Download Chapter 5: Elemental and Hydrologic Cycles

Chapter 5: Elemental and Hydrologic Cycles
I. In contrast to energy, which moves in one direction through ecosystems, the transformation of matter
is cyclical. All materials vital to life are continually recycled from the abiotic environment to
organisms and back to the environment.
II. Biogeochemical cycles are cycles of matter such as carbon, nitrogen, phosphorus, i.e., the
elemental cycles, and water.
A. Carbon dioxide (CO2) is the most important gas of the carbon cycle. Methane (CH4) also
becomes significant in anaerobic environments.
1. Carbon enters plants, algae, and cyanobacteria (and many chemoautotrophs) as
CO2, which is incorporated into organic molecules by photosynthesis (or similar
processes for carbon fixation).
2. Cell respiration by plants, by animals that eat plants, and by decomposers returns
CO2 to the atmosphere, making it available for producers again.
3. Combustion and weathering also return CO2 to the atmosphere.
4. The level of atmospheric CO2 has increased dramatically during the last half of the
20th century. This increase may cause human-induced changes in climate called
global warming.
B. There are actually three different nitrogen cycles. We will look at these three cycles starting
with nitrogen in organic forms like proteins and nucleic acids.
1. The oldest, which requires no oxygen (but can still happen if O2 is present).
a. Ammonification is the conversion of organic nitrogen to ammonia and
ammonium ions, NH4+. Ammonification is a special case within the
nitrogen cycle of the more general phenomenon (which you first heard
about in an earlier lecture) called mineralization, the conversion of any
element from an organic form to an inorganic form, i.e., Xorg 6 Xinorg.
b. Assimilation (also called “plant uptake”) is the biological conversion of
nitrates, ammonia, or ammonium into proteins and other nitrogencontaining compounds by plants. When microbes assimilate the same
inorganic forms of nitrogen, the process is also called immobilization,
the conversion of an element (in this case N) from an inorganic form to
an organic form, i.e., for some element X, Xinorg 6 Xorg. Immobilization
is mineralization backwards. Ordinary land plants living outside
wetlands (upland species) assimilate some N in the form of ammonium,
but they much prefer nitrate (See below.)
c. This simple, ancient nitrogen cycle still prevails in acidic conifer-dominated
forest soils, largely because nitrification (see below) does not work very
quickly at low pH.
2. The aerobic nitrogen cycle. In agricultural lands, this is the predominant N cycle.
a. As before, ammonification produces NH4+ from organic forms of nitrogen,
but now (before the plants get the N)...
b. Nitrification is the conversion of ammonia or ammonium to nitrate, (NO3-)
one of the main forms of nitrogen used by plants. Nitrification
absolutely requires O2, which is usually available since it constitutes
about 20% of the atmosphere. Nitrification is done primarily by
chemoautotrophs. These organisms are able to capture the potential
energy released during this process of nitrogen oxidation and use it for
growth. Nitrification actually occurs in two steps that are caused by
two different groups of chemoautotrophs:
i. Ammonia + O2 6 nitrite (NO2-) + water, which is done by
organisms whose generic names begin with “Nitroso...”, such
as Nitrosomonas or Nitrosococcus.
ii. Nitrite + O2 6 nitrate, which is done by organisms whose generic
names start with “Nitro” (but not “Nitroso”), such as
Nitrobacter or Nitrospira.
c. Upland plants love nitrate. Assimilation of NO3- into organic plant
compounds returns us to our starting point.
3. The complete nitrogen cycle requires nitrogen to be transformed in both aerobic and
anaerobic sites.
a. As before, ammonification creates NH4+ from organic N-containing
compounds, and nitrification converts the NH4+ to NO3-(aerobically).
Now we are ready for an anaerobic process that will not happen in the
presence of O2. Oddly, even agricultural soil contains many anaerobic
microsites, especially after a heavy rain.
b. Denitrification converts nitrate to nitrogen gas. Denitrification only occurs
under anaerobic conditions, such as you might find in a swamp or even
in portions of upland soil that is temporarily very wet following a rain.
Denitrification is performed by heterotrophic bacteria that are capable
of using nitrate as a substitute oxidizer in environments that temporarily
run out of oxygen. Alas, no true plant can use N in the form of N2 gas.
