Crassulacean acid metabolism
Crassulacean acid metabolism known as CAM photosynthesis, is a carbon fixation pathway that evolved in some plants as an adaptation to arid conditions. In a plant using full CAM, the stomata in the leaves remain shut during the day to reduce evapotranspiration, but open at night to collect carbon dioxide; the CO2 is stored as the four-carbon acid malate in vacuoles at night, in the daytime, the malate is transported to chloroplasts where it is converted back to CO2, used during photosynthesis. The pre-collected CO2 is concentrated around the enzyme RuBisCO, increasing photosynthetic efficiency; the mechanism was first discovered in plants of the family Crassulaceae. CAM was first suspected by de Saussure in 1804 in his Recherches Chimiques sur la Vegetation and refined by Aubert, E. in 1892 in his Recherches physiologiques sur les plantes grasses and expounded upon by Richards, H. M. 1915 in Acidity and Gas Interchange in Cacti, Carnegie Institution. The term CAM may have been coined by Ranson and Thomas in 1940, but they were not the first to discover this cycle.
It was observed in the succulent family Crassulaceae. Its name refers to acid metabolism in Crassulaceae, not the metabolism of "crassulacean acid". CAM is an adaptation for increased efficiency in the use of water, so is found in plants growing in arid conditions. During the night, a plant employing CAM has its stomata open, allowing CO2 to enter and be fixed as organic acids that are stored in vacuoles. During the day the stomata are closed, the carbon is released to the Calvin cycle so that photosynthesis may take place; the carbon dioxide is fixed in the cytoplasm of mesophyll cells by a PEP reaction similar to that of C4 pathway. But, unlike the C4 mechanism, the resulting organic acids are stored in vacuoles for use; the latter cannot operate during the night because the light reactions that provide it with ATP and NADPH cannot take place. During the day, the CO2-storing organic acids are released from the vacuoles of the mesophyll cells and enter the stroma of the chloroplasts where an enzyme releases the CO2, which enters into the Calvin cycle.
The most important benefit of CAM to the plant is the ability to leave most leaf stomata closed during the day. Plants employing CAM are most common in arid environments. Being able to keep stomata closed during the hottest and driest part of the day reduces the loss of water through evapotranspiration, allowing such plants to grow in environments that would otherwise be far too dry. Plants using only C3 carbon fixation, for example, lose 97% of the water they uptake through the roots to transpiration - a high cost avoided by plants able to employ CAM; the C4 pathway bears resemblance to CAM. CAM concentrates it temporally, providing CO2 during the day, not at night, when respiration is the dominant reaction. C4 plants, in contrast, concentrate CO2 spatially, with a RuBisCO reaction centre in a "bundle sheath cell" being inundated with CO2. Due to the inactivity required by the CAM mechanism, C4 carbon fixation has a greater efficiency in terms of PGA synthesis. Plants with CAM must control storage of CO2 and its reduction to branched carbohydrates in space and time.
At low temperatures, plants using CAM open their stomata, CO2 molecules diffuse into the spongy mesophyll's intracellular spaces and into the cytoplasm. Here, they can meet phosphoenolpyruvate, a phosphorylated triose. During this time, the plants are synthesizing a protein called PEP carboxylase kinase, whose expression can be inhibited by high temperatures and the presence of malate. PEP-C kinase phosphorylates its target enzyme PEP carboxylase. Phosphorylation enhances the enzyme's capability to catalyze the formation of oxaloacetate, which can be subsequently transformed into malate by NAD+ malate dehydrogenase. Malate is transported via malate shuttles into the vacuole, where it is converted into the storage form malic acid. In contrast to PEP-C kinase, PEP-C is synthesized all the time but inhibited at daylight either by dephosphorylation via PEP-C phosphatase or directly by binding malate; the latter is not possible at low temperatures, since malate is efficiently transported into the vacuole, whereas PEP-C kinase inverts dephosphorylation.
