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83 Cards in this Set
- Front
- Back
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biomining ore definition |
rock that has some useful mineral embedded in it; metals like iron, lead, gold, copper, uranium |
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biomining mining definition |
extracting the ore from the earth |
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biomining refinement definition + types |
extracting of minerals from the rock/ore classical refinement involved using: - smelting using heat - chemicals (toxic to environment) |
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biomining definition |
the use of microbes to extract rock minerals environmentally friendly useful for low grade ores |
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biomining microbial extraction three factors |
- composition of rock and mineral in the ore - temperature - toxicity of metals - type of microbes |
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biomining microbial extraction composition of rock in ore |
iron sulfide sediments dissolve better by acid producing bacteria = Thiobacillius ferrooxidans; used for iron, copper, lead limestone dissolve better by alkaline conditions produced by algae; used for selenium, uranium, radium |
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biomining microbial extraction composition of mineral in ore |
ex: extracting copper requires different chemistries than gold or lead |
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biomining microbial extraction temperature |
extractions can generate lots of heat (exothermic) that often use thermophilic Archae |
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biomining microbial extraction toxicity of metals |
metals extracted during biomining are toxic to the microbes that extract them they must be removed after extraction or genetically engineered to become more resistant |
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biomining microbial extraction type of microbes |
usually lithotrophic Archae |
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composting definition |
conversion of solid organic wastes into nutrient rich humus = natural fertilizer controlled oxidation event that requires organics with specific carbon:nitrogen ratios, O2, water variable microbes involved throughout process |
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composting physical structure |
- can use drums, tumblers, or piles - starts when organics are added in set ratios (veggie/fruit scraps, lawn trimmings) provide N2 - brown, dry wastes (branches, leaves, cardboard) high carbon contents - animal/human manure - nutrient rich - layered appropriately and add something |
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composting
microbial process |
- mesophilic bacteria + fungi begin decomp. resulting oxidation causes temp. to rise significantly - thermophilic bacteria + fungi + actinomycetes begin replacing mesophiles (temp. will continue to rise + peaks @ 70-80 C) - maturation phase begins and temp. drops to 40-50 C; mildly thermophilic fungi (Aspergillus) degrade most cellulose + mesophilic microbes will begin growth again - takes ~ a year; slower in winter + must constantly oxygenate + water |
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wastewater treatment
three types |
- sewage - "grey" water - liquid industrial waste cannot be discarded in untreated form into lakes/rivers |
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wastewater treatment goals of treatment |
- reduce existing microbes in water - reduce organic + inorganics to limit microbial growth - remove toxic chemicals + waste |
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wastewater treatment BOD acronym measurement mechanism interpretation + goal |
"biochemical oxygen demand" - measurement: microbial oxygen-consuming capacity of water - mechanism: pump a bottle of water full of O2 + let sit for 5 days, measure how but O2 is left at the end - interpretation: more O2 consumed, more organics matter being oxidized, higher level of contamination - goal: lowest BOD possible |
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wastewater treatment primary wastewater treatment two major components |
two major components for physical separation: - screens and grates to filter larger materials - settling tank where other particulate matter will sink to the bottom over the course of hours - called sludge = anoxic digestion - liquid in tank goes to aerobic treatment |
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wastewater treatment secondary wastewater treatment two stages |
- anoxic treatment of sludge in digesters - aerobic treatment of 1 prime supernatant |
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wastewater treatment secondary wastewater treatment anoxic treatment of sludge in digesters |
settled sludge from primary treatment mostly insoluble cellulose + fiber - added to a big tank with anaerobic bact. - secretions of hydrolytic enzymes degrades large polymers (proteins) into small monomers (AA) - fermentations by anaerobes yields acetate, hydrogen, CO2 (acetate used by methabnogens for to create methane = harvested for heat/power) |
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wastewater treatment secondary wastewater treatment aerobic treatment of primary treatment supernatant |
remaining organic matter wil be oxidied in tanks of aerobic bacteria two methods: - trickling filter - activated sludge |
