: Bacterial Diversity in the Sulfur Cycle 14.9 Dissimilative SulfateReducing Bacteria Couple oxidation of H t2re uction of SO , d4verse, aquatic/terrestrial environments. 2 physiological types: o Complete oxidizer oxidize acetate and other fatty acids completely to CO 2 o Incomplete oxidizer unable to oxidize acetate to CO 2 14.10 Dissimilative SulfurReducing Bacteria 0 2 Use respiratory S reduction to conserve energy, reduce S to H S,2but not to SO , m4st obligate anaerobes 14.11 Dissimilative SulfurOxidizing Bacteria Chemolithotrophs, oxidize reduced S compounds as electron donors, most obligate anaerobes. Either o Obligate chemolithotrophs grow autotrophically, convert CO int2 cell material, and contain Carboxysomes (increase rate of CO fix2 ion due to high concentration of RubisCO). o Mixotrophs 6 strategies used by aerobic sulfideoxidizers to cope with chemical instability of H S2in presence of O 2 o Thiothrix holdfast to position itself in high flow environment downstream of H S source 2 o Beggiatoa gliding motility to position at point where H S2and O c2occur o Thiomargarita separate temporally the oxidation of H S f2om the reduction of O 2 o Thioploca intracellular S granules and large vacuoles with NO , l3rge sheaths o Thiovulum rotation creates flow of water that generates gradients of H S2and O 2 o Symbiotic relationship with eukaryotic cell IV: Bacteria Diversity of the Nitrogen Cycle 14.12 Diversity of NitrogenFixing Bacteria Diazotrophs fix N 2into NH ,3nitrogenase irreversibly inhibited by O2 o Form symbiotic relationships, host provides hospitable environment and system for regulating O concentrations, symbiont provides supply of fixed N o Free living protecting nitrogenase from O, anoxic environments, fix N only at times when O is absent or 2 present in low concentrations 14.13 Diversity of Nitrifying and Dentrifying Bacteria and Archaea Denitrifies anaerobic respiration of inorganic N to gaseous products, facultative anaerobes/chemoorganotrophs Nitrifiers chemolitotrophically, reduced inorganic N compounds 2 physiological groups: o Ammonia oxidizers oxidize NH to3NO 2 o Nitrite oxidizers oxidize NO 2to NO 3 V: Diversity of Other Distinctive Chemotrophic Bacteria 14.14 Dissimilative IronReducing Bacteria Couple reduction of oxidized metal to cellular growth, using insoluble solid material as electron acceptor Possess outer membrane cytochromes that facilitate electron transfer with insoluble minerals 14.15 Dissimilative IronOxidizing Bacteria Couple the oxidation of Fe to cell growth, widespread Four function groups based on physiology: o Acidophilic aerobic ironoxidizing growth favored in ironrich acidic environments where soluble ferrous iron is present o Neutrophilic aerobic ironoxidizing ferrous Fe insoluble at neutral pH and chemical oxidation is spontaneous o Aerobic ironoxidizing 14.16 HydrogenMetabolizing Bacteria H 2is very electronegative, couple to any electron acceptor Hydrogenase enzyme binds H to2produce ATP or for reducing power for autotrophic growth, enzymes are oxygen sensitive. Grow aerobically on CO as electron donor 14.17 Methanotrophic and Methylotrophic Bacteria Methylotrophs grow using organic compounds lacking CC bonds Methanotrophs methane is substrate for growth Aerobic facultative methylotrophs are unable to use methane , but use other methylated compounds Methanotrophs possess the enzyme methane monooxygenase that catalyzes the incorporation of an O into CH 2 4 forming methanol (CH OH3 14.18 Acetic Acid Bacteria and Acetogens Acetic acid bacteria obligate aerobes, produce acetic acid, incomplete oxidation of alcohols and sugar accumulation of organic acids, can synthesize cellulose Acetogens obligate anaerobes, use acetyl CoA pathway 14.19 Predatory Bacteria Predatory bacteria predators that consume other bacteira, different methods of predation: o Epibiotic predators attach to surface and acquire nutirents from cytoplasm o Cytoplasmic predators invade host cells and replicate in cytoplasm o Periplasmic predators replicate within periplasmic space of their prey cells o Social predators swarming behavior to find prey, which they lyse and feed upon Bdellovibrio attachment, predator