Lecture 9a

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Lecture 9a

• Biogeochemical Cycling
• Chapter 14 Text

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Cycling Carbon, Nitrogen, Sulfur, Phosphorus

• Autotrophs use photosynthesis incorporates
  abiotic CO2, NO3, SO4, and PO4 into biotic cell
  compounds
• polysaccharides
• proteins
• lipids
• nucleic acids
• organic acids
• Heterotrophs use respiration to mineralize the
  biotic cell components back to inorganic
  compounds CO2, NO3, SO4, and PO4

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• Sometimes the products formed by microbes are
  detrimental to the biosphere
• sulfuric acid from acid mine drainage
• nitrous oxide from soil denitrification

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The environment of the Earth has changed since
life first appeared

• Early Earth before life evolved
• CO2 contributed 98 of atmospheric gases
• surface temperature was 290o C
• reducing conditions
• CO2 uv reduced organic compounds
• anaerobic thermophilic heterotrophs (archaea)
• Photosynthesis evolved 3.7-3.9 billion years ago
• CO2 sunlight CH2O
• O2 produced from photosynthesis 2 billion years
  ago. CO2 sunlight CH2O O2

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• Molecular nitrogen was abundant in atmosphere of
  early Earth
• Nitrogen was a limiting nutrient for early life
  forms
• Nitrogen-fixation metabolism developed before
  oxygen-producing photosynthesis
• nitrogen-fixing nitrogenase enzyme is sensitive
  to the presence of O2

N2-fixing heterocyst
Photosynthetic cells
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Earths environment today

• CO2 is 0.03 of atmospheric gases
• O2 is 20 of atmospheric gases
• N2 has increased from 1.9 before life appeared
  to 9 when N-fixation pathway evolved to 69
  today
• temperature is 13oC
• So, over long time scales, the evolution of life
  has led to evolution of the environment

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• Carbon
• largest reservoir or sink or source is in form of
  calcium carbonate rock found in Earths crust
• 1.2 x 1017 metric tons
• 2nd largest reservoir of carbon is as dissolved
  calcium carbonate in worlds oceans
• 3.8 x 1013 metric tons
• 3rd largest reservoir is buried fossil fuel
• 1.0 x 1013 metic tons
• 4th largest reservoir is dissolved and
  particulate organic matter in the oceans
• 2.1 x 1012 metric tons
• Atmospheric CO2 is relatively small source of
  carbon 6.7 x 1011 metric tons

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• The carbon reservoir (atmospheric CO2) most
  available for photosynthesis is relatively small
  compared to calcium carbonate reservoirs
• Humans have affected several of the smaller
  carbon reservoirs
• atmospheric CO2
• fossil fuel
• land biomass (deforestation)
• burning fossil fuel and deforestation have
  reduced organic C in land biomass and in
  subsurface

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Reduction of C in these reservoir results in
increase in C in atm.
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Transformations occurring on a contemporary time
scale

• The increase in atmospheric CO2 from burning
  fossil fuels and deforestation has not been as
  great as expected because the reservoir of
  calcium carbonate in ocean acts as a buffer
  between the atmospheric and sediment carbon
  reservoirs

CaCO3 H2CO3 HCO3- CO2
sediments
limestone
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Ocean as a CO2 sink

• Some of the CO2 released into atmosphere has been
  taken up by ocean
• Since CO2 is in equilibrium with bicarbonate and
  carbonate, more calcium carbonate is formed and
  deposited in ocean sediments

atmosphere
CO2
CaCO3 HCO3- CO2
ocean
sediment
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plants algae bacteria cyanobacteria protozoa
gt50
bacteria protozoa
Aquatic and terrestrial environments contribute
equally to global primary production. Plants
predominant in terrestrial, microbes in aquatic
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Detritus
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stopped
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Common forms of organic carbon
Single, most abundant compound
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Second most abundant compound
Plant storage product
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How are fungal, plant animal polysaccharides
degraded?

