Science Glossary

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The process in which radiant energy is retained by a substance. A further process always results from absorption, that is, the irreversible conversion of the absorbed radiation into some other form of energy within and according to the nature of the absorbing medium. The absorbing medium itself may emit radiation, but only after an energy conversion has occurred.


A horizontal movement of a mass of fluid, such as ocean or air currents. Can also refer to the horizontal transport of something (e.g., pollution, phytoplankton, ice, or even heat) by such movement.


The reflectivity of a material (e.g. vegetation, snow) summed over all wavelengths for a sunlit surface.


Physiological processes within a plant distribute nutrients to various plant parts according to growth needs and environmental and seasonal stresses. Processes include senescence and retranslocation .


Autotrophic respiration. The carbon that is returned to the atmosphere as CO2 during plant metabolism. Often abbreviated "Ra".


Biochemical Processes

Interaction of soil chemical properties and biology within the soil. These include:

  • Organic matter decomposition
  • Trace gas production/consumption

Elements are cycled between biotic and abiotic components of the biosphere .


Well-defined terrestrial environment (e.g., desert, tundra, or tropical forest). The complex of living organisms found in an ecological region.

Biophysical Processes

Physical processes modified by the ecosystem. These include:

  • Energy budget
  • Evaporation
  • Transpiration
  • Hydrology
  • Soil water dynamics
  • Soil temperature

That component of the Earth system that contains life in its various forms, which includes its living organisms and derived organic matter (e.g. litter, detrius, soil).



Plants use two principal carbon fixation cycles, the C3 and C4 cycles, during photosynthesis. C4 plants (notably tropical grasses) are disadvantaged relative to C3 plants (such as trees, shrubs, and cool-climate grasses) at high CO2/O2 ratios because of the additional energy expense needed to concentrate CO2in the bundle-sheath cells. At low CO2/O2, however, C4 plants can achieve a relatively high quantum yield by suppressing photorespiration. C4 photosynthesis is commonly associated with hot dry environments with warm-season precipitation and high light intensity , because C4 plants exhibit greater efficiency than C3 species with respect to water, light, and nitrogen use.
(Source: Climate Change as a Dominant Control on Glacial-Interglatial Variations in C3 and C4 Plant Abundance", Science, 31 August 2001, vol 293, pp. 1647-1651).

C3 Plants use rubisco to make a three-carbon compound as the first stable product of carbon fixation. These plants may lose up to 50% of their recently-fixed carbon through photorespiration. More than 95% of earth's plant species can be characterized as C3 plants.

C4 Plants use PEP carboxylase during initial carbon fixation to make a four-carbon compound that is subsequently transferred to specialized cells where carbon dioxide is internally released and refixed using rubisco. This phenomenon greatly reduces carbon loss by photorespiration, and in many cases, it completely inhibits it. Less than 1% of earth's plant species can be characterized as C4 plants.

A C4 photosynthetic pathway is a biochemical pathway used by certain plants to obtain carbon during photosynthesis. Such plants possess biochemical and anatomical CO2-concentrating mechanisms that increase the intercellular CO2 concentration at the site of fixation, which greatly reduces carbon losses by photorespiration. It is thought that the primary selective mechanism for the development of C4 photosynthesis is the low level of CO2 that has prevailed during the last 50 to 60 million years.

Also see CAM .

CAM (Crassulacean Acid Metabolism)

A carbon fixation scheme exhibited in many succulent plants. Also see C3/C4 Plants .



Reduction of nitrate or nitrite to molecular nitrogen or nitrogen oxide.


Dynamic Global Vegetation Model.



Science dealing with the interrelationships between living organisms and their environments.


Any natural unit or entity including living and non-living parts that interact to produce a stable system through cyclic exchange of materials.



Free Air CO2 Enrichment. Refers to algorithms and technology implementing the growth response of plants to elevated levels of atmospheric CO2. Examples of FACE field experiments include the FACE project at ORNL and the FACTS-I Project at Duke University.

FPAR (Fraction of Photosynthetically Active Radiation)

The fraction of incoming shortwave radiation that is photosynthetically active. See PAR .



Global atmosphere circulation model.

