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Pollution & Bioremediation > Biodegradation > Flashcards

Biodegradation Flashcards

1
Q

Abiotic mechanisms of degradation

A

Photochemical, chemical (ox/red), mechanical

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2
Q

Two biological mechanisms of degradation

A

Plants/Animals and Microorganisms

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3
Q

How plants and animals contribute to degradation

A

Direct/indirect consumption, compounds secreted, associated microorganisms

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4
Q

How do microorganisms contribute to degradation

A

Mineralization, modification or transformation

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5
Q

What is mineralization?

A

Conversion of organic compounds to CO2

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6
Q

How much of global biomass is microbial?

A

Greater than 50%

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7
Q

How many microbial species have never been cultured

A

Around 99% (holy shit)

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8
Q

What was the first evidence of cyanobacteria-like fossils and when did they appear?

A

Stromatolites, 3.5 BYA

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9
Q

What happened 2.5 BYA?

A

The great oxidation event, oxygenic photosynthesis (bc of microbes)

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10
Q

What are the two metabolic features of cyanobacteria?

A

Photosynthesis and nitrogen fixation

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11
Q

What does VBNC mean?

A

Viable but not culturable

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12
Q

How do we know microbes exist without culturing them?

A

Microscopy, respiration tests, molecular biology (16S rRNA seq)

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13
Q

Why is molecular biology important in microbiology?

A

It is needed to classify microorganisms - can’t do it on morphology alone

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14
Q

Central dogma of life

A

DNA – RNA – Protein

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15
Q

Why was 16S rRNA sequence important?

A

Helped form the tree of life and determine evolutionary relationships

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16
Q

Why is evolution important in terms of biodegradation?

A

Microbes have evolved to degrade certain pollutants because of selection pressures

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17
Q

Why are prokaryotes thought to have greater metabolic diversity?

A

Because of their high surface/volume ratio

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18
Q

Three characteristics of prokaryotes

A

Small size, rigid cell wall, metabolic diversity

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19
Q

Three characteristics of eukaryotes

A

Larger size, flexible cell walls, metabolic specialization

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20
Q

How is growth defined in the microbial world

A

Multiplication of cells by the successive division of mother cells into two daughter cells

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21
Q

What are the two divisions of metabolism?

A

Anabolism and catabolism

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22
Q

What does lithoautotrophic mean

A

Reduces non organic molecules

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23
Q

Oxidation

A

Removal of electrons

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24
Q

Reduction

A

Addition of electrons

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25
Q

Anabolism

A

Biosynthesis, requires energy

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26
Q

Catabolism

A

Enzymatic degradation, produces energy

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27
Q

Three divisions of the mineralization process

A

Glycolysis, TCA cycle, electron transport chain

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28
Q

Why do microbes degrade pollutants?

A

Because they can get energy out of it

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29
Q

What is an example of a terminal electron acceptor?

A

O2, nitrate

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30
Q

What is the proton gradient/PMF

A

Created during the ETC, used by cells to move and generate ATP

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31
Q

What is aerobic respiration?

A

O2 as TEA, creates water, results in PMF, PMF fuels ATP synthesis (oxidative phosphorylation)

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32
Q

How is the reducing power generated in aerobic respiration?

A

By the oxidation of the energy source

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33
Q

What is the overall process occurring in the ETC?

A

Oxidative phosphorylation

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34
Q

What are organic pollutants degraded better aerobically?

A

It is faster and results in the more complete oxidation to CO2

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35
Q

Why does O2 concentration in a soil aggregate decrease as you get closer to the middle?

A

The microbes in the middle are using up the oxygen faster than it can diffuse in

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36
Q

Availability to TEAs in soil varies with __

A

Depth

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37
Q

What are examples of metallic terminal electron acceptors

A

MnO2, Fe(OH)3

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38
Q

What is anaerobic respiration?

A

TEA is a compound other than O2

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39
Q

What is the TEA used by nitrate reducers?

A

NO3 -

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40
Q

What is the TEA used by sulfate reducers?

A

SO4 -

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41
Q

Where does anaerobic respiration occur?

A

Cytoplasm or periplasm

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42
Q

What are examples of organic TEAs in anaerobic respiration?

A

Fumarate, enzyme part of ETC, CO2 (methanogenesis)

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43
Q

Ammonium oxidizing =

A

Uses ammonium as electron DONOR

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44
Q

Reduction is __ of oxygen, __ of electron

A

Loss, gain

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45
Q

Oxidation is __ of oxygen, __ of electron

A

Gain, loss

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46
Q

What are the most abundant denitrifies in soil?

