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Decomposition and Mineralization
838 Ecological Processes | Decomposition and Mineralization
that supports cooperation between individuals and/or sufficient mating rate. At this threshold population level, the M-stability equals zero. M-stability does not necessarily imply local stability at the equilibrium state. The equilibrium can be unstable and the population system may follow a cyclic trajectory, but this population may have a strong M-stability if its average density does not change easily in response to additional mortality. Local stability can be lost if density dependence in mortality processes is delayed, whereas M-stability is supported even by delayed density-dependent processes. The conception of M-stability can be applied to the effect of harvest mortality on the average fish stock. If a fish population has a high M-stability then harvesting is partially compensated by the decrease in natural mortality which is density dependent, and hence causes a relatively small reduction in the average population density. However, fish populations with low M-stability can be easily depleted due to harvesting. The difference in M-stability can partially explain observed changes in the species composition of fish populations. A myth that fish populations have a ‘harvestable surplus’, which can be harvested without any effect on the stock (it is believed that harvest deaths are substituting for the deaths that would occur naturally), has led to the global depletion of fish populations. Mathematical models show that additional mortality is compensated only partially by the decrease in natural mortality and hence always draw population density to a lower level. Analysis of M-stability can help to estimate what reduction of harvest rates is needed to restore fish population levels. Another application of M-stability is the protection of endangered
populations. Species with low M-stability have a high risk of extinction because they do not have strong compensatory density-dependent mortality processes. Large mammals belong to this category because they have low mortality and low fecundity; hence, the densitydependent component of mortality is weak. These species require most intensive conservation efforts.
See also: Classical and Augmentative Biological Control; Metapopulation Models; Parasitism; Predation; Stability.
Further Reading Begon M and Mortimer M (1981) Population Ecology: A Unified Study of Animals and Plants. Oxford: Blackwell. Begon M, Townsend CR, and Harper JL (2006) Ecology: From Individuals to Ecosystems, 4th edn. Malden, MA: Blackwell. Berryman AA (1981) Population Systems: A General Introduction. New York: Plenum. Beverton RJH and Holt SJ (2004) On the Dynamics of Exploited Fish Populations. Caldwell, NJ: Blackburn. Caughley G (1978) Analysis of Vertebrate Populations. Chichester: Wiley. May RM (1973) Stability and Complexity in Model Ecosystems. Princeton, NJ: Princeton University Press. Namboodiri K (1996) A Primer of Population Dynamics. New York: Plenum. Pielou EC (1976) Population and Community Ecology. New York: Gordon and Breach Science Publishers. Sharov AA (1992) Life-system approach: A system paradigm in population ecology. Oikos 63: 485–494. Sharov AA (1996) Quantitative population ecology. http://www.ento.vt.edu/~sharov/PopEcol/popecol.html (accessed December 2007). Varley GC and Gradwell GR (1960) Key factors in population studies. Journal of Animal Ecology 29: 399–401. Varley GC, Gradwell GR, and Hassell MP (1973) Insect Population Ecology: An Analytical Approach. Oxford: Blackwell.
Decomposition and Mineralization L Wang and P D’Odorico, University of Virginia, Charlottesville, VA, USA ª 2008 Elsevier B.V. All rights reserved.
Introduction Mechanisms and Processes Dynamics of Selected Ecosystems
Anthropogenic Impacts Common Study Methods Further Reading
Introduction
with consequent liberation of energy. Decomposition is an important component in global carbon budget; without decomposition, the atmospheric CO2 pool could be depleted literally in one decade based on the current annual rates of net photosynthesis (without considering the effect of biological feedbacks). Moreover, soil organic matter is one of the largest and most dynamic reservoirs of carbon in the global carbon cycle. The carbon stored in soil organic
Decomposition can be considered the inverse process of production, because it is a metabolic degradation of organic matter (such as plant residues, animal tissues, and microbial material) into simple organic and inorganic compounds. Decomposition is essentially a process of breakdown of the carbon skeleton existing in the organic compounds
Ecological Processes | Decomposition and Mineralization
matter is 2400 petagrams (Pg, 1015 g), which is about twice as much the amount stored in vegetation (550 Pg) and atmosphere (750 Pg), together. A better understanding of processes involved in the dynamics of soil organic matter is crucial to predict future changes in atmospheric CO2 concentrations. Decomposition and the subsequent mineralization are also an indispensable process for sustaining life on Earth, as they are the only processes enabling massive recycling of chemical elements in the biosphere. Most nutrients cycle from an inorganic form in the soil solution to vegetation and back to the soil solution through decomposition and subsequent mineralization. Mineralization is the conversion of nutrients and other substances from an organically bound form to a water-soluble inorganic form. Decomposition and mineralization are closely related processes. In fact, mineralization is often considered as part of the decomposition process; however, decomposition does not always lead to mineralization. Decomposition is associated with carbon cycling whereas mineralization is with nutrient cycling. Part of decomposition processes such as fragmentation and chemical alteration could be classified as mineralization, if inorganic nutrients or other simple bases (e.g., NH3, (PO4)3 ) are lost from the complex organic compounds during these processes. Mineralization is a vital process in ecosystem dynamics since most plant essential nutrients (such as nitrogen, phosphorus, and sulfur) are made available to plant uptake through the process of mineralization (Figure 1).
Mechanisms and Processes Overview Decomposition is comprised of a series of interacting physical, chemical, and biological processes. In general, three major processes are involved in terrestrial Organic matter
decomposition: leaching, fragmentation, and chemical alteration. Leaching is a physical process through which ions (such as Kþ, Mg2þ, and Ca2þ) and small water-soluble organic compounds (such as sugars, amino acids, and amino sugars) dissolve in water and move out of the decomposed organic material. Leaching could happen even from green leaves still attached to the plants. These soluble materials move into the soil matrix where they are taken up by plant roots or soil microbes, adsorbed to soil minerals, or leached and transported through the soil column by water drainage. Leaching losses are greatest in environments with high precipitation and negligible in dry environments. Fragmentation is a physical process through which fresh detritus is broken down into smaller particles. During fragmentation, some chemical bases can break off from organic compounds thereby contribute to nutrient mineralization. Fragmentation also provides more fresh surfaces that can be used by microbial colonization thereby facilitating further decomposition. Biological factors are major contributors of litter fragmentation. Fragmentation is a byproduct of the feeding activities of larger animals and the direct product from the feeding of smaller organisms such as protozoan, potworm, and earthworms. Abiotic factors such as freeze–thaw and wetting–drying cycles can also facilitate litter fragmentation. Through chemical alteration, the final stage of the decomposition process, litter fragments are further broken down into simple organic and inorganic compounds. The complete decomposition, that is, the release of all the energy fixed in organic compounds, may take thousands of years if it happens at all. One of the most commonly known products of incomplete decomposition is fossil fuel, on which our modern societies heavily rely. Decomposition
Inorganic material
Plant tissue
C
Animal tissue
C mineralization
CO2
Animal waste
Litter
Microbes
N mineralization
Leaching
N
Fragmentation
P
P mineralization
Figure 1 The process of decomposition and mineralization.
