Theoretical production ecology
Encyclopedia
Theoretical production ecology tries to quantitatively study the growth of crops.
The plant is treated as a kind of biological factory, which processes light
, carbon dioxide
, water
and nutrients into harvestable parts.
Main parameters kept into consideration are temperature, sunlight, standing crop biomass, plant production distribution, nutrient and water supply.
Unit of modelling usually is the crop
, the assembly of plants per standard surface unit. Analysis results for an individual plant are generalised to the standard surface, e.g. the Leaf Area Index
is the generalised surface of all crop leaves per surface unit.
Two cycles of biochemical reactions constitute the basis of plant production, the light reaction and the dark reaction.
Climate:
Crop:
Care:
As of 2005, several crop production models are in use. The crop growth model SUCROS has been developed during more than 20 years and is based on earlier models. Its latest revision known dates from 1997. The IRRI
and Wageningen University
more recently developed the rice growth model ORYZA2000. This model is used for modeling rice growth. Both crop growth models are open source
. Other more crop-specific plant growth models exist as well.
computer programming language. The model can and has been applied to a variety of weather regimes and crops. Because the source code of Sucros is open source
, the model is open to modifications of users with FORTRAN programming experience.
The official maintained version of SUCROS comes into two flavours: SUCROS I, which has non-inhibited unlimited crop growth (which means that only solar radiation and temperature determine growth) and SUCROS II, in which crop growth is limited only by water shortage.
. This model, too, is programmed in FORTRAN. The scope of this model is limited to rice
, which is the main food crop for Asia.
has sponsored a number of applicable crop growth models for various major US crops, such as cotton
, soy bean, wheat
and rice
. http://www.ars.usda.gov/Research/docs.htm?docid=6339
Other widely-used models are the precursor of SUCROS (SWATR), CERES, several incarnations of PLANTGRO, SUBSTOR, the FAO-sponsored CROPWAT, AGWATER and the erosion-specific model EPIC. http://www.italocorotondo.it/tequila/module5/irrig_crops/crop_grow_mod.htm
A less mechanistic growth and competition model, called the Conductance Model, has been developed, mainly at Warwick-HRI, Wellesbourne, UK. This model simulates light interception and growth of individual plants based on the lateral expansion of their crown zone areas. Competition between plants is simulated by a set algorithms related to competition for space and resultant light intercept as the canopy closes. Some versions of the model assume overtopping of some species by others. Although the model cannot take account of water or mineral nutrients, it can simulate individual plant growth, variability in growth within plant communities and inter-species competition. This model was written in Matlab. See Benjamin and Park (2007) Weed Research 47, 284-298 for a recent review.
The plant is treated as a kind of biological factory, which processes light
Light
Light or visible light is electromagnetic radiation that is visible to the human eye, and is responsible for the sense of sight. Visible light has wavelength in a range from about 380 nanometres to about 740 nm, with a frequency range of about 405 THz to 790 THz...
, carbon dioxide
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
, water
Water
Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...
and nutrients into harvestable parts.
Main parameters kept into consideration are temperature, sunlight, standing crop biomass, plant production distribution, nutrient and water supply.
Modelling
Modelling is essential in theoretical production ecology.Unit of modelling usually is the crop
Agriculture
Agriculture is the cultivation of animals, plants, fungi and other life forms for food, fiber, and other products used to sustain life. Agriculture was the key implement in the rise of sedentary human civilization, whereby farming of domesticated species created food surpluses that nurtured the...
, the assembly of plants per standard surface unit. Analysis results for an individual plant are generalised to the standard surface, e.g. the Leaf Area Index
Leaf Area Index
Leaf Area Index The Global Climate Observing System defines LAI as "one half the total green leaf area per unit groundsurface area. On sloping surfaces, the LAI should be projected to the normal to the slope. LAI is expressed in terms of square meters of leaf per square meter of ground...
is the generalised surface of all crop leaves per surface unit.
Processes
The usual system of describing plant production divides the plant production process into at least five separate processes, which are influenced by several external parameters.Two cycles of biochemical reactions constitute the basis of plant production, the light reaction and the dark reaction.
- In the light reaction, sunlight photons are absorbed by chloroplasts which split waterWaterWater is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...
into an electron, proton and oxygen radical which is recombined with another radical and released as molecular oxygenOxygenOxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
. The recombination of the electron with the proton yields the energy carriers NADH and ATPAdenosine triphosphateAdenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
. The rate of this reaction often depends on sunlight intensity, leaf area indexLeaf Area IndexLeaf Area Index The Global Climate Observing System defines LAI as "one half the total green leaf area per unit groundsurface area. On sloping surfaces, the LAI should be projected to the normal to the slope. LAI is expressed in terms of square meters of leaf per square meter of ground...