A

Pseudomonas and Alcaligenes

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47
Q

What do denitrifiers reduce NO3 to?

A

N2O and N2 (gaseous products)

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48
Q

What bacteria degrade toluene under anaerobic conditions?

A

Thauera aromatica and Azoarcus tolylyticus

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49
Q

What does Geobacter metallireducens GS15 do?

A

Fe-reducing bacterium that degrades toluene

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50
Q

What are three taxonomic groups of sulfate reducing bacteria

A

Desulfovibrio, Desulfuromonas, Desulfosarcina

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51
Q

What do methanogenic archaea use as an electron donor and acceptor?

A

H2 donor, CO2 acceptor

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52
Q

What do fermenters use as terminal electron acceptors?

A

Organic molecules

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53
Q

What are the products of fermentation in soil?

A

Acetate, formate, butyrate, lactate, succinate, etc.

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54
Q

Example of fermenting bacteria found in soil

A

Clostridium

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55
Q

What is special about Shewanella oneidensis?

A

It has a lot of terminal electron acceptors, and can live as a heterotroph or lithoautotroph

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56
Q

What does Geobacter do?

A

Uses acetate as an energy source to convert uranium 6 to uranium 4 (ferric iron to ferrous iron)

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57
Q

What is involved in the remediation of arsenic contaminated ground water?

A

Oxygenate the system, microbes use Fe, arsenite and Mn as electron donors, arsenite precipitates are arsenate

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58
Q

What form of mercury is in the atmosphere?

A

Hg0

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59
Q

What form of mercury enters aquatic environments?

A

Hg2+

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60
Q

What does Mg2+ turn into under anaerobic conditions?

A

Methylmercury (CH3Hg+)

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61
Q

Hg demethylation is an __ and __ process

A

Aerobic and anaerobic

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62
Q

What is the function of MerB

A

Can detoxify methylmercury by converting it back to Hg2+

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63
Q

What is the function of MerA

A

Can convert Hg2+ back to Hg0 (elemental form)

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64
Q

Photoautotroph: energy source, carbon source

A

Light, CO2

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65
Q

Photoheterotroph: energy source, carbon source

A

Light, Organic compounds

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66
Q

Chemoautotrophs/lithotrophs: energy source, carbon source

A

Inorganic compounds, CO2

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67
Q

Chemoheterotrophs: energy source, carbon source

A

Organic compounds, organic compounds

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68
Q

Auto =

A

CO2 is carbon source

69
Q

Hetero =

A

Organic compounds are carbon source

70
Q

What are chemolithoautotrophs?

A

Bacteria able to oxidize reduced inorganic compounds to synthesis ATP and fix CO2

71
Q

Ammonium-oxidizing nitrifying bacteria

A

Use NH4+ as sole energy source and oxidize it to NO2, have monooxygenase that may attack TCE

72
Q

Nitrite-oxidizing nitrifying bacteria

A

Use NO2 as sole energy source and oxidize it to NO3

73
Q

What two bacteria play a critical role in the nitrogen cycle?

A

Ammonium and nitrite-oxidizing nitrifying bacteria

74
Q

What is the sole energy source of sulfur-oxidizing bacteria?

A

Inorganic reduced sulfur compounds, such as elemental S, H2S, or thiosulfate

75
Q

Sulfur-oxidizing bacteria oxidize __ to __ using ___

A

oxidize reduced sulfur compounds to SO4 2-, using O2

76
Q

Why is thiobacillus denitrificans a special sulfur-oxidizing bacteria?

A

It can use NO3 as an electron acceptor in the absence of oxygen

77
Q

Why are H2-oxidizing bacteria facultative chemolithoautotrophs?

A

They can use H2 or organic compounds as their energy source

78
Q

Why type of biochemical pathways occur in soil (from top to bottom)?

A

Oxygen respiration, denitrification, sulfate reduction, methanogenesis

79
Q

How would you stimulate biodegradation?

A

Add more of the terminal electron acceptor of the bacteria you are trying to stimulate

80
Q

Examples of reduced organic compounds as electron donors

A

Carbs, CH4

81
Q

Examples of reduced inorganic compounds as electron donors

A

H2S, Fe2+, NH4+

82
Q

Aerobic resp electron acceptors

A

O2 (to H2O)

83
Q

Anaerobic resp electron acceptors

A

Various, eg NO3- (to NH4)

84
Q

What does NAD(P)H provide?