In daylight, plants using CAM close their guard cells and discharge malate, subsequently transported into chloroplasts. There, depending on plant species, it is cleaved into pyruvate and CO2 either by malic enzyme or by PEP carboxykinase. CO2 is introduced into the Calvin cycle, a coupled and self-recovering enzyme system, used to build branched carbohydrates; the by-product pyruvate can be further degraded in the mitochondrial citric acid cycle, thereby providing additional CO2 molecules for the Calvin Cycle. Pyruvate can be used to recover PEP via pyruvate phosphate dikinase, a high-energy step, which requires ATP and an additional phosphate. During the following cool night, PEP is exported into the cytoplasm, where it is involved in fixing carbon dioxide via malate. Plants use CAM to different degrees; some are "obligate CAM plants", i.e. they use only CAM in photosynthesis, although they vary in the amount of CO2 they are able to store as organic acids. Other plants show "inducible CAM", in which they are able to switch between using either the C3 or C4 mechanism and CAM depending on
Photorespiration refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. The desired reaction is the addition of carbon dioxide to RuBP, a key step in the Calvin–Benson cycle, however 25% of reactions by RuBisCO instead add oxygen to RuBP, creating a product that cannot be used within the Calvin–Benson cycle; this process reduces the efficiency of photosynthesis reducing photosynthetic output by 25% in C3 plants. Photorespiration involves a complex network of enzyme reactions that exchange metabolites between chloroplasts, leaf peroxisomes and mitochondria; the oxygenation reaction of RuBisCO is a wasteful process because 3-phosphoglycerate is created at a reduced rate and higher metabolic cost compared with RuBP carboxylase activity. While photorespiratory carbon cycling results in the formation of G3P around 25% of carbon fixed by photorespiration is re-released as CO2 and nitrogen, as ammonia. Ammonia must be detoxified at a substantial cost to the cell.
Photorespiration incurs a direct cost of one ATP and one NADH. While it is common to refer to the entire process as photorespiration, technically the term refers only to the metabolic network which acts to rescue the products of the oxygenation reaction. Addition of molecular oxygen to ribulose-1,5-bisphosphate produces 3-phosphoglycerate and 2-phosphoglycolate. PGA is the normal product of carboxylation, productively enters the Calvin cycle. Phosphoglycolate, inhibits certain enzymes involved in photosynthetic carbon fixation, it is relatively difficult to recycle: in higher plants it is salvaged by a series of reactions in the peroxisome and again in the peroxisome where it is converted into glycerate. Glycerate by the same transporter that exports glycolate. A cost of 1 ATP is associated with conversion to 3-phosphoglycerate, within the chloroplast, free to re-enter the Calvin cycle. Several costs are associated with this metabolic pathway. Hydrogen peroxide is a dangerously strong oxidant which must be split into water and oxygen by the enzyme catalase.
The conversion of 2× 2Carbon glycine to 1 C3 serine in the mitochondria by the enzyme glycine-decarboxylase is a key step, which releases CO2, NH3, reduces NAD to NADH. Thus, 1 CO2 molecule is produced for every 2 molecules of O2; the assimilation of NH3 occurs via the GS-GOGAT cycle, at a cost of one ATP and one NADPH. Cyanobacteria have three possible pathways, they are unable to grow if all three pathways are knocked out, despite having a carbon concentrating mechanism that should reduce the rate of photorespiration. The oxidative photosynthetic carbon cycle reaction is catalyzed by RuBP oxygenase activity: RuBP + O2 → Phosphoglycolate + 3-phosphoglycerate + 2H+ During the catalysis by RuBisCO, an'activated' intermediate is formed in the RuBisCO active site; this intermediate is able to react with either CO2 or O2. It has been demonstrated that the specific shape of the RuBisCO active site acts to encourage reactions with CO2. Although there is a significant "failure" rate, this represents significant favouring of CO2, when the relative abundance of the two gases is taken into account: in the current atmosphere, O2 is 500 times more abundant, in solution O2 is 25 times more abundant than CO2.
