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Midterm

BIOL 241 Notes - Before Midterm.docx

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Department
Biology
Course
BIOL 241
Professor
Barbara Butler
Semester
Fall

Description
BIOL 241 – Applied Microbiology Lecture One – Microbial Ecology Microbial ecology – study of interrelationships between microorganisms and their environments Ecosystem – community of organism and their natural environment Guild – a grouping of metabolic organisms related to each other who share the same resources Community – sets of population that interact with each other Objectives in Microbial Ecology - Understanding biodiversity of microorganisms in nature and interactions in communities - Measurement of microbial activities in nature and monitoring of effects on ecosystem Activities measured include: - Primary Production of organic matter (phototrophic, chemolithotrophic activity) - Decomposition of organic matter (chemoorganotrophic/heterotrophic activity) - Biogeochemical Cycling of elements Microorganisms in Nature - Live in common habitats suited to higher organisms, also in extreme environments - Necessities for growth include available resources suitable for physiochemical conditions Extremophlies – psychrophiles, thermophiles, hyperthermophiles - Live in habitats of extreme conditions Note: Halobacterium is not Bacteria, but Archaea Niche: functional role of an organism with an ecosystem Prime Niche: where everything is optimal for an organism Microenvironment: where a microorganism lives, metabolizes within its habitat Nutrient Levels and Growth Rates - Microbial life in nature often differs from microbial life in lab culture - Growth rate measured by doubling time (i) Entry of nutrients into an ecosystem is often intermittent (ii) Distribution of resources in nature is often non-uniform (iii) Competition for resources is likely Surfaces and Biofilms - Biofilm – a community of microorganisms embedded in an organic polymer matrix (extracellular polymeric substances, EPS) adhering to a surface - Physicochemical gradients within mature biofilm result in a number of potential microenvironments within a small area Advantages to Biofilm Mode: - Protection from toxicants, predators, immune system cells - Ability to remain within a favourable niche - Cooperative interactions possible - Nutrient trapping Disadvantages: - Highly competitive - Localized biomass can be efficiently preyed upon - Infected by virus Problems Resulting from Biofilm Formation - Pipe clogging - Accelerated corrosion of pipelines and structural steelwork - High microbial numbers in portable water distribution systems - Increased drag on ship’s hull - Periodontal disease Exploitation of Biofilms - Slow sand filtration (water purification) - Microbial leaching of low-grade ores - Vinegar production Microbial mats: specialized microbial communities often composed mainly of photosynthetic prokaryotes - Macroscopic; often layered - Distinction between these and other biofilms is dependence on photosynthetic primary productivity as source of energy Interactions Between Microbial Populations Negative Effect - Competition – outcome depends on innate capabilities of nutrient uptake, metabolic rates - Antagonism – specific inhibitor or metabolic product may impede growth/metabolism of others Positive Effect - Cooperative interactions – interacting microbes must share same/nearyby microenvironment Syntrophy – microorganisms together carry out transformation neither can conduct alone Microbes can carry out complementary metabolic interactions - Symbioses – relationships between two or more organisms that share a particular ecosystem Lecture Two – Bacteria-Bacteriophage Interactions Virus: a genetic element containing either RNA or DNA that replicates in cells but is characterized by having an extracellular state Importance of Interaction - Potential controller of microbial population size - Phage infection may influence phenotype of host prokaryote - Phage – host prokaryote interaction been exploited in molecular biology Virus particles (virions) are metabolically alert; contain nucleic acid surrounded by protein caspid and sometimes other macromolecular components (envelope) Virus Replication: Lytic Cycle - Attachment: highly specific interaction between viral proteins and specific receptor on host cell surface - Penetration of host bacterium is complex; obligatory for phage replication to