penetrates the cell, replicated in periplasmic space Myxobacteria form fruiting bodies Lecture: Categories of diversity: Hydrogen oxidation oxidizes H vis aerobic/anaerobic process as electron acceptor, produces water, Homoacetogens autotrophic, produces acetate (one product) from H and CO 2 Methylotrophy methane as source of C (electron donor) and energy, grow using reduced C compounds containing one or more C atoms but no CC bonds o Aerobic/anaerobic o Methane is being oxidized Nitrogen fixation assimilating atmospheric nitrogen into organic compounds Denitrification aerobic respiration in which nitrate is reduced 2o N under anoxic conditions Nitrification microbial oxidation of ammonia to nitrate (N3 to N3 ) Iron oxidation Fe is oxidized to Fe spontaneously in moderate pH conditions Iron reduction reduction of oxidized iron species (adding more bonds to H) 0 Sulfur oxidation oxidation of reduced sulfur compounds (H 2, S , and thiosulfate) 2 S4 Sulfur reduction reduction of oxidized iron species (adding more bonds to H) Oxygenic phototrophy use of light to synthesize ATP and NADPH by noncyclic photophosphorylation with the production of O2 from water Anoxygenic phototrophy use of light energy to synthesize ATP by cyclic photophosphorylation without O 2 production Microbial Diversity: Less than 1% of microorganisms viewed under a microscope have been cultivated (uncultivated majority) 90% characterized genera are from 4 phyla Epsilonproteobacteria gram , motile spirilla, oxidase and catalase positive, pathogenic to humans/animals o Abundant in oxicanoxic interfaces in S rich environments (hydrothermal vents) o Many are autotrophs (using H 2 formate, sulfide, or thiosulphate as electron donor) o Pathogenic and nonpathogenic representatives Helicobacter pylori most well studied member of the Epsilonproteobacteria o Gramnegative, slowgrowing organism. o Common human pathogen causing gastritis and stomach ulcers (lives on the mucous lining of stomach) o Multisubunit urease enzyme allows survival in acidic pH conditions and colonize the gastric environment. Result: bicarbonate production, neutralizes environment survive in acidic pH Sulfurospirillum freeliving bacteria capable of a variety of metabolisms. o S oxidation and nitrate reduction, reduction of TCE o Members of this genera have also been identified as symbionts of Alvinella pompejana Nautilli lithotrophica: Member of the family Nautilaiales, predominant microorganisms living as episympbionts on Alvinella pompejana Anammox: anoxic ammonia oxidation, by Planctomycetes o Anammoxosome is compartment where anammox reactions occur protects cell from hydrazine o Anammox is very beneficial in the treatment of sewage and wastewater, important in N cycling 4/11: Microbial Diversity: Bacteria Readings: 15.115.21 I: Proteobacteria 15.1 Alphaproteobacteria Oligotrophic prefer to grow in environments that have low nutrient concentration Rhizobiales, key genera: Bartonella, Methylobacterium, Pelagibacter, Rhizobium, Agrobacterium o Largest and most metabolically diverse order (phototrophs, chemolithotrophs, symbionts, nitrogenfixing bacteria, pathogens, and chemoorganotrophs), 9 different genera o Bartonella human pathogens Rickettsiales key genera: Rickettsia, Wolbachia, Rickettsia o Small, coccoid or rodshaped cells, most are obligate intracellular parasites o Causative agent of several human diseases (typhus, rocky mountain spotted fever) 15.2 Betaproteobacteria Rhodocyclales, key genera: Rhodocyclus, Zooglea o Wide range of metabolic and ecological characteristics o Rhodocyclus purple nonsulfur bacterium, grows best via photoheterotrophs and can also grow via photoautotrophy and respiration, anoxygenic, purple pigment, input of electrons other than S o Zooglea chemoorganotroph that produces thick capsule, important in wastewater treatment Neisseriales Key genera: Neisseria, Chromobacterium o Neisseria isolated from animals, pathogenic, cocci o Chromobacterium rodshaped, facultative aerobe, produce purple pigment violacein Opportunistic pathogen can be pathogenic, but infection doesn’t always occur 15.3/4 Gammaprotebacteria Pseudomonads polar flagella, oxidase