NH4+ PO43– HPO42– H2PO4–
Chemical alteration
Soil organic matter
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S
S mineralization
SO42–
840 Ecological Processes | Decomposition and Mineralization
Carbon mineralization is about the same as carbon decomposition if we exclude the leaching process. Nitrogen (N) and phosphorus (P) mineralization, however, although related to decomposition, are distinctprocesses. In particular, P mineralization is less-tightly linked to decomposition than N mineralization due to the chemical structure of P containing compounds. In fact, because the N atoms are directly bonded to carbon skeletons of organic matter (C–N), N is generally released as dissolved organic N (DON) in the breakdown of these skeletons, that is, in the course of the decomposition process (e.g., during fragmentation or chemical alteration). On the other hand, because P atoms can form ester linkages C–O–P, P can be released (i.e., mineralized) independent of the decomposition of organic matter, that is, with no breakdown of the carbon skeleton. N mineralization starts with the release of DON associated with decomposition. Both plants (through the mycorrhizal fungi associated with plant roots) and soil microbes can take up DON, although in most cases soil microbes outcompete plants for DON uptake. When microbial needs for DON are met, microbes break down the remaining DON using the energy released by the breakdown of the carbon skeleton and secrete NHþ 4 to the surrounding soil matrix. This process is known as ‘N mineralization’. When DON is insufficient to meet the microbial N requirement, soil microbes absorb additional N from the pool of inorganic N (e.g., NHþ 4 , NO3 ) in the soil solution, a process known as ‘immobilization’. Immobilization also includes the removal of inorganic N from the soil solution by chemical fixation.
Decomposers Fungi are an important class of decomposers due to their abundance and ability to decompose rather recalcitrant organic material. In fact, fungi are able to secrete enzymes that are capable of breaking down virtually all classes of plant compounds. Thus, fungi can decompose substrates such as fresh plant litter and some structural materials (e.g., lignin, chitin, and keratin) that are initially almost inaccessible to other decomposers. Moreover, fungi account for a large fraction of the soil microbial biomass, as they contribute to about 60–90% of the microbial biomass in forest soils and to 50% in grassland soils. Fungi have extensive hyphae networks, which make it possible to acquire carbon (e.g., from forest litter) and nutrients (e.g., from mineral soil) from different locations. Mycorrhizae are symbiotic associations between plant roots and fungi. Based on conservative estimates, approximately 95% of all vascular plant species have the potential to form this mutualistic association with mycorrhizal fungi. Approximately 70% of all plant families include species, which develop specialized
endomycorrhizae called vesicular arbuscular mycorrhizae (VAM) or just arbuscular mycorrhizae (AM). In these associations, plants receive nutrients from fungi – especially the less mobile groups (e.g., phosphates), while providing, in return, fungi with carbohydrates. Mycorrhizal fungi play a role in the decomposition process by breaking down proteins into amino acids. Under certain conditions, mycorrhizal fungi have been found to turn into aggressive decomposers capable of decomposing humus that used to be considered stabilized. Bacteria are another major group of decomposers. Like fungi, bacteria spores are ubiquitous in air, water, and both dead and live organic matter. There is a wide range of types of soil bacteria. Recent studies have shown that bacteria are able to degrade cellulose/hemicellulose, lignin, and even intact fiber walls. Due to their small size and large surface to volume ratio, bacteria are able to rapidly absorb soluble substrates and to reproduce quickly in substrate-rich conditions. In substrate-rich environments such as the rhizosphere or dead animal carcasses, bacteria tend to undergo population ‘explosions’ and thereby become the dominant decomposers. These populations collapse as the freely available resources are consumed. Bacteria decomposition seems to be more common in situations where fungi are under stress. Bacteria have also been found to degrade substrates resistant to fungal decay. Soil fauna can be classified into three categories based on the size: microfauna (less than 0.1 mm), mesofauna (between 100 mm and 2 mm), and macrofauna (between 2 mm and 20 mm), though some researchers adopt slightly different size criteria. Soil fauna used to be considered an important contributor to litter decomposition; however it was later recognized that, soil microorganisms such as fungi and bacteria are the dominant functional groups of decomposers. In fact, complex organic polymers, such as lignin, can be degraded exclusively by these microorganisms. Soil fauna affect decomposition through the processes of litter fragmentation, bacteria/fungi grazing, and soil structure alteration. They graze either directly on microorganisms or on dead organic matter inhabited by bacteria and fungi. Moreover, soil fauna spread the populations and increase the turnover rate of microbial communities, thus enhancing the rates of organic matter decomposition. Therefore, despite its limited direct participation in the decomposition process, the overall influence of soil fauna on the turnover of soil organic matter should not be underestimated especially in warm environments. Temporal and Spatial Patterns Litter mass decreases exponentially with time in the course of the decomposition process. In general, leaf litter typically loses 30–70% of its mass in the first year and
Ecological Processes | Decomposition and Mineralization
another 20–30% in the following 5–10 years. Only a few of the important chemical changes occurring during decomposition have been completely understood, while most of these reactions still need to be investigated. The organic compounds in plant tissues can be grouped into several broad classes on the basis of their different rates of decomposition. These organic compounds are typically grouped (from fast to slow decomposition) into (1) sugars, starches, and simple proteins, (2) crude proteins, (3) hemicellulose, (4) cellulose, (5) fats and waxes, and (6) lignin and phenolic compounds. A three-stage model is often used to describe the chemical changes and rate-regulating factors contributing to decomposition. These stages include an early, a late, and a near-humus stage. At the early stage, the decomposition of water-soluble substances and unshielded hemicellulose/cellulose is stimulated by high levels of nutrients; at the late stage, the degradation rate of lignin determines the rate of litter decomposition, while higher N levels decrease the decomposition rates; in the near-humus stage, the rate of litter decomposition tends to zero, while the total amount and the lignin content of the residual soil organic material remain constant. An alternative, commonly accepted three-phase model of litter decomposition, considers the following phases: (1) leaching of cell solubles; (2) fragmentation and chemical alteration; this second phase occurs slowly and includes most of the fragmentation and alteration of the litter structure; (3) chemical alteration of litter detritus mixed with mineral soils. In this final phase, decomposition occurs at a slower pace. Climate determines regional patterns of decomposition. In general, regions with higher temperature and soil moisture tend to experience higher decomposition rates. However, decomposition is limited under water logging conditions typical of wetland environments. At a given location, most decomposition occurs near the ground surface, where soils are substrate-rich, due to the presence of relatively high amounts of leaf and root litter.