, leaf angle and amount of chloroplasts per leaf surface unit. The maximum theoretical gross production rate under optimum growth conditions is approximately 250 kg per hectare per day. - The dark reaction or Calvin cycle ties atmospheric carbon dioxideCarbon dioxideCarbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
and uses NADH and ATP to convert it into sucroseSucroseSucrose is the organic compound commonly known as table sugar and sometimes called saccharose. A white, odorless, crystalline powder with a sweet taste, it is best known for its role in human nutrition. The molecule is a disaccharide composed of glucose and fructose with the molecular formula...
. The available NADH and ATP, as well as temperature and carbon dioxideCarbon dioxideCarbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
levels determine the rate of this reaction. Together those two reactions are termed photosynthesisPhotosynthesisPhotosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...
. The rate of photosynthesis is determined by the interaction of a number of factors including temperature, light intensity and carbon dioxide. - The produced carbohydrates are transported to other plant parts, such as storage organs and converted into secondary products, such as amino acids, lipids, celluloseCelluloseCellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....
and other chemicals needed by the plant or used for respiration. Lipids, sugars, cellulose and starchStarchStarch or amylum is a carbohydrate consisting of a large number of glucose units joined together by glycosidic bonds. This polysaccharide is produced by all green plants as an energy store...
can be produced without extra elements. The conversion of carbohydrates into amino acids and nucleic acids requires nitrogen, phosphorusPhosphorusPhosphorus is the chemical element that has the symbol P and atomic number 15. A multivalent nonmetal of the nitrogen group, phosphorus as a mineral is almost always present in its maximally oxidized state, as inorganic phosphate rocks...
and sulfurSulfurSulfur or sulphur is the chemical element with atomic number 16. In the periodic table it is represented by the symbol S. It is an abundant, multivalent non-metal. Under normal conditions, sulfur atoms form cyclic octatomic molecules with chemical formula S8. Elemental sulfur is a bright yellow...
. ChlorophyllChlorophyllChlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...
production requires magnesiumMagnesiumMagnesium is a chemical element with the symbol Mg, atomic number 12, and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the Earth's crust and ninth in the known universe as a whole...
, while several enzymes and coenzymes require trace elements. This means, nutrient supply influences this part of the production chain. Water supply is essential for transport, hence limits this too. - The production centers, i.e. the leaves, are sources, the storage organs, growth tips or other destinations for the photosynthetic production are sinks. The lack of sinks can be a limiting factor for production too, as happens e.g. in apple orchards where insects or night frost have destroyed the blossoms and the produced assimilates cannot be converted into apples. BiennialBiennial plantA biennial plant is a flowering plant that takes two years to complete its biological lifecycle. In the first year the plant grows leaves, stems, and roots , then it enters a period of dormancy over the colder months. Usually the stem remains very short and the leaves are low to the ground, forming...
and perennial plantPerennial plantA perennial plant or simply perennial is a plant that lives for more than two years. The term is often used to differentiate a plant from shorter lived annuals and biennials. The term is sometimes misused by commercial gardeners or horticulturalists to describe only herbaceous perennials...
s employ the stored starch and fats in their storage organs to produce new leafs and shoots the next year. - The amount of crop biomass and the relative distribution of biomass over leafs, stems, roots and storage organs determines the respirationRespiration (physiology)'In physiology, respiration is defined as the transport of oxygen from the outside air to the cells within tissues, and the transport of carbon dioxide in the opposite direction...
rate. The amount of biomass in leafs determines the leaf area indexLeaf Area IndexLeaf Area Index The Global Climate Observing System defines LAI as "one half the total green leaf area per unit groundsurface area. On sloping surfaces, the LAI should be projected to the normal to the slope. LAI is expressed in terms of square meters of leaf per square meter of ground...
, which is important in calculating the gross photosynthetic production. - extensions to this basic model can include insect and pest damage, intercroppingIntercroppingIntercropping is the practice of growing two or more crops in proximity. The most common goal of intercropping is to produce a greater yield on a given piece of land by making use of resources that would otherwise not be utilized by a single crop. Careful planning is required, taking into account...
, climatical changes, etc.
