The effects of planned engineers are for the most part evident, as suggested earlier. Contrarily, the effects of associated engineers are largely indirect, subtle, and incompletely understood. To summarize them, it is convenient to think of the overall agroecosystem as having seven compartments into which matter enters and exits, and six processes whereby matter is transferred between compartments, some of which are strictly trophic, others of which are engineering. The seven compartments are plants, herbivores, carnivores, detritus, organic soup, humus, and nutrients, and the six processes are photosynthesis and nutrient absorption, primary consumption, secondary consumption, death, comminution, and catabolism. In this way the decomposition subsystem of ecosystems can be seen as fitting in with the trophic-based ideas of elementary ecology, and the main engineering aspects (i.e., comminution and catabolism) emerge as a simple subcomponent of the trophic hierarchy. We refer to these engineers as decomposition engineers. Their inclusion as engineers may be questionable in the spirit of the definition of engineers explicitly excluding trophic effects, but we feel they play such an important part in the modification of the environment that it is justified including them as a major category of ecosystem engineering (e.g., exo-digestion clearly modifies the environment for organisms other than the exodigester; the soil organic matter is regarded by most researchers as a physical fact of soil chemistry, yet it is clearly engineered by these decomposition engineers).
However, this framework excludes one of the more important aspects of ecosystem engineering in the soil—those organisms whose activities directly affect the macrostructure of the soil. These are the digging and tunneling organisms, such as termites, ants, and earthworms, and the fungi whose mycelia act to bind particles together into peds as well as make physical connections among different peds, engineering a structural integrity beyond the simple ped structure. Termites are especially important in the tropical agroecosystems of Africa and South America (Black and Okwakol 1997, Jones 1990, Dangerfield et al. 1998, Martius 2001), earthworms are universally important (Lawton 1994, Fragoso et al. 1997, Edwards 1994, Edwards and Bohlen 1996), and ants are likely important but have not received the attention they deserve (Folgarait 1998). For clarity of presentation, we refer to them as soil structure engineers.
Engineers in the soil reach their maximum importance in the process of decomposition. Decomposition of any piece of plant or animal matter is completed over a period of hundreds or thousands of years, yet the bulk of the decomposition occurs within one or a few years, depending on climatic conditions. The decomposition process thus has two components, the rapid cycle and the slow cycle. The rapid cycle is responsible for the mineralization of nutrients, while the slow cycle is responsible for the production of humus, and thus the contribution of organic matter to soil physical and chemical structure. Which materials go to which cycle depends on both the chemical makeup of the constituents and the activities of the microbial soil engineers.
In natural ecosystems the relevant process is the introduction of litter to the soil. This is almost always a seasonal phenomenon, even in seemingly nonseasonal tropical rain forests. In most forms of agriculture this seasonality is exaggerated because of planting and harvesting cycles, although many forms of permanent culture, especially in tropical regions, do not have such a strict cycle imposed by Homo sapiens, and can be expected to correspond more or less to the patterns of natural systems. In a non-managed system it is a reasonable expectation that the yearly seasonal cycle will result in something close to a complete cycling of nutrients through the fast cycle. But many agroecosystems are seemingly not at such an equilibrium state and have either rapid decomposition, such that most of the fast cycle is completed before the end of the seasonal cycle, or accumulate organic material because of slow decomposition. This timing of decomposition with the seasonal cycle is an important concept when it comes to the ecological management of decomposition, and is one of the reasons why various forms of composting activities have become part and parcel of many agroecosystems (Insam et al. 2002). Vermiculture, with its worm engineers, has become one of the most common forms (Hendrix and Edwards 1994, Frederickson et al. 1997, Berc et al. 2004).
At a mechanistic level, the process of decomposition can be thought of as involving three main transformations, all occurring simultaneously—leaching, catabolism, and comminution (Swift et al. 1979). Leaching is generally the transport of materials from one place to another, frequently through runoff or percolation of water. Catabolism is the chemical process whereby larger molecules are broken down into smaller ones. Comminution is the physical reduction in size of the organic material, a physical rather than a chemical process. All three transformations are strongly influenced by ecosystem engineers.
