Biodegradation Flashcards
Abiotic mechanisms of degradation
Photochemical, chemical (ox/red), mechanical
Two biological mechanisms of degradation
Plants/Animals and Microorganisms
How plants and animals contribute to degradation
Direct/indirect consumption, compounds secreted, associated microorganisms
How do microorganisms contribute to degradation
Mineralization, modification or transformation
What is mineralization?
Conversion of organic compounds to CO2
How much of global biomass is microbial?
Greater than 50%
How many microbial species have never been cultured
Around 99% (holy shit)
What was the first evidence of cyanobacteria-like fossils and when did they appear?
Stromatolites, 3.5 BYA
What happened 2.5 BYA?
The great oxidation event, oxygenic photosynthesis (bc of microbes)
What are the two metabolic features of cyanobacteria?
Photosynthesis and nitrogen fixation
What does VBNC mean?
Viable but not culturable
How do we know microbes exist without culturing them?
Microscopy, respiration tests, molecular biology (16S rRNA seq)
Why is molecular biology important in microbiology?
It is needed to classify microorganisms - can’t do it on morphology alone
Central dogma of life
DNA – RNA – Protein
Why was 16S rRNA sequence important?
Helped form the tree of life and determine evolutionary relationships
Why is evolution important in terms of biodegradation?
Microbes have evolved to degrade certain pollutants because of selection pressures
Why are prokaryotes thought to have greater metabolic diversity?
Because of their high surface/volume ratio
Three characteristics of prokaryotes
Small size, rigid cell wall, metabolic diversity
Three characteristics of eukaryotes
Larger size, flexible cell walls, metabolic specialization
How is growth defined in the microbial world
Multiplication of cells by the successive division of mother cells into two daughter cells
What are the two divisions of metabolism?
Anabolism and catabolism
What does lithoautotrophic mean
Reduces non organic molecules
Oxidation
Removal of electrons
Reduction
Addition of electrons
Anabolism
Biosynthesis, requires energy
Catabolism
Enzymatic degradation, produces energy
Three divisions of the mineralization process
Glycolysis, TCA cycle, electron transport chain
Why do microbes degrade pollutants?
Because they can get energy out of it
What is an example of a terminal electron acceptor?
O2, nitrate
What is the proton gradient/PMF
Created during the ETC, used by cells to move and generate ATP
What is aerobic respiration?
O2 as TEA, creates water, results in PMF, PMF fuels ATP synthesis (oxidative phosphorylation)
How is the reducing power generated in aerobic respiration?
By the oxidation of the energy source
What is the overall process occurring in the ETC?
Oxidative phosphorylation
What are organic pollutants degraded better aerobically?
It is faster and results in the more complete oxidation to CO2
Why does O2 concentration in a soil aggregate decrease as you get closer to the middle?
The microbes in the middle are using up the oxygen faster than it can diffuse in
Availability to TEAs in soil varies with __
Depth
What are examples of metallic terminal electron acceptors
MnO2, Fe(OH)3
What is anaerobic respiration?
TEA is a compound other than O2
What is the TEA used by nitrate reducers?
NO3 -
What is the TEA used by sulfate reducers?
SO4 -
Where does anaerobic respiration occur?
Cytoplasm or periplasm
What are examples of organic TEAs in anaerobic respiration?
Fumarate, enzyme part of ETC, CO2 (methanogenesis)
Ammonium oxidizing =
Uses ammonium as electron DONOR
Reduction is __ of oxygen, __ of electron
Loss, gain
Oxidation is __ of oxygen, __ of electron
Gain, loss
What are the most abundant denitrifies in soil?
Pseudomonas and Alcaligenes
What do denitrifiers reduce NO3 to?
N2O and N2 (gaseous products)
What bacteria degrade toluene under anaerobic conditions?
Thauera aromatica and Azoarcus tolylyticus
What does Geobacter metallireducens GS15 do?
Fe-reducing bacterium that degrades toluene
What are three taxonomic groups of sulfate reducing bacteria
Desulfovibrio, Desulfuromonas, Desulfosarcina
What do methanogenic archaea use as an electron donor and acceptor?
H2 donor, CO2 acceptor
What do fermenters use as terminal electron acceptors?
Organic molecules
What are the products of fermentation in soil?
Acetate, formate, butyrate, lactate, succinate, etc.
Example of fermenting bacteria found in soil
Clostridium
What is special about Shewanella oneidensis?
It has a lot of terminal electron acceptors, and can live as a heterotroph or lithoautotroph
What does Geobacter do?
Uses acetate as an energy source to convert uranium 6 to uranium 4 (ferric iron to ferrous iron)
What is involved in the remediation of arsenic contaminated ground water?
Oxygenate the system, microbes use Fe, arsenite and Mn as electron donors, arsenite precipitates are arsenate
What form of mercury is in the atmosphere?
Hg0
What form of mercury enters aquatic environments?
Hg2+
What does Mg2+ turn into under anaerobic conditions?