But, N2 created by denitrification is not lost forever, because we have...
c. Nitrogen fixation is the conversion of nitrogen gas (N2), the most abundant
gas in the atmosphere but which plants cannot use directly, to ammonia
(NH3), another gas, or its dissolved form, ammonium ions (NH4+),
which plants are able to use, although it is not the form of N that most
upland plants “prefer”. Before humans figured out how to make
ammonia from a mixture of molecular nitrogen and hydrogen (H2)
gases, symbiotic nitrogen fixation was the most effective way (on a
per acre basis) of converting N2 to a plant useable form. The N2-fixing
mutualism between rhizobia and leguminous plant roots is not the only
example of such a mutualism. A group of filamentous bacteria in the
genus Frankia form similar N-fixing associations with the roots of nonleguminous plants like bayberries and sweetfern. Even some nitrogenfixing cyanobacteria have formed a mutualism with the fern Azolla,
which often occurs floating in flooded low-land rice fields, and with an
ancient group of plants called cycads, which look a lot like short palms
but are actually more closely related to cone-bearing plants like pines.
4. Humans have more than doubled the amount of fixed nitrogen, i.e., a form of N
other than N2, entering the global nitrogen cycle. This is largely the result of
fertilizer production and application, but nitrogen oxides produced by internal
combustion engines are another significant source of fixed N. The excess
nitrogen is contributing to water-quality problems, air pollution, acid deposition,
global warming, and depletion of stratospheric ozone.
C. The phosphorus cycle has no biologically important gaseous compounds, which is really too
bad, because the phosphorous-containing gas that is more-or-less analogous to
ammonia is phosphine, PH3, which is quite toxic, marvelously foul smelling, and
explosive on contact with air.
1. Phosphorus erodes from rock as inorganic phosphate ions such as HPO42- and
H2PO4- and is absorbed from the soil by the roots of plants.
2. Plants incorporate phosphorus into organic compounds, most notably into DNA and
RNA. No phosphorus 6 no genes. Animals obtain the phosphorus they need
from their diets. Decomposers release inorganic phosphate (which, by
definition, they produce by mineralization) into the environment.
3. Phosphorus can be lost from biological cycles for millions of years when it washes
into the ocean and is deposited in sea beds.
4. There no processes in the phosphorus cycle that are analogous to nitrification or
denitrification.
5. There is a mutualism important to the phosphorus cycle that is vaguely similar to
nitrogen fixation, the symbiosis between mycorrhizal fungi, (See text, p. 72.)
which are far more efficient than plants at finding and solubilizing phosphates in
soils, and the plant roots which give these fungi sugars in exchange for
phosphate. This offers an attractive parallel with the mutualism between
nitrogen-fixing bacteria and the higher plants on or with which they grow.
6. Inorganic phosphorus in the form of phosphate (HPO42- and H2PO4- ) has a
surprisingly high affinity for clay particles considering that phosphates are
anions. Most clay particles are also negatively charged, so they might have
been expected to repel phosphate the same way they repel chloride (Cl-),
nitrate (NO3-), and sulfate (SO42-), but they don’t. The chemical explanation
for why phosphate behaves differently in soil from other ions is more detailed
than we need for the purposes of this course. It bears mentioning, however,
that the kinds of clays that are most abundant in very old, highly weather soils,
such as those under tropical rainforests are the ones with the most powerful
phosphorus-binding capacity. Phosphates go into the soil from fertilizer only to
get tightly tied up so plants can find this fertilizer element. This is just one more
reason why it is very difficult to farm rainforest soils using conventional
methods.
D. The hydrologic cycle, which continuously renews the supply of water that is essential to life,
involves an exchange of water between the land, the atmosphere, and organisms.
1. Water enters the atmosphere by evaporation and transpiration and leaves the
atmosphere as precipitation. Air is tremendously desiccating. Most people do
not know that pumping air with 97% relative humidity through soil will
eventually make it too dry to support plant growth. Fortunately, a relatively
thin, very dry layer at the surface of bare soil usually prevents water from
moving to the surface (where it can evaporate) from greater depths.
2. On land, water filters through the ground or runs off to lakes, rivers, and the ocean.
Groundwater (in “aquifers”) is stored in underground caverns and porous layers
of rock. The movement of surface water from land to ocean is called runoff.