Chapter 25
BIOGEOCHEMISTRY I: NUTRIENT CYCLING
The life of the ecosystem depends on the flow of energy and the recycling of matter through the
ecosystem.
Energy and matter flow together through the ecosystem as organic matter.
The link between energy and matter begins with photosynthesis.
TYPES OF NUTRIENT CYCLES
Nutrients move through the ecosystem in biogeochemical cycles.
The cycles involve the exchange of elements between the atmosphere, rocks, water and
organisms.
There are two types of biogeochemical cycles: gaseous and sedimentary.
In gaseous cycles, the nutrients accumulate in the atmosphere and the oceans
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They have a global influence.
Nitrogen, oxygen and carbon dioxide.
In sedimentary cycles, the main reservoirs are rock and soil.
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Available forms of the nutrients occur as dissolved salts in soil water, lakes, ocean, etc.
The cycle consists of salt-solution phase and a rock phase.
MODEL OF NUTRIENT CYCLES
All biogeochemical cycles involve inputs, internal cycling and outputs.
INPUTS
The input of nutrients to the ecosystem depends on the type of biogeochemical cycle:
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Nutrients with gaseous cycle enter the ecosystem via the atmosphere.
Nutrients with a sedimentary cycle enter the ecosystem after the weathering of rocks.
Air, snow, rain and animals supplement the nutrients in the soil.
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Wetfall refers to nutrients carried by precipitation.
Dryfall brings nutrients in the form of airborne particles and aerosols.
Water trickling down the forest canopy and stems carries dust particles that had settled on the
leaves.
Epiphytic lichens remove nutrients as the water flows
Water drainage is the major input for aquatic ecosystems.
INTERNAL CYCLING
Nutrients are stored in living tissues.
As old tissues die, nutrients are returned to the soil.
Mineralization is the release of organically bound nutrients into an inorganic form available for
plants and microbes. Detritivores oxidize organic compounds into smaller and simpler products.
These nutrients are once again available to plants for uptake and incorporation into new tissues.
Nutrients stored in trunk, limbs, bark and roots is removed from short-term cycling.
Nutrients accumulated in soil organic matter prevent rapid losses from the system.
Nutrients tightly bound to organic matter have to be released through the activity of
decomposers.
Ecosystem processes influencing the rate of nutrient cycling.
The rate at which nutrients cycle through the ecosystem is directly related to the rates at which
primary productivity and decomposition occur.
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Primary productivity determines the rate at which nutrients are transferred from inorganic
to organic form (nutrient uptake).
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Decomposition determines the rate of transformation of organic nutrients into inorganic
form (nutrient release).
These two processes are interdependent.
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Reduced nutrient availability can have the combined effect or reducing both the nutrient
concentration of plant tissues (primarily leaf tissues) and net primary productivity.
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This reduction lowers the total amount of nutrients retuned to the soil in dead organic
matter.
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Reduced quantity and concentration of organic matter entering the decomposer food
chain increases immobilization and reduces the availability of nutrients for uptake by
plants.
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Conversely, high nutrient availability encourages high plant tissue concentrations and
high net primary productivity.
Climate
Temperature and moisture influence the rate of microbial activity.
Low temperature and dry conditions inhibit microbial activity.
Rate of litter decay depends on the chemical composition of the litter, temperature, humidity and
pH.
 Decomposition rate is fastest for material containing little lignin, in warm and moist
conditions.
 Low pH slows decay.
Tropical rain forests are characterized by having
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a high rate of net primary productivity
higher annual rates of litter input to the forest floor
very low mass of litter on the forest floor
high rate of decomposition
organic matter is being consumed by decomposers at about the same rate at which it is
falling to the forest floor.
Boreal forests, which are found in cooler northern latitudes, have…
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low rate of net primary productivity
low rates of litter input
extremely low rates of decomposition
high accumulation of litter on the forest floor.
Moving in latitude from south to north, the rate of decomposition decreases, the accumulation of
litter increases, and the input of forest litter decreases.
There is an inverse relationship between the biomass o forest floor and biomass of the litter
input, e. g. in tropical rain forest, the input into the forest floor is high but the accumulation is
very low if any.
The rate of decomposition affects the amount of litter that accumulates on the forest floor.
More nutrients are tied up in dead organic matter in the cooler, more northern forest
ecosystems, resulting in a slower rate of internal nutrient cycling.
Species characteristics affect the nutrient cycling.
Zooplankton and phytoplankton absorb nutrients quickly, are short-lived, grow rapidly and return
the nutrients to the available nutrient pool. Recycling is fast.