The ability of RuBisCO to specify between the two gases is known as its selectivity factor, it varies between species, with angiosperms more efficient than other plants, but with little variation among the vascular plants. A suggested explanation into RuBisCO's inability to discriminate between CO2 and O2 is that it is an evolutionary relic: The early atmosphere in which primitive plants originated contained little oxygen, the early evolution of RuBisCO was not influenced by its ability to discriminate between O2 and CO2. Photorespiration rates are increased by: Factors which influence this include the atmospheric abundance of the two gases, the supply of the gases to the site of fixation, the length of the liquid phase. For example, when the stomata are closed to prevent water loss during drought: this limits the CO2 supply, while O2 production within the leaf will continue. In algae, it has been predicted that the increase in ambient CO2 concentrations predicted over the next 100 years may reduce the rate of photorespiration in most plants by around 50%.
At higher temperatures RuBisCO is less able to discriminate between CO2 and O2. This is. Increasing temperatures reduce the solubility of CO2, thus reducing the concentration of CO2 relative to O2 in the chloroplast. Certain species of plants or algae have mechanisms to reduce uptake of molecular oxygen by RuBisCO; these are referred to as Carbon Concentrating Mechanisms, as they increase the concentration of CO
A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separate from the other eukaryotic life kingdoms of plants and animals. A characteristic that places fungi in a different kingdom from plants and some protists is chitin in their cell walls. Similar to animals, fungi are heterotrophs. Fungi do not photosynthesize. Growth is their means of mobility, except for spores, which may travel through the water. Fungi are the principal decomposers in ecological systems; these and other differences place fungi in a single group of related organisms, named the Eumycota, which share a common ancestor, an interpretation, strongly supported by molecular phylogenetics. This fungal group oomycetes; the discipline of biology devoted to the study of fungi is known as mycology. In the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more related to animals than to plants.
Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and parasites, they may become noticeable when fruiting, either as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment, they have long been used in the form of mushrooms and truffles. Since the 1940s, fungi have been used for the production of antibiotics, more various enzymes produced by fungi are used industrially and in detergents. Fungi are used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, that are toxic to animals including humans; the fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies.
Fungi can break down manufactured materials and buildings, become significant pathogens of humans and other animals. Losses of crops due to fungal diseases or food spoilage can have a large impact on human food supplies and local economies; the fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, estimated at 2.2 million to 3.8 million species. Of these, only about 120,000 have been described, with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. Since the pioneering 18th and 19th century taxonomical works of Carl Linnaeus, Christian Hendrik Persoon, Elias Magnus Fries, fungi have been classified according to their morphology or physiology. Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, which has sometimes challenged the historical groupings based on morphology and other traits.
Phylogenetic studies published in the last decade have helped reshape the classification within Kingdom Fungi, divided into one subkingdom, seven phyla, ten subphyla. The English word fungus is directly adopted from the Latin fungus, used in the writings of Horace and Pliny; this in turn is derived from the Greek word sphongos, which refers to the macroscopic structures and morphology of mushrooms and molds. The word mycology is derived from the Greek logos, it denotes the scientific study of fungi. The Latin adjectival form of "mycology" appeared as early as 1796 in a book on the subject by Christiaan Hendrik Persoon; the word appeared in English as early as 1824 in a book by Robert Kaye Greville. In 1836 the English naturalist Miles Joseph Berkeley's publication The English Flora of Sir James Edward Smith, Vol. 5. Refers to mycology as the study of fungi. A group of all the fungi present in a particular area or geographic region is known as mycobiota, e.g. "the mycobiota of Ireland". Before the introduction of molecular methods for phylogenetic analysis, taxonomists considered fungi to be members of the plant kingdom because of similarities in lifestyle: both fungi and plants are immobile, have similarities in general morphology and growth habitat.