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wastewater treatment secondary wastewater treatment aerobic treatment of 1 p. supernatant trickling filter method |
- bed of crushed rocks created - sprayed with nutrients so microbial biofilms form - supernatant is sprayed on top of these rocks - biofilms will absorb organics as water trickles through the rocks to the bottom - bottom = water, NO3, NH3, SO4, PO4 |
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wastewater treatment secondary wastewater treatment aerobic treatment of 1 p. supernatant activated sludge method |
- supernatant from 1 p. treatment is put into an aerated tank with slime forming bacgeria - bacteria clump up (= flocs) as they digest organics from water - water pumped into clarifying tank, where flocs settle out - treated water sits on top |
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wastewater treatment tertiary wastewater treatment |
water leaving 2 p. is clean enough to be released back into environment (BOD drop of 95%) chlorine, UV light, ozone are commonly applied to kill any remaining microbes if necessary if there's contamination with lots of inorganics, toxins, pesticides = treatment needed |
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bioremediation definition |
clean up of dangerous chemical toxins, oil, nuclear waste, and other pollutants from the environment by organisms in situ = on site clean up of waste ex situ = off site removal of contaminated water, soil, etc and treating it can involve variety of organisms: phytoremedation (using plants to remove toxins from soil) and microbes (reliable for metabolic potential + speed) |
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bioremediation types of environmental pollutants |
- heavy metals (mercury, cadmium, lead, copper, nickel, chromium, cobalt) - petroleum wastes ( long chain hydrocarbons) - nuclear wastes (radionuclides) - xenobiotics (synthetic chemicals not naturally found in biome) |
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bioremediation petroleum products |
bacteria can degrade aliphatic/aromatic hydrocarbons aerobically or anaerobically aerobic: molecular oxygen is chemically added to hydrocarbon chain by oxygenase enzyme to start oxidation - faster option anaerobic: bact./fungi/algae will attach to hydrophobic oil droplets as they float on water; secrete surfactant to solubilize them before oxidizing them into CO2 |
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bioremediation xenobiotics |
in most pesticides, dyes, medications, and chlorinated solvents degradation efficiency relies on similiarity to natural compounds - if microbes have never seen it, they biologically have no enzymes to break it down absorption into sediment will inhibit breakdown |
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bioremediation nuclear waste |
waste will take thousands of years to naturally degrade dual threat: high levels of radiation (uranium) and presence of many heavy metals Deinococcus radiodurans and Geobactor species can repair their own DNA very well; can use natural or genetically engineered strains to immobilize radioactive metals + other toxic parts of NW |
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industrial fermentation definition + types of microbes used |
use of microbes to synthesize commercial products on a large scale with the goal to enhance natural fermentation reactions so microbes overproduce the intended products major types used: bacteria and fungi (molds+yeasts) |
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industrial fermentation three fermentation products |
- biomass production - biotransformation - extra/intracellular metabolites |
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industrial fermentation three fermentation products biomass production |
microbial cells themselves are the target product - dried yeast for baking or brewing - yeast/algae extracts as human/animal nutrient supplements - growth of genetically "pure" starts for industry |
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industrial fermentation three fermentation products biotransformations |
conversion of specific substrates into specific products |
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industrial fermentation three fermentation products extracellular metabolites |
- released from cells at different stages of their growth - growth curve: lag phase, log phase, stationary phase, death/prolonged death phase - primary v. secondary metabolites |
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industrial fermentation three fermentation products extracellular metabolites primary metabolites |
released during log phase when cells feowing at max rate + healthy usually are products of basic metabolic pathwats used for energy extraction production of alcohols, citric acids, and amino acids occur during active growth |
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industrial fermentation three fermentation products extracellular metabolites secondary metabolites |
released during stationary phase when cells are running out of nutrients and becoming unhealthy not required for growth production is highly dependent on growth medium; often produced in higher quantities than 1 p. + include many types of toxins ex: all natural antibiotics, fungicides |
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industrial fermentation three fermentation products intracellular metabolites |