Forest trees are large, grow slowly, and store large quantities of nutrients in their biomass for
longer periods. These nutrients are removed from short-term cycling.
Trees and shrubs store nutrients in long and short term structures, e.g. bark, trunks, leaves,
flowers, fruits, etc.
Species differ in their concentration of nutrients and their ability to recycle them.
OUTPUTS
The export of nutrients from the ecosystem must be upset by inputs if a net decline is not to
occur.
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Carbon is exported to the atmosphere as CO2 via the process of respiration.
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Organic matter can be removed by runoff water into streams and rivers.
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Herbivores can transport nutrients from one ecosystem to another.
Large quantities of nutrients are bound tightly in organic matter; they are not available until
released by activities of decomposers.
Farming and logging carry a substantial amount of nutrients out the ecosystem. These losses
must be replaced by the application of fertilizers.
Clear-cut logging alters the internal cycling causing the leaching of nutrients:
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Clear-cut logging increases the amount of radiation including direct sunlight, reaching
the ground. This results in an increase in soil temperature that promotes decomposition
resulting in an increase in net mineralization rate.
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This happens at the time when the demand is low due to the removal of vegetation. This
causes an increase in leaching of nutrients from the ecosystem in surface waters.
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This is the result of uncoupling nutrient decomposition and nutrient uptake in net primary
productivity.
Fire increases the loss of nutrients volatilization and airborne particulate.
Nitrates in ash are quickly mineralized. Surface runoff increases after fire and leaches nutrients
from the soil.
CONTRASTING NUTRIENT CYCLING IN TERRESTRIAL AND AQUATIC
ECOSYSTEMS.
Nutrient cycling, the link between primary productivity and decomposition, are an essential
feature of all ecosystems.
There is a separation between the zone of decomposition and the zone of productivity.
In terrestrial ecosystems, plants exit in both zones: roots in the soil, canopy exposed to light.
In deep aquatic ecosystems, decomposition occurs in the benthic zone and is separated from
the photic zone where productivity is carried out by phytoplankton.
Epilimnion:
 Rather warm due to solar radiation.
 Dissolved oxygen is high.
 Lower density water.
Hypolimnion:
 Cold.
 Low in oxygen.
 Higher density water.
Metalimnion is the region of the fast drop in temperature, thermocline.
The colder deep water is relatively nutrient rich; the surface, warmer water is nutrient poor.
In autumn and winter, the surface waters cool and approach the temperature of the
hypolimnion; the surface water become denser and sink and the thermocline breaks down; the
displaced deep water moves to the surface: this is called the turnover.
Winter turnover brings nutrients to the surface.
Nutrients are used up as the spring and summer progress and productivity declines.
There are two parts to the carbon cycle, the atmosphere and the water cycles.
MAJOR BIOGEOCHEMICAL CYCLES
CARBON CYCLE
The main reservoir of carbon is in the form of CO2 in the atmosphere, but there is a
considerable amount of carbon tied up in the biosphere.
Carbon is intimately tied to the energy flow through the ecosystem: just as energy passes
through the food chain so does carbon.
The concentration of CO2 fluctuates throughout the day. In daytime is low and increases at
night time.
There is a seasonal change in the production and utilization of CO2. During the spring growing
season there is an increase in respiration and production of CO2. in the autumn there is a
decline in CO2 production.
In aquatic environments, at pH < 4.3, most CO2 is found as dissolved gas, at pH between 4.3
and 8.3, mostly as HCO3‾, and at pH > than 8.3 as CO32-.
Carbonates deposited as sediment on the bottom of the oceans are taken into the lower layers
of the earth crust and eventually released as CO2 during volcanic activity.
Carbon dioxide is a green-house gas that tends to keep the earth surface warm, e.g. water
remains liquid.
NITROGEN CYCLE
The cycle has four stages:
1. Nitrogen has to be fixed, converted to a usable form (NH3, NO31-), before it can be used
by organisms.
2. Mineralization or ammonification that is the conversion of amino acids to ammonia.
3. Nitrification: the conversion (oxidation) of ammonia to nitrites and nitrates.
4. Denitrification, the conversion of nitrates to atmospheric nitrogen, N2.
Nitrogen fixation can occur through
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lightning in the atmosphere:10% of the fixed nitrogen; ~35 mg N/ha/year.
through the action of nitrogen-fixing bacteria associated with the roots of plants,
especially leguminous plants, soil bacteria and cyanophytes: 90% of the fixed nitrogen;
1.4 - 7.0 kg N/ha/year in natural ecosystems.