Controlling Factors Decomposition and mineralization rates are largely controlled both by biotic and abiotic factors. Biotic factors include mainly substrate quantity and quality (i.e., nutrient content), and the type and size of microbial community; abiotic factors include variables such as soil temperature, moisture, and pH, which determine the soil environmental conditions. Biotic factors Substrate quality and quantity
Substrate quantity and quality are major biotic factors controlling the rates of decomposition. Litter quality is determined by three general characteristics: (1) the type of
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chemical bonds present in the organic compounds, (2) the amount of energy released by their decay, and (3) the size and structure of these compounds and their nutrient content. Glucose and other simple sugars have high carbon quality for microbial decomposer, followed by cellulose and hemicellulose. Lignin, a structural compound second only to cellulose in quantitative importance in most plant tissues, has a content ranging from 2% to more than 50% in plant dry weight. These polyphenols dramatically slow the decomposition and mineralization rates. The quality of organic matter is generally expressed (especially in biogeochemical models) in terms of the C/N ratios of litter, soil organic matter, and microbial biomass, though the mechanistic role of C/N ratios in the decomposition and mineralization processes is still not completely understood. Because microbes are generally more N limited than carbon limited, lower C/N ratios in plant residues usually lead to higher decomposition rates. The C/N ratios of plant residues range from 10:1 to 100:1. The C/N ratios of soil organic matter remain rather constant with a typical value of 10. The C/N ratios of microbial biomass range from 5 (e.g., tropical arable soil) to 10 (e.g., tropical dry forest). Microbial biomass is the most readily decomposable pool of organic material due to the simple structure and high quality of both carbon and nutrients. The microbial decomposition rates are followed by those of plant litter and soil organic matter. In most systems, if the C/N ratio of soil organic matter exceeds about 25:1, net N immobilization occurs instead of net mineralization. Microbial community composition
The composition of microbial communities is another important factor determining the rates of decomposition due to the different types and rates of enzyme production in different microbial communities. These enzymes are major players in breakdown of different classes of substrates. In addition, different microbial decomposers have different tolerance to soil moisture and temperature conditions, with consequent effects on the rates of decomposition and mineralization. For example, because fungi are usually less sensitive to water stress than bacteria, they may play a more important role in organic matter decomposition in arid and semiarid environments. Abiotic factors Temperature
Soil temperature may affect microbial activity both directly and indirectly, through its impact on other factors such as soil moisture and litter quantity. Higher temperatures are associated with higher rates of microbial activity. Moreover, changes in soil temperature also affect the microbial community composition. The effect of temperature is also modulated by other factors. For example, in water limited environments higher temperatures do not necessarily lead to higher decomposition rates if the soil is dry. In cold
842 Ecological Processes | Decomposition and Mineralization
climates, temperature fluctuations determine freeze–thaw cycles, which kill soil microbes, release pulses of available nutrients, and lead to higher rates of decomposition and N mineralization in the subsequent growing season. Soil moisture
Conditions of limited soil water availability reduce the rate of microbial activity due to the emergence of conditions of microbial water stress due to dehydration, and to the reduction in the size of the water films coating the soil grains. Low moisture contents limit the mobility and the supply of substrate to the soil microbes by diffusion through the soil solution. In wet soils, microbial activity is limited by the low soil aeration and the consequent limitations in the amounts of oxygen available for the decomposition process. Thus, under water-logging conditions typical of wetland soils, decomposition is for most part inhibited due to the limited supply of oxygen to the soil microbes and to the limited transport of the CO2 produced in the decomposition process (soil respiration). The optimal environment for microbial activity is provided by a warm soil that is both moist and aerated. These conditions are met with intermediate moisture contents between those of dry and completely saturated soils. The effect of soil moisture is also modulated by other factors – in energy-limited environment, for example, boreal forest, higher moisture does not necessarily lead to higher decomposition rates. Soil moisture fluctuations, typical of arid and semiarid environments, are associated with pulses in the rates of decomposition and mineralization, with consequent pulses in the availability of soil mineral nutrients. Other abiotic factors such as solar irradiance, soil pH, and soil physical properties (e.g., clay content) also affect the decomposition rates. For example, it has been found that in arid environments litter decomposition can undergo a process of photodegradation, which provides a shortcut in the cycling of soil carbon.
Dynamics of Selected Ecosystems Arid and Semiarid Environments Arid and semiarid lands occupy an increasingly large portion of the world’s land surface. Decomposition processes in arid and semiarid environment have some unique characteristics due to the distinct physical environment, for example, low rainfall and relatively high solar radiation. In these ecosystems: (1) leaching is not an important decomposition process as opposed to temperate and tropical environments; (2) fragmentation and chemical alteration may be separated both temporally and spatially; (3) the ultimate location of plant litter is more important than its physical–chemical structure; (4) a variable quantity of the litter input in a desert ecosystem can be buried under the soil surface. The buried litter decomposes more
rapidly than surface litter though it goes through the same pathway of chemical transformation as the surface litter; and (5) photodegradation may dominate aboveground litter decomposition. This process provides a shortcut in the carbon cycle, with a substantial fraction of vegetation carbon being lost directly to the atmosphere without cycling through the soil organic matter pools. Aquatic Ecosystems Aquatic ecosystems comprise the largest portion of the biosphere and include both freshwater and marine ecosystems. The sources of organic matter in these systems can be both internal (autochthonous) and external (allochthonous). In general, the autochthonous material has higher available N concentration and is structurally easier to decompose than the allochthonous plant residues. Decomposition in aquatic ecosystems follows similar patterns as in terrestrial environments (i.e., it involves leaching, fragmentation, and chemical alteration), though with some major differences due to the aquatic environment. A major form of organic matter in aquatic ecosystems is the particulate organic matter (POM). POM can come from both autochthonous and allochthonous sources. The allochthonous sources include terrestrial leaves and small twigs, which are usually colonized by fungi and fragmented by shredders, leading to the formation of POM. Autochthonous POM is derived from the fragmentation of dead organisms and other organic material. POM is partly ingested, digested, and mineralized by organisms and microorganisms before settling on the bottom. The remaining organic matter that reaches the bottom is further broken down by bacteria both through aerobic and anaerobic processes. Another important component of organic matter in aquatic ecosystems is the dissolved organic matter (DOM). Major sources of DOM in the water column are (1) exudates excreted by macroalgae, phytoplankton, and zooplankton and (2) autolysis – the remains of phytoplankton and zooplankton. DOM is taken up by bacteria and converted into bacterial biomass without undergoing any breakdown into inorganic compounds. This bacterial biomass is later consumed by the zooplankton, which in turn, excretes nutrients in the form of exudates, contributing to a significant portion of the suspended material in the water column. Bacteria then take these exudates (even at very low concentration) to obtain both carbon and nutrients, and a new cycle starts. Thus, in contrast to terrestrial ecosystems, bacteria in aquatic systems act as converters rather than as decomposers, whereas phytoplankton and zooplankton play major roles in the release of available nutrients. Boreal Forests Boreal forests are among the best-studied ecosystems in terms of litter decomposition and mineralization. In these
Ecological Processes | Decomposition and Mineralization
forests - and in forest ecosystems in general - litterfall is the largest source of soil organic material, in that it can account for more than 50% of net primary productivity (NPP). Due to the low energy environment (low temperature and solar radiation), litter decomposition in boreal forests is slow. In these environments, the initial leaching from leaf litter is generally slow, while microbial degradation is the major decomposition process. The chemical changes of litter biomass in boreal forests have been well documented. The concentrations of N, P, S, Fe, Pb, Cu, and Zn in litter increase with time during decomposition. However, these relationships are empirical and have not been fully explained. The concentration of K normally decreases with time until it reaches a minimum value, and, then, it slowly increases, probably due to the fact that K is the most mobile element among all plant nutrients and its leaching may start as soon as the trees shed their leaves. Mg is another mobile nutrient and its leaching pattern is similar to that of K, though at a slower pace. Ca concentration usually increases in the early stage of decomposition until it reaches a maximum value, and then it decreases. The concentration of Mn, in contrast to most of the other elements, decreases almost linearly throughout the decomposition process.