usually proteins; made by fermenting microbes that can be mass produced + harvested includes many pigments and most commercial enzymes requires cells to be broken open in order to release desired product |
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industrial fermentation three stages |
- upstream process - fermentation process - downstream process |
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industrial fermentation upstream process definition |
isolation of microbes that make product genetic manipulation of microbe for max production media preparation + fermenter set up |
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industrial fermentation fermentation process definition |
seed and scale up production monitor / control optimal conditions for product synthesis |
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industrial fermentation downstream process definition |
lyse cells if necessary harvest - concentrate - purify product formulation, packaging, distribution |
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industrial fermentation upstream process microbial properties + selection |
growing microbes to produce product in large, cheap system - profit is #1 concern - genetic flexibility and stability - ideal involves waste products from other industries - non-pathogenic to curb FDA regulation - rapid growth + make product quickly |
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industrial fermentation upstream process isolation of species two sampling approachs |
objective approach: purposely go into likely environment for microbe w/ desired trait shotgun approach: collecting samples from any environment and screening for presence of microbes with desired trait |
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industrial fermentation upstream process isolation of species |
once sample is collected: - need to enrich for desired type of microbe - need to kill/repress other microbes survivors will be separated via streak plating into pure colonies using selective agars colonies would be chosen to be screened for desired qualities as well as non-toxicity, stability |
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industrial fermentation upstream process strain improvement general |
- many selected strains don't naturally produce massive quantities of given product / other issues therefore not economically viable - important to modify the isolated species to: increase productivity + gene expression + cell size/growth rates decrease costs + toxicity to humans + other compounds that could harm production/purification alter permeability to ease metabolite exports |
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industrial fermentation upstream process strain improvement genetic recombination v. mutagenesis |
GR: when changes must be made to the microbe's genome using (prokaryotic) transformation, transduction, or conjugation OR (eukaryotic) sexual reproduction - enables microbes to gain new abilities or enhance new ones MUTA: can wait for natural mutants or induce mutations using radiation, transposons, or chemical mutagens; use high throughput assays |
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industrial fermentation upstream process strain maintence |
genetically altered strains must be maintained so they don't revert to original form because of their hyper productive state that isn't natural |
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industrial fermentation upstream process genetic (structural) instability |
when microbes lose abilities (like plasmids) when not faced with selective pressure therefore need to be continually selected for mutations/plasmid presence can also freeze stocks in liquid nitrogen |
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industrial fermentation upstream process growth media conditions |
growth media accounts for most of production costs all media must have carbon for ATP and biosynthesis; nitrogen; phosphorus; sulfur; and trace minerals (vitamins/other growth factors) differs depending on microbe and product |
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industrial fermentation upstream process growth media conditions primary v. secondary metabolite production |
1 p. - optimal growth wanted to stay in log phase; need excess nutrient stimulation continuously 2 p. - want optimal growth for some time, then force whole culture to enter stationary phase; need to have at least one limiting nutrient to starve the culture |
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industrial fermentation upstream process growth media conditions materials |
undefined carbon sources: leftover whey, molasses, cellulose, sulfite waste liquor, malt extract nitrogen sources: peptone, yeast extract, corn steep liquid |
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industrial fermentation upstream process fermenter types (how they're fed) |
batch: closed system w/ growth harvested when completed, all nutrients gone fed batch: given fresh nutrients but still harvested once growth is complete continuous: fresh nutrients come in, old media out while cells stay in log phase forever |
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industrial fermentation upstream process fermenter types (how microbes grow) solid state |
solid state fermenters: microbes are grown on solid substrate + kept moist for growth without any free flowing media over them ideal for filamentous fungi - natural growth; cheaper method used to isolate degradative enzymes (cellulases) |