GPP (Gross Primary Production)

The amount of carbon taken up in photosynthesis. GPP denotes the total amount of carbon fixed in the process of photosynthesis by plants in an ecosystem, such as a stand of trees. GPP is measured on photosynthetic tissues, principally leaves. Global total GPP is estimated to be about 120 Gt C yr-1.

Growth Respiration

Respiration associated with photosynthesis. Respiration in which energy is used for the construction of new biomass.


Heterotrophic respiration

The release of CO2 during the process of decomposition of organic matter in the soil by soil animals, fungi, and other decomposer organisms. Often abbreviated "Rh".



Total solar irradiance describes the radiant energy emitted by the sun over all wavelengths that falls each second on 1 square meter outside the earth's atmosphere--a quantity proportional to the " solar constant " observed earlier in this century. It measures the solar energy flux in watts m-2.



Leaf Area Index. The area of foliage per unit area of ground. Conventionally this refers to the ratio of the area of the upper side of the leaves in a canopy projected onto a flat surface to the area of the surface under the canopy. This as also been called single-sided LAI or projected LAI. Occasionally LAI has been used in reference the total surface area of leaves, sometimes referred to as double-sided LAI. If a leaf is flat, the double-sided LAI is about twice that of the single-sided LAI. If the leaf is cylindrical, the double-sided LAI will be more than twice the single-sided LAI.

Latent Heat

Energy released or absorbed when water changes state (melts, freezes, vaporizes, or condenses). The latent heat of evaporation is often represented by the symbol "LE".

The heat that is either released or absorbed by a unit mass of a substance when it undergoes a change of state, such as during evaporation, condensation, or sublimation.


A structural substance in a plant that is very resistant to decomposition.

Longwave Radiation

The radiation emitted in the spectral wavelength greater than 4 micrometers corresponding to the radiation emitted from the Earth and atmosphere. It is sometimes referred to as 'terrestrial radiation' or 'infrared radiation,' although somewhat imprecisely.


Maintenace Respiration

Respiration involved with turnover and repair of plant material. Respiration in which energy is used to maintain living biomass.

Methane (CH4)

A hydrocarbon that is a greenhouse gas. Methane is produced through anaerobic (without oxygen) decomposition of waste in landfills, animal digestion, decomposition of animal wastes, production and distribution of natural gas and oil, coal production , and incomplete fossil fuel combustion.



NBP (Net Biome Production)

Net Biome Production denotes the net production of organic matter in a region containing a range of ecosystems (a biome) and includes, in addition to heterotrophic respiration , other processes leading to loss of living and dead organic matter (harvest, forest clearance, and fire, etc.). NBP is appropriate for the net carbon balance of large areas (100-1000 km2) and longer periods of time (several years and longer). In the past, NBP has been considered to be close to zero . Compared to the total fluxes between atmosphere and biosphere, global NBP is comparatively small; NBP for the decade 1989-1998 has been estimated to be 0.7  1.0 Gt C yr-1— about 1 percent of NPP and about 10 percent of NEP . Source: .

NEE (Net Ecosystem Exhange)

The integration the fluxes of CO2 into and out of the vegetation. The equation is:

NEE = GPP — Recosystem

NEP (Net Ecosystem Production)

The net gain or loss of C by the ecosystem. The equation is (ignoring lateral fluxes):

NEP = NPP — Rheterotrophic — Fremoved — Fdisturbance — Fleached

Net Ecosystem Production denotes the net accumulation of organic matter or carbon by an ecosystem. Over a short time scale, NEP is the difference between the rate of production of living organic matter (NPP) and the decomposition rate of dead organic matter (heterotrophic respiration, RH). Global NEP is estimated to about 10 Gt C yr-1. Source:

Net Momentum



Oxidation of ammonium to nitrite or nitrate.

Nitrogen Fixation

The conversion of atmospheric nitrogen to forms usable in biological processes (ammonium and nitrate).

Nitrous Oxide (N2O)

A powerful greenhouse gas with a global warming potential of 310 X CO2. Major sources of nitrous oxide include soil cultivation practices, especially the use of commercial and organic fertilizers, fossil fuel combustion, nitric acid production, and biomass burning.

NOx (Nitrogen Oxides)

Gases consisting of one molecule of nitrogen and varying numbers of oxygen molecules. Nitrogen oxides are produced in the emissions of vehicle exhausts and from power stations. In the atmosphere, nitrogen oxides can contribute to formation of photochemical ozone (smog), can impair visibility, and have health consequences; they are thus considered pollutants.