Nitrogen fixation requires 160 Kcal/mole (1 mole of N = 28 g).
In agricultural ecosystems, approximately 200 species of leguminous plants are important
nitrogen fixers.
1. Fixation:
In natural ecosystems, about 1200 species of bacteria, cyanobacteria and legumes are involved
in nitrogen fixation.
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Rhizobium is the bacterium genus associated with legumes. Rhizobium is aerobic.
Azotobacter and Clostridium are free-living aerobic genera found in the soil.
These three genera require Mo as an activator.
All these species are inhibited by the accumulation of nitrates and ammonia in the soil.
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About 40 known species of cyanobacteria are important nitrogen fixers.
They are found in terrestrial and aquatic habitats and require Mo for nitrogen fixation.
They are active over a wide range of temperatures, from polar seas to freshwater ponds
to hot springs.
Other plants are also involved in nitrogen fixation: some epiphytes in tropical forests,
epiphyllic algae and bacteria, and phycobiont algae in lichens.
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2. Mineralization or ammonification:
Proteins require nitrogen.
Plants take it the form of ammonia and nitrate.
Nitrogen in organic compounds of dead animals and plants is unavailable to plants and must be
transformed by decomposers into inorganic compounds.
Proteins found in dead plant and animals are broken down by bacteria and fungi, and oxidized
to CO2, H2O and NH3 with yield of energy. Examples:
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RNH2 (Organic N) + heterotrophic (ammonifying) bacteria → NH3 (ammonia) + R.
NH2CH2COOH + 1½ O2 → 2CO2 + H2O + NH3 + 178 kcal
In soils NH3 is rapidly converted to NH4+ when hydrogen ions are plentiful (pH < 7.5).
When microbes have too much N for their own requirements they excrete the excess as NH4+
into the soil.
In high pH soils NH4+ (ion in solution) is unstable and changes to NH3 (gas) which can be lost
via volatilization.
Denitrification occurs largely in arid calcareous soils and in soils with low exchange capacity
(sandy soils) as NH4+ is not held.
NH4+ is held by the soils cation exchange capacity (negative charge sites) and thus will not
leach, but can be lost when soil erosion occurs.
NH3 and NH4+ are absorbed by plant roots and incorporate into amino acids and passed through
the food chain.
3. Nitrification:
During nitrification NH4+ is oxidized to nitrate (NO31-) and nitrite (NO21-).
Two groups of bacteria are involved:
1. Nitrosomas bacteria use ammonia as their sole source of energy.
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NH3 + 1½ O2 → HNO2 + H2 → NO21- + H+ + 165 kcal
2. Nitrobacter uses the energy left in nitrite by oxidizing it to nitrate.
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NO21- + 1½ O2 → NO31- + energy.
Nitrosomas oxidizes 35 moles of nitrogen for each mole of CO2 assimilated; Nitrobacter oxidizes
100 moles of nitrogen for every mole of CO2 assimilated.
Nitrates are absorbed by plants and incorporated into organic acids.
Most plant species prefer nitrate to ammonium.
Nitrates leach more readily than ammonium and eventually may end in aquatic ecosystems.
4. Denitrification:
Some organisms degrade nitrates to obtain oxygen.
These denitrifiers are fungi and the bacterium Pseudomonas, both facultative anaerobes.
They prefer oxygenated environments but if oxygen is deficient, they turn to nitrates as the
source of oxygen atoms.
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C6H12O6 + 4NO3- → 6CO2 + 6H2O + 2N2 (g)
Denitrifiers use nitrates as the terminal electron acceptors.
About 10% of the fixed nitrogen may be lost through denitrification.
Under aerobic condition, some denitrifiers produce NO and N2O.
Denitrification results in environmental pollution (destroys ozone) and also contributes to global
warming since nitrous oxides do have a minor effect as a greenhouse gas.
“Nitrous oxide (N2O) is a gaseous nitrogen oxide that is present at a concentration of about 350
ppb in the atmosphere. The concentration of this compound was maintained below 300 ppb in
the global nitrogen cycle before the 20th century. However, recent reports suggest that the
atmospheric concentration of N2O is now increasing at a rate as high as 0.3% per year. N2O has
a 200- to 300-fold-stronger greenhouse effect than carbon dioxide (CO2) and has the potential
to destroy the ozone layer. Therefore, the N2O balance is critical to the natural environment. The
proposed sources of N2O are chemical industries, burning fossil fuels, and biomass, as well as
soil denitrification of nitrogenous compounds resulting from excess agricultural fertilizer. Another
critical source of N2O is wastewater treatment plants, in which considerable amounts of nitrogen
pollutants removed from treated water are released into the atmosphere as N2O, as well as
dinitrogen (N2).” Appl Environ Microbiol. 2003 June; 69(6): 3152–3157. 2003.