• Polysaccharides are too large to get into cell
• extracellular and cell surface enzymes are used
• Polysaccharidase enzymes
• cellulases
• chitinase
• amylase

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Cellulases

• b-1,4-endoglucanase
• cleaves internal linkages between glucose
  subunits creating shorter glucan chains
• b-1,4-exoglucanase
• cleaves two glucose subunits from reducing end of
  chain liberating disaccharide
• Cellobiase
• hydrolyzes disaccharide into single glucose
  subunits

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Relative rates of degradation
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Cross-section of plant tissue
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Lignin subunits
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Lignin phenylpropene-based polymer
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• Lignin is the 3rd most abundant plant polymer
• Basic building blocks are the aromatic amino
  acids tyrosine and phenylalanine
• These are converted to phenylpropene subunits
• 500-600 subunits are randomly polymerized

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Lignin degradation

• Non-specific enzyme peroxide-dependent lignin
  peroxidase
• Produce oxygen-based free radicals that react
  with lignin polymer to release phenylpropene
  residues
• Since oxygen radicals are involved, lignin
  degradation is strictly an aerobic process.
• The degradation of aromatic pollutants such as
  toluene, benzene, and xylenes proceeds through
  pathways similar to lignin degradation.

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Lignin degradation pathway
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Methane

• Methane production is mediated primarily by
  microbial processes.
• Environments where methanogenesis is carried out
  microbiologically
• Rice paddies
• Wetlands
• Rumen
• Landfills
• Termite gut
• Methane is formed when CO2 serves as a terminal
  electron acceptor during anaerobic respiration
• 4H2 CO2 CH4 2H2O
  (autotrophic metabolism)

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• Methane can also be produced by heterotrophic
  metabolism of acetate, methanol and formate,
  which are formed as by-products of fermentations
  carried out by other populations of microbes
  growing close-by.

H2 CH3COOH CH4 CO2
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Methane oxidation

• Group of microbes called methanotrophs have the
  ability to use methane as a carbon and energy
  source
• CH4 O2 CH3OH HCHO HCOOH CO2

methanol formaldehyde formic acid
carbon dioxide
Methane monooxygenase can also cometabolize
chlorinated organic compds such as TCE
under aerobic conditions
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Methylotrophs

• Microbes that can utilize other C1 compounds
  besides methane
• Carbon monoxide (CO)
• CO H2O CO2 H2
• H2 O2 2H2O
• Pseudomonas carboxydoflava (chemoautotroph)
• Carbon cycling by methanogens, methanotrophs and
  methylotrophs
• CO2 CH4 CH3OH HCHO HCOOH
  CO2

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Common pollutant
Breakdown product of hemi- cellulose
Plant and animal tissues
Formed from plant cyanides
Industrial pollutant
Generated by plants, fungi, bacteria industrial
pollutant
Most common organic S compound in
environment- algal origin
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Nitrogen cycling
nitrogen fixation
N2
-3 valence state
ammonia assimilation
anaerobic ammonia oxidation
N2H4
NH4
amino acids
ammonification
assimilatory nitrate reduction
Proteins
nitrification
NH2OH
denitrification
NO2-
aerobic nitrite oxidation
NO3-
5 valence state
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Nitrogen

• Usually limiting nutrient for microbes and plants
• bacteria need a C/N of 4-5
• fungi need a C/N of 10
• balance point C/N is 20 because N is better
  conserved than C
• 4th most abundant element in biosphere
• Makes up 12 of cell dry weight

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N-fixation

• Ultimately, all forms of nitrogen come from
  atmospheric N

Table 14.11
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N fixation

• Atmospheric N is fixed into NH3 by over 100
  different free-living bacteria, actinomycetes,
  and cyanobacteria
• Highly conserved nifH gene encodes
  iron-containing reductase component of
  nitrogenase enzyme compled
• N-fixation is an energy-intensive process
• N2 16ATP 8 e- 8H 2NH3 16ADP
  16Pi H2

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Rates of N-fixation
N-fixing system N fixation (kg N/hectare/year
Rhizobium-legume 200-300 Anabaena-Axolla 100-
120 Cyanobacteria-moss 30-40 Rhizosphere
associations 2-25 Free-living 1-2
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Nitrogen cycling
nitrogen fixation
N2
-3 valence state
ammonia assimilation
anaerobic ammonia oxidation
N2H4
NH4
amino acids
ammonification
assimilatory nitrate reduction
Proteins
nitrification
NH2OH
denitrification
NO2-
aerobic nitrite oxidation
NO3-
5 valence state
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Ammonification or ammonia assimilation?

