Final Flashcards
What causes organic pollutant degradation?
Abiotic and biological mechanisms
What are abiotic mechanisms of organic pollutant degradation?
Nonbiological mechanisms The types are: - photochemical - chemical (oxidation, reduction) - mechanical (wind, water, mixing, dilution)
What are biological mechanisms of organic pollutant degradation?
Types:
- Plants and animals
- Microorganisms (most important)
What are the different plant and animal biological mechanisms?
Direct consumption
Indirect degradation via:
- Compounds secreted by organisms
- Associated microbes biodegrade contaminants
- These microbes include rhizosphere and biofilm on roots
What are the different microorganism biological mechanisms?
Mineralization
- Conversion of organic compounds to CO2
Modification or transformation
- End product may be more or less of a pollution problem after
What are microbes?
Microscopic organisms of:
- Plants and animals (called protozoa)
- Bacteria (even visible bacteria)
- Archae
- Viruses & prions
What is microbial hegemony?
The significant roles of microorganisms on earth
Dominance in global biomass with over 50% as microbial
Predominant influence over global biogeochemical cycling
Supremacy in extraordinary metabolic capacity
What is the importance of microbial evolution in biodegradation?
Have been exposed to every imaginable organic compound and environment over the last 3-4 billion years of their existence
Have complex metabolic processes that evolved for biodegradation
Failures:
- Only ~1% of microbial species have been cultured
- we don’t know much about metabolic pathways
Why are only ~1% of microbes cultured?
The vast majority of bacteria and archaea can’t be grown in culture
Some can be viable-but-not-culturable (Called VBNC)
Tests to determine microbes that can’t be grown in culture
Microscopy: direct microscopic counts can exceed viable counts by several orders of magnitude
Respiration tests
Molecular biology (types: 16S rRNA sequences, the “molecular clock”, the position on tree of life)
What is the central dogma of life?
An explanation of the flow of genetic information within a biological system
DNA -> RNA -> protein
What is the tree of life?
The study of phylogenetic relationships between all cells: done by comparing the 16S rRNA sequences
- Proves that the greatest diversity in the living world is within the microbial world
- Was able to split the two branches of microbes: bacteria and archaea
Bacteria on the tree of life
Include some well-known species
Majority of species have never been characterized
Found in every niche on the planet
Archaea on the tree of life
Organisms previously thought to be limited to extreme environments (such as anaerobic sediments, hot springs, etc)
Dominate extreme environment niches, but are found everywhere (are ubiquitous)
Have unique physiological properties
What happened with the Last Common Ancestor?
Gave rise to two branches: bacteria and archaea/eukarya
What is the evolution of metabolic capabilities in bacteria?
Genetics -> physiology -> ecological niche -> genetics
Ecological niche consists of:
- competition
- change in conditions
These factors are part of the selective pressure that stimulate the evolution of metabolic capacities in microbes
Importance of the evolution of metabolic capabilities in bacteria for biodegradation:
Microbes have been around since an anaerobic atmosphere
They have evolved many different/complex metabolic strategies
Can be used to degrade many toxic pollutants
High probability of finding a species that can bioremediate a particular pollution
- May have to use culture-based and/or molecular methods to find useful microbes
Where do you look for microbial pollution biodegraders?
Soil & water in contaminated sites b/c
- biodegrades should be enriched and selected for in these environments
What occurred 2.5 billion years ago?
Great oxidation event
When the amount of oxygen in the air increased so the atmosphere became aerobic
Due to oxygenic photosynthesis from microbes
What are the key properties of prokaryotes?
Small size: 1-2 um High surface to volume ratio Developed biochemical pathways (favors chemistry) Metabolically diverse - Alternate energy sources - Light, organics, inorganics, alternate oxidants - O2, metals, CO2 Rigid cell wall
What are the key properties of Eukaryotes?
Larger cell size (10-25um) Complex structures (multicellular) Flexible cell walls Metabolic specialization - O2 respiration - Organic C as fuel
Microbial bioenergetics consists of:
Metabolism and thermodynamics
How do cells grow?
Living cells are dynamic open systems in constant interaction with the immediate environment, where they obtain the raw material for the production of ATP and building blocks
They need to synthesize the building blocks (monomers) and harvest energy so biochemical reactions can occur, and the cell can grow
What are the two sets of reactions of metabolism?
