Encyclopedia of Global Resources part 55 pps

Genetic diversity Category: Ecological resources Genetic diversity includes the inherited traits encoded in the deoxyribonucleic acid (DNA) of all living organisms and can be examined on four levels: among species, among populations, within populations, and within individuals. Populations with higher levels of diversity are better able to adapt to changes in the envi- ronment, are more resistant to the deleterious effects of inbreeding, and provide more opportunities for animal and plant breeders to cultivate types or varieties with qualities desired by humans. Background Genetic diversity is the most fundamental level of biological diversity because genetic material is responsi- ble for the variety of life. For new species to form, genetic material must change. Changes in the inherited properties of populations occur deterministically through gene flow (mating between individual organisms representing formerly separated populations) and through natural or artificial selection (which occurs when some types of individuals breed more successfully than others). Change can also occur randomly through mutations or genetic drift (when the relative proportions of genes change by chance in small populations). Populations with higher levels of diversity tend to do better—to have more survival options—as surroundings change than do populations (particularly smaller ones) with lower levels of genetic diversity. Preservation Efforts Conservation efforts directed at maintaining genetic diversity involve both germ plasm preservation (germ plasm kept in a steady state for periods of time) and germ plasm conservation (germ plasm kept in a natural, evolving state). The former usually involves ex situ laboratory techniques in which genetic resources are removed from their natural habitats. They include seminatural strategies such as botanical gardens, ar- boretums, nurseries, zoos, farms, aquariums, and captive fisheries as well as completely artificial methods such as seed reserves or “banks,” microbial cultures (preserving bacteria, fungi, viruses, and other micro - organisms), tissue cultures of parts of plants and ani - mals (including sperm storage), and gene libraries (involving storage and replication of partial segments of plant or animal DNA). Conservation areas are the preferred in situ (at the natural or original place) means of protecting genetic resources. Ideally these include preserving the number and relative proportions of species and the genetic diversity they represent, the physical features of the habitat, and all ecosystem processes. It is not always enough, however, to maintain the ecosystem which the threatened species inhabits. It is sometimes necessary to take an active interventionist position in order to save a species. Controversial strategies can include reintroduction of captive species into the wild, sometimes after they have been genetically manipulated. Direct management of the ecosystem may also be attempted either by lessening human exploitation and interference or by reducing the number of natural predators or competitors. However, management of a specific conservation area varies in terms of what is valued and how preservation is accomplished. Crop Diversity One area of keen interest that illustrates the issues in- volved with the preservation of any kind of genetic diversity is how to preserve crop germ plasm. Largely conserved in gene banks, crop germ plasm was historically protected by farmers who selected for success in differing environments and other useful traits. Tradi- tionally cultivated varieties (landraces) diversified as people spread into new areas. Colonial expansion produced new varieties as farmers adapted to new conditions and previously separated plant species in- terbred; other species were lost when some societies declined and disappeared. By the early 1900’s, field botanists and agronomists were expressing concern about the rapidly escalating loss of traditionally cultivated varieties. This loss accel- erated after the 1940’s as high-yielding hybrids of ce- real and vegetable crops replaced local landraces. Wild relatives of these landraces are also disappearing as their habitats are destroyed through human activity. Gene banks preserve both kinds of plants because, as argued by Nikolai Ivanovich Vavilov in 1926, crop plant improvement can best be accomplished by taking advantage of these preserved genetic stocks. Vavilov also noted that genetic variation for most cultivated species was concentrated in specific regions, his “centers of diversity,” most of which are regions where crop species originated. The vulnerability to parasites and climate of an agri - 488 • Genetic diversity Global Resources culture that relies on one or a few variet - ies of crops necessitates the maintenance of adequate reserves of genetic material for breeding. In addition to the preservation of