Like plants, fungi grow in soil and, in the case of mushrooms, form conspicuous fruit bodies, which sometimes resemble plants such as mosses. The fungi are now considered a separate kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago; some morphological and genetic features are shared with other organisms, while others are unique to the fungi separating them from the other kingdoms: Shared features: With other euka
Ecosystem ecology is the integrated study of living and non-living components of ecosystems and their interactions within an ecosystem framework. This science examines how ecosystems work and relates this to their components such as chemicals, soil and animals. Ecosystem ecology examines physical and biological structures and examines how these ecosystem characteristics interact with each other; this helps us understand how to maintain high quality water and economically viable commodity production. A major focus of ecosystem ecology is on functional processes, ecological mechanisms that maintain the structure and services produced by ecosystems; these include primary productivity and trophic interactions. Studies of ecosystem function have improved human understanding of sustainable production of forage, fiber and provision of water. Functional processes are mediated by regional-to-local level climate and management, thus ecosystem ecology provides a powerful framework for identifying ecological mechanisms that interact with global environmental problems global warming and degradation of surface water.
This example demonstrates several important aspects of ecosystems: Ecosystem boundaries are nebulous and may fluctuate in time Organisms within ecosystems are dependent on ecosystem level biological and physical processes Adjacent ecosystems interact and are interdependent for maintenance of community structure and functional processes that maintain productivity and biodiversityThese characteristics introduce practical problems into natural resource management. Who will manage which ecosystem? Will timber cutting in the forest degrade recreational fishing in the stream? These questions are difficult for land managers to address while the boundary between ecosystems remains unclear. We need better understanding of the interactions and interdependencies of these ecosystems and the processes that maintain them before we can begin to address these questions. Ecosystem ecology is an inherently interdisciplinary field of study. An individual ecosystem is composed of populations of organisms, interacting within communities, contributing to the cycling of nutrients and the flow of energy.
The ecosystem is the principal unit of study in ecosystem ecology. Population and physiological ecology provide many of the underlying biological mechanisms influencing ecosystems and the processes they maintain. Flowing of energy and cycling of matter at the ecosystem level are examined in ecosystem ecology, but, as a whole, this science is defined more by subject matter than by scale. Ecosystem ecology approaches organisms and abiotic pools of energy and nutrients as an integrated system which distinguishes it from associated sciences such as biogeochemistry. Biogeochemistry and hydrology focus on several fundamental ecosystem processes such as biologically mediated chemical cycling of nutrients and physical-biological cycling of water. Ecosystem ecology forms the mechanistic basis for regional or global processes encompassed by landscape-to-regional hydrology, global biogeochemistry, earth system science. Ecosystem ecology is philosophically and rooted in terrestrial ecology; the ecosystem concept has evolved during the last 100 years with important ideas developed by Frederic Clements, a botanist who argued for specific definitions of ecosystems and that physiological processes were responsible for their development and persistence.
Although most of Clements ecosystem definitions have been revised by Henry Gleason and Arthur Tansley, by contemporary ecologists, the idea that physiological processes are fundamental to ecosystem structure and function remains central to ecology. Work by Eugene Odum and Howard T. Odum quantified flows of energy and matter at the ecosystem level, thus documenting the general ideas proposed by Clements and his contemporary Charles Elton. In this model, energy flows through the whole system were dependent on biotic and abiotic interactions of each individual component. Work demonstrated that these interactions and flows applied to nutrient cycles, changed over the course of succession, held powerful controls over ecosystem productivity. Transfers of energy and nutrients are innate to ecological systems regardless of whether they are aquatic or terrestrial. Thus, ecosystem ecology has emerged from important biological studies of plants, terrestrial and marine ecosystems. Ecosystem services are ecologically mediated functional processes essential to sustaining healthy human societies.