Aerobic Denitrifying Bacteria That Produce Low Levels of Nitrous Oxide
Naoki Takaya,1 Maria Antonina B. Catalan-Sakairi,1 Yasushi Sakaguchi,1 Isao Kato,1 Zhemin Zhou,1 and Hirofumi Shoun2*
SULFUR CYCLE
Sulfur is a component of some amino acids, enzymes and other compounds.
The sulfur cycle has a sedimentary and a gaseous phase.
In long-term sediments, sulfur is tied up in organic (coal, oil, peat) and inorganic deposits,
released by weathering, organic decomposition, erosion and industrial production, and carried
to terrestrial and aquatic ecosystems in solution.
Most of sulfur first appears in the atmosphere as H2S.
H2S appears in the atmosphere from combustion of fossil fuels, volcanic eruptions,
decomposition of animal and plant tissues.
H2S oxidizes quickly into SO2, which reacts with water to form H2SO4 and is carried to back to
the earth as weak solutions of sulfuric acid, SO42- and H+.
During the decomposition of phytoplankton, dimethyl sulfide (CH3)2S is released and some of it
is lost to the atmosphere and some is decomposed in the ocean water.
It is rarely a limiting nutrient and is usually absorbed as SO4-2 .
Sulfate is absorbed by plants and incorporated into sulfur containing amino acids, which are
passed down the food chain.
Decomposition of organisms releases sulfate and hydrogen sulfide
Sulfate-reducing bacteria release sulfur found in dead organic matter as H2S and SO4-2.
Purple bacteria found in salt marshes and estuarine mudflats utilize SH2 as an oxygen acceptor
to reduce CO2.
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6 CO2 + 3 H2S + 6 H2O + sunlight  C6H12O6 + 3 H2SO4  H+ + SO4-2
Sulfur in the presence of iron and under anaerobic conditions forms ferrous sulfide, FeS2, which
is highly insoluble.
Ferrous sulfide when exposed to air reacts with oxygen and forms sulfuric acid, H2SO4, and
ferrous sulfate, FeSO4, and other sulfur compounds in aquatic ecosystems.
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These substances destroy aquatic life.
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This is one of the major pollution problems created by mining that exposes pyrite,
FeS2 that overlies coal deposits.
PHOSPHORUS CYCLE
Phosphorus is a component of phospholipids, nucleic acids, ATP and other macromolecules.
Phosphorus occurs in the atmosphere only in negligible amounts. The phosphorous cycle has
no atmospheric reservoir.
None of the phosphorous compounds has any appreciable vapor pressure.
Soil solution contains about 3 x 10-6 % phosphorus but plants contain about 3% phosphorus.
Most forms of phosphate are insoluble.
The main reservoir of phosphorous is rock and natural phosphate deposits, from which the
elements are released by weathering, leaching, erosion and mining.
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Soil phosphorus is mostly in the form of apatite: [Ca5(PO4)3 (Cl, OH)]
Ca3(PO4)2 is soluble in acid solutions and under reducing conditions.
Phosphorus is scarce and a limiting mineral in almost all ecosystems.
Al and Fe phosphates are insoluble in acid conditions.
There are biotic and abiotic portions of the cycle.
In marine and freshwater systems, the phosphorus cycles involves three major fractions:
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Particulate organic phosphorus (POP) found in dead organic matter and
phytoplankton.
Dissolved organic phosphorus (DOP) excreted by organisms, especially
zooplankton.
Dissolved inorganic phosphorus (DIP), mostly as orthophosphate, PO43-.
The uptake of phosphorus by phytoplankton and bacteria are responsible for the low phosphorus
concentration in surface water.
Zooplankton and detritus-feeders feed on bacteria and phytoplankton and excrete large
amounts in their wastes
The recycling of P in freshwater ecosystems is very fast, just a few minutes.
Part of the phosphorus in aquatic ecosystems is deposited in sediments, and remains
unavailable for a long period of time.
Return of phosphorus from the oceans to the land is very slow.
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It returns mostly in animal form, e. g. skeleton of sea animals and guano.
Phosphates form insoluble compounds below pH 5.5 and above 7.0.
Mycorrhizae are important in the uptake of phosphorus (H2PO4-).