Anthropogenic Impacts Human activities significantly modify several aspects of ecosystem function in many environments around the world. Decomposition is unavoidably altered in most ecosystems. Effects of N Deposition Dry and wet deposition and fertilization add significant amounts of N both to aquatic and terrestrial ecosystems. In most systems, the increase in soil N content leads to higher levels of foliar N and, hence, to higher litter N contents. The higher substrate quality (high litter and soil N levels) generally results in higher rates of decomposition. In some ecosystems, (e.g., Scots pine and Norway spruce forests), however, N fertilization has also been found to increase the amount of lignin in the litter, with consequent reduction in the decomposition rates, suggesting that the effect of N fertilization on decomposition could be complicated and counterintuitive. Effects of Heavy Metal Pollution Some heavy metals tend to accumulate in the soil, due to their high affinity both with soil organic matter and with mineral particles. This accumulation eventually exceeds the toxicity threshold tolerable by soil microorganisms and soil fauna – the major drivers of the decomposition process. The direct effect of heavy metal accumulation on plant uptake depends on soil properties – soils with
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neutral pH and high clay content can immobilize large amounts of heavy metals, while the chemical composition of leaves is not significantly affected by the heavy metals in the soil. However, plants growing on these soils are only temporarily protected against heavy metals until the soil retention potential for these metals is reached. In acidic soils, the low pH increases the solubility of most heavy metals leading to the uptake of heavy metals by vegetation, and to their accumulation in the plant tissues (e.g., leaves). Because all heavy metals are potentially toxic, there is some concern about the possible increase in heavy metal content in the plant leaves, and its consequent deleterious effects on ecosystem function.
Common Study Methods Decomposition Methods The use of litter bags is one of most common field techniques for litter decomposition studies to the point that it has become a sort of standard method in studies on decomposition. This method is used both for the quantitative assessment of litter biomass loss and for studies on its chemical changes. In this method, a bag is filled generally with 1–10 g of litter dried at room temperature until a constant moisture level is reached. High temperatures are avoided in the preparation of these litter samples to prevent important changes in microbial community and fiber structure. The bag is first exposed to field conditions for a specific time period, and then it is brought back to the laboratory for reweighing and performing chemical analyses on the remaining litter using techniques such as atomic emission spectrometry (AES), atomic absorption spectrometry (AAS), and inductively coupled plasma spectrometry (ICP). A typical litter bag size is between 10 10 cm and 20 20 cm and it is made of biologically resistant polyester or nylon. Nylon is not used in N studies because this material contains N. Mesh size and incubation time depends on aim of the study and the precision required. Sometimes a certain mesh size is purposely employed to exclude particular groups of soil fauna in order to determine their functional significance to decomposition processes. The number of replicate bags is important for the accuracy in mass loss estimation and the minimum of bags must be sufficient to estimate the decomposition rate constant k adequately. The study methods for woody detritus decomposition are analogous to the litter bags method, though they usually do not use litter confinement. Other methods commonly used to investigate decomposition include microcosm studies, or laboratory and field techniques based on the measurement of concentration and fluxes of soil CO2 through time. These measurements allow separating the different contributions to soil organic matter loss (e.g., carbon mineralization vs. leaching).
844 Chemical Ecology | Defense Strategies of Marine and Aquatic Organisms
Mineralization Methods The buried bag technique is a common approach to measuring N mineralization. It consists of (1) collecting soil core samples and measuring the initial concentration of inorganic N; (2) reburing subsamples of this core in polyethylene bags for specific period of time; and (3) measuring the inorganic N after incubation. The net rate of N mineralization is calculated by the difference in N concentrations between the two measurements. The buried bag method is relatively simple, cost effective, and provides results that can be compared with other studies, due to its widespread use in many different ecosystems around the world. The major problem of this method arises from the disturbance of the soil sample. For example, the method eliminates plant uptake, with a consequent increase in soil inorganic N. In N limited systems, this increase leads to higher microbial N immobilization, which, in turn, results in the underestimation of plant uptake. The mineralization rates of other nutrients essential to plants, such as P and S, can also be measured using buried bags with appropriate adjustments. Several other methods can be used to determine the rates of N mineralization, including the N budget analysis (ideally for large temporal scales), the ‘super sinks’ analysis (e.g., ion exchange resin), the use of substrate analogs, as well as the use of isotope tracer and dilution measurements. Over the last decade, the general notion of N mineralization has evolved; the concept of N mineralization as the driving process in the N cycle has been replaced by the idea that exoenzyme-driven depolymerization is the rate-limiting
step in the generation of bioavailable N. This new N cycling paradigm does not invalidate the traditional methods of net mineralization measurement as fundamental tools in the study of N cycling, but caution needs to be used in the interpretation of the results. Net mineralization is an indirect indicator of N availability and not the key step of N cycling. See also: Biodegradation.
Further Reading Austin AT and Vivanco L (2006) Plant litter decomposition in a semiarid ecosystem controlled by photodegradation. Nature 442: 555–558. Berg B and Laskowski R (2006) Advances in Ecological Research, Vol. 38: Litter Decomposition: A Guide to Carbon and Nutrient Turnover. London: Elsevier. Brady N and Weil RR (2004) Elements of the Nature and Properties of Soils, 2nd edn. Upper Saddle River, NJ: Pearson/Prentice-Hall. Chapin FS, Matson PA, and Mooney HA (2002) Principles of Terrestrial Ecosystem Ecology. New York: Springer. Parton W, Silver WL, Burke I, et al. (2007) Global-scale similarities in nitrogen release patterns during long-term decomposition. Science 315: 361–363. Sala OE, Jackson RB, Mooney HA, and Howarth RW (eds.) (2000) Methods in Ecosystem Science. New York: Springer. Schimel JP and Bennett J (2004) Nitrogen mineralization: Challenges of a changing paradigm. Ecology 85: 591–602. Schlesinger W (1997) Biogeochemistry: An Analysis of Global Change, 2nd edn. New York: Academic Press. Smith RL and Smith TM (2001) Ecology and Field Biology, 6th edn. San Francisco, CA: Benjamin Cummings. Vitousek P (2004) Nutrient Cycling and Limitation-Hawaii as a Model System. Princeton, NJ: Princeton University Press.
Defense Strategies of Marine and Aquatic Organisms D Spiteller, Max Planck Institute for Chemical Ecology, Jena, Germany ª 2008 Elsevier B.V. All rights reserved.
Introduction Mechanical Defense and Defensive Behavior Defense of Microalgae and Macroalgae Sea Grass Defense Toxins of Cyanobacteria Sponge Defense Coral Defense
Bryozoan Defense Defense of Other Marine Invertebrates Fish Defense Marine Crustacean Defense Conclusions Further Reading
Introduction
high competition for limited resources and living space, efficient defense strategies are crucial for them. Therefore marine organisms are forced to use powerful chemical defense strategies. Some of the most toxic natural products such as brevetoxin (LD100 zebrafish 3 ng ml1) or palytoxin (LD50 mouse <100 ng kg1) have been isolated from marine organisms.