Soil ecosystem engineers are remarkably diverse, ranging in size from bacteria to snails. Furthermore these organisms do not fall into the same neat trophic categories as do the organisms in the herbivore-carnivore subsystem of the ecosystem. With the absence of either primary producer or herbivore in the decomposition subsystem, it is not surprising that trophic levels are not easily definable—all organisms are carnivores and top carnivores in a sense. Consequently a variety of alternative trophic classification schemes have been devised. One of the simplest is a two-way crossed classification, with the mode of nutrient acquisition (absorptive versus ingestive) crossed with the size of the organism (micro versus macro). This classification does not preclude the classic plant-herbivore-carnivore trophic system, but may be more useful when thinking of the decomposition subsystem, especially from the point of view of the nontrophic ideas of ecosystem engineering. We here discuss the absorptive versus ingestive categories.
Absorptive organisms involved in decomposition are mainly bacteria and fungi. They are the primary forces for decomposing highly commu-tated material, and are effectively the last stage in the decomposition process, engineering the catabolism that releases nutrients. For any given input into the cascading decomposition process, the microabsorp-tive organisms become more important as the system cascades through its full long-term cycle. Although special mechanisms may be important for various species and species groups, they all have a similar fundamental operation. The organism excretes exoenzymes, which create a digestive zone around its body, engineering a locally modified environment. The exoenzymes break down relatively large molecules outside of the body of the decomposing organism, and these smaller molecules then are absorbed and enter the normal intracellular metabolic process. Since a great part of digestion is external to the organism, digestion itself must be thought of as an engineering activity.
Absorptive organisms also share a strictly engineering characteristic the extent of which is not yet known, but the importance of which may be great. A number of studies report on complex interactions among various adsorptive microorganisms (e.g., Forlani et al. 1995, Nagarajah et al. 1970). For example, it is known that some bacteria concentrate near the surface of fungal hyphae, presumably for the purpose of scavenging on the products of the exodigestion of the fungi (Swift et al. 1979). In recognition of the basic processes involved in exodigestion, it would be surprising indeed if bacteria, and perhaps even fungi, did not regularly scavenge on the products of the exodigestion of other absorptive organisms. This process, if indeed it occurs and is common, has important implications for the long-term sustainability of decomposer ecosystems and places great emphasis on the potential role of biodiversity therein. Suppose, for example, the decomposition environment is composed of Cellulomonas (which produces cellulase as an exoenzyme) and Bacillus (which produces peptidases as exoenzymes). Is it possible that the Cellulomonas can obtain a fraction of its nitrogen nutrition from the small peptides produced near the body surface of Bacillus and the latter can obtain a fraction of its carbon from the carbohydrate products produced near the surface of Cellulomonas (from its digestion of cellulose)? Indeed, could Bacillus survive better in a cellulose-rich environment that contained Cellulomonas than one that didn't, through its ability to scavenge the products of exodigestion of Cellulomonas? If such a process actually operates to a significant extent in nature, bacterial engineers that have no obvious function in the actual decomposition process may in fact act as ecological buffers, providing exodigestive products on which other bacteria can scavenge when their preferred resource is temporarily in short supply. The significance of such complexity for questions of microbial biodiversity is obvious, and punctuates the strong connection between biodiversity and ecosystem engineering.
In contrast to absorptive organisms, ingesters are typically involved at a higher level in the decomposition process, usually more associated with comminution and less with catabolism—ingested resources are converted to constituent tissues, cells, and extracellular macromolecules and ejected as feces, returned to the soil organic material pool upon death, and, to a far lesser extent, released into the environment as metabolic products of catabolized molecules. The very idea of comminution is fundamentally one of engineering, thus implicating all ingesters as ecosystem engineers.
