Transcript BIOGEOCHEMICAL CYCLING - University of KwaZulu

BIOGEOCHEMICAL CYCLING
 A biogeochemical cycle is a circuit or pathway by which a
chemical element or molecule moves through both biotic
and abiotic compartments of an ecosystem.
 In effect, the element is recycled, although in some such
cycles there may be places (called "sinks") where the
element is accumulated or held for a long period of time.
 The elements, chemical compounds, and other forms of
matter are passed from one organism to another and from
one part of the biosphere to another through the
biogeochemical cycles.
The Nitrogen Cycle
 The nitrogen cycle represents one of the most important
nutrient cycles found in terrestrial ecosystems.
 Nitrogen is used by living organisms to produce a number of
complex organic molecules like amino acids, proteins, and
nucleic acids.
 The store of nitrogen in the atmosphere, where it exists as a
gas (mainly N2), plays an important role for life.
 Other major stores of nitrogen include organic matter in
soil and the oceans.
 Despite its abundance in the atmosphere, nitrogen is often
the most limiting nutrient for plant growth.
 This problem occurs because most plants can only take up
nitrogen in two forms:
 ammonium ion (NH4+),
 the ion nitrate (NO3-) and urea (NH2)2CO.
 Most plants obtain the nitrogen they need as inorganic
nitrate from the soil solution.
 Ammonium is used less by plants for uptake because in
large concentrations it is extremely toxic.
 Animals receive the required nitrogen they need for
metabolism, growth, and reproduction by the
consumption of living or dead organic matter
containing molecules composed partially of nitrogen.
Four processes involved in the cycling of nitrogen
through the biosphere:
 Nitrogen fixation
 Decay
 Nitrification
 Denitrification
Nitrogen fixation
 The process by which nitrogen is taken from its relatively
inert molecular form (N2) in the atmosphere and converted
into nitrogen compounds (such as, notably, ammonia,
nitrate and nitrogen dioxide) useful for other chemical
processes.
 Microorganisms that fix nitrogen are called diazotrophs. They
have the nif gene.
 Nitrogen fixation also occurs as a result of non-biological
processes.
 These include lightning, industrially through the Haber-Bosch
Process, and combustion.
 Biological nitrogen fixation was discovered by the Dutch
microbiologist Martinus Beijerinck.
 Biological Nitrogen Fixation (BNF) occurs when atmospheric
nitrogen is converted to ammonia by a pair of bacterial enzymes
called nitrogenase.
 The formula for BNF is:
N2 + 8H+ + 8e− + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi
 Although ammonia (NH3) is the direct product of this reaction, it is
quickly protonated into ammonium (NH4+).
 In free-living diazotrophs, the nitrogenase-generated ammonium is
assimilated into glutamate through the glutamine synthetase/
glutamate synthase pathway.
 In most bacteria, the nitrogenase enzymes are very susceptible
to destruction by oxygen (and many bacteria cease production of
the enzyme in the presence of oxygen).
DECAY
 The body of a living organism begins to decompose (as
part of a succession) shortly after death.
 Such decomposition can be simplified in two stages:
 In the first stage, it is limited to the production of
vapors.
 In the second stage, liquid materials form and the
flesh or plant matter begins to decompose.
 Decomposition begins at the moment of death, caused
by two factors:
 Autolysis, the breaking down of tissues by the body's
own internal chemicals and enzymes;
 Putrefaction, the breakdown of tissues by bacteria.
 These processes release gases that are the chief
source of the characteristic odor of dead bodies.
 These gases swell the body.
NITRIFICATION
 Biological oxidation of ammonia with oxygen into nitrite
followed by the oxidation of these nitrites into nitrates.
 Nitrification is an important step in the nitrogen cycle in soil,
discovered by the Russian microbiologist, Sergei Winogradsky.
 The oxidation of ammonia into nitrite, and the subsequent oxidation
to nitrate is performed by two different bacteria (nitrifying bacteria).
 The first step is done by bacteria of (amongst others) the genus
Nitrosomonas and Nitrosococcus.
 The second step (oxidation of nitrite into nitrate) is (mainly) done by
bacteria of the genus Nitrobacter, with both steps producing energy
to be coupled to ATP synthesis.
 NH3 + O2 → NO2− + 3H+ + 2e−
 NO2− + H2O → NO3− + 2H+ + 2e−

Nitrification also plays an important role in the removal of nitrogen from
municipal wastewater.

The conventional removal is nitrification, followed by denitrification.

The cost of this process resides mainly in aeration (bringing oxygen in
the reactor) and the addition of an external carbon source (e.g. methanol)
for the denitrification.

In most environments both organisms are found together, yielding nitrate
as the final product. It is possible however to design systems in which
selectively nitrite is formed (the Sharon process).

Together with ammonification, nitrification forms a mineralization
process which refers to the complete decomposition of organic material,
with the release of available nitrogen compounds. This replenishes the
nitrogen cycle.
Denitrification
 The process of reducing nitrate and nitrite (highly
oxidised forms of nitrogen available for consumption
by many groups of organisms), into gaseous nitrogen,
which is far less accessible to life forms but makes up the
bulk of our atmosphere.
 It can be thought of as the opposite of nitrogen fixation,
which converts gaseous nitrogen into a more biologically
available form.
 The process is performed by heterotrophic bacteria
(such as Paracoccus denitrificans, Thiobacillus
denitrificans, and various pseudomonads) from all main
proteolytic groups.
 Denitrification takes place under special conditions in both
terrestrial and marine ecosystems.
 In general, it occurs when oxygen (which is a more favourable
electron acceptor) is depleted, and bacteria turn to nitrate in order
to respire organic matter
 Because our atmosphere is rich with oxygen, denitrification only
takes place in some soils and groundwater, wetlands, poorly
ventilated corners of the ocean, and in seafloor sediments.
 Denitrification proceeds through some combination of the
following steps:
nitrate → nitrite → nitric oxide → nitrous oxide → dinitrogen gas
 Or expressed as a redox reaction:
 2NO3- + 10e- + 12H+ → N2 + 6H2O
a process
where water
bodies receive
excess
nutrients that
stimulate
excessive plant
growth
 The Sulfur Cycle
 An important distinction between cycling of sulfur and
cycling of nitrogen and carbon is that sulfur is "already
fixed".
 That is, plenty of sulfate anions (SO42-) are available for
living organisms to utilize.
 By contrast, the major biological reservoirs of nitrogen
atoms (N2) and carbon atoms (CO2) are gases that
must be pulled out of the atmosphere.
Important reactions of the sulfur cycle include:
 Assimilative sulfate reduction
 sulfate (SO42-) is reduced to organic sulfhydryl groups
(R-SH) by plants, fungi and various prokaryotes.
 The oxidation states of sulfur are +6 in sulfate and -2 in
R-SH.
 Desulfuration
 organic molecules containing sulfur can be
desulfurated, producing hydrogen sulfide gas (H2S),
 oxidation state = -2.
 Oxidation of hydrogen sulfide
 produces elemental sulfur (So), oxidation state = 0.
 This reaction is done by the photosynthetic green and
purple sulfur bacteria and some chemolithotrophs.
 Further oxidation of elemental sulfur
 by sulfur oxidizers produces sulfate.
 Dissimilative sulfur reduction
 elemental sulfur can be reduced to hydrogen sulfide.
 Dissimilative sulfate reduction
 sulfate reducers generate hydrogen sulfide from sulfate.