Catabolic
Anabolic
What is the electron donor of eukaryotes?
Organic carbon
What is the electron acceptors of eukaryotes?
Oxygen
Do many bacteria use carbon as an electron donor? If yes, what happens?
True
Organic C is electron donor, oxygen is electron acceptor
What does lithoautotrophic prokaryotes mean?
Litho- -autotrophic = nonorganic eating
What are some electron donors of lithoautotrophic prokaryotes?
Hydrogen gas, hydrogen sulfur…
What are some electron acceptors of lithoautotrophic prokaryotes?
Oxygen
Ferric hydroxide to iron (called iron respiration)
True/false different microbes can use different types of metabolisms to produce energy.
True
Via redox reactions (also called oxidation reduction reactions)
What is oxidation?
The removal of electrons from an atom or molecule
Can only occur with reduction (electron must be accepted by another atom or molecules)
What is reduction?
The addition of electrons to an atom or molecule
What happens to the energy released during redox reactions?
Captured in the form of energy-rich chemical bonds (becomes ATP)
What is NADH?
A reducing power
Can take in the electron released by oxidation
What are ATP and NADH required for?
Cellular metabolism
What is anabolism?
Biochemical reactions involved in the synthesis of compounds and macromolecules such as proteins and nucleic acids
Biosynthesis
What is catabolism?
Biochemical reactions that break down compounds (mostly to allow cells to generate chemical energy)
What is an example of catabolism?
The oxidation of carbohydrates (sugars) during respiration (aerobic or anaerobic) or fermentation
What happens if glucose is the main nutrient for a bacterium?
Will be transported across the membrane
Then it will be oxidized to CO2 in 3 steps (IMPORTANT)
1. Glycolysis: Glucose (6 C) will be broken into 2 molecules of pyruvate (3 C) (produces 2ATP)
2. Krebs cycle or tricarboxylic acids cycle: Complete combustion of pyruvate to CO2 through a cyclic set of reactions (produces 2 ATP)
3. Oxidative phosphorylation: some reactions lead to the reduction of coenzymes (NADH, FADH) that will be further oxidized in the respiratory chain (electron transport system) which produces the proton motive force (produces the most ATP molecules: 34 ATP)
Why do microbes biodegrade pollutants?
They can get energy
What is atrazine?
Pesticide
What is toluene and xylene?
Hydrocarbons
What is dichloroethane (DCE)?
A solvent (a chlorinated hydrocarbon)
Process of the electron transfer system:
Electrons flow from the reduced coenzymes to a terminal electron acceptor (TEA) such as O2 (microorganisms can use different TEAs) via the electron transport chain (ETC)
Flow of electrons down ETC causes ETC to pump protons (H+) out of the cell, resulting in the proton motive force (PMF)
The PMF is used for different work (membrane transport, flagellar rotation…) and allows synthesis of ATP during respiration
What is aerobic respiration?
Overall process called oxidative phosphorlation
The use of O2 as the TEA
Reducing power (NADH…) generated by oxidation of energy source
Electrons transferred to ETC then to TEA (O2 -> H2O)
Results in (H+)/pH gradient
H+ gradient fuels processes like ATP synthesis
In what condition are organic pollutants better degraded (aerobic or anaerobic respiration)?
Aerobic
It is faster and more efficient
It results in more complete oxidation to CO2
Why is anaerobic respiration important in biodegradation?
Many contaminated environments quickly become anaerobic
With anaerobic respiration of microbes, biodegradation is not limited by O2 as long as there are alternative TEAs
What are the O2 concentrations within soil aggregates?
Aerobic zones (outside) ->
Microaerophilic zones ->
Anaerobic zones (center)
Percent of oxygen decreases as it moves farther from external surface
The soil environment is a heterogeneous microbial habitat
What is a heterogeneous microbial habitat?
Contains both aerobic and anaerobic zones (O2 conc. decreases with depth into soil due to diffusion and utilization of O2 on the surface)
- O2 can be depleted within 1 mm below surface
Varies greatly (even within a soil aggregate)
Different micro-habitats and food sources
How do terminal electron acceptors work in energy generation?