Methylmercury (CH3Hg+)
Hg demethylation is an __ and __ process
Aerobic and anaerobic
What is the function of MerB
Can detoxify methylmercury by converting it back to Hg2+
What is the function of MerA
Can convert Hg2+ back to Hg0 (elemental form)
Photoautotroph: energy source, carbon source
Light, CO2
Photoheterotroph: energy source, carbon source
Light, Organic compounds
Chemoautotrophs/lithotrophs: energy source, carbon source
Inorganic compounds, CO2
Chemoheterotrophs: energy source, carbon source
Organic compounds, organic compounds
Auto =
CO2 is carbon source
Hetero =
Organic compounds are carbon source
What are chemolithoautotrophs?
Bacteria able to oxidize reduced inorganic compounds to synthesis ATP and fix CO2
Ammonium-oxidizing nitrifying bacteria
Use NH4+ as sole energy source and oxidize it to NO2, have monooxygenase that may attack TCE
Nitrite-oxidizing nitrifying bacteria
Use NO2 as sole energy source and oxidize it to NO3
What two bacteria play a critical role in the nitrogen cycle?
Ammonium and nitrite-oxidizing nitrifying bacteria
What is the sole energy source of sulfur-oxidizing bacteria?
Inorganic reduced sulfur compounds, such as elemental S, H2S, or thiosulfate
Sulfur-oxidizing bacteria oxidize __ to __ using ___
oxidize reduced sulfur compounds to SO4 2-, using O2
Why is thiobacillus denitrificans a special sulfur-oxidizing bacteria?
It can use NO3 as an electron acceptor in the absence of oxygen
Why are H2-oxidizing bacteria facultative chemolithoautotrophs?
They can use H2 or organic compounds as their energy source
Why type of biochemical pathways occur in soil (from top to bottom)?
Oxygen respiration, denitrification, sulfate reduction, methanogenesis
How would you stimulate biodegradation?
Add more of the terminal electron acceptor of the bacteria you are trying to stimulate
Examples of reduced organic compounds as electron donors
Carbs, CH4
Examples of reduced inorganic compounds as electron donors
H2S, Fe2+, NH4+
Aerobic resp electron acceptors
O2 (to H2O)
Anaerobic resp electron acceptors
Various, eg NO3- (to NH4)
What does NAD(P)H provide?
Reducing power for biochemical reactions
Gram negative cell
Thin peptidoglycan, outermembrane
Gram positive cell
Thick peptidoglycan, no outermembrane
What are 3 basic biogeochemical cycles
Carbon, nitrogen, sulfur
Respiration: carbon cycle
Ch2O is oxidized to CO2
Photosynthesis: carbon cycle
CO2 is reduced to CH2O and O2 is released
Lithotrophy
CO2 is reduced to organic biomass CH2O
Methanotrophy
CH4 is oxidized to CH2O
Methanogenesis
CO2 is reduced to CH4
Anaerobic lithotrophy
CO2 is reduced to organic biomass CH2O
Fermentation
Organic molecules are catabolized into smaller products
How is CO2 fixed in aerobic conditions
By oxygenic photosynthetic organisms (cyanobacteria, algae, plants etc) and some chemolithoautotrophic bacteria (nitrifying, sulfur-oxidizing)
How is CO2 fixed until anaerobic conditions?
By anoxygenic photosynthetic bacteria (Rhodospirillum, chlorobium)
How is organic matter oxidized back to CO2
Via aerobic respiration, anaerobic respiration and fermentation
What oxidizes CH4 to CO2
Methanotrophs (methylosinus, methylococcus)
What is methane monooxygenase (MMO)
Enzyme that methanotrophs have to oxidize CH4, can also oxidize TCE
What is happening as the permafrost thaws
It introduces previously unavailable organic carbon into the expanding layer of active soil
Reduced S compounds are good…
Energy sources
Oxidized forms of S are good…
Electron acceptors for anaerobic respiration
Dissimilatory sulfate reduction
Bacteria degrading pollutants via anaerobic respiration is sulfate is abundant as a TEA, SO4- –> H2S
Sulfide oxidation
H2S –> S0, aerobic
Sulfur oxidation
S0 –> SO4-, aerobic
Phototrophic oxidation
SO4- –> S0, and H2S –> S0, anaerobic
Sulfur respiration
S0 –> H2S, anaerobic
What is an example of a sulfate reducing bacteria
Desulfovibrio
What is the energy source and TEA of Desulfovibrio
H2/organic carbon, sulfate
Dissimilatory nitrate reduction
Anaerobic respiration where nitrate is TEA
How does addition of N-fertilizer help in bioremediation?
Stimulates mineralization by decreasing C/N ratio
What is nitrogenase
Enzyme that N2 fixing bacteria have to reduce N2 to NH4+
What happens to NH4+ under aerobic conditions?
Bacterial nitrification oxidizes it to NO2 then NO3
Nitrosomonas sp.
Oxidize NH4+ to NO2-, have ammonium monooxygenase
Nitrobacter sp.
Oxidize NO2- to NO3-
What is denitrification
Reduction of NO3- to N2 by bacteria
What are three fates of various contaminants?
