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Integrated Biosphere Simulator
IBIS-2 is the version 2 of the land-surface model Integrated Biosphere Simulator (IBIS), which includes several major improvements and additions to the prototype model developed by Foley et al. 996 IBIS was designed to explicitly link land surface and hydrological processes, terrestrial biogeochemical cycles, and vegetation dynamics within a single physically consistent framework IBIS Functionality The model considers transient changes in vegetation composition and structure in response to environmental change and is, therefore, classified as a Dynamic Global Vegetation Model ( DGVM) This new version of IBIS has improved representations of land surface physics, plant physiology, canopy phenology, plant functional type (PFT) differences, and carbon allocation. Furthermore, IBIS-2 includes a new belowground biogeochemistry submodel, which is coupled to detritus production (litterfall and fine root turnover). All process are organized in a hierarchical framework and operate at diff ...
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Biogeochemical Cycle
A biogeochemical cycle (or more generally a cycle of matter) is the pathway by which a chemical substance cycles (is turned over or moves through) the biotic and the abiotic compartments of Earth. The biotic compartment is the biosphere and the abiotic compartments are the atmosphere, hydrosphere and lithosphere. There are biogeochemical cycles for chemical elements, such as for calcium, carbon, hydrogen, mercury, nitrogen, oxygen, phosphorus, selenium, iron and sulfur, as well as molecular cycles, such as for water and silica. There are also macroscopic cycles, such as the rock cycle, and human-induced cycles for synthetic compounds such as polychlorinated biphenyls (PCBs). In some cycles there are reservoirs where a substance can remain or be sequestered for a long period of time. Overview Energy flows directionally through ecosystems, entering as sunlight (or inorganic molecules for chemoautotrophs) and leaving as heat during the many transfers between tro ...
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Vegetation
Vegetation is an assemblage of plant species and the ground cover they provide. It is a general term, without specific reference to particular taxa, life forms, structure, spatial extent, or any other specific botanical or geographic characteristics. It is broader than the term ''flora'' which refers to species composition. Perhaps the closest synonym is plant community, but ''vegetation'' can, and often does, refer to a wider range of spatial scales than that term does, including scales as large as the global. Primeval redwood forests, coastal mangrove stands, sphagnum bogs, desert soil crusts, roadside weed patches, wheat fields, cultivated gardens and lawns; all are encompassed by the term ''vegetation''. The vegetation type is defined by characteristic dominant species, or a common aspect of the assemblage, such as an elevation range or environmental commonality. The contemporary use of ''vegetation'' approximates that of ecologist Frederic Clements' term earth cov ...
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Dynamic Global Vegetation Model
A Dynamic Global Vegetation Model (DGVM) is a computer program that simulates shifts in potential vegetation and its associated biogeochemical and hydrological cycles as a response to shifts in climate. DGVMs use time series of climate data and, given constraints of latitude, topography, and soil characteristics, simulate monthly or daily dynamics of ecosystem processes. DGVMs are used most often to simulate the effects of future climate change on natural vegetation and its carbon and water cycles. DGVMs generally combine biogeochemistry, biogeography, and disturbance submodels. Disturbance is often limited to wildfires, but in principle could include any of: forest/land management decisions, windthrow, insect damage, ozone damage etc. DGVMs usually "spin up" their simulations from bare ground to equilibrium vegetation (e.g. climax community) to establish realistic initial values for their various "pools": carbon and nitrogen in live and dead vegetation, soil organic matter, e ...
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Physiology
Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemical and physical functions in a living system. According to the classes of organisms, the field can be divided into medical physiology, animal physiology, plant physiology, cell physiology, and comparative physiology. Central to physiological functioning are biophysical and biochemical processes, homeostatic control mechanisms, and communication between cells. ''Physiological state'' is the condition of normal function. In contrast, '' pathological state'' refers to abnormal conditions, including human diseases. The Nobel Prize in Physiology or Medicine is awarded by the Royal Swedish Academy of Sciences for exceptional scientific achievements in physiology related to the field of medicine. Foundations Cells Although there are ...
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Phenology
Phenology is the study of periodic events in biological life cycles and how these are influenced by seasonal and interannual variations in climate, as well as habitat factors (such as elevation). Examples include the date of emergence of leaves and flowers, the first flight of butterflies, the first appearance of migratory birds, the date of leaf colouring and fall in deciduous trees, the dates of egg-laying of birds and amphibia, or the timing of the developmental cycles of temperate-zone honey bee colonies. In the scientific literature on ecology, the term is used more generally to indicate the time frame for any seasonal biological phenomena, including the dates of last appearance (e.g., the seasonal phenology of a species may be from April through September). Because many such phenomena are very sensitive to small variations in climate, especially to temperature, phenological records can be a useful proxy for temperature in historical climatology, especially in the ...
