Microbiology Exam 3 (Autosaved) PDF

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Microbiology Exam 3 Ch. 13 Microbial Evolution - Bacteria and Archaea are generally HAPLOID and ASEXUAL, they have several mechanisms for HORIZONTAL GENE TRANSFER that result in the asymmetrical exchange of genetic material uncoupled from reproduction, and their genomes can be remarkably HETEROGENOUS and HIGHLY DYNAMIC 13.5 The Evolutionary Process - Evolution is a change in ALLELE frequencies in a population of organisms over time resulting in descent with modification o New alleles arise from a result of MUTATION and RECOMBINATION, and changes in allele frequencies can occur through a variety of processes Origins of Genetic Diversity - Mutations – random changes in DNA sequence that accumulate over time and they are a fundamental source of the natural variation that drives the evolutionary process o Several forms like substitutions, deletions, insertions, and duplications  Duplication events produce a redundant copy of a gene that can be modified by further mutation without losing the function encoded by the original gene. Hence, duplications allow for the DIVERSIFICATION of gene function - Recombination – a process by which segments of DNA are broken and rejoined to create new combinations of genetic material o Can cause reassortment of genetic material already present in a genome o Also required for the INTEGRATION into the genome of DNA acquired through horizontal gene transfer o Can be classified as either HOMOLOGOUS or NONHOMOLOGOUS  H: requires short segments of highly similar DNA sequence flanking the region of DNA being transferred  NH: mediated by several mechanisms that share in common the fact that they DO NOT require high levels of sequence similarity to initiate successful DNA integration Selection and Genetic Drif - Selection is defined on the basis of FITNESS – the ability of an organism to produce progeny and contribute to the genetic makeup of future generations o Most mutations are NEUTRAL with respect to fitness and they have no effect on the cell, as a result of the degeneracy of the genetic code  These mutations are DELETERIOUS  These DECREASE the fitness of an organism by disrupting gene function  Some mutations can be BENEFICIAL, increasing the FITNESS of an organism, and the mutations are favored by natural selection, INCREASING in frequency in a population over time  REMEMBER: all mutations occur by CHANCE; the selective nature of the environment does NOT cause adaptive mutations but simply select for

the growth and reproduction of those organisms that have incurred mutations that provide a fitness advantage - Genetic Drif – random process that can cause gene frequencies to change over time, resulting in evolution in the absence of natural selection o This occurs because members of a population will have more offspring that others simply as a result of chance; over time these chance events can result in evolutionary change in the absence of selection o Most powerful in small populations and in populations that experience frequent “bottleneck” events o The latter occur when a population experiences a severe reduction in population size followed by regrowth from the cells that remain  EX: GD important in evolution of pathogens because each new infection is caused by a small number of cell colonizing a new host New Traits Can Evolve Quickly in Microorganisms - A change in environment or the introduction of cells to a new environment can cause rapid evolutionary changes in microbial populations o Rapid populations o The heritable variation already present in a population provides the raw material upon which natural selection acts following such a change in the selective environment 2 - Experimental evolution: examples of Rhodobacter and E.coli (pgs. 373-375) Speciation of Microogranisms Can Take a Long Time - Molecular Clock – estimation of the time since 2 lineages have emerged o Ex: the strains of E.coli, harmless strain K-12 and pathogenic strain O157:H7 diverged about 4.5 million years ago 13.6 The Evolution of Microbial Genome - Genome sequencing of E.coli strain K-12 and two pathogenic strains showed that only 39% of their genes were shared among all 3 genomes o Core genome – genes shared by all strains of a species  The size of the core genome can be expected to DECREASE as the evolutionary distance of strains INCREASES o Pan genome – the core genome plus genes that AREN’T shared by all strains of a species and which are ofen acquired through horizontal gene transfer o Genomes are HIGHLY DYNAMIC (they can shrink or enlarge relatively quickly over time) Gene Deletions in Microbial Genomes Microbial Phylogeny and Systematics - Uses Polyphasic approach to taxonomy using 3 kinds of methods – phenotypic, genotypic, and phylogenetic – for the identification and description of bacteria o Phenotypic analysis examines the morphological, metabolic, physiological, and chemical characteristics of the cell o Genotypic = characteristics of genome