Many marine and aquatic organisms such as algae, dinoflagellates, nematodes, sponges, tunicates, barnacles, bryozoans, nudibranches, and fishes have soft bodies which are an easy target for predators, bacteria, and fungi. In addition, since marine organisms have to face
that supports cooperation between individuals and/or sufficient mating rate. At this threshold population level, the M-stability equals zero. M-stability does not necessarily imply local stability at the equilibrium state. The equilibrium can be unstable and the population system may follow a cyclic trajectory, but this population may have a strong M-stability if its average density does not change easily in response to additional mortality. Local stability can be lost if density dependence in mortality processes is delayed, whereas M-stability is supported even by delayed density-dependent processes. The conception of M-stability can be applied to the effect of harvest mortality on the average fish stock. If a fish population has a high M-stability then harvesting is partially compensated by the decrease in natural mortality which is density dependent, and hence causes a relatively small reduction in the average population density. However, fish populations with low M-stability can be easily depleted due to harvesting. The difference in M-stability can partially explain observed changes in the species composition of fish populations. A myth that fish populations have a ‘harvestable surplus’, which can be harvested without any effect on the stock (it is believed that harvest deaths are substituting for the deaths that would occur naturally), has led to the global depletion of fish populations. Mathematical models show that additional mortality is compensated only partially by the decrease in natural mortality and hence always draw population density to a lower level. Analysis of M-stability can help to estimate what reduction of harvest rates is needed to restore fish population levels. Another application of M-stability is the protection of endangered
populations. Species with low M-stability have a high risk of extinction because they do not have strong compensatory density-dependent mortality processes. Large mammals belong to this category because they have low mortality and low fecundity; hence, the densitydependent component of mortality is weak. These species require most intensive conservation efforts.
See also: Classical and Augmentative Biological Control; Metapopulation Models; Parasitism; Predation; Stability.
Further Reading Begon M and Mortimer M (1981) Population Ecology: A Unified Study of Animals and Plants. Oxford: Blackwell. Begon M, Townsend CR, and Harper JL (2006) Ecology: From Individuals to Ecosystems, 4th edn. Malden, MA: Blackwell. Berryman AA (1981) Population Systems: A General Introduction. New York: Plenum. Beverton RJH and Holt SJ (2004) On the Dynamics of Exploited Fish Populations. Caldwell, NJ: Blackburn. Caughley G (1978) Analysis of Vertebrate Populations. Chichester: Wiley. May RM (1973) Stability and Complexity in Model Ecosystems. Princeton, NJ: Princeton University Press. Namboodiri K (1996) A Primer of Population Dynamics. New York: Plenum. Pielou EC (1976) Population and Community Ecology. New York: Gordon and Breach Science Publishers. Sharov AA (1992) Life-system approach: A system paradigm in population ecology. Oikos 63: 485–494. Sharov AA (1996) Quantitative population ecology. http://www.ento.vt.edu/~sharov/PopEcol/popecol.html (accessed December 2007). Varley GC and Gradwell GR (1960) Key factors in population studies. Journal of Animal Ecology 29: 399–401. Varley GC, Gradwell GR, and Hassell MP (1973) Insect Population Ecology: An Analytical Approach. Oxford: Blackwell.
Decomposition and Mineralization L Wang and P D’Odorico, University of Virginia, Charlottesville, VA, USA ª 2008 Elsevier B.V. All rights reserved.
Introduction Mechanisms and Processes Dynamics of Selected Ecosystems
Anthropogenic Impacts Common Study Methods Further Reading
Introduction
with consequent liberation of energy. Decomposition is an important component in global carbon budget; without decomposition, the atmospheric CO2 pool could be depleted literally in one decade based on the current annual rates of net photosynthesis (without considering the effect of biological feedbacks). Moreover, soil organic matter is one of the largest and most dynamic reservoirs of carbon in the global carbon cycle. The carbon stored in soil organic
Decomposition can be considered the inverse process of production, because it is a metabolic degradation of organic matter (such as plant residues, animal tissues, and microbial material) into simple organic and inorganic compounds. Decomposition is essentially a process of breakdown of the carbon skeleton existing in the organic compounds
Ecological Processes | Decomposition and Mineralization
matter is 2400 petagrams (Pg, 1015 g), which is about twice as much the amount stored in vegetation (550 Pg) and atmosphere (750 Pg), together. A better understanding of processes involved in the dynamics of soil organic matter is crucial to predict future changes in atmospheric CO2 concentrations. Decomposition and the subsequent mineralization are also an indispensable process for sustaining life on Earth, as they are the only processes enabling massive recycling of chemical elements in the biosphere. Most nutrients cycle from an inorganic form in the soil solution to vegetation and back to the soil solution through decomposition and subsequent mineralization. Mineralization is the conversion of nutrients and other substances from an organically bound form to a water-soluble inorganic form. Decomposition and mineralization are closely related processes. In fact, mineralization is often considered as part of the decomposition process; however, decomposition does not always lead to mineralization. Decomposition is associated with carbon cycling whereas mineralization is with nutrient cycling. Part of decomposition processes such as fragmentation and chemical alteration could be classified as mineralization, if inorganic nutrients or other simple bases (e.g., NH3, (PO4)3 ) are lost from the complex organic compounds during these processes. Mineralization is a vital process in ecosystem dynamics since most plant essential nutrients (such as nitrogen, phosphorus, and sulfur) are made available to plant uptake through the process of mineralization (Figure 1).
Mechanisms and Processes Overview Decomposition is comprised of a series of interacting physical, chemical, and biological processes. In general, three major processes are involved in terrestrial Organic matter
decomposition: leaching, fragmentation, and chemical alteration. Leaching is a physical process through which ions (such as Kþ, Mg2þ, and Ca2þ) and small water-soluble organic compounds (such as sugars, amino acids, and amino sugars) dissolve in water and move out of the decomposed organic material. Leaching could happen even from green leaves still attached to the plants. These soluble materials move into the soil matrix where they are taken up by plant roots or soil microbes, adsorbed to soil minerals, or leached and transported through the soil column by water drainage. Leaching losses are greatest in environments with high precipitation and negligible in dry environments. Fragmentation is a physical process through which fresh detritus is broken down into smaller particles. During fragmentation, some chemical bases can break off from organic compounds thereby contribute to nutrient mineralization. Fragmentation also provides more fresh surfaces that can be used by microbial colonization thereby facilitating further decomposition. Biological factors are major contributors of litter fragmentation. Fragmentation is a byproduct of the feeding activities of larger animals and the direct product from the feeding of smaller organisms such as protozoan, potworm, and earthworms. Abiotic factors such as freeze–thaw and wetting–drying cycles can also facilitate litter fragmentation. Through chemical alteration, the final stage of the decomposition process, litter fragments are further broken down into simple organic and inorganic compounds. The complete decomposition, that is, the release of all the energy fixed in organic compounds, may take thousands of years if it happens at all. One of the most commonly known products of incomplete decomposition is fossil fuel, on which our modern societies heavily rely. Decomposition
Inorganic material
Plant tissue
C
Animal tissue
C mineralization
CO2
Animal waste
Litter
Microbes
N mineralization
Leaching
N
Fragmentation
P
P mineralization
Figure 1 The process of decomposition and mineralization.
