Primary nutritional groups are groups of organisms, divided in relation to the nutrition mode according to the sources of energy and carbon, needed for living, growth and reproduction. The sources of energy can be light and organic or inorganic compounds; the sources of carbon can be of organic or inorganic origin. 
The terms aerobic respiration, anaerobic respiration and fermentation do not refer to primary nutritional groups, but simply reflect the different use of possible electron acceptors in particular organisms, such as O2 in aerobic respiration, or nitrate (NO3−), sulfate (SO42−) or fumarate in anaerobic respiration, or various metabolic intermediates in fermentation. Because all ATP-generating steps in fermentation involve modifications of metabolic intermediates instead of the use of an electron transport chain fermentation is often referred to as substrate-level phosphorylation.
Some bacteria can alternate phototrophy and chemotrophy, depending on availability of light.
The electrons from reducing equivalents (electron donors) are needed by both phototrophs and chemotrophs, to keep running reduction-oxidation reactions that transfer energy in the anabolic processes of ATP synthesis (in heterotrophs) or biosynthesis (in autotrophs). The electron donors are taken up from the environment.
Organotrophic organisms are often also heterotrophic, using organic compounds as sources of electrons and carbon at the same time. Similarly, lithotrophic organisms are often also autotrophic, using inorganic sources of electrons and CO2 as inorganic carbon source.
Some lithotrophic bacteria can utilize diverse sources of electrons, depending on availability of possible donors.
For example, plants use water as electron donor to biosynthesis, being lithotrophs. Animals use organic compounds as electron donors to synthesize ATP, being organotrophs (plants also do it, but this is not taken into account). Both use oxygen in respiration as electron acceptor, but this character is not used to define them as lithotrophs.
|Electron donor||organic compound||organo-|
|Carbon source||organic compound||hetero-|
A chemoorganoheterotrophic organism is one that requires organic substrates to get its carbon for growth and development, and that produces its energy from the oxidation and reduction (redox) of an organic compound. This group of organisms may be further subdivided according to what kind of organic substrate and compound they use. Decomposers are examples of Chemoorganoheterotrophs which obtain carbon and electron reactions from dead organic matter. Herbivores and carnivores are examples of organisms that obtain carbon and electron reactions from living organic matter.
Chemoorganotrophs are organisms which oxidize the chemical bonds in organic compounds as their energy source. Chemoorganotrophs also attain the carbon molecules that they need for cellular function from these organic compounds. The organic compounds that they oxidize include sugars (i.e. glucose), fats and proteins.
All animals are chemoheterotrophs (meaning they oxidize chemical compounds as a source of energy and carbon), as are fungi, protozoa, and some bacteria. The important differentiation amongst this group is that chemoorganotrophs oxidize only organic compounds while chemolithotrophs instead use inorganic compounds as a source of energy.
|Photoorganoheterotroph||Some bacteria (Rhodobacter)|
|Photolithoheterotroph||Purple non-sulfur bacteria and Green non-sulfur bacteria|
|Photolithoautotroph||Some bacteria (blue green algae), some eukaryotes (eukaryotic algae, land plants). Photosynthesis.|
|Chemoorganoheterotroph||Predatory, parasitic, and saprophytic prokaryotes. Some eukaryotes (heterotrophic protists, fungi, animals)|
|Chemoorganoautotroph||Some archaea (anaerobic methanotrophic archaea). Chemosynthesis.|
|Chemolithoheterotroph||Some bacteria (Oceanithermus profundus)|
|Chemolithoautotroph||Some bacteria (Nitrobacter), some archaea (Methanobacteria). Chemosynthesis.|
Some, usually unicellular, organisms can switch between different metabolic modes, for example between photoautotrophy, photoheterotrophy, and chemoheterotrophy in Chroococcales  Such mixotrophic organisms may dominate their habitat, due to their capability to use more resources than either photoautotrophic or organoheterotrophic organisms. 
All sorts of combinations may exist in nature. For example, most cyanobacteria are photoautotrophic, since they use light as an energy source, water as electron donor, and CO2 as a carbon source. Fungi are chemoorganotrophic since they use organic carbon as both an electron donor and carbon source. Eukaryotes are generally easy to categorise. All animals are heterotrophic, as are fungi. Plants are generally photoautotrophic. Some eukaryotic microorganisms, however, are not limited to just one nutritional mode. For example, some algae live photoautotrophically in the light, but shift to chemoorganotrophy in the dark. Even higher plants retained their ability to respire heterotrophically on the starch at night which had been synthesised phototrophically during the day.