- SSU rRNA is highly conserved 13.7 Molecular Phylogeny: Making Sense of Molecular Sequences Obtaining DNA Sequences - PCR primers can be designed to target any region of DNA from any organism Sequence Alignment - The purpose is to add gaps to molecular sequences in order to establish positional homology, that is, to be sure that each position in the sequence was inherited from a common ancestor of all organisms under consideration o Critical to phylogenetic analysis because the assignment of mismatches and gaps caused by deletions is in effect an explicit hypothesis of how the sequences have diverged from a common ancestral sequence Limitations of Phylogenetic Trees - Genes encoding SSU rRNAs appear to be transferred HORIZONTALLY at very low frequencies, and rRNA gene phylogenies agree largely with those prepared from other genes that encode genetic information functions o Provide accurate record of organismal phylogeny o Many microbial genomes contain genes that have been acquired by HGT at some point in their evolutionary history, and this has important implications for microbial evolution 13.8 The Species Concept in Micro - Phylogenetic species concept defines a microbial species pragmatically as a group of strains that share certain characteristic traits and which are genetically COHESIVE and share a unique recent common ancestor o Developed to facilitate taxonomy o Species of Bacteria and Archaea are defined OPERATIONALLY as a group of strains sharing a high degree of similarity in many traits and sharing a recent common ancestor for their SSU rRNA genes How Many Species of Bacteria and Archaea Exist? - The diversity of both in Earth is unquestionably higher than that of all plants and animal species combined o 10,000 species can coexist in a single gram of soil 13.9 Taxonomic Methods in Systematics - Multilocus sequencing typing (MLST) – method in which several different “housekeeping” genes from several related organisms are sequenced and the sequences are used collectively to distinguish the organisms o Has found its greatest use in clinical microbiology, where it has been used to differentiate strains of various pathogens - Genome Fingerprinting – rapid approach for evaluating polymorphisms between strains of a species o Fingerprints are fragments of DNA generated from individual genes or whole genomes o REP-PCR is based on the presence of highly conserved repetitive DNA elements interspersed randomly around the bacterial chromosome

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o o Making Sense of Microbial Diversity Phylogenetic diversity – the component of microbial diversity that deals with EVOLUTIONARY RELATIONSHIPS between organisms o It encompasses the genetic and genomic diversity of evolutionary lineages and so can be defined on the basis of with GENES or ORGANISMS o Also defined on the basis of ribosomal RNA gene phylogeny, which is thought to reflect the phylogenetic history of the entire organism Functional Diversity – the component of microbial diversity that deals with diversity in form and function as it relates to microbial physiology and ecology o Functional trait is shared between divergent organisms with dissimilar 16S ribosomal RNA gene sequences  1. Gene loss – a situation where a trait present in the common ancestor of several lineages is subsequently lost in some lineages but retained in others that over evolutionary time became quite divergent  2. Convergent evolution – a trait has evolved INDEPENDENTLY in two or more lineages and is not encoded by HOMOLOGOUS genes shared by these lineages  3. Horizontal Gene Transfer – a situation where genes that confer a particular trait are homologous and have been exchanged between distantly related lineages Overview of Phototrophic Bacteria The first phototrophic organisms were ANOXYGENIC phototrophs, organisms that DO NOT generate O2 as a product of photosynthesis o Instead of H20, these early phototrophs likely used H2, Fe2+, or H2S as the electron donor for photosynthesis o Oxygenic photosynthesis is known only within the Cyanobacteria o All phototrophic bacteria use chlorophyll-like pigments and various accessory pigments to harvest energy from light and transfer this energy to a membranebound reaction center where it used to drive electron transfer reactions that ultimately result in the production of ATP  2 different Reaction Centers: PSII and PSI  Anoxygenic phototrophs have one RC or the other Cyanobacteria Oxygenic, phototrophic bacteria Contains chlorophyll A and uses Calvin-Benson Cycle Contain phycobilins – function as accessory pigments in photosynthesis Has unicellular, colonial and filamentous forms o UNICELLULAR: Synechococcus and Prochlorococcus are the most abundant phototrophs in the ocean  Both contribute 80% of marine photosynthesis o COLONIAL: Microcystis – create toxins that are found in lakes