species known to be useful, many people advocate preservation of wild species for aesthetic reasons as well as for their unknown future potential. The Maintenance of Productivity Farmers in developed nations change crop varieties every four to ten years in order to maintain consistent levels of food production. This necessitates an on- going search for new breeds with higher yields and an ability to withstand several environmental challenges, including re- sistance to multiple pests and drought. Over time, older varieties either mutate, become less popular at the marketplace, or are unable to adapt to new conditions. However, farmers from developing nations are not always able to take advantage of the new breeds or afford the expensive support systems, including chemical fertilizers. More- over,not all types of cropshavebenefitedequallyfrom conservation efforts. Another tension between the world’s developing and developed nations concerns ownership of genetic diversity. The Convention on Biological Diver- sity, signed by 167 nations in 1992, states that genetic materials are under the sovereign control of the countries in which they are found. This policy is particularly controversial regarding medicinal plants, because “biodiversity prospecting” for new drugs has economically benefited either individuals or corporations based in the developed countries. Joan C. Stevenson Further Reading Carroll, Scott P., and Charles W. Fox, eds. Conservation Biology: Evolution in Action. New York: Oxford Uni- versity Press, 2008. Frankham, Richard, Jonathan D. Ballou, and David A. Briscoe. Introduction to Conservation Genetics. Line drawings by Karina H. McInness. New York: Cam- bridge University Press, 2002. _______. A Primer of Conservation Genetics. Line draw - ings by Karina H. McInness. New York: Cambridge University Press, 2004. Hawkes, J. G. The Diversity of Crop Plants. Cambridge, Mass.: Harvard University Press, 1983. Hunter, Malcolm L., Jr., and James P. Gibbs. Funda- mentals of Conservation Biology. 3d ed. Malden, Mass.: Blackwell, 2007. Lowe, Andrew, Stephen Harris, and Paul Ashton. Eco- logical Genetics: Design, Analysis, and Application. Malden, Mass.: Blackwell, 2004. Orians, Gordon H., et al., eds. The Preservation and Val- uation of Biological Resources. Seattle: University of Washington Press, 1990. Plucknett, Donald L., et al. Gene Banks and the World’s Food. Princeton, N.J.: Princeton University Press, 1987. Van der Werf, Julius, Hans-Ulrich Graser, Richard Frankham, and Cedric Gondro, eds. Adaptation and Fitness in Animal Populations: Evolutionary and Breeding Perspectives on Genetic Resource Management. London: Springer, 2009. See also: Animal breeding; Biodiversity; Biological invasions; Biotechnology; Conservation; Conserva- tion biology; Fisheries; Forest management; Genetic prospecting; Genetic resources; Monoculture agriculture; Plant domestication and breeding; Plants as a medical resource; Species loss; United Nations Con - vention on Biological Diversity. Global Resources Genetic diversity • 489 The Hawaiianmonkseal is anendangered species partly because ofitslevel of genetic diversity, which is the lowest among all animals studied. (©Henry Fu/Dreams- time.com) Genetic engineering. See Animal breeding; Biotechnology; Plant domestication and breeding Genetic prospecting Categories: Obtaining and using resources; scientific disciplines As the world’s population continues to grow, the search expands for plant and animal species whose genes can lead to new medicines, better crops, and products that make daily life easier. If not undertaken with great care, however, this twenty-first century “gold rush” has the potential to wreak havoc on many of the most frag- ile ecosystems of the world as well as on the indigenous populations that rely upon them. Definition There is no universally agreed upon definition for the term “genetic prospecting” or the synonym “biological prospecting (bioprospecting).” However, the United Nations University Institute for Advanced Studies defines these terms as “the collection, research, and use of biological and/or genetic material for purposes of applying the knowledge derived there from for scientific and/or commercial purposes. Bioprospecting entails the search for economically valuable genetic and biochemical resources from nature.” Overview Estimates indicate that more than 80 percent of the world’spopulationusestraditionalmedicinesderived from local plants or animals for basic medical needs. In addition, at least 25 percent of prescription drugs used in the United States contain at least one active ingredient that has been derived from genetic prospecting. In fact, the creation of new medicinal and agricultural products from living materials is more than a $2-billion-per-year industry. Much of the information about which plants or animals may yield genetic opportunities for medicine has come from indigenous knowledge