Water provision and filtration, production of biomass in forestry and fisheries, removal of greenhouse gases such as carbon dioxide from the atmosphere are examples of ecosystem services essential to public health and economic opportunity. Nutrient cycling is a process fundamental to forest production. However, like most ecosystem processes, nutrient cycling is not an ecosystem characteristic which can be “dialed” to the most desirable level. Maximizing production in degraded systems is an overly simplistic solution to the complex problems of hunger and economic security. For instance, intensive fertilizer use in the midwestern United States has resulted in degraded fisheries in the Gulf of Mexico. Regrettably, a “Green Revolution” of intensive chemical fertilization has been recommended for agriculture in developed and developing countries; these strategies risk alteration of ecosystem processes that may be difficult to restore when applied at broad scales without adequate assessme
An ecosystem model is an abstract mathematical, representation of an ecological system, studied to better understand the real system. Using data gathered from the field, ecological relationships—such as the relation of sunlight and water availability to photosynthetic rate, or that between predator and prey populations—are derived, these are combined to form ecosystem models; these model systems are studied in order to make predictions about the dynamics of the real system. The study of inaccuracies in the model will lead to the generation of hypotheses about possible ecological relations that are not yet known or well understood. Models enable researchers to simulate large-scale experiments that would be too costly or unethical to perform on a real ecosystem, they enable the simulation of ecological processes over long periods of time. Ecosystem models have applications in a wide variety of disciplines, such as natural resource management and environmental health and wildlife conservation. Ecological modelling has been applied to archaeology with varying degrees of success, for example, combining with archaeological models to explain the diversity and mobility of stone tools.
There are two major types of ecological models, which are applied to different types of problems: analytic models and simulation / computational models. Analytic models are relatively simple systems, that can be described by a set of mathematical equations whose behavior is well-known. Simulation models on the other hand, use numerical techniques to solve problems for which analytic solutions are impractical or impossible. Simulation models tend to be more used, are considered more ecologically realistic, while analytic models are valued for their mathematical elegance and explanatory power. Ecopath is a powerful software system which uses simulation and computational methods to model marine ecosystems, it is used by marine and fisheries scientists as a tool for modelling and visualising the complex relationships that exist in real world marine ecosystems. The process of model design begins with a specification of the problem to be solved, the objectives for the model. Ecological systems are composed of an enormous number of biotic and abiotic factors that interact with each other in ways that are unpredictable, or so complex as to be impossible to incorporate into a computable model.
Because of this complexity, ecosystem models simplify the systems they are studying to a limited number of components that are well understood, deemed relevant to the problem that the model is intended to solve. The process of simplification reduces an ecosystem to a small number of state variables and mathematical functions that describe the nature of the relationships between them; the number of ecosystem components that are incorporated into the model is limited by aggregating similar processes and entities into functional groups that are treated as a unit. After establishing the components to be modeled and the relationships between them, another important factor in ecosystem model structure is the representation of space used. Models have ignored the confounding issue of space. However, for many ecological problems spatial dynamics are an important part of the problem, with different spatial environments leading to different outcomes. Spatially explicit models attempt to incorporate a heterogeneous spatial environment into the model.
A spatial model is one that has one or more state variables that are a function of space, or can be related to other spatial variables. After construction, models are validated to ensure that the results are acceptably accurate or realistic. One method is to test the model with multiple sets of data that are independent of the actual system being studied; this is important. Another method of validation is to compare the model's output with data collected from field observations. Researchers specify beforehand how much of a disparity they are willing to accept between parameters output by a model and those computed from field data. One of the earliest, most well-known, ecological models is the predator-prey model of Alfred J. Lotka and Vito Volterra; this model takes the form of a pair of ordinary differential equations, one representing a prey species, the other its predator. D X d t = α. X − β. X. Y d Y d t = γ. β. X. Y − δ. Y where, Volterra devised the model to explain fluctuations in fish and shark populations observed in the Adriatic Sea after the First World War.