occur - Permissive cells allow virus multiplication to occur - Once viral components have been synthesized by host’s metabolic machinery, new viral particles self-assemble - Mature phage particles released when host cell lyses Time Course of Events in Phage T4 Infection - T4 is a dsDNA bacteriophage that infects E. coli - An example of lytic phage - Attachment of T4 bacteriophage to cell wall of E. coli and injection of DNA Infection by Temperate Bacteriophage - Post-infection alternatives are lysis (replication and release of mature virus), or lysogenization (integration of viral DNA into host DNA) - Lysogens are bacterial cells carrying integrated phage genome (prophage), which is passed from one generation to the next during bacterial cell division - Integration of lambda phage DNA into host DNA - Lysogens can be induced to produce mature virus and lyse Influences of Bacteriophages on Lives of Their Hosts Generalized transduction: when host gene is accidentally packaged into lytic phage and transferred to new host cell Specialized transduction: when a specific gene adjacent to the site where a lysogenic phage integrates into host genome is accidentally packaged and transferred to new host cell Bacteriophages are important in microbial communities: - Lysogeny: most bacteria isolated from nature are lysogens - Where ever aquatic ecosystems have been assessed, viruses are consistently the most abundant biological entities present Lecture Three – Terrestrial and Aquatic Environments as Microbial Habitats Soils: may be organic (rare) or (commonly) inorganic - Soil formation requires many years (1000s) and is very omplex - Microbial activities contribute, as do physical and chemical processes - Animals living in soil also contribute to soil structure Microenvironments within a soil aggregate - Clay, mineral, organic matter surfaces - Air-failled, water-filled pore space Determinants of microbial activity in soil - Water availability -> affectes oxygen availability - Nutrient status – microbial activity may be limited by C, N or P availability Plants: greatly influence soil habitat, as well as serving as potential habitat Rhizosphere: soil that surrounds plant roots an environment that is significantly different from bulk soil environment – rhizosphere effect Rhizoplane: actual root surface Source of root exudates (sugars, amino acids, hormones, vitamins) Phyllosphere: surface of plant leaf Deep Terrestrial Subsurface As a Microbial Habitat - Biosphere extends ~10 km below ground surface - Subsurface inhabitants – pokaryotes, few microeukaryotes - Low-nutrient habitat – low metabolic activity - Practical interest: remedial potential of deep surface microbiota in event of pollutant reflux Aquatic Environments as Microbial Habitats - Species composition affected by physics, chemical characteristics of environment - Niches based generally on oxygen and sunlight Freshwater Environments Lakes: oxygen produced near surface, may be depleted at depth due to low solubility, consumption Anaerobic inhabitants in deeper regions Rivers: flow, turbulence affect degree of re-oxygenation Organic matter, nutrient inputs affect productivity, may lead to oxygen depletion Marine Environment Open ocean: low primary productivity, often limiting N, P, Fe resulting in low heterotrophic avtivity Photic zone: 300 meters down in oceans, 10s meters in lakes Inshore areas: nutrient rich -> greater productivity Deep Sea Habitats - 75% ocean water at depths greater than 1000m - Dark, cold (2-3 degrees C), under high hydrostatic pressure, low nutrient input - Low microbial activity -> psychrotolerant or psychrophilic, barotolerant or barophilic - Cold, wet desert Hydrothermal vents: thrives with population and productivity (analogous to oases in desert) - Driven by geothermal energy - Microbe-animal symbioses - Free-living microorganisms - Include S-oxidizing chemolithotrophs 2+ 2+ - Methanotrophs, nitrifiers, H-, Fe-2 Mn - oxidizers Tube Worms - Can be 2+ m long - Lack mouth, gut, anus - Possess trophosome – spongy tissue packed with S granules and S-oxidizing bacteria - Traps oxygen, HS in blood and deliver to bacteria 2 Lecture Four – Biogeochemical Cycling: Carbon Cycle Land: major site of CO fixation; soil humus very slowly biodegraded 2 Atmospheric CO: rapid2y cycles Oceans: site of CO fixation, organic matter decomposition; less influence than land reservoir 2 Sediments, rock: largest reservoir (>99.5%), extremely long