NH4+ PO43– HPO42– H2PO4–
Chemical alteration
Soil organic matter
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S
S mineralization
SO42–
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Carbon mineralization is about the same as carbon decomposition if we exclude the leaching process. Nitrogen (N) and phosphorus (P) mineralization, however, although related to decomposition, are distinctprocesses. In particular, P mineralization is less-tightly linked to decomposition than N mineralization due to the chemical structure of P containing compounds. In fact, because the N atoms are directly bonded to carbon skeletons of organic matter (C–N), N is generally released as dissolved organic N (DON) in the breakdown of these skeletons, that is, in the course of the decomposition process (e.g., during fragmentation or chemical alteration). On the other hand, because P atoms can form ester linkages C–O–P, P can be released (i.e., mineralized) independent of the decomposition of organic matter, that is, with no breakdown of the carbon skeleton. N mineralization starts with the release of DON associated with decomposition. Both plants (through the mycorrhizal fungi associated with plant roots) and soil microbes can take up DON, although in most cases soil microbes outcompete plants for DON uptake. When microbial needs for DON are met, microbes break down the remaining DON using the energy released by the breakdown of the carbon skeleton and secrete NHþ 4 to the surrounding soil matrix. This process is known as ‘N mineralization’. When DON is insufficient to meet the microbial N requirement, soil microbes absorb additional N from the pool of inorganic N (e.g., NHþ 4 , NO3 ) in the soil solution, a process known as ‘immobilization’. Immobilization also includes the removal of inorganic N from the soil solution by chemical fixation.
Decomposers Fungi are an important class of decomposers due to their abundance and ability to decompose rather recalcitrant organic material. In fact, fungi are able to secrete enzymes that are capable of breaking down virtually all classes of plant compounds. Thus, fungi can decompose substrates such as fresh plant litter and some structural materials (e.g., lignin, chitin, and keratin) that are initially almost inaccessible to other decomposers. Moreover, fungi account for a large fraction of the soil microbial biomass, as they contribute to about 60–90% of the microbial biomass in forest soils and to 50% in grassland soils. Fungi have extensive hyphae networks, which make it possible to acquire carbon (e.g., from forest litter) and nutrients (e.g., from mineral soil) from different locations. Mycorrhizae are symbiotic associations between plant roots and fungi. Based on conservative estimates, approximately 95% of all vascular plant species have the potential to form this mutualistic association with mycorrhizal fungi. Approximately 70% of all plant families include species, which develop specialized
endomycorrhizae called vesicular arbuscular mycorrhizae (VAM) or just arbuscular mycorrhizae (AM). In these associations, plants receive nutrients from fungi – especially the less mobile groups (e.g., phosphates), while providing, in return, fungi with carbohydrates. Mycorrhizal fungi play a role in the decomposition process by breaking down proteins into amino acids. Under certain conditions, mycorrhizal fungi have been found to turn into aggressive decomposers capable of decomposing humus that used to be considered stabilized. Bacteria are another major group of decomposers. Like fungi, bacteria spores are ubiquitous in air, water, and both dead and live organic matter. There is a wide range of types of soil bacteria. Recent studies have shown that bacteria are able to degrade cellulose/hemicellulose, lignin, and even intact fiber walls. Due to their small size and large surface to volume ratio, bacteria are able to rapidly absorb soluble substrates and to reproduce quickly in substrate-rich conditions. In substrate-rich environments such as the rhizosphere or dead animal carcasses, bacteria tend to undergo population ‘explosions’ and thereby become the dominant decomposers. These populations collapse as the freely available resources are consumed. Bacteria decomposition seems to be more common in situations where fungi are under stress. Bacteria have also been found to degrade substrates resistant to fungal decay. Soil fauna can be classified into three categories based on the size: microfauna (less than 0.1 mm), mesofauna (between 100 mm and 2 mm), and macrofauna (between 2 mm and 20 mm), though some researchers adopt slightly different size criteria. Soil fauna used to be considered an important contributor to litter decomposition; however it was later recognized that, soil microorganisms such as fungi and bacteria are the dominant functional groups of decomposers. In fact, complex organic polymers, such as lignin, can be degraded exclusively by these microorganisms. Soil fauna affect decomposition through the processes of litter fragmentation, bacteria/fungi grazing, and soil structure alteration. They graze either directly on microorganisms or on dead organic matter inhabited by bacteria and fungi. Moreover, soil fauna spread the populations and increase the turnover rate of microbial communities, thus enhancing the rates of organic matter decomposition. Therefore, despite its limited direct participation in the decomposition process, the overall influence of soil fauna on the turnover of soil organic matter should not be underestimated especially in warm environments. Temporal and Spatial Patterns Litter mass decreases exponentially with time in the course of the decomposition process. In general, leaf litter typically loses 30–70% of its mass in the first year and
Ecological Processes | Decomposition and Mineralization
another 20–30% in the following 5–10 years. Only a few of the important chemical changes occurring during decomposition have been completely understood, while most of these reactions still need to be investigated. The organic compounds in plant tissues can be grouped into several broad classes on the basis of their different rates of decomposition. These organic compounds are typically grouped (from fast to slow decomposition) into (1) sugars, starches, and simple proteins, (2) crude proteins, (3) hemicellulose, (4) cellulose, (5) fats and waxes, and (6) lignin and phenolic compounds. A three-stage model is often used to describe the chemical changes and rate-regulating factors contributing to decomposition. These stages include an early, a late, and a near-humus stage. At the early stage, the decomposition of water-soluble substances and unshielded hemicellulose/cellulose is stimulated by high levels of nutrients; at the late stage, the degradation rate of lignin determines the rate of litter decomposition, while higher N levels decrease the decomposition rates; in the near-humus stage, the rate of litter decomposition tends to zero, while the total amount and the lignin content of the residual soil organic material remain constant. An alternative, commonly accepted three-phase model of litter decomposition, considers the following phases: (1) leaching of cell solubles; (2) fragmentation and chemical alteration; this second phase occurs slowly and includes most of the fragmentation and alteration of the litter structure; (3) chemical alteration of litter detritus mixed with mineral soils. In this final phase, decomposition occurs at a slower pace. Climate determines regional patterns of decomposition. In general, regions with higher temperature and soil moisture tend to experience higher decomposition rates. However, decomposition is limited under water logging conditions typical of wetland environments. At a given location, most decomposition occurs near the ground surface, where soils are substrate-rich, due to the presence of relatively high amounts of leaf and root litter.