Parameters
Important parameters in theoretical production models thus are:Climate:
- Temperature - The temperature determines the speed of respirationRespiration (physiology)'In physiology, respiration is defined as the transport of oxygen from the outside air to the cells within tissues, and the transport of carbon dioxide in the opposite direction...
and the dark reaction. A high temperature combined with a low intensity of sunlight means a high loss by respiration. A low temperature combined with a high intensity of sunlight means that NADH and ATP heap up but cannot be converted into glucose because the dark reaction cannot process them swiftly enough.
- Light - Light, also called photosynthetic Active Radiation (PAR) is the energy source for green plant growth. PAR powers the light reaction, which provides ATP and NADPH for the conversion of carbon dioxide and water into carbohydrates and molecular oxygenOxygenOxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
. When temperature, moisture, carbon dioxide and nutrient levels are optimal, light intensity determines maximum production level.
- Carbon dioxide levels - Atmospheric carbon dioxide is the sole carbon source for plants. About half of all proteins in green leaves have the sole purpose of capturing carbon dioxide.
- Although CO2 levels are constant under natural circumstances, CO2 fertilization is common in greenhouses and is known to increase yields by on average 24% http://www.eurekalert.org/pub_releases/2004-02/jaaj-cdf020504.php.
- C4 plantsC4 carbon fixationC4 carbon fixation is one of three biochemical mechanisms, along with and CAM photosynthesis, used in carbon fixation. It is named for the 4-carbon molecule present in the first product of carbon fixation in these plants, in contrast to the 3-carbon molecule products in plants. fixation is an...
like maizeMaizeMaize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
and sorghumSorghumSorghum is a genus of numerous species of grasses, one of which is raised for grain and many of which are used as fodder plants either cultivated or as part of pasture. The plants are cultivated in warmer climates worldwide. Species are native to tropical and subtropical regions of all continents...
can achieve a higher yield at high solar radiation intensities, because they prevent the leaking of captured carbon dioxide due of the spatial separation of carbon dioxide capture and carbon dioxide use in the dark reaction. This means that their photorespirationPhotorespirationPhotorespiration, or "'photo-respiration'", is a process in plant metabolism by which RuBP has oxygen added to it by the enzyme , instead of carbon dioxide during normal photosynthesis. This is the beginning step of the Calvin-Benson cycle...
is almost zero. This advantage is sometimes offset by a higher rate of maintenance respirationMaintenance respirationMaintenance respiration refers to metabolism occurring in an organism that is needed to maintain that organism in a healthy, living state...
. In most models for natural crops, carbon dioxide levels are assumed to be constant.
Crop:
- Standing crop biomass - Unlimited growth is an exponential processExponential growthExponential growth occurs when the growth rate of a mathematical function is proportional to the function's current value...
, which means that the amount of biomass determines the production. Because an increased biomass implies higher respiration per surface unit and a limited increase in intercepted light, crop growth is a sigmoid functionSigmoid functionMany natural processes, including those of complex system learning curves, exhibit a progression from small beginnings that accelerates and approaches a climax over time. When a detailed description is lacking, a sigmoid function is often used. A sigmoid curve is produced by a mathematical...
of crop biomass.
- Plant production distribution - Usually only a fraction of the total plant biomass consists of useful products, e.g. the seeds in pulses and cerealCerealCereals are grasses cultivated for the edible components of their grain , composed of the endosperm, germ, and bran...
s, the tubers in potatoPotatoThe potato is a starchy, tuberous crop from the perennial Solanum tuberosum of the Solanaceae family . The word potato may refer to the plant itself as well as the edible tuber. In the region of the Andes, there are some other closely related cultivated potato species...
and cassavaCassavaCassava , also called yuca or manioc, a woody shrub of the Euphorbiaceae native to South America, is extensively cultivated as an annual crop in tropical and subtropical regions for its edible starchy tuberous root, a major source of carbohydrates...
, the leafs in sisalSisalSisal is an agave that yields a stiff fibre traditionally used in making twine, rope and also dartboards. The term may refer either to the plant or the fibre, depending on context...
and spinachSpinachSpinach is an edible flowering plant in the family of Amaranthaceae. It is native to central and southwestern Asia. It is an annual plant , which grows to a height of up to 30 cm. Spinach may survive over winter in temperate regions...
etc. The yield of usable plant portions will increase when the plant allocates more nutrients to this parts, e.g. the high-yielding varieties of wheatWheatWheat is a cereal grain, originally from the Levant region of the Near East, but now cultivated worldwide. In 2007 world production of wheat was 607 million tons, making it the third most-produced cereal after maize and rice...
and riceRiceRice is the seed of the monocot plants Oryza sativa or Oryza glaberrima . As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies...
allocate 40% of their biomass into wheat and rice grains, while the traditional varieties achieve only 20%, thus doubling the effective yield.