NPP (Net Primary Production)

Net gain of carbon by plants. (GPP minus autotrophic respiration).

Net Primary Production denotes the net production of organic matter by plants in an ecosystem-that is, GPP reduced by losses resulting from the respiration of the plants (autotrophic respiration). Global NPP is estimated to be about half of the GPP — that is, about 60 Gt C yr-1. Source:


PAR (Photosynthetically Active Radiation)

The wavelengths absorbed by chlorophyll, and therefore active in the photosynthetic processes. These wavelengths are between 0.4 and 0.7 microns and essentially make up the visible spectrum.


Plant functional type. Both a conceptual and algorithmic view the role of a plant species or archtypical plant representation in ecosystem modeling.


The timing of plant behaviors, governed by increasing or decreasing day length and/or growing degree days. These behaviors include the greening up of plants, senescence of plants, leaf production, and leaf drop.


The specialized vascular plant tissue used for the transportation of dissolved sugars and other organic solutes within a plant.


A process that begins when rubisco fixes molecular oxygen, as opposed to carbon dioxide, which ultimately leads to the evolution of CO2 from plants. This process of carbon loss is stimulated by conditions of high light, temperature and oxygen concentration.


Carbohydrates, including glucose and sucrose among others, that are produced from the end products of photosynthesis.


The process by which plants use sunlight, water, and carbon dioxide to produce their food.

Plant Functional Type

A plant functional type (PFT) in terms of the IRC model, is a plant type plus soil within a landscape. A plant is defined from a database of parameters derived from empirical data. Soil is a realistic approximations to soil survey map units, whose texture and structure directly affect plant production and organic matter decomposition. The landscape provides the topographic influences upon the local environment. A PFT is simulated as a cohort which can be created through disturbance and aggregated with similar cohorts.


Plant processes. These include:

PPFD (Photosynthetic Photon Flux Density)

PAR (Photosynthetically Active Radiation) expressed in umol m-2 sec-1.



The change in rate of a process with an increase in temperature of 10 degrees Celcius. It's usually between 2 and 3 for biological and chemical reactions. If R1 and R2 are the rates at temperatures T1 and T2, respectively, then

R2 = R1 * Q10([T2-T1]/10)


Radiative Forcing

A change in the balance between incoming solar radiation and outgoing infra-red radiation. Without any radiative forcing, solar radiation coming to the Earth would continue to be approximately equal to the infra-red radiation emitted from the Earth. The addition of greenhouse gases traps and increased fraction of the infra-red radiation, reradiating it back toward the surface and creating a warming influence (i.e., positive radiative forcing because incoming solar radiation will exceed outgoing infra-red radiation).

Radiative Transfer

The transfer of short wave energy from the sun and long wave energy from the environment to entities such as plants, snow pack, and soil. A theory dealing with the propagation of electromagnetic radiation through a medium.

Respiration (cellular)

The cellular process by which sugars and other organic compounds are broken down to release stored energy and to obtain carbon skeletons used in the growth and maintenance of the cell.

The oxidation of carbohydrate to CO2 and H20 in living cells. An intracellular process in which molecules, particularly pyrutvate in the Krebs cycle, are oxidized with the release of energy and CO2. The complete breakdown of sugar or other organic compounds to carbon dioxide and water is termed aerobic respiration, although the first steps of the process are anaerobic.

In plant vegetation there are two main types of respiration. The first is called dark respiration (Rd) and includes various pathways of substrate oxidation such as glycolysis, the oxidative pentose phosphate pathway and the tricarboxylic acid (TCA or Krebs) cycle. These conserve some of the free energy in carbohydrate in the high energy bonds of ATP, reduced pyridine nucleotide (NADH) and FADH2. The term dark respiration also covers the further oxidation of NADH and FADH2 by transfer of electrons through the various electron transfer complexes of the mitochondrial electron transport pathway. The second type of respiration in plants is called photorespiration. This is the pathway of CO2 production via the photorespiratory carbon oxidation (PCO) cycle. The same enzyme (Rubisco) that catalysis the carboxylation of RuBP as the first step of the PCR cycle can also catalyse the oxygenation of RuBP to phosphoglycollate as the first step of the PCO cycle.