o FILAMENTOUS – unicellular cyano can fix N2 only at night when photosynthesis does NOT occur, but filamentous fixes N2 during the day and by forming specialized cells called HETEROCYSTS  Heterocysts: are surrounded by a thickened cell wall that slows the diffusion of O2 into the cell and permits NITROGENASE activity to occur in an anoxic environment  Anabaena has heterocysts and is a genus found in soil; when they die, it enriches the soil to plant grains 15.4 Purple Sulfur Bacteria - ANAEROBE - Anoxygenic phototrophs that use H2S as an electron donor for photosynthesis - They are found in illuminated anoxic zones where H2S is present o Such habitats are lakes, marine sediments and “sulfur springs”, where H2S produced geochemically or biologically can support the growth of purple sulfur bacteria  Also found in microbial mats and in SALT marsh sediments o Use PSII (Q-type RC) which contain the bacteriochlorophyll a or b, and carry out CO2 fixation by the Calvin Cycle - Form 2 families: Chromatiaceae and Ectothiorhodospiraceae o Chromatium store S0 granules inside their cells and have vesicular intracellular photosynthetic membrane systems o Ectothiorhodospora oxidize H2S to S0 that is deposited OUTSIDE the cell  Both these genera are extremely halophilic (salt loving) and are found in saline lakes, soda lakes, and salterns, where abundant levels of SO42support sulfate-reducing bacteria, the organisms that produce H 2S - Observed in MERMICTIC (permanently stratified) lakes o Form layers because they have denser (usually saline) water on the bottom and less dense (usually freshwater) water nearer the surface o If sufficient sulfate is present to support sulfate reduction, sulfide is produced in the sediment and diffuses upward into the anoxic bottom waters. The presence of sulfide and light in the anoxic layers of the lake allow purple sulfur bacteria to form dense cell masses 15.5 Purple Nonsulfur Bacteria - Most metabolically versatile of all microbes - They are photoheterotrophs (a condition where light is the energy source and an organic compound is the carbon source) o Species are able to use a wide range of carbon sources and electron donors for photosynthesis, including organic acids, amino acids, sugars, and even aromatic compounds o Use Q-type photosystem (PSII) and contain either bacteriochlorophyll a or b - Reside within the Alphaproteobacteria o Rhodospirillum o Rhodobacter

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Can conserve energy photoautotrophically using: o H2 o Low levels of H2S o Even Fe2+ as the electron donor for photosynthesis with CO2 fixation carried out by the Calvin Cycle - Some species can grow aerobic respiration in the dark while others can grow by ANAEROBIC fermentation - All can fix N2 15.5 Green Sulfur Bacteria - Have LITTLE metabolic versatility and they are NONMOTILE and strictly ANAEROBIC ANOXYGENIC phototrophic bacteria - Like purple sulfur bacteria, green sulfur bacteria oxidize hydrogen sulfide (H2S) as an electron donor for autotrophic growth, oxidizing it first to sulfur (S0) and then to sulfate (SO42-) o But unlike most purple sulfur bacteria, the S0 produced by green sulfur bacteria is deposited only OUTISDE the cell o Autotrophy is supported NOT by the reactions of the Calvin Cycle, but instead by a reversal of steps in the CITRIC ACID CYCLE - Contain bacteriochlorophyll c, d, or e and house these pigments in unique structures called CHLOROSOMES o Chlorosomes are oblong bacteriochlorophyll-rich bodies bound by a thin, nonunit membrane and attached to the cytoplasmic membrane in the periphery of the cell o Chlorosomes function to funnel energy into the photosystem, and this eventually leads to ATP synthesis - Uses FeS-type photosystem (PSI) - Tend to have a GREATER TOLERANCE of H2S than do other anoxygenic phototrophs o Typically found at the greatest depths of all phototrophic microorganisms in lakes or microbial mats, where light intensities are LOW and H2S levels are HIGH o Chlorobium is genus 15.6 Green Nonsulfur Bacteria - Filamentous anoxygenic phototrophs that are capable of gliding motility - Contain Q-type (PSII) RC compared to Green Bacteria - Uses the 3-hydroxypropionate bi-cycle pathway to support autotrophic growth - Chloroflexus is the genus 15.9 Dissimilative Sulfate-Reducers - OBLIGATE ANAEROBES - Produce H2S - Use H2 or organic compounds as ELECTRON DONORS for growth, and the range of organics used is fairly broad - Species of Archaeoglobus (an ARCHAEON) are THEMOPHILIC, found in hot springs and oil reserves - Desulfovibrio is in an anoxic lactate-sullfate medium containing Fe2+

o Black insoluble ferrous sulfide is formed in medium using THIOGLYCOLATE tube 15.11 Dissimilative Sulfur-Oxidizers - H2S is produced by sulfate-reducing bacteria which is released into oxygenated waters (where O2 acts as electron ACCEPTOR to oxidize HsS) - Chemolitotrophs - Oxidation of H2S to H2SO4 is SPONTANEOUS and rapid in presence of O2 (H2S is chemically instable with O2 but aerobic sulfide-oxidizers have different strategies) - Most are OBLIGATE AEROBES o Thiomargaritas can reduce NO3- in DENITRIFICATION intracellular  Nonmotile; its ecological strategy is to separate in time the oxidation of H2S from the reduction of O2  To accomplish this, it contains a GIANT VACUOLE that fills with high concentrations of NITRATE (NO3-)  This vacuole can fill almost the entire volume of cell  Cells live in sulfide-rich marine sediments that are mixed occasionally with O2 rich waters, such as that in salt marshes. When buried in sediments, cells oxidize H2S to S0 ANAEROBICALLY by reducing NO3- stored in the vacuole to ammonium (NH4 +). They then store the S0 as INTRACELLULAR GRANULES. When turbulent waters mix the cells into the water column where H2S is lacking, they switch to the AEROBIC oxidation of stored S0. The energy they gain from S0 oxidation is used to refill their vacuole with NO3from the water column so they will be able to survive the next period of ANOXIA - Others are FACULATATIVE CHEMILITHOTROPHS o Facultative in the sense that they can grow either chemolithotrophically (and thus, also as autotrophs) or chemoorganotrophically o Beggiatoa can obtain energy from the oxidation of inorganic sulfur compounds but lack enzymes of the Calvin Cycle  They are FILAMENTOUS  They thus require ORGANIC COMPOUNDS as carbon sources  Organisms that use a mix of carbon and energy sources, for example those that simultaneously assimilate carbon from both CO2 and organic sources are MIXOTROPHS  uses gliding motility to position itself at the point where H2S and O2 cooccur in an environment Thiobacillus - The oxidation of H2S, S0, or thiosulfate by Thiobacillus generates SULFURIC ACID (H2SO4), and thus thiobacilli are ACIDOPHILIC o Acidithiobacillus ferooxidans can grow CHEMOLITHOTROPHICALLY by the oxidation of Fe2+ and is a major biological agent for the oxidation of this metal  Iron pyrite (FeS2) is a major source of ferrous iron as well as of sulfide  The oxidation of FeS2, especially in mining operations, can be both beneficial (because bioleaching of the ore releases the iron from