Controlling Factors Decomposition and mineralization rates are largely controlled both by biotic and abiotic factors. Biotic factors include mainly substrate quantity and quality (i.e., nutrient content), and the type and size of microbial community; abiotic factors include variables such as soil temperature, moisture, and pH, which determine the soil environmental conditions. Biotic factors Substrate quality and quantity
Substrate quantity and quality are major biotic factors controlling the rates of decomposition. Litter quality is determined by three general characteristics: (1) the type of
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chemical bonds present in the organic compounds, (2) the amount of energy released by their decay, and (3) the size and structure of these compounds and their nutrient content. Glucose and other simple sugars have high carbon quality for microbial decomposer, followed by cellulose and hemicellulose. Lignin, a structural compound second only to cellulose in quantitative importance in most plant tissues, has a content ranging from 2% to more than 50% in plant dry weight. These polyphenols dramatically slow the decomposition and mineralization rates. The quality of organic matter is generally expressed (especially in biogeochemical models) in terms of the C/N ratios of litter, soil organic matter, and microbial biomass, though the mechanistic role of C/N ratios in the decomposition and mineralization processes is still not completely understood. Because microbes are generally more N limited than carbon limited, lower C/N ratios in plant residues usually lead to higher decomposition rates. The C/N ratios of plant residues range from 10:1 to 100:1. The C/N ratios of soil organic matter remain rather constant with a typical value of 10. The C/N ratios of microbial biomass range from 5 (e.g., tropical arable soil) to 10 (e.g., tropical dry forest). Microbial biomass is the most readily decomposable pool of organic material due to the simple structure and high quality of both carbon and nutrients. The microbial decomposition rates are followed by those of plant litter and soil organic matter. In most systems, if the C/N ratio of soil organic matter exceeds about 25:1, net N immobilization occurs instead of net mineralization. Microbial community composition
The composition of microbial communities is another important factor determining the rates of decomposition due to the different types and rates of enzyme production in different microbial communities. These enzymes are major players in breakdown of different classes of substrates. In addition, different microbial decomposers have different tolerance to soil moisture and temperature conditions, with consequent effects on the rates of decomposition and mineralization. For example, because fungi are usually less sensitive to water stress than bacteria, they may play a more important role in organic matter decomposition in arid and semiarid environments. Abiotic factors Temperature
Soil temperature may affect microbial activity both directly and indirectly, through its impact on other factors such as soil moisture and litter quantity. Higher temperatures are associated with higher rates of microbial activity. Moreover, changes in soil temperature also affect the microbial community composition. The effect of temperature is also modulated by other factors. For example, in water limited environments higher temperatures do not necessarily lead to higher decomposition rates if the soil is dry. In cold
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climates, temperature fluctuations determine freeze–thaw cycles, which kill soil microbes, release pulses of available nutrients, and lead to higher rates of decomposition and N mineralization in the subsequent growing season. Soil moisture
Conditions of limited soil water availability reduce the rate of microbial activity due to the emergence of conditions of microbial water stress due to dehydration, and to the reduction in the size of the water films coating the soil grains. Low moisture contents limit the mobility and the supply of substrate to the soil microbes by diffusion through the soil solution. In wet soils, microbial activity is limited by the low soil aeration and the consequent limitations in the amounts of oxygen available for the decomposition process. Thus, under water-logging conditions typical of wetland soils, decomposition is for most part inhibited due to the limited supply of oxygen to the soil microbes and to the limited transport of the CO2 produced in the decomposition process (soil respiration). The optimal environment for microbial activity is provided by a warm soil that is both moist and aerated. These conditions are met with intermediate moisture contents between those of dry and completely saturated soils. The effect of soil moisture is also modulated by other factors – in energy-limited environment, for example, boreal forest, higher moisture does not necessarily lead to higher decomposition rates. Soil moisture fluctuations, typical of arid and semiarid environments, are associated with pulses in the rates of decomposition and mineralization, with consequent pulses in the availability of soil mineral nutrients. Other abiotic factors such as solar irradiance, soil pH, and soil physical properties (e.g., clay content) also affect the decomposition rates. For example, it has been found that in arid environments litter decomposition can undergo a process of photodegradation, which provides a shortcut in the cycling of soil carbon.
Dynamics of Selected Ecosystems Arid and Semiarid Environments Arid and semiarid lands occupy an increasingly large portion of the world’s land surface. Decomposition processes in arid and semiarid environment have some unique characteristics due to the distinct physical environment, for example, low rainfall and relatively high solar radiation. In these ecosystems: (1) leaching is not an important decomposition process as opposed to temperate and tropical environments; (2) fragmentation and chemical alteration may be separated both temporally and spatially; (3) the ultimate location of plant litter is more important than its physical–chemical structure; (4) a variable quantity of the litter input in a desert ecosystem can be buried under the soil surface. The buried litter decomposes more
rapidly than surface litter though it goes through the same pathway of chemical transformation as the surface litter; and (5) photodegradation may dominate aboveground litter decomposition. This process provides a shortcut in the carbon cycle, with a substantial fraction of vegetation carbon being lost directly to the atmosphere without cycling through the soil organic matter pools. Aquatic Ecosystems Aquatic ecosystems comprise the largest portion of the biosphere and include both freshwater and marine ecosystems. The sources of organic matter in these systems can be both internal (autochthonous) and external (allochthonous). In general, the autochthonous material has higher available N concentration and is structurally easier to decompose than the allochthonous plant residues. Decomposition in aquatic ecosystems follows similar patterns as in terrestrial environments (i.e., it involves leaching, fragmentation, and chemical alteration), though with some major differences due to the aquatic environment. A major form of organic matter in aquatic ecosystems is the particulate organic matter (POM). POM can come from both autochthonous and allochthonous sources. The allochthonous sources include terrestrial leaves and small twigs, which are usually colonized by fungi and fragmented by shredders, leading to the formation of POM. Autochthonous POM is derived from the fragmentation of dead organisms and other organic material. POM is partly ingested, digested, and mineralized by organisms and microorganisms before settling on the bottom. The remaining organic matter that reaches the bottom is further broken down by bacteria both through aerobic and anaerobic processes. Another important component of organic matter in aquatic ecosystems is the dissolved organic matter (DOM). Major sources of DOM in the water column are (1) exudates excreted by macroalgae, phytoplankton, and zooplankton and (2) autolysis – the remains of phytoplankton and zooplankton. DOM is taken up by bacteria and converted into bacterial biomass without undergoing any breakdown into inorganic compounds. This bacterial biomass is later consumed by the zooplankton, which in turn, excretes nutrients in the form of exudates, contributing to a significant portion of the suspended material in the water column. Bacteria then take these exudates (even at very low concentration) to obtain both carbon and nutrients, and a new cycle starts. Thus, in contrast to terrestrial ecosystems, bacteria in aquatic systems act as converters rather than as decomposers, whereas phytoplankton and zooplankton play major roles in the release of available nutrients. Boreal Forests Boreal forests are among the best-studied ecosystems in terms of litter decomposition and mineralization. In these
Ecological Processes | Decomposition and Mineralization
forests - and in forest ecosystems in general - litterfall is the largest source of soil organic material, in that it can account for more than 50% of net primary productivity (NPP). Due to the low energy environment (low temperature and solar radiation), litter decomposition in boreal forests is slow. In these environments, the initial leaching from leaf litter is generally slow, while microbial degradation is the major decomposition process. The chemical changes of litter biomass in boreal forests have been well documented. The concentrations of N, P, S, Fe, Pb, Cu, and Zn in litter increase with time during decomposition. However, these relationships are empirical and have not been fully explained. The concentration of K normally decreases with time until it reaches a minimum value, and, then, it slowly increases, probably due to the fact that K is the most mobile element among all plant nutrients and its leaching may start as soon as the trees shed their leaves. Mg is another mobile nutrient and its leaching pattern is similar to that of K, though at a slower pace. Ca concentration usually increases in the early stage of decomposition until it reaches a maximum value, and then it decreases. The concentration of Mn, in contrast to most of the other elements, decreases almost linearly throughout the decomposition process.