A

Reducing power for biochemical reactions

85
Q

Gram negative cell

A

Thin peptidoglycan, outermembrane

86
Q

Gram positive cell

A

Thick peptidoglycan, no outermembrane

87
Q

What are 3 basic biogeochemical cycles

A

Carbon, nitrogen, sulfur

88
Q

Respiration: carbon cycle

A

Ch2O is oxidized to CO2

89
Q

Photosynthesis: carbon cycle

A

CO2 is reduced to CH2O and O2 is released

90
Q

Lithotrophy

A

CO2 is reduced to organic biomass CH2O

91
Q

Methanotrophy

A

CH4 is oxidized to CH2O

92
Q

Methanogenesis

A

CO2 is reduced to CH4

93
Q

Anaerobic lithotrophy

A

CO2 is reduced to organic biomass CH2O

94
Q

Fermentation

A

Organic molecules are catabolized into smaller products

95
Q

How is CO2 fixed in aerobic conditions

A

By oxygenic photosynthetic organisms (cyanobacteria, algae, plants etc) and some chemolithoautotrophic bacteria (nitrifying, sulfur-oxidizing)

96
Q

How is CO2 fixed until anaerobic conditions?

A

By anoxygenic photosynthetic bacteria (Rhodospirillum, chlorobium)

97
Q

How is organic matter oxidized back to CO2

A

Via aerobic respiration, anaerobic respiration and fermentation

98
Q

What oxidizes CH4 to CO2

A

Methanotrophs (methylosinus, methylococcus)

99
Q

What is methane monooxygenase (MMO)

A

Enzyme that methanotrophs have to oxidize CH4, can also oxidize TCE

100
Q

What is happening as the permafrost thaws

A

It introduces previously unavailable organic carbon into the expanding layer of active soil

101
Q

Reduced S compounds are good…

A

Energy sources

102
Q

Oxidized forms of S are good…

A

Electron acceptors for anaerobic respiration

103
Q

Dissimilatory sulfate reduction

A

Bacteria degrading pollutants via anaerobic respiration is sulfate is abundant as a TEA, SO4- –> H2S

104
Q

Sulfide oxidation

A

H2S –> S0, aerobic

105
Q

Sulfur oxidation

A

S0 –> SO4-, aerobic

106
Q

Phototrophic oxidation

A

SO4- –> S0, and H2S –> S0, anaerobic

107
Q

Sulfur respiration

A

S0 –> H2S, anaerobic

108
Q

What is an example of a sulfate reducing bacteria

A

Desulfovibrio

109
Q

What is the energy source and TEA of Desulfovibrio

A

H2/organic carbon, sulfate

110
Q

Dissimilatory nitrate reduction

A

Anaerobic respiration where nitrate is TEA

111
Q

How does addition of N-fertilizer help in bioremediation?

A

Stimulates mineralization by decreasing C/N ratio

112
Q

What is nitrogenase

A

Enzyme that N2 fixing bacteria have to reduce N2 to NH4+

113
Q

What happens to NH4+ under aerobic conditions?

A

Bacterial nitrification oxidizes it to NO2 then NO3

114
Q

Nitrosomonas sp.

A

Oxidize NH4+ to NO2-, have ammonium monooxygenase

115
Q

Nitrobacter sp.

A

Oxidize NO2- to NO3-

116
Q

What is denitrification

A

Reduction of NO3- to N2 by bacteria

117
Q

What are three fates of various contaminants?

A

Water, groundwater, soil/sediment

118
Q

Biomagnification

A

Increase in a pollutant in tissues of organisms at successive levels of a food chain

119
Q

Bioaccumulation

A

Increase in the concentration of a compound within an organism compared to the level found in the environment

120
Q

Biodegradation

A

Degradation of a pollutant by a living organism

121
Q

Bioremediation

A

Remediation of a contaminated site by using the biodegradative capacity of biology

122
Q

What are the 3 conditions for biodegradation/remediation?

A
  1. contaminant must be biodegradable
  2. environmental conditions must allow it
  3. microorganisms must be present
123
Q

Xenobiotic compounds

A

Man-made compounds with uncommon structures or properties

124
Q

Why are xenobiotics a pollution problem?

A

Toxicity, carcinogenicity, recalcitrance

125
Q

Recalcitrance

A

A compound that is attacked poorly because of molecular complexity (does not fit into the enzymatic pocket of the organism)

126
Q

What makes xenobiotics so complex

A

Halogen (or other) substitutions, H replaced by Cl ,Fl, or Br, or nitro/sulfo groups

127
Q

What is a source of a natural xenobiotic compound?

A

Forest fires (lignin + Cl ions = chloroorganics), volcanoes

128
Q

Pollutants and microbes are more easily located in __ compared to __

A

Soil, water

129
Q

Why don’t we use GMO to clean up contamination?