Prokaryotes show a great diversity of nutritional categories. For example, purple sulfur bacteria and cyanobacteria are generally photoautotrophic whereas purple non-sulfur bacteria are photoorganotrophic. Some bacteria are limited to only one nutritional group, whereas others are facultative and switch from one mode to the other, depending on the nutrient sources available.
An autotroph or primary producer, is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) from simple substances present in its surroundings, generally using energy from light (photosynthesis) or inorganic chemical reactions (chemosynthesis). They are the producers in a food chain, such as plants on land or algae in water (in contrast to heterotrophs as consumers of autotrophs). They do not need a living source of energy or organic carbon. Autotrophs can reduce carbon dioxide to make organic compounds for biosynthesis and also create a store of chemical energy. Most autotrophs use water as the reducing agent, but some can use other hydrogen compounds such as hydrogen sulfide. Some autotrophs, such as green plants and algae, are phototrophs, meaning that they convert electromagnetic energy from sunlight into chemical energy in the form of reduced carbon.
Autotrophs can be photoautotrophs or chemoautotrophs. Phototrophs use light as an energy source, while chemotrophs use electron donors as a source of energy, whether from organic or inorganic sources; however in the case of autotrophs, these electron donors come from inorganic chemical sources. Such chemotrophs are lithotrophs. Lithotrophs use inorganic compounds, such as hydrogen sulfide, elemental sulfur, ammonium and ferrous iron, as reducing agents for biosynthesis and chemical energy storage. Photoautotrophs and lithoautotrophs use a portion of the ATP produced during photosynthesis or the oxidation of inorganic compounds to reduce NADP+ to NADPH to form organic compounds.Biomass (ecology)
The biomass is the mass of living biological organisms in a given area or ecosystem at a given time. Biomass can refer to species biomass, which is the mass of one or more species, or to community biomass, which is the mass of all species in the community. It can include microorganisms, plants or animals. The mass can be expressed as the average mass per unit area, or as the total mass in the community.
How biomass is measured depends on why it is being measured. Sometimes, the biomass is regarded as the natural mass of organisms in situ, just as they are. For example, in a salmon fishery, the salmon biomass might be regarded as the total wet weight the salmon would have if they were taken out of the water. In other contexts, biomass can be measured in terms of the dried organic mass, so perhaps only 30% of the actual weight might count, the rest being water. For other purposes, only biological tissues count, and teeth, bones and shells are excluded. In some applications, biomass is measured as the mass of organically bound carbon (C) that is present.
The total live biomass on Earth is about 550–560 billion tonnes C, and the total annual primary production of biomass is just over 100 billion tonnes C/yr. The total live biomass of bacteria may be as much as that of plants and animals or may be much less. The total number of DNA base pairs on Earth, as a possible approximation of global biodiversity, is estimated at (5.3±3.6)×1037, and weighs 50 billion tonnes. In comparison, the total mass of the biosphere has been estimated to be as much as 4×1012 tonnes of carbon.Cascade effect (ecology)
An ecological cascade effect is a series of secondary extinctions that is triggered by the primary extinction of a key species in an ecosystem. Secondary extinctions are likely to occur when the threatened species are: dependent on a few specific food sources, mutualistic (dependent on the key species in some way), or forced to coexist with an invasive species that is introduced to the ecosystem. Species introductions to a foreign ecosystem can often devastate entire communities, and even entire ecosystems. These exotic species monopolize the ecosystem's resources, and since they have no natural predators to decrease their growth, they are able to increase indefinitely. Olsen et al. showed that exotic species have caused lake and estuary ecosystems to go through cascade effects due to loss of algae, crayfish, mollusks, fish, amphibians, and birds. However, the principal cause of cascade effects is the loss of top predators as the key species. As a result of this loss, a dramatic increase (ecological release) of prey species occurs. The prey is then able to overexploit its own food resources, until the population numbers decrease in abundance, which can lead to extinction. When the prey's food resources disappear, they starve and may go extinct as well. If the prey species is herbivorous, then their initial release and exploitation of the plants may result in a loss of plant biodiversity in the area. If other organisms in the ecosystem also depend upon these plants as food resources, then these species may go extinct as well. An example of the cascade effect caused by the loss of a top predator is apparent in tropical forests. When hunters cause local extinctions of top predators, the predators' prey's population numbers increase, causing an overexploitation of a food resource and a cascade effect of species loss. Recent studies have been performed on approaches to mitigate extinction cascades in food-web networks.Chemosynthesis
In biochemistry, chemosynthesis is the biological conversion of one or more carbon-containing molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic compounds (e.g., hydrogen gas, hydrogen sulfide) or methane as a source of energy, rather than sunlight, as in photosynthesis. Chemoautotrophs, organisms that obtain carbon through chemosynthesis, are phylogenetically diverse, but also groups that include conspicuous or biogeochemically-important taxa include the sulfur-oxidizing gamma and epsilon proteobacteria, the Aquificae, the methanogenic archaea and the neutrophilic iron-oxidizing bacteria.
