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Bios 312 Notes from 4/8 and 4/11

by: Cara Cahalan

Bios 312 Notes from 4/8 and 4/11 Bios 312

Marketplace > University of Nebraska Lincoln > Biology > Bios 312 > Bios 312 Notes from 4 8 and 4 11
Cara Cahalan
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These are notes for test 4 that include microbial diversity and bacterial diversity. Includes book notes and notes from lecture.
Karrie Weber
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This 7 page Bundle was uploaded by Cara Cahalan on Tuesday April 12, 2016. The Bundle belongs to Bios 312 at University of Nebraska Lincoln taught by Karrie Weber in Spring 2016. Since its upload, it has received 22 views. For similar materials see Microbiology in Biology at University of Nebraska Lincoln.


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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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