A

It could turn into another contaminant, since we are introducing another man-made compound into a system to clean up a man-made problem

130
Q

What does bioavailable mean?

A

Available to biological systems for utilization as energy and C sources or to be biotransformed

131
Q

What can make a pollutant less bioavailable?

A

If it is heavily bound to something

132
Q

What are 6 parameters that need to be considered for optimal bioremediation?

A

Soil moisture, soil type, aeration, redox potential, pH and temperature

133
Q

Petroleum hydrocarbons are more quickly degraded under what conditions?

A

Aerobic

134
Q

How can you increase aeration in a system?

A

Tilling, adding bulking agents, venting aquifers

135
Q

Biodegradation or organic contaminants under anoxic conditions occurs under…

A

Denitrifying, methanogenic, sulphate-reducing and iron-reducing conditions

136
Q

What compounds are best degraded under anaerobic conditions?

A

BTEX, PAHs, Halogenated organic compounds (TCE, PCBs)

137
Q

How can anaerobic degradation be enhanced?

A

Adding a supply of appropriate electron acceptors

138
Q

What is reductive dechlorination?

A

Use of the chlorinated structures as the TEA, sub of Cl with H

139
Q

What is the range of pH in soils

A

2.5 - 11

140
Q

What pH is optimal for the degradation of petroleum hydrocarbons

A

7 - 8

141
Q

How can you increase the pH in a soil system

A

Add lime to acid soils

142
Q

How can increasing the pH of a soil system be an issue?

A

Can effect water solubility and absorptions of contaminants in soil sediments (like heavy metals)

143
Q

What is the Q10 value

A

A change of 10oC will generally increase or decrease an enzymes activity by 2-fold

144
Q

How can you increase the temperature of a soil/water system

A

It is very difficult to do, but you could add compost materials to stimulate thermophilic biodegradation

145
Q

Soil moisture content (%)/water content

A

Amount of water present in soil expressed as the ratio of dry weight to wet weight

146
Q

Water activity (Aw)

A

Measures water actually available for microbial use

147
Q

What two water measurements are always taken when dealing with a contaminated soil system

A

Soil moisture content and water holding capacity

148
Q

Water holding capacity (WHC)

A

Amount of water a soil can hold before becoming saturated

149
Q

What is the optimal soil moisture content for aerobic microbial activity

A

60-80% WHC

150
Q

What is the optimal soil moisture content for hydrocarbon degradation

A

30-90% WHC

151
Q

WHC greater than 100% creates __ conditions

A

Anoxic

152
Q

How can you dry out a soil system

A

Adding gypsum or bulking agents like alfalfa

153
Q

What are the two nutrients that become rate limiting very quickly in contaminated environments

A

N and P

154
Q

What is the rate limiting nutrient for heterotrophs in non-contaminated systems

A

Carbon

155
Q

Biostimulation

A

Treating contaminated sites with N and P (or sometimes O) – increase C:N ratio, increase biomass and degradative activity

156
Q

What are oleophilic fertilizers

A

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

157
Q

Cometabolism

A

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

158
Q

What is an example of cometabolism

A

Cyclohexane is cometabolized in the presence of propane by Myobacterium, allowing Pseudomonas to grow using cyclohexanol

159
Q

An ecological niche is the site of…

A

Competition and change in conditions

160
Q

What is the difference between terminal and subterminal alkane biodegradation

A

The position of the carbon that is oxidized

161
Q

What are the 4 major steps of mineralization of an alkane

A
  1. Oxidation to primary alcohol via monooxygenase (or dioxygenase)
  2. Formation of fatty acid
  3. Beta oxidation of fatty acids to acetyl-CoA
  4. Oxidation of acetyl-CoA via the TCA cycle and the glyoxylate shunt
162
Q

How are phenolic/aromatic rings degraded?

A

They are first oxidized to catechol under aerobic conditions

163
Q

Monooxygenases

A

One oxygen atom is transferred to the substrate, the other is reduced (produces water)

164
Q

Dioxygenases

A

Both oxygen atoms are transferred to the substrate

165
Q

What enzyme cleaves catechol rings via the ortho pathway

A

catechol 1,2-dioxygenase

166
Q

What enzyme cleaves catechols via the meta pathway

A

catechol 2,3-dioxygenase

167
Q

Which is the preferred pathway for catechol cleavage

A

Ortho

168
Q

What is the problem with the meta pathway

A

It produces acetaldehyde which is toxic

169
Q

What enzyme do fungi use to degrade PAHs

A

Cyt P-450 monooxygenase

Pollution & Bioremediation (2 decks)

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