Many microorganisms in dark regions of the oceans use chemosynthesis to produce biomass from single carbon molecules. Two categories can be distinguished. In the rare sites at which hydrogen molecules (H2) are available, the energy available from the reaction between CO2 and H2 (leading to production of methane, CH4) can be large enough to drive the production of biomass. Alternatively, in most oceanic environments, energy for chemosynthesis derives from reactions in which substances such as hydrogen sulfide or ammonia are oxidized. This may occur with or without the presence of oxygen.
Many chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic associations between chemosynthesizers and respiring heterotrophs are quite common. Large populations of animals can be supported by chemosynthetic secondary production at hydrothermal vents, methane clathrates, cold seeps, whale falls, and isolated cave water.
It has been hypothesized that chemosynthesis may support life below the surface of Mars, Jupiter's moon Europa, and other planets. Chemosynthesis may have also been the first type of metabolism that evolved on Earth, leading the way for cellular respiration and photosynthesis to develop later.Energy flow (ecology)
In ecology, energy flow, also called the calorific flow, refers to the flow of energy through a food chain, and is the focus of study in ecological energetics. In an ecosystem, ecologists seek to quantify the relative importance of different component species and feeding relationships.
A general energy flow scenario follows:
Solar energy is fixed by the photoautotrophs, called primary producers, like green plants. Primary consumers absorb most of the stored energy in the plant through digestion, and transform it into the form of energy they need, such as adenosine triphosphate (ATP), through respiration. A part of the energy received by primary consumers, herbivores, is converted to body heat (an effect of respiration), which is radiated away and lost from the system. The loss of energy through body heat is far greater in warm-blooded animals, which must eat much more frequently than those that are cold-blooded. Energy loss also occurs in the expulsion of undigested food (egesta) by excretion or regurgitation.
Secondary consumers, carnivores, then consume the primary consumers, although omnivores also consume primary producers. Energy that had been used by the primary consumers for growth and storage is thus absorbed into the secondary consumers through the process of digestion. As with primary consumers, secondary consumers convert this energy into a more suitable form (ATP) during respiration. Again, some energy is lost from the system, since energy which the primary consumers had used for respiration and regulation of body temperature cannot be utilized by the secondary consumers.
Tertiary consumers, which may or may not be apex predators, then consume the secondary consumers, with some energy passed on and some lost, as with the lower levels of the food chain.