Different TEAs available in different niches
Availability of TEAs differs with depth
Key parts of major biogeochemical cycles (C, N, and S)
Many organisms use metallic terminal electron acceptors that vary with depth
Some organisms able to use only one compound, some can use multiple (mostly from adjacent zones)
What is anaerobic respiration?
Electrons transferred to compounds other than oxygen
Examples:
- Denitrification (electron acceptor = NO3-)
- Sulfate reduction (electron acceptor = SO4-)
- Fermentation (electron acceptor = fumarate)
- Methanogenesis (electron acceptor = CO2)
Denitrification
An anaerobic respiration biodegradation
Use NO3- as TEA. Reduce it to gaseous N2O and N2
Most abundant bacteria: Pseudomonas and Alcaligenes
Reductions catalyzed by reductases located in membrane or periplasmic space that are part of the ETC
Important process in the nitrogen cycle
Ex. Thauera aromatica, Azoarcus tolutytics are both toluene degrading bacteria
Iron-reducing and manganese-reducing bacteria
An anaerobic respiration biodegradation
Use iron or manganese as TEAs
Ex.
Geobacter metallireducens GS15 degrade toluene under iron-reducing conditions
Sulfate-reducing bacteria
An anaerobic respiration biodegradation
Use sulfate as the TEA
Taxonomic groups = Desulfovibrio, Desulforomonas, Desulfosarcina
Desulfobacula toluolica degrade toluene under sulfate-reducing conditions
Methanogenic archaea
An anaerobic respiration biodegradation
Use CO2 as TEA
Use H2 as energy and electron source OR ferment acetate
Important bacteria for atmospheric trace gases
IMPORTANT in anaerobic degradation of toluene in sediment or activated sludge reactors
Fermentation in biodegradation
Use organic molecules as TEAs
Products in soil/sediment are acetate, formate, butyrate, lactate, succinate, caproate…
Clostridium is a fermenting bacteria
What is species Thauera aromatica?
A toluene degrading denitrifiers (anaerobic)
What is the species Azoarcus tolulyticus?
A toluene degrading denitrifiers (anaerobic)
What is species Geobacter metallireducens GS15?
An Fe-reducing bacterium degrading toluene under anaerobic conditions
What is species Desulfobacula toluolica?
Degrading toluene bacteria under sulfate-reducing conditions
What is genus Clostridium?
Fermenting bacteria in soil
What is the most metabolically efficient redox reaction?
Aerobic iron oxidation
What is the best reductant?
CH2O (organic carbon) (oxidized)
What is the worst reductant?
H2O (water) (oxidized)
What is the best oxidant?
O2 (oxygen) (reduced)
What is the worst oxidant?
CO2 (carbon dioxide) (reduced)
What is Shewanella oneidensis?
The super microbe
Extremely versatile with its electron acceptors (strains reduce multiple electron acceptors)
Donors: formate, lactate, pyruvate, amino acids, H2
Acceptors: O2, NO3-, NO2-, Mn (IV,III), Fe (III), Fumarate, DMSO, TMAO, S^0, S2O3^2-, U(VI), Cr (VI)
What is Geobacter spp.?
A cousin of Shewanella oneidensis
Energy source = organic carbon (acetate)
Reduces U (vi) to U (iv) and Fe3+ to Fe2+
U (vi) is highly soluble in water
U (iv) is highly insoluble and will precipitate out of water
How would you increase Geobacter numbers and activity in a Uranium contaminated aquifer?
Increase the amount of organic carbon and increase the number of Geobacter spp.
What is the bioremediation process of arsenic contaminated groundwater?
Using aerobic lithoautotrophic bacteria
Water cycles through oxygenation tanks containing bacteria that oxidize arsenite, iron, and manganese
Produces oxidized form of arsenic (arsenate)
- it chemically precipitates with iron and manganese for convenient removal
Electron donor = Fe2+, Mn2+, and arsenite
Electron acceptor = oxygen (O2)
How does mercury biodegradation occur?
Mercury concentrates in living tissues and is highly toxic
Mercury in atmosphere = elemental mercury (Hg^0) which is volatile
- Oxidized to mercuric ion (Hg2+) (how it enters aquatic environments
Hg2+ is metabolized by microorganisms which form methylmercury (CH3Hg+) (extremely soluble and neurotoxic compound)
Bacteria can transform methyl mercury into nontoxic form
How to define microbial nutritional categories?
