Introduction to Biogeochemical Cycles

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The following slides are provided by Dr.
Vincent OFlaherty.
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Symbiotic nitrogen fixation

• 1. Legume symbioses
• Most NB examples of nitrogen-fixing symbioses are
  the root nodules of legumes (peas, beans, clover,
  etc.).
• Bacteria are Rhizobium species, but the root
  nodules of soybeans, chickpea and some other
  legumes are formed by small-celled rhizobia
  termed Bradyrhizobium

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• Bacteria "invade" the plant and cause the
  formation of a nodule by inducing localised
  proliferation of the plant host cell
• Chemicals called lectins act as signal molecules
  between Rhizobium and its plant host - v.
  specific
• Bacteria form an infection thread and
  eventually burst into the plant cells - cause
  cells to proliferate - form nodules

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• Bacteria always separated from the host cytoplasm
  by being enclosed in a membrane
• In nodules - plant tissues contain the
  oxygen-scavenging molecule - leghaemoglobin
• Function of this molecule is to reduce the amount
  of free O2, protects the N-fixing enzyme
  nitrogenase, which is irreversibly inactivated by
  oxygen

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• Bacteria are supplied with ATP (80), substrates
  and an excellent growth environment by the plant
  -carry out N-fixation
• Bacteria provide plant with fixed N - major
  advantage in nutrient poor soils

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Other symbiotic associations

• 2. Frankia form nitrogen-fixing root nodules
  (sometimes called actinorhizae) with several
  woody plants of different families, such as alder
• 3. Cyanobacteria often live as free-living
  organisms in pioneer habitats such as desert
  soils (see cyanobacteria) or as symbionts with
  lichens in other pioneer habitats

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The nitrogen cycle

• Diagram shows an overview of the nitrogen cycle
  in soil or aquatic environments
• At any time a large proportion of the total fixed
  nitrogen will be locked up in the biomass or in
  the dead remains of organisms

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• So, the only nitrogen available to support new
  growth will be that which is supplied by NITROGEN
  FIXATION from the atmosphere (pathway 6)
• or by the release of ammonium or simple organic
  nitrogen compounds through the decomposition of
  organic matter (pathway 2 (AMMONIFICATION/MINERALI
  SATION)

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• Other stages in this cycle are mediated by
  specialised groups of microorganisms -
  NITRIFICATION AND DENITRIFICATION

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Nitrification

• Nitrification - conversion of ammonium to nitrate
  (pathway 3-4)
• Brought about by the nitrifying bacteria,
  specialised to gain energy by oxidising ammonium,
  while using CO2 as their source of carbon to
  synthesise organic compounds (chemoautotrophs)
• The nitrifying bacteria are found in most soils
  and waters of moderate pH, but are not active in
  highly acidic soils

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• Found as mixed-species communities (consortia)
  because some - Nitrosomonas sp. - are
  specialised to convert ammonium to nitrite (NO2-)
  while others - Nitrobacter sp. - convert nitrite
  to nitrate (NO3-)
• Accumulation of nitrite inhibits Nitrosomonas, so
  depends on Nitrobacter to convert this to
  nitrate, and Nitrobacter depends on Nitrosomonas
  to generate nitrite
• Nitrate leaching from soil is a serious problem
  in Ireland

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Denitrification

• Denitrification - process in which nitrate is
  converted to gaseous compounds (nitric oxide,
  nitrous oxide and N2).
• Several types of bacteria perform this conversion
  when growing on organic matter in anaerobic
  conditions
• Use nitrate in place of oxygen as the terminal
  electron acceptor. This is termed anaerobic
  respiration and can be illustrated as follows

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• In aerobic respiration (as in humans), organic
  molecules are oxidised to obtain energy, while
  oxygen is reduced to water
• C6H12O6 6 O2 6 CO2 6 H2O energy
• In the absence of oxygen, any reducible substance
  such as nitrate (NO3-) could serve the same role
  and be reduced to nitrite, nitric oxide, nitrous
  oxide or N2

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• Conditions in which we find denitrifying
  organisms (1) a supply of oxidisable organic
  matter, and (2) absence of oxygen but
  availability of reducible nitrogen sources
• Common denitrifying bacteria include several sp.
  of Pseudomonas, Alkaligenes and Bacillus. Their
  activities result in substantial losses of N into
  the atmosphere, roughly balancing the amount of
  nitrogen fixation that occurs/year

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Microbial N-Fixation
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Other Biogeochemical cycles P and S

• Other major nutrient cycles include S and P
• Sulfur cycle involves the cycling of elemental
  Sulfur (So), Sulphate (SO42-) and hydrogen
  sulphide (H2S) and organic matter (-SH)

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The Sulfur Cycle

• Some major steps in the sulfur cycle include
• 1.Assimilative reduction of sulfate (SO42-) into
  -SH groups in proteins (cysteine) carried out by
  virtually all bacteria
• 2.Release of -SH to form H2S during excretion and
  decomposition

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• 3.Oxidation of H2S by chemolithotrophs to form
  sulfur (So) and sulfate (SO42-)
• 4.Dissimilative reduction of sulfate (SO42-) by
  anaerobic respiration of sulfate-reducing
  bacteria.
• 5.Anerobic oxidation of H2S and S by anoxygenic
  phototrophic bacteria (purple and green bacteria)

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The Sulfur Cycle
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• The sulfur cycle includes more steps. Sulfur
  compounds undergo some interconversions due to
  chemical and geologic processes (slow flux)
• Human impact on the S-cycle is through the
  production of SO2 through fossil fuel combustion

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The Phosphorus Cycle

• The major reservoir of P is locked in a slow
  geochemical flux between rocks n sediments and
  soils release slowly over millennia
• The ecosystem phase of the phosphorus cycle moves
  faster than the sediment phase. All organisms
  require phosphorus for synthesizing
  phospholipids, NADPH, ATP, nucleic acids, and
  other compounds. Plants absorb phosphorus v.
  quickly, and herbivores get phosphorus by eating
  plants

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• Carnivores get phosphorus by eating herbivores.
  Eventually both of these organisms will excrete
  phosphorus as a waste
• Then DECOMPOSITION will release phosphorus into
  the soil. Plants absorb the phosphorus from the
  soil and they recycle it within the ecosystem

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