A final link in the food chain are decomposers which break down the organic matter of the tertiary consumers (or whichever consumer is at the top of the chain) and release nutrients into the soil. They also break down plants, herbivores and carnivores that were not eaten by organisms higher on the food chain, as well as the undigested food that is excreted by herbivores and carnivores. Saprotrophic bacteria and fungi are decomposers, and play a pivotal role in the nitrogen and carbon cycles.The energy is passed on from trophic level to trophic level and each time about 90% of the energy is lost, with some being lost as heat into the environment (an effect of respiration) and some being lost as incompletely digested food (egesta). Therefore, primary consumers get about 10% of the energy produced by autotrophs, while secondary consumers get 1% and tertiary consumers get 0.1%. This means the top consumer of a food chain receives the least energy, as a lot of the food chain's energy has been lost between trophic levels. This loss of energy at each level limits typical food chains to only four to six links.Index of biology articles
Biology is the study of life and its processes. Biologists study all aspects of living things, including all of the many life forms on earth and the processes in them that enable life. These basic processes include the harnessing of energy, the synthesis and duplication of the materials that make up the body, the reproduction of the organism and many other functions. Biology, along with chemistry and physics is one of the major disciplines of natural science.Invasive species
An invasive species is a species that is not native to a specific location (an introduced species), and that has a tendency to spread to a degree believed to cause damage to the environment, human economy or human health.The term as most often used applies to introduced species that adversely affect the habitats and bioregions they invade economically, environmentally, or ecologically. Such species may be either plants or animals and may disrupt by dominating a region, wilderness areas, particular habitats, or wildland–urban interface land from loss of natural controls (such as predators or herbivores). This includes plant species labeled as exotic pest plants and invasive exotics growing in native plant communities. The European Union defines "Invasive Alien Species" as those that are, firstly, outside their natural distribution area, and secondly, threaten biological diversity. The term is also used by land managers, botanists, researchers, horticulturalists, conservationists, and the public for noxious weeds.The term "invasive" is often poorly defined or very subjective and some broaden the term to include indigenous or "native" species, that have colonized natural areas - for example deer considered by some to be overpopulating their native zones and adjacent suburban gardens in the Northeastern and Pacific Coast regions of the United States.The definition of "native" is also sometimes controversial. For example, the ancestors of Equus ferus (modern horses) evolved in North America and radiated to Eurasia before becoming locally extinct. Upon returning to North America in 1493 during their hominid-assisted migration, it is debatable as to whether they were native or exotic to the continent of their evolutionary ancestors.Notable examples of invasive plant species include The kudzu vine, Andean pampas grass, and yellow starthistle. Animal examples include the New Zealand mud snail, feral pigs, European rabbits, grey squirrels, domestic cats, carp and ferrets.Invasion of long-established ecosystems by organisms from distant bio-regions is a natural phenomenon, but has been accelerated massively by humans, from their earliest migrations though to the age of discovery, and now international trade.Lipogenesis
Lipogenesis is the metabolic process through which acetyl-CoA is converted to triglyceride for storage in fat. The triglycerides in fat are packaged within cytoplasmic lipid droplets. The process begins with acetyl-CoA, which is an organic compound used to transfer energy from metabolism of carbohydrates, fatty acids, and ethanol. Through the citric acid cycle, acetyl-CoA is broken down to produce ATP, which is then an energy source for many metabolic processes, including protein synthesis and muscle contraction.
Lipogenesis encompasses both fatty acid and triglyceride synthesis, with the latter being the process by which fatty acids are esterified to glycerol before being packaged into very-low-density lipoprotein (VLDL). Fatty acids are produced in the cytoplasm of cells by repeatedly adding two-carbon units to acetyl-CoA. Triglycerides, on the other hand, are produced in the endoplasmic reticulum of cells by bonding three fatty acid molecules to a glycerol molecule. Both processes take place mainly in liver and adipose tissue. After being packaged into VLDL, the resulting lipoprotein is then secreted by the liver directly into the blood for delivery to peripheral tissues.Mesopredator release hypothesis
The mesopredator release hypothesis is an ecological theory used to describe the interrelated population dynamics between apex predators and mesopredators within an ecosystem, such that a collapsing population of the former results in dramatically-increased populations of the latter. This hypothesis describes the phenomenon of trophic cascade in specific terrestrial communities.
A mesopredator is a medium-sized, middle trophic level predator, which both preys and is preyed upon. Examples are raccoons, skunks, snakes, cownose rays, and small sharks.Metabolism
Metabolism (, from Greek: μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. (The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary metabolism or intermediate metabolism).
Metabolic reactions may be categorized as catabolic - the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration); or anabolic - the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts - they allow a reaction to proceed more rapidly - and they also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.
The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions.
A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants. These similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention because of their efficacy.Mixotroph
A mixotroph is an organism that can use a mix of different sources of energy and carbon, instead of having a single trophic mode on the continuum from complete autotrophy at one end to heterotrophy at the other. It is estimated that mixotrophs comprise more than half of all microscopic plankton. There are two types of eukaryotic mixotrophs; those who have their own chloroplasts, and those with endosymbionts and others who require them through kleptoplasty or by enslaving the entire phototrophic cell.Possible combinations are photo- and chemotrophy, litho- and organotrophy, auto- and heterotrophy or other combinations of these. Mixotrophs can be either eukaryotic or prokaryotic. They can take advantage of different environmental conditions.If a trophic mode is obligate, then it is always necessary for sustaining growth and maintenance; if facultative, it can be used as a supplemental source. Some organisms have incomplete Calvin cycles, so they are incapable of fixing carbon dioxide and must use organic carbon sources.Organotroph
An organotroph is an organism that obtains hydrogen or electrons from organic substrates. This term is used in microbiology to classify and describe organisms based on how they obtain electrons for their respiration processes. Some organotrophs such as animals and many bacteria, are also heterotrophs. Organotrophs can be either anaerobic or aerobic.
