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Lecture 9a Biogeochemical Cycling Chapter 14 Text Anaerobic ammonia oxidation Anammox reaction NH4+ NO2- N2H2 (hydrazine) Carried out by a monophyletic cluster of ... – PowerPoint PPT presentation

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Title: Lecture 9a


1
Lecture 9a
  • Biogeochemical Cycling
  • Chapter 14 Text

2
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

3
  • Sometimes the products formed by microbes are
    detrimental to the biosphere
  • sulfuric acid from acid mine drainage
  • nitrous oxide from soil denitrification

4
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

5
  • 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
6
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

7
  • 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

8
  • 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

9
Reduction of C in these reservoir results in
increase in C in atm.
10
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
11
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
12
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
13
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14
Detritus
15
stopped
16
Common forms of organic carbon
Single, most abundant compound
17
Second most abundant compound
Plant storage product
18
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

19
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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21
Relative rates of degradation
22
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23
Cross-section of plant tissue
24
Lignin subunits
25
Lignin phenylpropene-based polymer
26
  • 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

27
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.

28
Lignin degradation pathway
29
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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31
  • 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
32
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
33
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

34
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
35
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
36
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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38
N-fixation
  • Ultimately, all forms of nitrogen come from
    atmospheric N

Table 14.11
39
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

40
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
41
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
42
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

43
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
44
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

45
Nitrification
  • Step 2
  • NO2- 1/2O2 NO3- DG -18 kcal/mol
  • 100 mols NO2 required to fix 1 mol CO2

46
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
47
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

48
Anammox reaction
NH4 1.32NO2- 0.066HCO3- 0.13H ? 1.02N2
0.26NO3- 2.03H2O 0.066CH2O0.5N0.15
49
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)
50
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
51
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

52
Nitrous oxide
Outer membrane
Nitric oxide
periplasm
Inner membrane
53
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-
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