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industrial fermentation upstream process fermenter types (how microbes grow) submerged fermenters |
microbes grow completely submerged in liquid broth; typical set up for most applications ideal for bacteria, yeasts, some fungi media comp. is important variable = can be easily manipulated compared to solid state |
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industrial fermentation upstream process fermenter types (how microbes grow) submerged fermenters - aerobic structures |
most are continuous batch systems with one pipe supplying nutrients + another harvesting product - sparger at bottom bubbles sterile compressed O2 - impeller powered by motor to mix culture, distributing air/nutrients - cooling system monitored using probes to determine temperature, pH, and O2 of culture |
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industrial fermentation upstream process fermenter types (how microbes grow) submerged fermenters - anaerobic structures |
similar structure to aerobic fermenter without continuous oxygenated air no air OR will pump in N2 or CO2 |
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industrial fermentation upstream process fermenter scale up |
start in lab in test tubes/beaker to measure plausability of idea move up to lab fermenter (1-10 L) to test media, pH, temp, oxygen, other factors moves to plant to test (300-3000 L) before full scale industrial fermentation (10k+ L) |
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industrial fermentation downstream process definition |
all steps following completion of fermentation goal: to efficiently and safely pilot target product while maximizing recover and minimizing cost can involve the processing of media or cells -purification methods vary (enzymes require maintaining of biological activity structure) |
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industrial fermentation downstream process cell separation definition + three methods |
separation of product cells from growth medium depending on its media viscosity, and microbial arrangement / shape - centrifugation: spin + pellet cells - flocculation / sedimentation: natural or induced clumping - filtration: using pressure to force liquid out of small pores |
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industrial fermentation downstream process cell disruption |
required when a product is in cell cytosol, periplasm, or organelles (euk) issues: - damage lysosomes: releases hydrolytic enzyomes - releases DNA: makes media viscous - generate heat: can denature proteins types: mechanical v. non-mechanical |
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industrial fermentation downstream process cell disruption mechanical methods |
- pressure: (ex. French press) cells placed under immense pressure; bursting occurs when cells try to pass through small pores - high speed bead mills running cells through grinding beads - sonication high energy sound waves sent into cells to pop them |
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industrial fermentation downstream process cell disruption non-mechanical methods |
- chemical disruption: applying mild detergents/cell wall degrading enzymes (lysozymes) - repeated freeze-thawing: ice crystals form and pop holes in membranes - osmotic lysis: cells put into hypotonic solution (pure water) so they'll expand + explode, releasing proteins |
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industrial fermentation downstream process product recovery |
the separation and purification of product away from growth media and cell debris if product was released from cells, first step is centrifuge lysate so product is in suspension |
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industrial fermentation downstream process product recovery recovering protein products from solution |
commonly done by adding a compound to precipitate proteins in solution spin out protein into a pellet; resuspend protein pellet = crude pellet mixture |
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industrial fermentation downstream process product recovery recovering other products from solution |
common method is liquid-liquid extraction for alkaloids, antibiotics, sterioids, vetaminds - add some organic solvent to solution - hydrophobic products stay in organic layer, separating from other components alcohol + acetone purification usually involves distillation - using heat to vaporize everything but desired product |
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industrial fermentation downstream process product recovery further purification |
chromatography is most common way to achieve further purification of product types: - affinity: ligand binding - gel fitration: size - high performance liquid: HPLC - ion-exchange: charge |
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microbial biocontrol definition |
the use of microbes to purposely reduce the number of some other undesirable species like agricultural pests, pathogens, water contaminants (invasive species) three types of biocontrol: - biochemical: purified microbial toxin is applied to other species - direct: live microbe is applied to other species - genetic: gene encoding microbial toxin is put into genome of what is being protected like a plant |
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microbial biocontrol what is being protected? |
commerically important plant crops (usually) protection against insects feeding on them, fungi/protozoa trying to kill them, invasive plant species and weeds can also be used to control animals that are invasive, pests, or overpopulating |