Water, groundwater, soil/sediment
Biomagnification
Increase in a pollutant in tissues of organisms at successive levels of a food chain
Bioaccumulation
Increase in the concentration of a compound within an organism compared to the level found in the environment
Biodegradation
Degradation of a pollutant by a living organism
Bioremediation
Remediation of a contaminated site by using the biodegradative capacity of biology
What are the 3 conditions for biodegradation/remediation?
- contaminant must be biodegradable
- environmental conditions must allow it
- microorganisms must be present
Xenobiotic compounds
Man-made compounds with uncommon structures or properties
Why are xenobiotics a pollution problem?
Toxicity, carcinogenicity, recalcitrance
Recalcitrance
A compound that is attacked poorly because of molecular complexity (does not fit into the enzymatic pocket of the organism)
What makes xenobiotics so complex
Halogen (or other) substitutions, H replaced by Cl ,Fl, or Br, or nitro/sulfo groups
What is a source of a natural xenobiotic compound?
Forest fires (lignin + Cl ions = chloroorganics), volcanoes
Pollutants and microbes are more easily located in __ compared to __
Soil, water
Why don’t we use GMO to clean up contamination?
It could turn into another contaminant, since we are introducing another man-made compound into a system to clean up a man-made problem
What does bioavailable mean?
Available to biological systems for utilization as energy and C sources or to be biotransformed
What can make a pollutant less bioavailable?
If it is heavily bound to something
What are 6 parameters that need to be considered for optimal bioremediation?
Soil moisture, soil type, aeration, redox potential, pH and temperature
Petroleum hydrocarbons are more quickly degraded under what conditions?
Aerobic
How can you increase aeration in a system?
Tilling, adding bulking agents, venting aquifers
Biodegradation or organic contaminants under anoxic conditions occurs under…
Denitrifying, methanogenic, sulphate-reducing and iron-reducing conditions
What compounds are best degraded under anaerobic conditions?
BTEX, PAHs, Halogenated organic compounds (TCE, PCBs)
How can anaerobic degradation be enhanced?
Adding a supply of appropriate electron acceptors
What is reductive dechlorination?
Use of the chlorinated structures as the TEA, sub of Cl with H
What is the range of pH in soils
2.5 - 11
What pH is optimal for the degradation of petroleum hydrocarbons
7 - 8
How can you increase the pH in a soil system
Add lime to acid soils
How can increasing the pH of a soil system be an issue?
Can effect water solubility and absorptions of contaminants in soil sediments (like heavy metals)
What is the Q10 value
A change of 10oC will generally increase or decrease an enzymes activity by 2-fold
How can you increase the temperature of a soil/water system
It is very difficult to do, but you could add compost materials to stimulate thermophilic biodegradation
Soil moisture content (%)/water content
Amount of water present in soil expressed as the ratio of dry weight to wet weight
Water activity (Aw)
Measures water actually available for microbial use
What two water measurements are always taken when dealing with a contaminated soil system
Soil moisture content and water holding capacity
Water holding capacity (WHC)
Amount of water a soil can hold before becoming saturated
What is the optimal soil moisture content for aerobic microbial activity
60-80% WHC
What is the optimal soil moisture content for hydrocarbon degradation
30-90% WHC
WHC greater than 100% creates __ conditions
Anoxic
How can you dry out a soil system
Adding gypsum or bulking agents like alfalfa
What are the two nutrients that become rate limiting very quickly in contaminated environments
N and P
What is the rate limiting nutrient for heterotrophs in non-contaminated systems
Carbon
Biostimulation
Treating contaminated sites with N and P (or sometimes O) – increase C:N ratio, increase biomass and degradative activity
What are oleophilic fertilizers
Special fertilizers that have N and P that stick to the hydrocarbons in oil so that when microbes come to degrade them they have an energy source close by
Cometabolism
Gratuitous metabolic transformation of a substance by a microbe growing on another substrate – substrate is not incorporated into microorganisms biomass and the microorganism does not derive energy from the transformation of the substrate
What is an example of cometabolism
Cyclohexane is cometabolized in the presence of propane by Myobacterium, allowing Pseudomonas to grow using cyclohexanol
An ecological niche is the site of…
Competition and change in conditions
What is the difference between terminal and subterminal alkane biodegradation
The position of the carbon that is oxidized
What are the 4 major steps of mineralization of an alkane
- Oxidation to primary alcohol via monooxygenase (or dioxygenase)
- Formation of fatty acid
- Beta oxidation of fatty acids to acetyl-CoA
- Oxidation of acetyl-CoA via the TCA cycle and the glyoxylate shunt
How are phenolic/aromatic rings degraded?
They are first oxidized to catechol under aerobic conditions
Monooxygenases
One oxygen atom is transferred to the substrate, the other is reduced (produces water)
Dioxygenases
Both oxygen atoms are transferred to the substrate
What enzyme cleaves catechol rings via the ortho pathway
catechol 1,2-dioxygenase
What enzyme cleaves catechols via the meta pathway
catechol 2,3-dioxygenase
Which is the preferred pathway for catechol cleavage
Ortho
What is the problem with the meta pathway
It produces acetaldehyde which is toxic
What enzyme do fungi use to degrade PAHs
Cyt P-450 monooxygenase