The transport of minerals and food from the leaves of a plant to storage when the leaves senesce.


A bifunctional enzyme that can fix carbon dioxide or molecular oxygen, which leads to photosynthesis or photorespiration , respectively. Rubisco is the most abundant enzyme on earth.



The process of plant degeneration that generally occurs at the end of the growing season. It is typically characterized by increasing respiration, decreasing growth rates, chlorophyll breakdown, and mobilization of nitrogen out of leaves and into other plant organs.

Sensible Heat

Thermal energy advective in the air from adjacent land mass, usually aided by convection from deep soil layers or from the earth. Often represented by the symbol H. The excess radiative energy that has passed from the Earth's surface to the atmosphere through advection, conduction, and convection processes.


The process of increasing the carbon content of a carbon pool other than the atmosphere.

Shade-intolerant species

Plants that typically grow in places that receive lots of direct sunlight. They generally have high relative growth rates, highly-regulated stomata and thin leaves.

Shade-tolerant species

Plants that typically grow in places that receive less than full sunlight, such as the lower levels of a forest. They generally have low relative growth rates, open stomata and thick densely-packed leaves.


Any process or mechanism which removes a greenhouse gas, an aerosol, or a precursor of a greenhouse gas from the atmosphere. A given pool (reservoir) can be a sink for atmospheric carbon if, during a given time interval, more carbon is flowing into it than is flowing out. Opposite of source .

Solar constant

(as defined for planet Earth) is the power collected at the top of the atmosphere by a unit area perpendicular to the light path.

SOM (Soil Organic Matter)

Organic matter contained within the soil.


A carbon pool (reservoir) can be a source of carbon to the atmosphere if less carbon is flowing into it than is flowing out of it. Opposite of sink .

Shortwave Radiation

The radiation received from the sun and emitted in the spectral wavelengths less than 4 microns. It is also called 'solar radiation'.


Small pores in plant leaves through which water vapor and carbon dioxide diffuse during transpiration and photosynthesis (carbon fixation), respectively.

Stomatal Conductance

A plant property related to the ease with which water vapor escapes from plant leaves through small pores in the leaves know as stomata.


Region of the atmosphere between the troposphere and mesosphere , having a lower boundary of approximately 8 km at the poles to 15 km at the equator and an upper boundary of approximately 50 km. Depending upon latitude and season, the temperature in the lower stratosphere can increase, be isothermal, or even decrease with altitude, but the temperature in the upper stratosphere generally increases with height due to absorption of solar radiation by ozone.


The change in numbers and kinds of organisms leading to a stable community. Replacement of communities, one by another, on an area.



Terrestrial carbon model.

Trace Gas

Any one of the less common gases found in the Earth's atmosphere. Nitrogen, oxygen, and argon make up more than 99 percent of the Earth's atmosphere. Other gases, such as carbon dioxide, water vapor, methane, oxides of nitrogen, ozone, and ammonia, are considered trace gases. Although relatively unimportant in terms of their absolute volume, they have significant effects on the Earth's weather and climate.


The long distance transport of water, minerals, or food within a plant; most often used to refer to food transport.


The process by which water vapor is lost from plants, evaporating from cell walls just below the surface of the leaf and diffusing into the air through small stomatal pores.


The atmospheric layer separating the stratosphere from the troposphere . It marks the transition from temperatures that decrease with increasing height within the troposphere , to an atmospheric region that experiences increasing temperatures with height.


The lower atmosphere, to a height of 8-15 km above Earth, where temperature generally decreases with altitude, clouds form, precipitation occurs, and convection currents are active. See atmosphere.

Turbulent Exchange


Vapor Pressure Deficit

A measure of the "dryness" of the air. A high vapor pressure deficit corresponds to a low relative humidity and/or high temperature, while a low vapor pressure deficit corresponds to a high relative humidity and/or low air temperature.

Vegetation Dynamics


WUE (Water Use Efficiency)

A higher water use efficiency in a plant means less water is lost while fixing a molecule of CO2. C4 and CAM species have an enhanced ability to utilize light while restricting water loss. Although it may be defined in a number of ways, it is basically the amount of organic matter produced by a plant divided by the amount of water used by the plant in producing it.