of natural resources. In fact, most of the plants that have been prospected have come from the world’s great rain for - ests, especially those of the Southern Hemisphere, and have been identified by the indigenous peoples who inhabit these areas. It should be noted that the term “genetic prospecting” may also be used to de- scribe the search for compounds of promise in plants or animals that have never been used for medicines or cures by indigenous cultures. According to the report of the United Nations Convention on Biological Diversity (2004), many pros- pectors are now turning their attention to the world’s remaining frontiers, including the Antarctic ice fields, hydrothermal vents deep in the world’s oceans, and the deep seafloor. The unique genes of many extrem- ophiles (organisms that live in extreme conditions) are expected to yield great opportunities for new medicines well into the second half of the twenty-first century. A real concern that has been partially addressed by the United Nations in the landmark 1993 Conven- tion on Biological Diversity is that of “biopiracy,” “genetic piracy,” or “biocolonialism.” These terms refer to the appropriation of genetic materials without the express informed consent of the indigenous peoples, that landowners, or the appropriate government. For instance, making use of indigenous knowledge of the healing powers of a particular plant to find, replicate, and market a new drug without com- pensating those whose knowledge was the foundation of the work is a form of genetic piracy. For this reason, many countries in the tropical belt have written strict laws on genetic prospecting, including appropriate consent of, and compensation to, the host nation and its people. Kerry L. Cheesman See also: Genetic resources; Plants as a medical resource; Resources as a medium of economic exchange; Resources as a source of international conflict; United Nations Convention on Biological Diversity. Genetic resources Category: Plant and animal resources The raw material used in biotechnology is the genetic code found within the DNA of living organisms. While not viewed as a natural resource historically, genetic material has, with the advent of modern biotechnology, become a commodity that not only can be manipulated 490 • Genetic prospecting Global Resources to improve agricultural yield but also can be used as a source by which to produce novel pharmaceutical or chemical products. Background Biotechnology can be defined as the use of living organisms to achieve human goals; in this sense, humans have used biotechnology throughout history to provide themselves with such things as food, cloth- ing, shelter, cosmetics, and medicine. Starting around 10,000 b.c.e., humans began to alter the genetic makeup of the plants and animals that they used by ar- tificially selecting certain traits in the crops and live- stock that they were breeding. Because farmers lived in different areas around the world with varying environmental conditions, the varieties of domesticated organism that eventually developed initially preserved what is known as “genetic diversity.” Every organism on Earth has a particular genome, its entire set of DNA, which is specific to that particular living thing. Therefore, genetic diversity is at its greatest when the widest variety of organisms available are in existence in a particular area. The term “biodiversity” refers to the number of different species (or other taxonomi- cal units) that inhabit a given ecosystem or geograph- ical area. Genetic Erosion of Plants and Animals A process known as “genetic erosion” decreases the biodiversity of cultivated areas. In this process, local species are lost from an area as they are replaced by less diverse, domesticated varieties. Human activities such as urbanization, the replacement of traditional agriculture with more modern techniques, and the introduction of high-yield varieties of crops have been blamed for such erosion of genetic resources. One example can be seen in the crops that are utilized for food in modern society. Among the 300,000 or so flowering plants that have been characterized to date, estimates indicate that humankind has used around 7,000 of these throughout history to satisfy basic human needs. However, only 30 of these account for 95 percent of the world’s dietary calories, less than 10 account for 75 percent, and a mere 3 (corn, wheat, and rice) make up nearly 50 percent of the caloric intake of humankind. Not only has the number of different crops decreased over time, but also the variety of crop species has declined. Such a narrow genetic base of crops puts the food supply at risk from pests or diseases that affect a specific type of crop. Apparently, humans, in their eagerness to improve crop varieties, have somehow robbed the Earth of a portion of the genetic diversity that has taken millions of years to develop. Traditional subsis- tence