Nov 26, 2013
In addition to energy, all organisms require specific chemical elements to meet their
biochemical requirements for metabolism and growth. Organisms get these elements by
absorbing them from the environment or by consuming other organisms
Iron is required by all organisms for several metabolic functions. However,
organisms obtain this iron from different sources in very different ways. However,
the ultimate source of iron is solid minerals in earths crust which are subjected to
chemical transformations as they move through the different physical and biological
components of ecosystems.
Biogeochemistry is the study of the physical, chemical, and biological factors that influence the
movement and transformation of elements (nutrients and non nutrients like tracers or
Understanding biogeochemistry is important in determining the availability of nutrients which
are chemical elements required for metabolism and growth. Nutrients must be in certain forms
for uptake by organisms. The rate of physical and chemical transformations determines the
supply of nutrients.
Nutrient Requirements & Sources
All organisms share similar nutrient
requirements. However, the ways in which
these nutrients are obtained, the chemical
forms of those nutrients that are taken up, and
relative amounts of those nutrients that are
required vary greatly. Nutrients enter
ecosystems through the chemical breakdown
of minerals in rocks of the earths crust, or
through fixation of atmospheric gases
Amounts and specific nutrients required vary
according to the organisms mode of energy
acquisition (autotrophs vs heterotrophs),
mobility, and thermal physiology (ectotherm
Differences in nutrient requirements are reflected in the chemical composition of organisms.
Carbon (C) is the main component of structural compounds in plants; nitrogen (N) is largely tied up in enzymes. C:N ratios reflect relative concentrations of biochemical machinery in cells:
Animals have lower C:N ratios (6 for humans); plants have C:N ratios of 10–40. As a result,
herbivores must consume more food than carnivores to get enough nutrients such as N.
All plants require a set of essential nutrients. Some species have specific requirements. Some 4
and CAM plants require sodium. (All animals require it for maintaining pH and osmotic balance.)
Some plants that host N-fixing bacteria require cobalt. Some plants in selenium-rich soil require
it, but it is toxic to most plants.
Plants and microorganisms take up nutrients in simple, soluble forms from the environment.
Using the simple forms, they synthesize the larger forms required for their metabolism and
Animals mostly get nutrients in food as large, complex molecules. They take them up by
consuming living organisms, or detritus. Some of these are broken down; others are absorbed
intact, such as some amino acids.
Ultimate Source of Nutrients
All nutrients are ultimately derived from two abiotic sources: Minerals in rocks and gases in the
atmosphere. Over time, they accumulate in ecosystems in organic forms.
Nutrients may be cycled within an ecosystem, repeatedly passing through organisms and the
soil or water. They may even be cycled internally within an organism (stored or mobilized for
use as needs change)
The breakdown of minerals in rock supplies ecosystems with nutrients such as potassium,
calcium, magnesium and phosphorous.
Minerals: solid substances with characteristic chemical properties, derived from
several geologic processes
Rocks: collections of different minerals.
Elements are released from rock minerals by weathering, which is a two step process.
The first step is Mechanical weathering. This is the physical breakdown of rocks.
Expansion and contraction processes (freeze–thaw and drying–rewetting cycles) break
rocks into smaller pieces. Plant roots and gravity (e.g., landslides) also contribute.
Mechanical weathering exposes minerals to the processes of chemical weathering in
which the minerals are subjected to chemical reactions that release soluble forms of the
mineral elements (nutrients).
Weathering is one of the processes that result in soil formation.
Soil is a mix of mineral particles, organic matter (mostly decomposing plant matter),
water, and organisms. The water contains dissolved organic matter, minerals, and gases
(the soil solution).
Soil properties influence availability of nutrients to plants:
Texture: determined by particle size. The coarsest particles are sand.
Intermediate sized particles are silt. Clays are the smallest particles (< 2 μm).
Clays have a semicrystalline structure and negative charges on the surface that
can hold onto cations and exchange them with the soil solution. As a result, clay 2+ +
particles can serve as a reservoir for some nutrient ions such as Ca , K , and
Mg . A soils ability to hold and exchange these cations is known as Cation
exchange capacity. It is determined by the amount and types of clay particles
present in the soil. Texture also influences soil water-holding capacity, and thus
movement of nutrients in the soil solution. Soils with a high proportion of sand
have large spaces between the particles, and do not hold water well. Water
drains through quickly.