Determine:
- Source of energy (photo- or chemo-)
- Source of electrons
- Source of carbon (-autotroph or -heterotroph)
Where do the two-part nutritional category names photoautotrophs and chemoheterotrophs come from?
Consideration of energy and carbon sources
Photoautotroph:
Photo- = light energy -autotroph = CO2 carbon source
Chemoheterotroph/heterotrophs:
Chemo- = organic compounds for energy -heterotroph = organic carbon source (plants/animals)
Where does the three-part nutritional category name chemolithoautotroph come from?
Energy, electron, and carbon sources
Chemolithoautroph:
Chemo- = chemical energy
- litho- = uses inorganic electron molecules
- autotroph = CO2 carbon source
Heterotrophic carbon utilization:
Heterotrophs assimilate organic compounds
Take up organic compounds and then use them as a source of carbon in own biosynthetic reactions
Types of chemolithoautotrophs:
Able to oxidize reduced inorganic compounds to synthesize ATP for biosynthesis and fix CO2 Ammonium-oxidizing nitrifying bacteria Nitrite-oxidizing nitrifying bacteria Sulfur-oxidizing bacteria H2-oxidizing bacteria
Ammonium-oxidizing nitrifying bacteria
Chemilithoautotroph
Uses inorganic compound NH4+ as energy source
Oxidize NH4+ to NO2-
Have a monooxygenase (ammonia monooxygenase, AMO) which may attack some pollutants (trichloroethylene, TCE)
Genuses Nitrosomonas & Nitrovibrio
Between ammonium-oxidizing and nitrite-oxidizing nitrifying bacteria, convert NH4+ to NO3- (a rate-limiting step)
Nitrite-oxidizing nitrifying bacteria
Chemolithoautotroph
Use inorganic compound NO2- as energy source
Oxidize NO2- to NO3-
Genus Nitrobacter
Between ammonium-oxidizing and nitrite-oxidizing nitrifying bacteria, convert NH4+ to NO3- (a rate-limiting step)
Sulfur-oxidizing bacteria
Chemolithoautotroph
Genus Thiobacillus
Use a variety of inorganic reduced sulfur compounds as energy source
- Such as S, H2S, S2O3
Oxidize reduced S compounds to SO4^2- using O2
Key enzymes: sulfide-, sulfur-, and sulphite-oxidases
Play critical role in S cycle by regenerating SO4 ^2- (main source of S for assimilation)
Exception is Thiobacillus denirificans
What is species Thiobacillus denitrificans?
Exception to sulfur-oxidizing bacteria
Uses NO3- as an electron acceptor in the absence of oxygen
H2-oxidizing bacteria
Chemolithoautotroph
Uses H2 as energy and electron source
Considered a facultative chemolithoautotroph because they can use organic compounds instead of H2
Species are Paracoccus denitrificans and Desulfovibrio vulgaris
The course of biodegradation TEAs through sediment:
Based on energy per molecule Begins with oxygen respiration (O2 -> H2O) Then denitrification (NO3- -> N2)) Then iron reduction Then sulfate reduction (SO4-2 -> H2S) Then methanogenesis (CO2 -> CH4)
What happens when TEAs are used up through sediment?
SO4- is used = leads to sulfide accumulation
CO2 is used = leads to CH4 accumulation
What does a purple gram stain indicate?
Gram-positive membrane
Found in Firmicutes and Actinobacteria (including Bacillus sp.)
Have thick cell wall outside of cytoplasmic membrane and have no outer membrane
What does a pink gram stain indicate?
Gram-negative membrane
Have thin cell wall in periplasmic space between the cytoplasmic and outer membranes
Have LPS and porins on outer wall not found in gram-positive membranes
What membranes do most of the bacterial phyla involved in biodegradation have?
Gram-negative membranes
What is biogeochemical cycling?