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microbial biocontrol human pathogens |
natural antibiotics: the use of natural products of one microbe to kill another phage: apply specific bacteriophages to water contamination with specific pathogen (non toxic to humans) |
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microbial biocontrol benefits |
- relatively non-toxic to other species due to specificity, no run off into waterways, no toxic byproducts - no bioaccumulation - persistence - will reproduce itself and continue to protect - less chance of resistance to arise |
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microbial biocontrol drawbacks |
- must compete with other microbes in environment - usually very specific - one biocontrol:one species targeted - may involve genetically engineered plants that may develop public resistance or spread |
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microbial biocontrol mechanisms of control |
- antibiosis - competition - induction of systematic resistance - pathogenesis / parasitism |
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microbial biocontrol mechanisms of control competition |
biocontrol agent competes for space or some limited resource w/in target organism; must have more efficient nutrient uptake mechanism / ability to colonize examples: using pseudomonas to produce iron binding siderophore enzymes |
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microbial biocontrol mechanisms of control pathogenesis/parasitism |
biocontrol agent attaches to and/or invades a target organisms = lead to inhibition or death attachment: block nutrient acquisition, destroy cuticle, alter surface in other deleterious ways invasion: gets inside target organism used w/ insect pests, nematodes, patho. fungi |
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microbial biocontrol mechanisms of control antibiosis |
secretion of chemicals by a biocontrol agent that influences the growth, health, metabolism, or reproduction of target organism includes: antibiotic producers, cell wall degrading enzymes (chitinases), and other toxins - can either apply organisms or purified chemical |
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microbial biocontrol mechanisms of control antibiosis Bt toxin + GMOs |
Bacillus thuringiensis secretes the Bt toxin - a crystalline protein that is eaten by insect/pest larvae - proteases in gut activate the toxin which will result in a pore being formed = kills 1990's: added Bt toxin into transgenic crop plants without any side effects (safety issues or spread problems) |
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microbial biocontrol mechanisms of control induction of systematic resistance |
- symbiotic rhizobia growing w/ plants can induce the plants to produce their own protective chemicals - rhi. secrete signaling molecules for plants (including ethylene) which signals cascade in plant cells = resistance to pathogens - plants increase thickness of cell wall = lignification - deposit a thick sugar named callose to block pathogens - synthesizes toxic peptides + proteins |
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microbial biocontrol requirements for success |
isolate or create a species / strain that: - colonizes and proliferates - competes well with other microbes - inexpensive = large production + distribution - non-pathogenic to host - persists for a long time in environment |
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microbial biocontrol three major agents |
- Bacillus species - Pseudomonas species - Trichoderma species |
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microbial biocontrol three major agents Bacillus |
- about half of all commercially available products - common soil endospores that survive harsh environments for long periods of time - most colonize roots + induce resistance or physically compete with pathogenic fungi - can secrete Bt and B.f. toxin |
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microbial biocontrol three major agents Trichoderma |
- mostly asexual reproducing fungi that are commonly isolated - effectively colonize woody/herbaceous material including diseased or wounded plant material - utilize all biocontrol mechanisms (genus) - target fungi and nematodes - produce a large number of lytic enzymes + anti-fungals |
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microbial biocontrol three major agents Pesudamonas |
- aerobic, gram negative bacteria - can utilize a large number of carbon sources - often used to treat seeds/roots before planting - aggressively compete with nearly all microbes; fight for nutrients + space by producing anti microbial agents - effectively attach to hyphae of fungi + kill |
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immunotechnology definition |
combination of imminology and biotechnology that involves application of immune components in the diagnosis, study, and treatment of disease theory: immune system produces proteins that are specific in ability to bind/recognize to foreign entities; system also creates powerful products to destroy foreign entities |
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immunotechnology two branches innate immune system |
the first line of defense against a pathogen always present + ready for infections; immediate response not specific for any particular pathogen cells involved: phagocytes, NK cells factors: lysozyme, AMPs |