agriculture, although it may have lacked the productivity of modern methods, actually increased the likelihood of a reasonable level of production by preserving the genetic diversity of the crops that were being grown. This is not to saythatusingplantsasafoodsource is their only economically viable use. Terrestrial plants have long been used as medicine or for other chemical applications. The recent loss of plant biodiversity is alarming for this reason also. Possibly, some undis- covered cure for a particular disease is at risk from disappearing permanently from the Earth, if it has not done so already.Ofthe remaining flowering plants on Earth, estimates indicate that one in four could become extinct by 2050. Compounding the problem, most of the world’s biodiversity is located in geo- graphically or politically unstable areas, namely in tropical or subtropical developing countries. A full two-thirds of all plant species known to humankind are located in the tropics; about 60,000 species are found in Latin America alone. Animals have also served as an important source of food and medicine throughout history and have also been submitted to artificial genetic selection, along with accompanying genetic erosion. Marine inverte- brates, in particular, have been investigated as a source of molecular compounds with medicinal properties. It has also been during more recent times that the importance of microorganisms in producing ther- apeutically relevant products has become known. While the full extent of microbial diversity remains unclear and bacterialdiversityinparticularappearsto follow different biogeographical patterns from those found for plants and animals, it is evident that many natural habitats that may harbor medicinally relevant microbes are disappearing rapidly. The worldwide loss of biodiversity comprises all types of living organisms, including plants, animals, fungi, protists, and bacteria. Paradigm Shift In the 1990’s, a significant shift occurred in the way that genetic resources were viewed as well as how their ownership was determined. Before this time, genetic resources were considered to be a common heritage of humankind andweretobetreated sothattheywere Global Resources Genetic resources • 491 used to the benefit of all. The only problem with this notion is that it gave host countries little economic incentive for conservation. Another reason for this paradigm shift was a revolution in biology which had taken place in the decade that preceded the change. Biological tools that allowed for genetic engineering had been developed during this time, thereby ex- panding the number of organisms amenable to biotechnology. These included those that could be artifi- cially selected for particular traits and bred with one another to any organism from which DNA could be extracted. This extracted DNA could then be intro- duced into a number of living vectors that may have been completely unrelated to the original source of genetic material. This new technology not only en - sured that virtually any organism could be used as a source of genetic innovation with a potential for prac - tical application but also decreased the cost of work- ing with genetic material to a level at which many more laboratories could afford to participate in genetic engineering efforts. The United Nations Convention on Biological Di- versity (CBD) was signed at a meeting in Rio de Ja- neiro, Brazil, in 1992 and went into effect the follow- ing year. The CBD affirmed the sovereign right of individual nations to their biodiversity and gave them a means by whichtoregulate access to their genetic resources, creating the stipulation that entities such as bioengineering firms secure informed written consent before collecting genetic material from any particular country. The export of a seed, microbe, or other plant- or animal-derived sample has been com- pared to exporting a verysmallchemicalfactory,com- plete with blueprints and its own source of venture capital. While most countries would not allow this to happen using conventional technology, prior to 1992 this had been the norm for biological goods. Despite the establishment of the CBD, a number of potential problems concerning genetic resources re- main. Developing countries are leery of corporations from developed nations that may, given the opportu- nity, engage in biopiracy. This includes taking advantage of indigenous knowledge and local technologies without providing adequate compensation. Genetic material is similar to electronic media in that it can be reproduced easily and relatively inexpensively, a fact that makes enforcing antipiracy legislation difficult. Conditions of contracts and changes in patent legislation must be followed closely by developing nations to ensure that undue control is not handed to foreign in- vestors. In addition, just because a country as a whole re- ceives compensation for a particular genetic resource