Organic matter decomposes into small inorganic molecules, which are immobilized by growing cells
Microbes play a great role in maintaining equilibrium between organic matter reservoir and mineralized reservoir
There is aerobic and anaerobic environment in each cycle
Important cycles: Nitrogen, Carbon, Sulfur
Cycles are altered by human activity
The carbon cycle is fixed into organic matter via:
Can be anaerobic or aerobic
Anaerobic: fixed by anoxygenic photosynthetic bacteria (Rhodospirillum, Chlorobium)
Aerobic: fixed by oxygenic photosynthetic organisms (cyanobacteria, algae, plants) and chemolithoautotrophic bacteria (nitrifying bacteria, sulfur-oxidizing bacteria)
What is merB
Breaks carbon-mercury bonds so methylmercury becomes mercuric ion
The carbon cycle:
- CO2 is fixed into organic matter (CH2O) under aerobic or anaerobic conditions
- Organic matter is oxidized back to CO2 via aerobic respiration or anaerobic respiration & fermentation
- Some organic matter and CO2 in anaerobic respiration can become CH4 by methanogens (diverse group of Archaea)
- CH4 is oxidized (aerobic) to CO2 by methanotrophs (group of bacteria: Methylosinus & Methylococcus)
What is carbon in organic matter?
-In soil/sediment, carbon in the organic matter can be active (living biomass) or inactive (dead)
What is the mineral reservoir of carbon?
Atmospheric or dissolved CO2 & calcareous rocks and coral
How do methanotrophs oxidize CH4
They possess a key enzyme (methane monooxygenase: MMO) that oxidized CH4 to methanol
Can be present on complex membrane structures
MMO can also oxidize trichloroethylene (TCE)
What is there a lot of in permafrost environments?
Organic carbon
The active layer of permafrost defrosts in the summer
- The active layer is becoming deeper so more organic carbon is being activated (and methane)
How much CO2 will be in atmosphere from permafrosts in 2100?
an extra 50ppm
How much CO2 is there in the environment today?
417ppm
What is the importance of sulfur?
Oxidized forms of S can be used as electron acceptors for anaerobic respiration (dissimilatory sulfate reduction)
Reduced forms of S are good energy sources
Sulfur is the most important element in the cell for amino acids
The Sulfur cycle (aerobic)
S^0 oxidized to sulfate (SO4-) (aerobic)
Dissimilatory sulfate reduction from SO4- to hydrogen sulfide (H2S) (anaerobic)
Sulfide oxidation from H2S to S^0 (aerobic)
The sulfur cycle (anaerobic)
Phototrophic oxidation of S^0 to H2S or SO4-
SO4- goes through dissimilatory sulfate reduction to H2S
H2S goes through sulfur respiration to S^0
What is an example of dissimilatory sulfate reduction?
sulfate-reducing bacteria (SRBs): Desulfovibrio
What does the dissimilatory sulfate reduction do?
Utilizes sulfate as a terminal electron acceptor
Uses H2 and/or organic carbon as an energy source
Therefore, SO4- becomes H2S
What is the importance of nitrogen?
Important element in cells for proteins and nucleic acids
Growth of organisms usually limited by nitrogen availability
Bacteria can use nitrate as a TEA (called dissimilatory nitrate reduction)
In bioremediation, adding N-fertilizer stimulates mineralization of organic matter by decreasing C/N ratio
What does nitrification do the ionic charge?
It alters the ionic charge of the fixed forms of nitrogen so that leaching occurs in soils
What happens in anaerobic denitrification?
Anaerobic respiration in soils and sediments returns molecular nitrogen to the atmosphere
The nitrate cycle (aerobic)
Nitrate oxidation: from nitrite (NO2-) to nitrate (NO3-)
Assimilation: Assimilatory NO3- reduction to R-NH2 ammonium assimilation to NH4+
Nitrification: Ammonium oxidation from NH4+ to NO2- using nitrifying bacteria with enzyme ammonium monooxygenase (AMO) or NO3-
Alternate root (from NO3- to NO2- through dissimilatory NO3- reduction (anaerobic)
The nitrate cycle (anaerobic)
Either:
- Nitrite ammonification: from NO2- to NH4+
- NH4+ to aerobic respiration
- Nitrite reduction: from NO2- to NO
- Denitrification: NO to N2O
- N2O to N2
- Nitrogen fixation: N2 to NH4+ (NH4+ to aerobic respiration)
Denitrification of NO3-: NO3- assimilated by microbes becoming organic matter or reduced to N2
How much of the atmosphere is N2 gas?