• Ammonification (mineralization) refers to the
  release of free ammonia from N-containing organic
  compounds
• occurs when C/N lt 20
• Ammonia assimilation (immobilization) refers to
  the incorporation of free ammonia into organic
  compounds
• occurs when C/N gt 20

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Nitrogen cycling
nitrogen fixation
N2
-3 valence state
ammonia assimilation
anaerobic ammonia oxidation
N2H4
NH4
amino acids
ammonification
assimilatory nitrate reduction
Proteins
nitrification
NH2OH
denitrification
NO2-
aerobic nitrite oxidation
NO3-
5 valence state
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Nitrification

• Catalyzed conversion of ammonia to nitrate
• Predominantly, an aerobic chemoautotrophic
  process
• amoA gene encoding ammonia monooxygenase is
  highly conserved
• STEP 1
• NH4 1/2 O2 NH2OH H ammonia
  monooxygenase
• NH2OH O2 NO2 H2O H DG -66
  kcal/mol
• Both Bacterial and Archaeal domains of life carry
  out this process

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Nitrification

• Step 2
• NO2- 1/2O2 NO3- DG -18 kcal/mol
• 100 mols NO2 required to fix 1 mol CO2

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Nitrogen cycling
nitrogen fixation
N2
-3 valence state
anaerobic ammonia oxidation
ammonia assimilation
N2H4
NH4
amino acids
ammonification
Proteins
assimilatory nitrate reduction
nitrification
NH2OH
denitrification
NO2-
aerobic nitrite oxidation
NO3-
5 valence state
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Anaerobic ammonia oxidation

• Anammox reaction
• NH4 NO2- N2H2 (hydrazine)
• Carried out by a monophyletic cluster of bacteria
  named Brocadiales related to the order
  Planctomycetales
• anammoxosome is organelle in which hydrazine is
  confined
• Anammox bacteria have not yet been obtained in
  pure culture, but they are routinely grown in
  enrichment cultures

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Anammox reaction
NH4 1.32NO2- 0.066HCO3- 0.13H ? 1.02N2
0.26NO3- 2.03H2O 0.066CH2O0.5N0.15
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Anaerobic ammonia oxidation pathway
PMF-driven reverse electron transport
ATP production
Generates ferrodoxin for CO2 reduction in
acetyl-CoA pathway
J. Gijs Kuenen, Nature Reviews Microbiology 6,
320-326 (April 2008)
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Nitrogen cycling
nitrogen fixation
N2
-3 valence state
ammonia assimilation
anaerobic ammonia oxidation
N2H4
NH4
amino acids
ammonification
Proteins
assimilatory nitrate reduction
nitrification
NH2OH
denitrification
NO2-
aerobic nitrite oxidation
NO3-
5 valence state
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Denitrification

• Reduction of nitrate or nitrite to N2 or various
  intermediates (nitric and nitrous oxide
• Anaerobic process
• Alternative to aerobic respiration
• Favored in saturated soils
• Major source of nitric and nitrous oxide
  emissions to the atmosphere
• Nitrite reductase gene nirS is highly conserved
  in different bacteria

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Nitrous oxide
Outer membrane
Nitric oxide
periplasm
Inner membrane
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Summary
Carbon cycle
Nitrogen cycle
N2
amino acids
NH4
N2H4
N2O
Proteins
NO
Conclusion
NH2OH
Life on Earth depends on these reactions carried
out by microbes in the environment
NO2-
NO3-