the sulfide material) and ecologically disastrous (the environment can become acidic and contaminated with toxic metals like aluminum, cadmium and lead) 15.12 Diversity of Nitrogen Fixers (assimilative) - Bacteria and Archaea are the only domains in which representatives exist that can conserve energy from the transformation of inorganic nitrogen species - Diazotrophs are microorganisms that fix dinitrogen gas (N2) into NH3 that can be assimilated as a source of nitrogen for cells o Requires ATP and the enzyme NITROGENASE o Nitrogenase is IRREVERSIBLY inhibited by O2 o There are OBLIGATE ANAEROBES o There are FACULATIVE AEROBES  Klebsiella will ofen fix N2 only when growing anaerobically (when O2 is absent or being low) o There are OBLIGATE AERBOBES  When Azotobacter are growing on N2 as a nitrogen source, extensive capsules or slime layers are typically produced  The high respiratory rate characteristics and the abundant capsular slime they produce help protect nitrogenase from O2  Able to grow on many different carbohydrates, alcohols, and organic acids, and METABOLISM is STRICTLY OXIDATIVE and wasteful  Cysts (like bacterial endospores) are resistant to desiccation, mechanical disintegration, and UV and ionizing radiation. They are not heat resistant though 15.13 Diversity of Nitrifiers and Denitrifiers - Denitrifiers (destroy NO3-) – microorganisms that grow by the ANAEROBIC respiration of inorganic nitrogen (NO3-, NO2-) reducing to the gaseous products NO, N2O, and N2 o They are typically FACULTATIVE AEROBES o They are chemoorganotrophs that use organic carbon as both carbon source and electron donor o Paracoccus is a genus of denitrifiers o FUN FACT: denitrifiers are big in agricultural soils where they cause the loss of nitrogen fertilizers and the PRODUCTION of N2O (nitrous oxide), which is dominant component of GREENHOUSE GASES produced by agricultural soil - Nitrifiers (PRODuce NO3-) – microrgnanisms able to grow chemolithotrophically at the expense of REDUCED inorganic nitrogen compounds (NH3, NO2-) o They are typically OBLIGATE AEROBES o They can grow autotrophically; fix CO2 by the Calvin Cycle o Ammonia oxidizers – oxidize NH3 to nitrite NO2 Ammonia monooxygenase is a key enzyme which oxidizes NH3 to hydroxylamine (NH2OH)

Nitrosomonas are abundant in sites with extensive protein decomposition (ammonification) and also in sewage treatment facilities o Nitrite oxidizers – the actual NITRATE-producing microorganisms, which oxidize NO2- to NO3 Use nitrite oxidoredctase, which oxidizes NO2- to NO3 Nitrobacter’s capacity for NO2- oxidation many have been acquired byhorizontal gene flow from nitrifying Proteobacteria  Nitrospira (NOT ON EXAM) is more abundant than Nitrobacter 15.6 Methanotrophs and Methylotrophs - Methylotrophs – organisms that grow using organic compounds lacking C-C bonds as electron donors in energy metabolism and as carbon sources o OBLIGATE AEROBES o Methylobacter - Methanotrophs – a subset of methylotrophs defined by their ability to use methane as a substrate for growth o OBLIGATE AEROBE o Possess a key enzyme, Methane Monooxygenase, which catalyzes the incorporation of an atom of oxygen from O2 into CH4, forming methanol (CH3OH)  Located in extensive internal membrane systems that are the site of methane oxidation o Methyltrophs unable to use methane LACK these ...