positive o Beggiatoa filamentous, gliding bacteria, in habitats rich2in H S (S springs, sewage water) Most grow mixotrophically with reduced sulfur compounds as electron donors and organic compounds as carbon sources o Purple Sulfur Bacteria all are in gamma Use hydrogen sulfide (H 2) as an electron donor for CO2 reduction in photosynthesis Sulfide oxidized to elemental S that is stored as globules either inside or outside cells Sulfur later disappears as it is oxidized to sulfat4 (SO ) II: Firmicutes, Teneritcutes, Actinobacteria 15.9 Tenericutes: The Mycoplasmas Lack cell walls, some of the smallest organisms mycoplasmas, live with animal/plant hosts o Contain lipoglycans stabilize cytoplasmic membrane, help attach to receptor cells Spiroplasma lack cell wall/flagella, motile by means of rotary motion 15.10 Actinobacteria Coryneform bacteria gram +, aerobic, nonmotile (Corynebacterium and Arthrobacter) Propanic acid bacteria in Swiss cheese, fermentative production of CO2 15.11 Actinobacteria: Mycobacterium Acidfastness presence of mycolic acids (lipids), slow growing and fast growing species M. tuberculosis slow grower, cause tuberculosis 15.12 Filamentous Actinobacteria Actinomycetes filamentous, aerobic gram + Streptomyces lack cross walls in vegetative phase, create spores (conidia), found in soil, produce antibiotics o Resistant to their own antibiotics, but sensitive to antibiotics created by other Streptomyces III: Bacteriodetes 15.13 Bacteriodales Obligately anaerobic fermentative species, in human intestinal tract, synthesize sphingolipid (collection of lipids characterized by longchain amino alcohol) B. thetaiotaomicron degrades polysaccharides, in large intestine 15.14 Cytophaglaes, Flavobacteriales, and Sphingobacteriales Cytophaglaes mostly obligate aerobes, degrade polysaccharides, cellulose degradation via: o Free cellulose secrete enzymes that degrade insoluble cellulose outside the cell o Physical contact of cellulose fibers with cellulase enzyme on outer surface of cell walls Flavobacteriales marine environments, degrade starch and proteins Sphingobacteriales degrade many complex polysaccharides, pigmented IV: Chlamydiae, Planctomycetes, and Verrucomicrobia 15.15 Chlamydiae Intracellular parasites of eukaryotes, unique lifestyle including: o Elementary body small dense cell, resistant to drying, infectious transmission o Reticulate body larger, divides via binary fission, after divisions converted back to elementary 15.16 Planctomycetes Budding, lack peptidoglycan, resistant to antibiotics, contain organellelike structures (nucleoid, anammoxosome) Planctomyces stalked bacterium, no cell wall/cytoplasm in stalks (protein), function in attachment 15.17 Verrucomicrobia Ferment sugars, symbiotic association with protists form prosthecae (cytoplasmic appendages) V: Hyperthermophilic Bacteria 15.18 Thermotogae and Thermodesulfobacteria Thermotoga: Form sheathlike envelopes, found in terrestrial hot springs, show homology to hyperthermophilic Archaea Thermodesulfobacteria thermophilic sulfatereducing bacterium, strict anaerobe, etherlinked lipids (rare) 15.19 Aquificae Aquifex obligate chemolithotroph and autotrophic hyperthermophile, tolerate lo2 O concentrations o Autotrophy reverse TCA cycle Thermocrinis chemolithotroph, forms filamentous cells IV: Other Bacteria 15.20 DeinococcusThermus Aerobic chemoorganotrophs, resistant to radioactivity D. radiodurans highly efficient in repairing DNA, unique arrangement of DNA plays role in radiation resistance, DNA in a stack of rings 15.21 Other Notable Phyla of Bacteria Acidobacteria acidic soils, ecological effects in soil, metabolically diverse Nitrospirae oxidizes nitrite to nitrate, autotroph Deferribacteres thermophilic dissimilative ferric ironreducer, reduce nitrate and metal oxides Chrysiogenetes couple oxidation of acetate to reduction of arsenate arsenite Synergistetes associated with animals in anoxic environments, in GI tract Fusobacteria obligate anaerobes, fermentative, in human microbiome Lecture: 4 phyla that are known most about: Firmicutes, Bacteriodetes, Achtinobacteria, Proteobacteria Proteobacteria Proteobacteria major phylum of Bacteria, includes