Ingestion in the case of macroingesters contributes mainly to the process of comminution and to a lesser extent to catabolism. Consider, for example, the earthworm, the great comminuter of temperate soils (Edwards and Bohlen 1996). Food is ingested through the mouth with the active participation of the pharynx, which operates as a pump. Food passes through the esophagus and arrives at the storage depot, the crop. From the crop, food is passed on to the gizzard, a muscular organ that grinds it, using small mineral particles that are also ingested. It is this physical grinding that has the main effect of comminution and is thus a major engineering process. The comminuted material is then passed to the intestine where digestion and absorption occurs. While earthworms produce a variety of enzymes, much of the digestion is accomplished through the use of symbiotic microorganisms, or simply by the microorganisms ingested with the organic matter.
Generally speaking, our present state of knowledge of the remarkably complex interactions that occur amongst all of these trophic-based engineers is slim. Yet, as a quick guide to the decomposition process, we can think of comminution and catabolism as working in sequence. Of course they do not in any real sense, but it is true that the first pass made by decomposing organisms at the organic material placed on or in the soil is dominated by comminution while the products of that comminution are acted on mainly by organisms that promote catabolism. Note that the products of comminution are not only a more finely dissected detritus but also the microorganisms that have incorporated the carbon from that detritus. So the engineering product of comminution might be most properly referred to as the soil organic "soup," since it includes both soil organic matter and soil microorganisms. It is thus not far off the track, as a heuristic device, to simply think of the organic detritus first being comminuted and then catabolized to form nutrients and humus. For the most part the initial comminution is accomplished by fungi and macroingestors, while the catabolism is accomplished mainly by fungi and bacteria. This view of the decomposition system is certainly too simplified to be useful in any active management plan, but it is a useful way to visualize the process of ecosystem engineering in the soil.
The actions of earthworms, ants and termites, other arthropods, and fungi and other organisms may induce major structural modifications to the soil. One of the most obvious effects is the creation of more pore space by tunneling activity of earthworms. Sometimes this effect can be spectacular. Hoeksema and Jongerius (1959) report an increase of from 75 to 100% porosity in orchard soils that have earthworms when compared to those without earthworms. However, published results are highly variable with some authors finding insignificant effects of earthworms (Springett et al. 1992), and most others reporting figures on the order of 25% of total soil pore space being earthworm burrows. Edwards and Bohlen (1996) are of the opinion that, on average "earthworm burrows constitute only about 5% of total soil volume."
An important effect of increasing porosity is on water infiltration. Earthworm burrows contribute substantially to this process, especially those that are open to the surface, which is to say those constructed by anecic species. However, it is well documented that endogeic species also contribute to the infiltrateability of soils (Joschko et al. 1992). Burrows must be connected to one another to be effective at water infiltration, and tillage can significantly disrupt the network of burrows, thus reducing their function as water conduits (Chan and Heenan 1993). Other agricultural activities, such as pesticide applications, have been shown to reduce water infiltration by as much as 93% because of increased earthworm mortality.
On the other hand, earthworms can contribute to soil erosion, a fact first noted by Darwin (1881). Surface-deposited casts are susceptible to being carried away by water, and the bare spots created by large anecic species on the surface of the soil near their burrow entrances make patches of bare soil that then can be eroded. However, in most studies thus far reported (Edwards and Bohlen 1996), the beneficial effect of infiltration due to earthworm burrows outweighs the effects of water erosion. From the point of view of ecosystem engineering, both infiltration and erosion are consequences of ecosystem engineering.
The role of termites and ants would seem obvious (Whitford 1994). With respect to termites it has long been part of conventional wisdom that their effect on physical structure is enormous, given the evident size of their nests in African and South American savannas. As summarized by Black and Okwakol (1997; also see Lavelle 2002) termites have been linked with increasing aggregate stability, with increasing water penetration into the soil (i.e., porosity), with increasing hydraulic conductivity, and with pedogenesis itself. Unfortunately ants have not been as vigorously studied as termites with respect to soil physical structure, although their effect could be enormous. For example, Perfecto and Vandermeer estimated that Atta cephalotes could be responsible for complete soil turnover in as short a period as 200 years in a lowland rain forest in Costa Rica (Perfecto and Vandermeer 1993). Clearly more studies are warranted since this particular species is a very evident component of neotropical forests and moves a great amount of soil. Other less conspicuous species could have trivial effects, or the cumulative effect of all ants could be great.
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