does not mean that a given region of that country will see any economic benefit. Two examples from the United States (which predate the CBD) include the cancer drug Taxol and Taq polymerase, an enzyme used in genetic engineering. These products were discovered respectively in Pacific yew bark from the Pa- cific Northwest and from hot springs in Yellowstone National Park. Despite the fact that both of these products have produced millions of dollars worth of profits, the regions of the country where they were first discovered ended up receiving little or no finan - cial benefit. This somewhat flawed system of compen - sation and financial incentive is not expected to work 492 • Genetic resources Global Resources A genetics professor at the Nova Southeastern University Oceano- graphic Center transfers fish samples into a test tube for purposes of genetic research. (Joe Rimkus, Jr./MCT/Landov) much better in developing countries. Historically, even when indigenous knowledge was used to develop a specific product, indigenous peoples often re- ceived little or no benefit from sharing their knowledge. Conservation Efforts The same year the CBD was signed, an interdepart- mental effort in the U.S. government created the In- ternational Conservation of Biodiversity Groups (ICBG) initiative. The objectives of the ICBG were to establish an inventory of species that have been used in traditional medicine, identify lead compounds for the treatment of human disease from this group, con- duct economic assessments of species in the host country, establish study plots in developing countries to study changes in rain-forest ecology, and train local scientists in the principles of drug-development and biodiversity conservation. Conservation of genetic resources typically fits into one of two categories, in situ or ex situ: The former is Latin for “in the place,” and the latter means “out of the place.” In situ conservation takes place on farms, for agricultural crops, or in natural reserves,forwildplants.Thistype of conservation preserves the evolutionary dynamics of the species in question. Ex situ conservation usually involves storing samples, called accessions, of seeds or vegeta- tive material for plants in what are known as gene banks. This type of conservation can also be applied to animals, where embryos or germ cells are stored frozen. This latter conservation technique has the disadvantage of being able to preserve only a small amount of the genetic diversity present in a given population but often plays a critical role in the preservation of many varieties of organisms, particularly those which are endangered or have already become extinct. Screening for Compounds Biological organisms of interest to the pharmaceutical or chemical industries are typically those which produce small organic compounds known as secondary metabolites. Some hypothesize that these compounds serve either defensive or signaling roles in the cell: Plants and animals use these compounds to de- fend themselves from potential predators, and microbes usethesetodefendthemselvesfrom and signal to the other organisms that surround them. Overall, more than one-half of the best-selling pharmaceuti - cals in use are derived from such natural products. Bioprospecting is the act of systematically searching through given genetic resources for compounds that may have a commercial application. Scientists are thus screening large numbers of extracts from plants, microbes, and marine organisms for secondary metabolites containing antifungal, antiviral, or antitu- mor activities. There are a number of hurdles that must be over- come before a specific activity can be gleaned from a particular natural product. Because most natural products consist of mixtures of crude extracts, a certain degree of purification must take place before a lead compound can be tested for a desired application. “Time-to-lead” is a term that refers to the degree of purification and structural characterization that is necessary before a sample can be effectively assayed for a given activity. Another issue is the continued supply of a given natural product. In the past several de- cades, techniques for the extraction, fractionation, and chemical identification of secondary metabolites have become more routine and less expensive to per- form. Before this was the case, it was often necessary to re-collectsamplesofparticularnaturalproducts for use in large-scale purifications. Frequently, develop- ers would then discover that it was impossible to re- produce the originally detected activity. Advances in genetic engineering as well as cell culture techniques have largely eliminated the need to re-collect an original sample. These advances actually make it more challenging for a supplier country to adequately charge for the use of a natural resource, because they can no longer rely on the need for re-collection of biological material to take