- Different plant organs have a different respiration rate, e.g. a young leaf has a much higher respiration rate than roots, storage tissues or stems do. There is a distinction between "growth respiration" and "maintenance respiration".
- Sinks, such as developing fruits, need to be present. They are usually represented by a discrete switch, which is turned on after a certain condition, e.g. critical daylength has been met.
Care:
- Water supply - Because plants use passive transport to transfer water and nutrients from their roots to the leafs, water supply is essential to growth, even so that water efficiency rates are known for different crops, e.g. 5000 for sugar cane, meaning that each kilogram of produced sugar requires up to 5000 liters of water.
- Nutrient supply - Nutrient supply has a twofold effect on plant growth. A limitation in nutrient supply will limit biomass production as per Liebig's Law of the MinimumLiebig's law of the minimumLiebig's Law of the Minimum, often simply called Liebig's Law or the Law of the Minimum, is a principle developed in agricultural science by Carl Sprengel and later popularized by Justus von Liebig...
. With some crops, several nutrients influence the distribution of plant products in the plants. A nitrogenNitrogenNitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
gift is known to stimulate leaf growth and therefore can work adversely on the yield of crops which are accumulating photosynthesis products in storage organs, such as ripening cereals or fruit-bearing fruit trees.
Phases in crop growth
Theoretical production ecology assumes that the growth of common agricultural crops, such as cereals and tubers, usually consists of four (or five) phases:- Germination - Agronomical research has indicated a temperature dependence of germination time (GT, in days). Each crop has a unique critical temperature (CT, dimension temperature) and temperature sum (dimensions temperature times time), which are related as follows.
- When a crop has a temperature sum of e.g. 150 °C·d and a critical temperature of 10 °C, it will germinate in 15 days when temperature is 20 °C, but in 10 days when temperature is 25 °C. When the temperature sum exceeds the threshold value, the germination process is complete.
- Initial spread - In this phase, the crop does not cover the field yet. The growth of the crop is linearly dependentLinear independenceIn linear algebra, a family of vectors is linearly independent if none of them can be written as a linear combination of finitely many other vectors in the collection. A family of vectors which is not linearly independent is called linearly dependent...
on leaf area index, which in its turn is linearly dependent on crop biomass. As a result, crop growth in this phase is exponential. - Total coverage of field - in this phase, growth is assumed to be linearly dependent on incident light and respiration rate, as nearly 100% of all incident light is intercepted. Typically, LAILaïLaï is a city in Chad, the capital of the region of Tandjilé. The town is served by Laï Airport.-References:...
is above two to three in this phase. This phase of vegetative growth ends when the plant gets a certain environmental or internal signal and starts generative growth (as in cereals and pulses) or the storage phase (as in tubers). - Allocation to storage organs - in this phase, up to 100% of all production is directed to the storage organs. Generally, the leafs are still intact and as a result, gross primary production stays the same. Prolonging this phase, e.g. by careful fertilization, water and pest management results directly in a higher harvest.
- Ripening - in this phase, leafs and other production structures slowly die off. Their carbohydrates and proteins are transported to the storage organs. As a result, the LAI and, hence, the primary production decreases.
- Initial spread - In this phase, the crop does not cover the field yet. The growth of the crop is linearly dependent
Existing plant production models
Plant production models exist in varying levels of scope (cell, physiological, individual plant, crop, geographical region, global) and of generality: the model can be crop-specific or be more generally applicable. In this section the emphasis will be on crop-level based models as the crop is the main area of interest from an agronomical point of view.As of 2005, several crop production models are in use. The crop growth model SUCROS has been developed during more than 20 years and is based on earlier models. Its latest revision known dates from 1997. The IRRI
International Rice Research Institute
The International Rice Research Institute is an international NGO. Its headquarters are in Los Baños, Laguna, Philippines, and it has offices in sixteen countries...
and Wageningen University
Wageningen University
Wageningen University and Research Centre is a Dutch public university in Wageningen, The Netherlands. It consists of Wageningen University, the Van Hall-Larenstein School of Higher Professional Education, and the former agricultural research institutes of the Dutch Ministry of Agriculture...
more recently developed the rice growth model ORYZA2000. This model is used for modeling rice growth. Both crop growth models are open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
. Other more crop-specific plant growth models exist as well.