79%
What is the problem with N2 gas in the atmosphere?
Only diazotrophs (a small proportion of bacterial and archaeal species) can fix N2
What does the enzyme nitrogenase do?
An N2-fixing bacteria that reduces N2 to NH4+
Ex. Rhizobium, Azotobacter, Azoarcus
What happens to NH4+ with assimilation?
Most microbes and plants can assimilate NH4+
There is a dynamic equilibrium between assimilation and mineralization (the ammonification of N from amino acids)
What happens with NH4+ with oxidization?
NH4+ can be oxidized to NO2- and NO3- by bacterial. nitrification under aerobic conditions
Bacterial examples are Nitrosomonas (for NO2-) and Nitrobacter (for NO3-)
- Both have complex membrane infoldings to facilitate nitrification
What is Nitrosomonas sp. for?
Oxidize NH4+ to NO2-
Possess ammonium monooxygenase (AMO) enzyme
What is Nitrobacter sp. for?
Oxidize NO2- to NO3-
Nitrate cycle in aquariums:
Urea/NH3 becomes nitrate (NO3-) Uses denitrifying bacteria to filter out nitrate Bacteria create biofilms on plastic Uses methanol as the electron donor Uses NO3 as electron acceptor
When does NO3 toxicity start manifesting?
Above 30mg NO3
Leads to infections, parasites, mortality rates
How many die per year due to pollution?
~9million
1 in 6 deaths
Main human sources of organic pollutants:
Domestic waste (plastics, antibiotics…)
Pulp and paper (Cellulosics…)
Agriculture (lignin, chloro-organics…)
Food processing (proteins, fats, carbs…)
Mining (metals…)
Textile industry (fluorocarbons…)
Chemical, pharmaceutical industries (dyes, solvents, paints, resins…)
Internal combustion engines (hydrocarbons…)
What is the fate of industrial contaminants when they are released into the environment?
If volatile = air pollution
If non-volatile & soluble = water and groundwater pollution
If non-volatile & non-soluble = soil pollution, mineralization (degradation to CO2), persistence in food chain
Examples of air pollution:
Carbon tetrachloride
CFCs
Examples of water pollution:
Pesticides
Examples of groundwater pollution:
Petrochemicals
Pesticides
Examples of mineralization:
PAHs
Petrochemicals
Examples of persistence in food chain:
PCBs
DDT
What is biomagnification?
The increase in a pollutant in tissues of organisms at successive levels of a food chain
Results in bioaccumulation at higher trophic levels
What is bioaccumulation?
The increase in concentration of a compound within an organism compared to the level found in the environment
Accumulates in tissue if not metabolized or excreted
Has negative health/reproductive effects
What is biodegradation?
Degradation of a pollutant through a living organism (usually a microbe)
What is bioremediation?
Remediation of a contaminated site by using biodegradative capacity of biology (usually microbiology)
What interactions need to happen for biodegradation and bioremediation to occur?
- The contaminant must be biodegradable
- The environmental physical/chemical parameters must allow biodegradation
- Biodegradative microorganisms must be present and active in the contaminated environment
What are xenobiotic compounds?
Compound alien to existing enzyme systems: man-made organic compounds with uncommon structures/properties
Not naturally occurring
Organic xenobiotics are often pollution problems due to:
- Toxicity
- Carcinogenicity (cancer causing)
- Recalcitrance (complexity)
What does recalcitrance mean?
A compound that is attacked poorly or not at all by microbial enzyme systems due to molecular complexity
- Oligomerization: converts monomers to macromolecular complexes
- Halogen substitutions: replacing H with chlorine, fluorine, or bromine
- Other substitutions: replacing H with nitro- or sulfo- groups
- Branching
- Large size: molecules are too big to fit into enzyme pockets with catalytic sites; large molecular organic contaminants are more hydrophobic so less bioavailable
Examples of xenobiotic compounds:
DDT Malathion 2,4-D Atrazine Monuron Chlorinated biphenyl (PCB) Trichloroethylene Mirex (KNOW) Kepone (KNOW) Benzaanthracene (KNOW) Benzoapyrene (KNOW)