place. This leaves two basic strategies for institutions seeking to benefit from international biotrade: becoming a low-cost supplier or becoming a value-added supplier. This latter strategy relies on the fact that selection of natural products for testing purposes does not have to occur randomly: Both chemotaxonomic and ethnomedical techniques can be applied to create a value-added product. Chemotaxonomic strategies rely on the selection of organisms from a related taxo- nomic group that are expected to produce a similar chemical category of substances as the original sample. An example of this can be seen in the soil-derived filamentous fungi as well as in the Actinobacteria. Since the antibiotics penicillin and streptomycin were isolated from the former group in the 1930’s and from the latter group a decade later,taxonomicallyre - lated groups have been successfully screened for sec - Global Resources Genetic resources • 493 ondary metabolites. In contemporary society, such compounds are used to treat cancer, arteriosclerosis, and infectious disease and are even used as immuno- suppressive agents. In ethnomedical selection, knowledge of the use of a natural product in traditional medicine is expected to increase the chance of get- ting positive results with a particular extract. This approach involves sending experts into the field to con- duct interviews with traditional healers. While this type of value-added product is more likely to generate a positive “hit,” it is time-consuming and therefore often slow to generate high numbers of potential compounds. Another disadvantage of this type of approach is that it has proven difficult to select with efficacy for agents against complex diseases like cancer, because indigenous traditional healers may be unfamiliar with such maladies. The most recent approach to the isolation of bio- active natural products eliminates the supply and sub- sequent screening of live organisms altogether. Be- cause it is actually the genetic data that are of interest to most researchers and not the isolated organism, collecting DNA from environmental samples and directly cloning it into a host vector is becoming more commonplace. While the nature of the organism which contributed its genetic material to any meta- genome, the collection of a large number of ge- nomes, may not be determined with any certainty, the end result of having a gene that produces a particular compound of interest has been achieved. This approach is especially adaptable to microorganisms that inhabit soil and water samples in high numbers, the DNA of which can be extracted with relative ease. This approach gained favor when it became evident that a minority of microbial diversity exists in those microbes amenable to being grown under laboratory conditions, and that vast amounts of biodiversity are present in the microorganisms, which resist culturing in the lab for some reason. While activity-based screening of cloned metagenomic libraries is, by definition, a random process, it is believed that new classes of useful compounds are bound to be discovered using this technique. James S. Godde Further Reading Esquinas-Alcazar, José. “Protecting Crop Genetic Di- versity for Food Security: Political, Ethical, and Technical Challenges.” Nature Reviews: Genetics 6, no. 12 (December, 2005): 946-953. Ferrer, Manuel, et al. “Metagenomics for Mining New Genetic Resources of Microbial Communities.” Journal of Molecular Microbiology and Biotechnology 16, nos. 1/2 (2009): 109-123. Reid, Walter V. “Gene Co-ops and the Biotrade: Trans- lating Genetic Resource Rights into Sustainable Development.” Journal of Ethnopharmacology 51, nos. 1-3 (April, 1996): 75-92. Schuster, Brian G. “A New Integrated Program for Natural Product Development and the Value of an Ethnomedical Approach.” Journal of Alternative and Complementary Medicine 7, no. 1 (2001): S61-S72. Singh, Sheo B., and Fernando Pelaez. “Biodiversity, Chemical Diversity, and Drug Discovery.” Progress in Drug Research 65, no. 141 (2008): 142-174. See also: Animal breeding; Biodiversity; Biotechnol- ogy; Genetic diversity; Genetic prospecting; Re- sources as a source of international conflict. Geochemical cycles Category: Geological processes and formations Geochemical cycles refer to the movement, or cycling, of elements through the biosphere and/or ecosystems. Both biotic (living) and abiotic (nonliving) compo- nents make up such systems. Background Geochemical cycles are generally considered to be those involving nutrient elements utilized by organisms in various ecosystems. Cycling involves both biological and chemical processes. While nearly all natural elements are cycled through both abiotic and living systems, certain elements are most commonly described in such systems. These include carbon, nitrogen, phosphorus, and a variety of lesser elements (including iron, sulfur, and trace elements such as copper and mercury). Although