Antonym: Lithotroph, Adjective: Organotrophic.Outline of biology
Biology – The natural science that involves the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy.Photoheterotroph
Photoheterotrophs (Gk: photo = light, hetero = (an)other, troph = nourishment) are heterotrophic phototrophs—that is, they are organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source. Consequently, they use organic compounds from the environment to satisfy their carbon requirements; these compounds include carbohydrates, fatty acids, and alcohols. Examples of photoheterotrophic organisms include purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria. Recent research has indicated that the oriental hornet and some aphids may be able to use light to supplement their energy supply.Phototroph
Phototrophs (Gr: φῶς, φωτός = light, τροϕή = nourishment) are the organisms that carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs often photosynthesize: they anabolically convert carbon dioxide into organic material to be utilized structurally, functionally, or as a source for later catabolic processes (e.g. in the form of starches, sugars and fats). All phototrophs either use electron transport chains or direct proton pumping to establish an electro-chemical gradient which is utilized by ATP synthase, to provide the molecular energy currency for the cell. Phototrophs can be either autotrophs or heterotrophs. As their electron and hydrogen donors are inorganic compounds [Na2S2O3 (PSB) and H2S (GSB)] they can be also called as lithotrophs, and so, some photoautotrophs are also called photolithoautotrophs. Examples of phototroph organisms: Rhodobacter capsulatus, Chromatium, Chlorobium etc.Productivity (ecology)
In ecology, productivity refers to the rate of generation of biomass in an ecosystem. It is usually expressed in units of mass per unit surface (or volume) per unit time, for instance grams per square metre per day (g m−2 d−1). The mass unit may relate to dry matter or to the mass of carbon generated. Productivity of autotrophs such as plants is called primary productivity, while that of heterotrophs such as animals is called secondary productivity.Pyruvate carboxylase
Pyruvate carboxylase (PC) encoded by the gene PC is an enzyme of the ligase class that catalyzes (depending on the species) the physiologically irreversible carboxylation of pyruvate to form oxaloacetate (OAA).
The reaction it catalyzes is:
pyruvate + HCO−3 + ATP → oxaloacetate + ADP + PIt is an important anaplerotic reaction that creates oxaloacetate from pyruvate. The enzyme is a mitochondrial protein containing a biotin prosthetic group, requiring magnesium or manganese and acetyl CoA.
Pyruvate carboxylase was first discovered in 1959 at Case Western Reserve University by M. F. Utter and D. B. Keech. Since then it has been found in a wide variety of prokaryotes and eukaryotes including fungi, bacteria, plants, and animals. In mammals, PC plays a crucial role in gluconeogenesis and lipogenesis, in the biosynthesis of neurotransmitters, and in glucose-induced insulin secretion by pancreatic islets. Oxaloacetate produced by PC is an important intermediate, which is used in these biosynthetic pathways. In mammals, PC is expressed in a tissue-specific manner, with its activity found to be highest in the liver and kidney (gluconeogenic tissues), in adipose tissue and lactating mammary gland (lipogenic tissues), and in pancreatic islets. Activity is moderate in brain, heart and adrenal gland, and least in white blood cells and skin fibroblasts.Sustainable gardening
Sustainable gardening includes the more specific sustainable landscapes, sustainable landscape design, sustainable landscaping, sustainable landscape architecture, resulting in sustainable sites. It comprises a disparate group of horticultural interests that can share the aims and objectives associated with the international post-1980s sustainable development and sustainability programs developed to address the fact that humans are now using natural biophysical resources faster than they can be replenished by nature.Included within this compass are those home gardeners, and members of the landscape and nursery industries, and municipal authorities, that integrate environmental, social, and economic factors to create a more sustainable future.
Organic gardening and the use of native plants are integral to sustainable gardening.