Parent material: The rock or mineral material that was broken down by
weathering to form a soil. Parent material may be bedrock (common), or
sediment deposited by glaciers (till), or by wind (loess), or by water. The
chemistry and structure of the parent material determines the rate of
weathering, and the amount and type of minerals released. Thus, it influences
soil characteristics such as fertility.
Example: Soils derived from limestone have high levels of Ca , K , and +
Mg . Soils derived from acidic granite have low concentrations of these
The chemistry and pH of the parent material exerts an influence on abundance, growth,
and diversity of plants in an ecosystem.
Gough et al. (2000) showed that variation in acidity of parent material pH was
correlated with differences in plant
species richness in Arctic ecosystems.
They surveyed Arctic vegetation
across gradients in soil acidity and
found that the number of plant
species increased as acidity
decreased. This variation was
attributed to the negative effects of
soil acidity on nutrient availability, as
well as its inhibitory effects on plant
Over time, soils undergo changes
associated with weathering,
accumulation/chemical alteration of
organic matter, leaching (movement of
dissolved organic matter and fine mineral
particles from upper to lower layers)
These processes form horizons, which are
layers of soil distinguished by their color,
texture, and permeability.
Climate influences rates of soil development (speeds weathering, leaching, etc). Soil
development is fastest in warm, wet conditions. Tropical forest soils have experienced
high rates of weathering and leaching for a long time, and are nutrient-poor. Most of the nutrients in these ecosystems are in the living tree biomass. In other terrestrial
ecosystems, the proportion of nutrients in the soil is greater. When tropical forests are
cleared and burned, the nutrients are lost in smoke and ash and soil erosion. These
ecosystems can take centuries to return to their previous state.
Organisms, especially plants, bacteria, and fungi, contribute organic matter to soils.
Organic matter is a reservoir of nutrients such as nitrogen and phosphorus. Organisms
can also increase chemicalweathering rates through the release of CO a2d organic
Once nutrients have entered an ecosystem, they are subjected to further modification as a
result of uptake by organisms and other chemical reactions. Chemical and biological
transformations in ecosystems alter the chemical form and supply of nutrients.
The most important nutrient transformation is the decomposition of organic matter, which
releases nutrients back into the ecosystem.
Detritus is an important source of nutrients, mainly nitrogen and phosphorous. Detritus
includes dead plants, animals, and microorganisms, and egested waste products.
Nutrients in detritus are made available by decomposition, the process by which
detritivores break down detritus to obtain
energy and nutrients.
Decomposition releases nutrients as simple,
soluble organic and inorganic compounds that
can be taken up by other organisms.
Organic matter is derived primarily from plant
matter (from above or below the surface). Fresh,
undecomposed organic matter on the soil
surface is known as litter (most abundant
substrate for decomposition including leaves,
stems, roots, dead animals). This litter is used by
animals, protists, bacteria, and fungi. Animals
such as earthworms, termites, and nematodes
consume the litter, breaking it up into
progressively finer particles. This fragmentation
increases surface area, which facilitates chemical breakdown.
Mineralization: Chemical conversion of organic matter into inorganic nutrients (nutrients not
associated with carbon). Heterotrophic microorganisms release enzymes into the soil that break
down organic macromolecules.
Abiotic and biotic controls on decomposition and mineralization determine nutrient availability
Rates of decomposition and mineralization are influenced by climate. Decomposition and
mineralization rates are faster in warm, moist conditions. Soil moisture also influences the availability of water and O2to microorganisms. Dry soils may
not provide enough water for detritovores to function. Wet
soils have low O concentrations, which inhibits detritivores
(hypoxic conditions). We want warm temps with
Not all of the nutrients released during mineralization
become available for uptake by autotrophs. This is because
some of the nutrients released are used by decomposers
themselves. The amount of nutrients released during
decomposition is dependent on the nutrient requirements of
decomposers, and the amount of energy the organic matter
The above factors can be approximated by the C:N ratio of detritus. This ratio represents energy
content to nutrient content ratio. Organic matter/detritus with high C:N will have a low net
release of nutrients because the heterotrophic microbes are limited more by nitrogen than by
The properties of carbon compounds influence decomposition rates. Not all of the carbon in
litter is equally available as an energy source for decomposers. The chemistry of that carbon
determines how rapidly the material can be decomposed.
Lignin strengthens plant cell walls, and is difficult for soil microbes to degrade. It
decomposes very slowly. The amount of lignin in cell walls varies with plant species. The
rate of nutrient release from plant
material containing high lignin (oak/pine)
is lower than that of material with low
lignin concentrations (maple/aspen)
Plant litter may co