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Plant Functional Type
Plant functional types (PFTs) is a system used by climatologists to classify plants according to their physical, phylogenetic and phenological characteristics as part of an overall effort to develop a vegetation model for use in land use studies and climate models. PFTs provide a finer level of modeling than biomes, which represent gross areas such as desert, savannah, deciduous forest. In creating a PFT model, areas as small as 1 km2 are modeled by defining the predominant plant type for that area, interpreted from satellite data or other means. For each plant functional type, a number of key parameters are defined, such as fecundity, competitiveness, resorption (rate at which plant decays and returns nutrients to the soil after death), etc.; the value of each parameter is determined or inferred from observable characteristics such as plant height, leaf area, etc. Climatologists and ecologists struggle to determine which minimal set of plant characteristics best model t ...
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Carbon
Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon makes up only about 0.025 percent of Earth's crust. Three isotopes occur naturally, C and C being stable, while C is a radionuclide, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity. Carbon is the 15th most abundant element in the Earth's crust, and the fourth most abundant element in the universe by mass after hydrogen, helium, and oxygen. Carbon's abundance, its unique diversity of organic compounds, and its unusual ability to form polymers at the temperatures commonly encountered on Earth, enables this element to serve as a common element of Carbon-based life, all known life. It is the second most abundant element in the human body by mass (about 18.5%) after oxygen. Th ...
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Evapotranspiration
Evapotranspiration (ET) is the combined processes by which water moves from the earth’s surface into the atmosphere. It covers both water evaporation (movement of water to the air directly from soil, canopies, and water bodies) and transpiration (movement of water from the soil, through roots and bodies of vegetation, on leaves and then into the air). Evapotranspiration is an important part of the local water cycle and climate, as well as measurement of it plays a key role in agricultural irrigation and water resource management. Definition Evapotranspiration is a combination of evaporation and transpiration, measured in order to better understand crop water requirements, irrigation scheduling, and watershed management. The two key components of evapotranspiration are: * Evaporation: the movement of water directly to the air from sources such as the soil and water bodies. It can be affected by factors including heat, humidity, and wind speed. * Transpiration: the mo ...
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Rubisco
Ribulose-1,5-bisphosphate carboxylase-oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme () involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate (also known as RuBP). It is probably the most abundant enzyme on Earth. Alternative carbon fixation pathways RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere. While many autotrophic bacteria and archaea fix carbon via the reductive acetyl CoA pathway, the 3-hydroxypropionate cycle, or the reverse Krebs cycle, these pathways are relatively small contributors to global carbon fixation compared to that catalyzed by RuBisCO. Phosphoenolpyruvate carboxylase, unlike RuBisCO, only te ...
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Photosynthesis
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in carbohydrate molecules, such as sugars and starches, which are synthesized from carbon dioxide and water – hence the name ''photosynthesis'', from the Greek ''phōs'' (), "light", and ''synthesis'' (), "putting together". Most plants, algae, and cyanobacteria perform photosynthesis; such organisms are called photoautotrophs. Photosynthesis is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. Although photosynthesis is performed differently by different species, the process always begins when energy from light is absorbed by proteins called reaction centers that contain green chlorophyll (and other colored) pigments/chromoph ...
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Soil Organic Matter
Soil organic matter (SOM) is the organic matter component of soil, consisting of plant and animal detritus at various stages of decomposition, cells and tissues of soil microbes, and substances that soil microbes synthesize. SOM provides numerous benefits to the physical and chemical properties of soil and its capacity to provide regulatory ecosystem services. SOM is especially critical for soil functions and quality. The benefits of SOM result from a number of complex, interactive, edaphic factors; a non-exhaustive list of these benefits to soil function includes improvement of soil structure, aggregation, water retention, soil biodiversity, absorption and retention of pollutants, buffering capacity, and the cycling and storage of plant nutrients. SOM increases soil fertility by providing cation exchange sites and being a reserve of plant nutrients, especially nitrogen (N), phosphorus (P), and sulfur (S), along with micronutrients, which the mineralization of SOM slowly ...
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