most commonly encountered bacteria, gram negative o o Most metabolically diverse of all Bacteria (chemolithotrophy, chemoorganotrophy, phototrophy) o 6 classes (alpha, beta, delta, gamma, epsilon, and zeta) Within classes there are pathogens and nonpathogens o Anaerobic chemoorganotrophic bacteria capable of Fe and S reduction Common in saturated soils and sediments Alphaproteobacteria: o Magnetospirillum magneticum move via magnetotaxis, nonpathogenic o Caulobacter crescentus model for cell differentiation because forms stalked and swarmer cell Betaproteobacteria: o Hydrogenophilales includes Thiobacillus denitrificans, denitrifying microorganism o Nitrosomonadales reduce into oxidized N species Gammaprotebacteria most wellknown for members of family Enterobacteraceae (in colon) o E. coli –feed on mucous secretions and produce vit K, some strains are pathogenic Different strains have different metabolic factors, don’t need to know all different strains o Enteric bacteria Salmonella (15.5) Deltaproteobacteria Key genera: Bdellovibrio, Myxococcus, Desulfovibrio, Geobacter, Syntrophobacter o Sulfate and sulfur reducers, dissimilative iron reducers, bacterial predators o Anaerobic chemoorganotrophic bacteria capable of iron and sulfur reduction Common in saturated soils and sediments o Myxococcalees Myxobacteria gliding bacteria that form multicellular structures (fruiting bodies) and show complex developmental life cycles, consumes dead organic matter or other bacterial cells Fruiting complex behavioral patterns Vegetative cells simple, nonflagellated rods that glide across surfaces Nutrients obtained through lysing other bacteria and utilizing released nutrients Under appropriate conditions, vegetative cells aggregate, construct fruiting bodies, and undergo differentiation into myxospores o Bdellovibrionales Bdevellovibrio prey on other bacteria, 2 stages of penetration, obligate aerobes, in soil, water, and marine environemtns, may be able to treat diseases (15.5)Epsilonproteobacteria Key genera: Campylobacter, Helicobacter o Campylobacter and Helicobacter Gramnegative, motile spirilla, oxidase and catalasepositive, pathogenic to humans and animals o Abundant in oxic–anoxic interfaces in sulfurrich environments (hydrothermal vents), autotrophs Using H 2 formate, sulfide, or thiosulphate as electron donor, pathogenic/nonpathogenic o Includes Heliobacter pylori common in stomach ulcers (15.68) Firmicutes Firmicutes: fermentative bacteria that produce lactic acid, 4 classes 11 orders 25 families and 240 species o Key genera: Bacillus, Clostridium, Sporosarcina Distinguished on the basis of cell morphology and on the shape and cellular position of endospore Generally found in soils, endospores are advantageous for soil microorganisms o Lactobacillus rod shaped, grows in chains, common in dairy, resistant to acidic conditions (low as 4) Lactobacillus reuteri heterofermentatic lactic acid bacterium. Colonizes stomach and intestine of animals. L. reuteri's produced folate and vitamin B12 and is used as a probiotic. o Bacillus anthracis is a grampositive, rodshaped bacterium, anthrax Habitat: Soil. facultative anaerobe st 1877: 1 organism shown to cause disease by Robert Koch and verified by Louis Pasteur. Deinococcus, deinococci Deinococcus radiodurans can withstand a lot of ionizing radiation One gray is the absorption of one joule of energy, in the form of ionizing radiation, by one kilogram of matter. Planctomyces Key genera: Planctomyces, Blastopirellula, Gemmata, Brocadia Gramnegative bacteria, divide by budding, stalked or appendaged, extensive cell compartmentalization (membrane closed nuclear structures) o Planctomyces is a stalked bacterium, primarily aquatic Gemmata equivalent of nucleus, nucleoid surrounded by nuclear envelope and contains ribosomes Brocadia anammoxidans different phenotypically from other Planctomyces due to anaerobic autotrophy Thermotogas Key genera: Thermotoga, Thermodesulfobacterium Thermotoga o Rodshaped, hyperthermophile (can grow at 90°C), anaerobic, fermentative, chemoorganotroph o 20% of genes likely originated from Archaea
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