SUCROS
SUCROS is programmed in the FortranFortran
Fortran is a general-purpose, procedural, imperative programming language that is especially suited to numeric computation and scientific computing...
computer programming language. The model can and has been applied to a variety of weather regimes and crops. Because the source code of Sucros is open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
, the model is open to modifications of users with FORTRAN programming experience.
The official maintained version of SUCROS comes into two flavours: SUCROS I, which has non-inhibited unlimited crop growth (which means that only solar radiation and temperature determine growth) and SUCROS II, in which crop growth is limited only by water shortage.
ORYZA2000
The ORYZA2000 rice growth model has been developed at the IRRI in cooperation with Wageningen UniversityWageningen University
Wageningen University and Research Centre is a Dutch public university in Wageningen, The Netherlands. It consists of Wageningen University, the Van Hall-Larenstein School of Higher Professional Education, and the former agricultural research institutes of the Dutch Ministry of Agriculture...
. This model, too, is programmed in FORTRAN. The scope of this model is limited to rice
Rice
Rice is the seed of the monocot plants Oryza sativa or Oryza glaberrima . As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies...
, which is the main food crop for Asia.
Other models
The United States Department of AgricultureUnited States Department of Agriculture
The United States Department of Agriculture is the United States federal executive department responsible for developing and executing U.S. federal government policy on farming, agriculture, and food...
has sponsored a number of applicable crop growth models for various major US crops, such as cotton
Cotton
Cotton is a soft, fluffy staple fiber that grows in a boll, or protective capsule, around the seeds of cotton plants of the genus Gossypium. The fiber is almost pure cellulose. The botanical purpose of cotton fiber is to aid in seed dispersal....
, soy bean, wheat
Wheat
Wheat is a cereal grain, originally from the Levant region of the Near East, but now cultivated worldwide. In 2007 world production of wheat was 607 million tons, making it the third most-produced cereal after maize and rice...
and rice
Rice
Rice is the seed of the monocot plants Oryza sativa or Oryza glaberrima . As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies...
. http://www.ars.usda.gov/Research/docs.htm?docid=6339
Other widely-used models are the precursor of SUCROS (SWATR), CERES, several incarnations of PLANTGRO, SUBSTOR, the FAO-sponsored CROPWAT, AGWATER and the erosion-specific model EPIC. http://www.italocorotondo.it/tequila/module5/irrig_crops/crop_grow_mod.htm
A less mechanistic growth and competition model, called the Conductance Model, has been developed, mainly at Warwick-HRI, Wellesbourne, UK. This model simulates light interception and growth of individual plants based on the lateral expansion of their crown zone areas. Competition between plants is simulated by a set algorithms related to competition for space and resultant light intercept as the canopy closes. Some versions of the model assume overtopping of some species by others. Although the model cannot take account of water or mineral nutrients, it can simulate individual plant growth, variability in growth within plant communities and inter-species competition. This model was written in Matlab. See Benjamin and Park (2007) Weed Research 47, 284-298 for a recent review.
External resources
- Wageningen UniversityWageningen UniversityWageningen University and Research Centre is a Dutch public university in Wageningen, The Netherlands. It consists of Wageningen University, the Van Hall-Larenstein School of Higher Professional Education, and the former agricultural research institutes of the Dutch Ministry of Agriculture...
, NetherlandsNetherlandsThe Netherlands is a constituent country of the Kingdom of the Netherlands, located mainly in North-West Europe and with several islands in the Caribbean. Mainland Netherlands borders the North Sea to the north and west, Belgium to the south, and Germany to the east, and shares maritime borders...
, Department of Theoretical production Ecology - Leuven UniversityKatholieke Universiteit LeuvenThe Katholieke Universiteit Leuven is a Dutch-speaking university in Flanders, Belgium.It is located at the centre of the historic town of Leuven, and is a prominent part of the city, home to the university since 1425...
, BelgiumBelgiumBelgium , officially the Kingdom of Belgium, is a federal state in Western Europe. It is a founding member of the European Union and hosts the EU's headquarters, and those of several other major international organisations such as NATO.Belgium is also a member of, or affiliated to, many...
, Department of Theoretical Production Ecology - SUCROS manual
- SUCROS download page
- ORYZA2000 project page
- Summary page with US government sponsored crop growth models