However, the equations have subsequently been applied more generally. Although simple, they illustrate some of the salient features of ecological models: modelled biological populations experience growth, interact with other populations and suffer mortality. A credible, simple alternative to the Lotka-Volterra preda
Reproduction is the biological process by which new individual organisms – "offspring" – are produced from their "parents". Reproduction is a fundamental feature of all known life. There are two forms of reproduction: sexual. In asexual reproduction, an organism can reproduce without the involvement of another organism. Asexual reproduction is not limited to single-celled organisms; the cloning of an organism is a form of asexual reproduction. By asexual reproduction, an organism creates a genetically identical copy of itself; the evolution of sexual reproduction is a major puzzle for biologists. The two-fold cost of sexual reproduction is that only 50% of organisms reproduce and organisms only pass on 50% of their genes. Sexual reproduction requires the sexual interaction of two specialized organisms, called gametes, which contain half the number of chromosomes of normal cells and are created by meiosis, with a male fertilizing a female of the same species to create a fertilized zygote; this produces offspring organisms whose genetic characteristics are derived from those of the two parental organisms.
Asexual reproduction is a process by which organisms create genetically similar or identical copies of themselves without the contribution of genetic material from another organism. Bacteria divide asexually via binary fission; these organisms do not possess different sexes, they are capable of "splitting" themselves into two or more copies of themselves. Most plants have the ability to reproduce asexually and the ant species Mycocepurus smithii is thought to reproduce by asexual means; some species that are capable of reproducing asexually, like hydra and jellyfish, may reproduce sexually. For instance, most plants are capable of vegetative reproduction—reproduction without seeds or spores—but can reproduce sexually. Bacteria may exchange genetic information by conjugation. Other ways of asexual reproduction include parthenogenesis and spore formation that involves only mitosis. Parthenogenesis is the development of embryo or seed without fertilization by a male. Parthenogenesis occurs in some species, including lower plants and vertebrates.
It is sometimes used to describe reproduction modes in hermaphroditic species which can self-fertilize. Sexual reproduction is a biological process that creates a new organism by combining the genetic material of two organisms in a process that starts with meiosis, a specialized type of cell division; each of two parent organisms contributes half of the offspring's genetic makeup by creating haploid gametes. Most organisms form two different types of gametes. In these anisogamous species, the two sexes are referred to as female. In isogamous species, the gametes are similar or identical in form, but may have separable properties and may be given other different names. For example, in the green alga, Chlamydomonas reinhardtii, there are so-called "plus" and "minus" gametes. A few types of organisms, such as many fungi and the ciliate Paramecium aurelia, have more than two "sexes", called syngens. Most animals and plants reproduce sexually. Sexually reproducing organisms have different sets of genes for every trait.
Offspring inherit one allele for each trait from each parent. Thus, offspring have a combination of the parents' genes, it is believed that "the masking of deleterious alleles favors the evolution of a dominant diploid phase in organisms that alternate between haploid and diploid phases" where recombination occurs freely. Bryophytes reproduce sexually, but the larger and commonly-seen organisms are haploid and produce gametes; the gametes fuse to form a zygote which develops into a sporangium, which in turn produces haploid spores. The diploid stage is small and short-lived compared to the haploid stage, i.e. haploid dominance. The advantage of diploidy, only exists in the diploid life generation. Bryophytes retain sexual reproduction despite the fact that the haploid stage does not benefit from heterosis; this may be an indication that the sexual reproduction has advantages other than heterosis, such as genetic recombination between members of the species, allowing the expression of a wider range of traits and thus making the population more able to survive environmental variation.
Allogamy is the fertilization of the combination of gametes from two parents the ovum from one individual with the spermatozoa of another. Self-fertilization known as autogamy, occurs in hermaphroditic organisms where the two gametes fused in fertilization come from the same individual, e.g. many vascular plants, some foraminiferans, some ciliates. The term "autogamy" is sometimes substituted for autogamous pollination and describes self-pollination within the same flower, distinguished from geitonogamous pollination, transfer of pollen to a different flower on the same flowering plant, or within a single monoecious Gymnosperm plant. Mitosis and meiosis are types of cell division. Mitosis occurs in somatic cells. Mitosis The resultant number of cells in mitosis is t