the cycling of elements is often thought of as occurring in a relatively rapid fashion, many of these elements spend long periods locked in abiotic systems. For example, carbon may be found in materials that require millions of years to cycle through ocean sediment back into the atmosphere. The fate of such elements depends on many factors, including their chemical properties and their ability to erode or 494 • Geochemical cycles Global Resources return to the atmosphere. Some chemical elements, such as carbon, oxygen, and nitrogen, are incorpo- rated into organisms from the atmosphere. Other elements, such as phosphorus, potassium, sulfur, and iron, are found mainly in rocks and sediments. Carbon and Oxygen Cycles The carbon and oxygen cycles are greatly dependent on each other. Molecular oxygen, which represents approximately 20 percent of the atmosphere, is used by organisms through a metabolic process called Global Resources Geochemical cycles • 495 C o o l i n g / s o l i di f i c a i t o n M e l t i n g M e l t i n g ( c r y s t a l l i z at i o n ) W e a t h e r n i g W e a t h e r i n g / t r a n s p o r a t i o n / d e p o s it i o n W e a t h e r i n g / t r a n s p o r a t i o n / d e p o s i t i o n L i t h i f i c a t i o n ( d ia g e n e s i s ) H e a t/ p r e s s u r e ( m e t a m o r p h i s m ) Igneous rocks Magma (melted rock) Metamorphic rocks Sedimentary rocks Sediment The Rock Cycle The rock cycle, the basic geochemical cycle, operates on a time scale of hundreds of millions to billions of years. It includes subcycles such as the oceanic cycle and the biological cycle, which could be called parts of the “atmospheric-hydrologic-biological-sedimentary” cycle. respiration. In these reactions, the oxygen reacts with reduced carbon compounds such as carbohydrates (sugars) and generates carbon dioxide (CO 2 ). Though carbon dioxide constitutes only a small pro- portion of the volume of the atmosphere (0.04 percent), it is in this form that it is used by primary producers such as plants. In the process of photosynthesis, utilizing sunlight as an energy source, plants and some microorganisms bind, or fix, the CO 2 , converting the carbon again into carbohydrates, re- sulting in growth of the plant or replication of the mi- croorganism. The complex carbohydrates that are generated in photosynthesis serve as the food source for consumers—organisms such as animals (including humans) that eat the plants. The carbohydrates are then broken down, regenerating carbon dioxide. In a sense, the combinations of respirationandphoto- synthesis represent the cycle of life. The concentra- tion of carbon dioxide in the atmosphere is a factor in regulating the temperature of Earth. Consequently, the release of large quantities of the gas into the atmosphere through the burning of fossil fuels could po- tentially alter the Earth’s climate. Nitrogen Cycle Nitrogen gas (N 2 ) represents 78 percent of the total volume of the atmosphere. However, because of the extreme stability of the bond between the two nitrogen atoms in the gas, plants and animals are unable to use atmospheric nitrogen directly as a nutrient. Nitrogen-fixing bacteria in the soil and in the roots of leguminous plants (peas, clover) are able to convert the gaseous nitrogen into nitrites and nitrates, chemical forms that can be used by plants. Animals then obtain nitrogen by consuming the plants. The decom- position of nitrogen compounds results in the ac- cumulation of ammonium (NH 4 + ) compounds in a process called ammonification. It is in this form that nitrogen is commonly found under conditions in which oxygen is limited. In this form, some of the nitrogen returns to the atmosphere. In the presence of oxygen, ammonium compounds are oxidized to nitrates (nitrification). Once the plant or animal has died, bacteria convert the nitrogenbackintonitrogen gas, and it returns to the atmosphere. Phosphorus Cycle Unlike carbon and nitrogen, which are found in the atmosphere, most of the phosphorus required for bi - otic nutrition is found in mineral form. Phosphorus is relatively water insoluble in this form; it is only grad - ually dissolved inwater. Availablephosphorus is therefore often growth-limiting in soils (it is second only to nitrogen as the scarcest of the soil nutrients). Ocean sediments may bring the mineral to the surface through uplifting of land, as along coastal areas, or by means of marine animals. Enzymatic breakdown of organic phosphate by bacteria and the consumption of marine organisms by seabirdscyclethephosphorus into forms available for use by plants. Deposition of guano (bird feces) along the American Pacific coast has long provided a fertilizer rich in phosphorus. Bacteria also play significant roles in the geochemical cycling of many other elements. Iron, despite its abundance in the Earth’s crust, is largely insoluble in water. Consequently, it is generally found in the