turnover time CO F2xation: via photosynthesis (mostly) and chemosynthesis (minor) Oxygenic photosynthesis: higher plants, eukaryotic microalgae, cyanobacteria Anoxygenic photosynthesis: purple and green sulfur bacteria Respiration: occurs in dark and light (by organotrophs, phototrophs, lithotrophs) Decomposition of organic matter: catabolic, energy-yielding reactions carried out by organotrophs Methanotrophs: specialize in metabolism of 1-C compounds Mathane monoozygenase (MMO) catalyses methane  methanol step Often microaerophilic “gradient organisms” Overall Process of Anoxic Decomposition (i) Hydrolysis of polymers (ii) Primary fermentations (iii) Secondary fermentations (H-produci2g fatty acid-oxidzing syntrophs) (iv) H consumption by methanogenesis and acetogenesis 2 - Sugar, amino acid fermentation provides subtrate for syntrophs - Syntrophs cannot operate unless H level is 2ow - Syntroph activity is critical to provide substrate for methanogens - Methanogenic (homoacetogenic) activity is critical to maintain low H level 2 Nitrogen Cycle - N is key component of biomass - Atmosphere is major reservoir of N (80% N)  cannot be2used by most organisms - N 2ixation conducted by few prokaryotes = critical to other organisms - Terrestrial and aquatic environments  recycling of ammonia and nitrate (common forms) - N is lost back to atmosphere via denitrification (NO  N) – carr3ed out 2y mostly facultative aerobes Nitrogen Fixation: Nitrogenase Complex Function - Nitrogenase complex is O-sensitive and subject to strict regulatory control 2 - Process requires a lot of energy - Activity of enzyme is therefore restricted - Required enzyme for nitrogenase: NIF gene - FeMO = the actual place of electrons passing  can be denatured by O 2 Nitrogen-Fixing Microorganisms Symbiotic (i) Legume-rhizobia symbioses: soybeans, clover, alfalfa (ii) Nonleguminous plants: Alnus (alder) and others with members of genus Free-Living Aerobes - Chemoorganotrophs including Azobacter, Klebsiella, Methylococcus and others - Phototrophs: many Cyanobacteria - Chemolithotrophs: Alcaligenes, some Thiobacillus and others Free-Living Anaerobes - Chemoorganotrophs including Clostridium, Desulfovibrio - Phototrophs including Cromacium, Thiocapsa, Chlorobium, Rhodospirillium - Chemolithotrophs: Methanosarcina, Methanococcus and other methanogens Heterocysts: modified cells found in certain filamentous cyanobacteria Lack photosystem II and thus do not produce oxygen but process nitrogenase and can conduct nitrogen fixation Major Metabolic Reactions and Nutrient Exchanges Occurring in the Bacteroid Bacteroid: rhizobial cells transformed into swollen, misshapen, branched shapes within the plant cell, possess nitrogenase activity, incapable of proliferation Symbiosome: bacteroids (singly or small groups) surrounded by portions of plant cell membrane; nitrogen fixation begins after symbiosome formation Leghemoglobin: oxygen binding protein; supplies oxygen to bacteroid and protects nitrogenase from oxygen inactivation Ammonification - Production of ammonia during decomposition of organic nitrogen compounds - Conducted by wide range of aerobes, anaerobes Oxic conditions: - Some NH vol3tilization to atmosphere - Assimilation by plants, microorganisms; production of new biomass - NH s4bject to nitrification Anoxic conditions: - NH t4nds to be stable and persist Nitrification - Conducted in well-drained, neutral pH soils, aquatic environments - Aerobic, chemolithotrophic energy metabolism - Two groups of microorganisms acting in sequence - Addition to high-protein materials to soil tends to encourage nitrification Anammox - Anoxic ammonia oxidation - Brocadia anammoxidans is an anaerobe able to oxidize ammonia, using nitrite as an electron acceptor, producing dinitrogen gas - Occurs in ammonia-rich habitats where oxic and anoxic microenvironments are in close juxtaposition Terminology Used in Microbiology Assimilatory reactions: nutrients are incorporated into biomass of an organism Dissimilatory reactions: when the compounds are not assimilated, but reduced as terminal electron acceptors in energy metabolism Denitrification - Dissimilatory reaction; oxidized N-compound is electron acceptor in energy metabolism - Most denitrifiers are facultative aerobes - Denitrification occurs in anoxic encironments Practical Implications of N Cycle Reactions Nitrogen fixation converts unusable nitrogen
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