Anthropogenic Impacts Human activities significantly modify several aspects of ecosystem function in many environments around the world. Decomposition is unavoidably altered in most ecosystems. Effects of N Deposition Dry and wet deposition and fertilization add significant amounts of N both to aquatic and terrestrial ecosystems. In most systems, the increase in soil N content leads to higher levels of foliar N and, hence, to higher litter N contents. The higher substrate quality (high litter and soil N levels) generally results in higher rates of decomposition. In some ecosystems, (e.g., Scots pine and Norway spruce forests), however, N fertilization has also been found to increase the amount of lignin in the litter, with consequent reduction in the decomposition rates, suggesting that the effect of N fertilization on decomposition could be complicated and counterintuitive. Effects of Heavy Metal Pollution Some heavy metals tend to accumulate in the soil, due to their high affinity both with soil organic matter and with mineral particles. This accumulation eventually exceeds the toxicity threshold tolerable by soil microorganisms and soil fauna – the major drivers of the decomposition process. The direct effect of heavy metal accumulation on plant uptake depends on soil properties – soils with
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neutral pH and high clay content can immobilize large amounts of heavy metals, while the chemical composition of leaves is not significantly affected by the heavy metals in the soil. However, plants growing on these soils are only temporarily protected against heavy metals until the soil retention potential for these metals is reached. In acidic soils, the low pH increases the solubility of most heavy metals leading to the uptake of heavy metals by vegetation, and to their accumulation in the plant tissues (e.g., leaves). Because all heavy metals are potentially toxic, there is some concern about the possible increase in heavy metal content in the plant leaves, and its consequent deleterious effects on ecosystem function.
Common Study Methods Decomposition Methods The use of litter bags is one of most common field techniques for litter decomposition studies to the point that it has become a sort of standard method in studies on decomposition. This method is used both for the quantitative assessment of litter biomass loss and for studies on its chemical changes. In this method, a bag is filled generally with 1–10 g of litter dried at room temperature until a constant moisture level is reached. High temperatures are avoided in the preparation of these litter samples to prevent important changes in microbial community and fiber structure. The bag is first exposed to field conditions for a specific time period, and then it is brought back to the laboratory for reweighing and performing chemical analyses on the remaining litter using techniques such as atomic emission spectrometry (AES), atomic absorption spectrometry (AAS), and inductively coupled plasma spectrometry (ICP). A typical litter bag size is between 10 10 cm and 20 20 cm and it is made of biologically resistant polyester or nylon. Nylon is not used in N studies because this material contains N. Mesh size and incubation time depends on aim of the study and the precision required. Sometimes a certain mesh size is purposely employed to exclude particular groups of soil fauna in order to determine their functional significance to decomposition processes. The number of replicate bags is important for the accuracy in mass loss estimation and the minimum of bags must be sufficient to estimate the decomposition rate constant k adequately. The study methods for woody detritus decomposition are analogous to the litter bags method, though they usually do not use litter confinement. Other methods commonly used to investigate decomposition include microcosm studies, or laboratory and field techniques based on the measurement of concentration and fluxes of soil CO2 through time. These measurements allow separating the different contributions to soil organic matter loss (e.g., carbon mineralization vs. leaching).
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Mineralization Methods The buried bag technique is a common approach to measuring N mineralization. It consists of (1) collecting soil core samples and measuring the initial concentration of inorganic N; (2) reburing subsamples of this core in polyethylene bags for specific period of time; and (3) measuring the inorganic N after incubation. The net rate of N mineralization is calculated by the difference in N concentrations between the two measurements. The buried bag method is relatively simple, cost effective, and provides results that can be compared with other studies, due to its widespread use in many different ecosystems around the world. The major problem of this method arises from the disturbance of the soil sample. For example, the method eliminates plant uptake, with a consequent increase in soil inorganic N. In N limited systems, this increase leads to higher microbial N immobilization, which, in turn, results in the underestimation of plant uptake. The mineralization rates of other nutrients essential to plants, such as P and S, can also be measured using buried bags with appropriate adjustments. Several other methods can be used to determine the rates of N mineralization, including the N budget analysis (ideally for large temporal scales), the ‘super sinks’ analysis (e.g., ion exchange resin), the use of substrate analogs, as well as the use of isotope tracer and dilution measurements. Over the last decade, the general notion of N mineralization has evolved; the concept of N mineralization as the driving process in the N cycle has been replaced by the idea that exoenzyme-driven depolymerization is the rate-limiting
step in the generation of bioavailable N. This new N cycling paradigm does not invalidate the traditional methods of net mineralization measurement as fundamental tools in the study of N cycling, but caution needs to be used in the interpretation of the results. Net mineralization is an indirect indicator of N availability and not the key step of N cycling. See also: Biodegradation.
Further Reading Austin AT and Vivanco L (2006) Plant litter decomposition in a semiarid ecosystem controlled by photodegradation. Nature 442: 555–558. Berg B and Laskowski R (2006) Advances in Ecological Research, Vol. 38: Litter Decomposition: A Guide to Carbon and Nutrient Turnover. London: Elsevier. Brady N and Weil RR (2004) Elements of the Nature and Properties of Soils, 2nd edn. Upper Saddle River, NJ: Pearson/Prentice-Hall. Chapin FS, Matson PA, and Mooney HA (2002) Principles of Terrestrial Ecosystem Ecology. New York: Springer. Parton W, Silver WL, Burke I, et al. (2007) Global-scale similarities in nitrogen release patterns during long-term decomposition. Science 315: 361–363. Sala OE, Jackson RB, Mooney HA, and Howarth RW (eds.) (2000) Methods in Ecosystem Science. New York: Springer. Schimel JP and Bennett J (2004) Nitrogen mineralization: Challenges of a changing paradigm. Ecology 85: 591–602. Schlesinger W (1997) Biogeochemistry: An Analysis of Global Change, 2nd edn. New York: Academic Press. Smith RL and Smith TM (2001) Ecology and Field Biology, 6th edn. San Francisco, CA: Benjamin Cummings. Vitousek P (2004) Nutrient Cycling and Limitation-Hawaii as a Model System. Princeton, NJ: Princeton University Press.
Defense Strategies of Marine and Aquatic Organisms D Spiteller, Max Planck Institute for Chemical Ecology, Jena, Germany ª 2008 Elsevier B.V. All rights reserved.
Introduction Mechanical Defense and Defensive Behavior Defense of Microalgae and Macroalgae Sea Grass Defense Toxins of Cyanobacteria Sponge Defense Coral Defense
Bryozoan Defense Defense of Other Marine Invertebrates Fish Defense Marine Crustacean Defense Conclusions Further Reading
Introduction
high competition for limited resources and living space, efficient defense strategies are crucial for them. Therefore marine organisms are forced to use powerful chemical defense strategies. Some of the most toxic natural products such as brevetoxin (LD100 zebrafish 3 ng ml1) or palytoxin (LD50 mouse <100 ng kg1) have been isolated from marine organisms.
Many marine and aquatic organisms such as algae, dinoflagellates, nematodes, sponges, tunicates, barnacles, bryozoans, nudibranches, and fishes have soft bodies which are an easy target for predators, bacteria, and fungi. In addition, since marine organisms have to face