form of precipitates of ferric (Fe +3 ) compounds, seen as brown deposits in water. Acids are often formed as by- products in the formation of ferric compounds. The bacterial oxidation of pyrite (FeS 2 ) is a major factor in the leaching process of iron ores and in the formation of acid mine drainage. Likewise, much of the sulfur found in the Earth’s crust is in the form of pyrite and gypsum (CaSO 4 ). Weathering processes return much of the sulfur to water-soluble forms; in the absence of air, the bacterial reduction of sulfate (SO 4 −2 ) to forms such as hydrogen sulfide (H 2 S) allows its return to the atmosphere. Since sulfide compounds are highly toxic to many organisms, bacterial reduction of sul- fates is of major biogeochemical significance. Richard Adler Further Reading Adriano, Domy C., ed. Biogeochemistry of Trace Metals. Boca Raton, Fla.: Lewis, 1992. Arms, Karen, et al. Biology: A Journey into Life.3ded. Fort Worth, Tex.: Saunders College, 1994. Bashkin, Vladimir N., and Robert W. Howarth. Mod- ern Biogeochemistry. Boston: Kluwer Academic, 2002. Heimann, Martin, ed. The Global Carbon Cycle. New York: Springer, 1993. Libes, Susan. Introduction to Marine Biogeochemistry.2d ed. Boston: Elsevier/Academic, 2009. Madigan, Michael T., et al. Brock Biology of Microorgan- isms. 12th ed. San Francisco: Pearson/Benjamin Cummings, 2009. Schlesinger, William H. Biogeochemistry: An Analysis of Global Change. 2d ed. San Diego, Calif.: Academic Press, 1997. 496 • Geochemical cycles Global Resources _______, ed. Biogeochemistry. Boston: Elsevier, 2005. Scientific American 223 (September, 1970). Special issue on geochemical cycles. See also: Biosphere; Carbon cycle; Carbonate minerals; Guano; Hydrology and the hydrologic cycle; Leaching; Nitrogen and ammonia; Nitrogen cycle; Phosphorus cycle; Sulfur cycle. Geodes Category: Mineral and other nonliving resources A host of different minerals may be found in the inte- rior of some geodes, and when cut open a geode typically makes a beautiful display. Definition Geodes are roughly spherically shaped bodies that are lined on the inside with inward-pro- jecting small crystals surrounded by a layer of crystallinequartz. Geodes are most frequently found in limestone beds, but they may also occur in volcanic rocks and in some shales. Overview Typically, a geode consists of a thin outer shell of dense chalcedonic silica (silicon dioxide) and an inner shell of crystals made of quartz or calcite. These crystals are often beautifully terminated, pointing toward the hollow inte- rior. New crystal layers frequently grow on the terminations of old layers, sometimes nearly or even completely filling the geode. Many geodes are filled with water, while others that have been exposed at the surface for some time are dry. Geodes typically range in size from less than 5 centimeters to more than 30 centimeters in diameter, but they can be much larger. Although the crystals are usually composed of quartz, they may also be composed of carbonate minerals, such as calcite, dolomite, and ar- agonite; of oxide minerals, such as hematite and magnetite; or of sulfide minerals, such as pyrite, calcopyrite, and sphalerite. In some ge - odes, there is an alternation of layers of silica and calcite, and almost all geodes show some kind of banding. When sulfide minerals are present, they are often the innermost crystals, whereas the carbonate minerals are typically next to the outermost layer of chalcedony (a fine-grained, fibrous variety of quartz). Some geodes are partially filled by mounds of banded chalcedony in which successive layers differ markedly in color and translucency. These layers form a colorful agate when stained. The origin of geodes is somewhat similar to the formation of large limestone caves. Groundwater dis- solves some of the limestone and forms a cavity in the rock, and the cavity is usually left filled with salty water. Silica-bearing waters then coagulate into a gel that surrounds the salt solution. The geode grows by expansion because of osmotic pressure between the salty water trapped inside the silica gel shell and fresh water on the outside of the gel. These pressures cause the geode to expand until equilibrium is reached. De- Global Resources Geodes • 497 Assorted geodes. (©Elena Elisseeva/Dreamstime.com) . micro - organisms), tissue cultures of parts of plants and ani - mals (including sperm storage), and gene libraries (involving storage and replication of partial segments of plant or animal DNA). Conservation. disadvantage of being able to preserve only a small amount of the genetic diversity present in a given population but often plays a critical role in the preservation of many varieties of organisms, particularly. appropriate consent of, and compensation to, the host nation and its people. Kerry L. Cheesman See also: Genetic resources; Plants as a medical resource; Resources as a medium of economic exchange; Resources