Dynamic Aquaria: Building Living Ecosystems

By Walter H. Adey and Karen Loveland

In its third edition, this praised book demonstrates how the living systems modeling of aquatic ecosystems for ecological, biological and physiological research, and ecosystem restoration can produce answers to very complex ecological questions. Dynamic Aquaria further offers an understanding developed in 25 years of living ecosystem modeling and discusses how this knowledge has produced methods of efficiently solving many environmental problems. Public education through this methodology is the additional key to the broader ecosystem understanding necessary to allow human society to pass through the next evolutionary bottleneck of our species. Living systems modeling as a wide spectrum educational tool can provide a primary vehicle for that essential step.

This third editon covers the many technological and biological developments in the eight plus years since the second edition, providing updated technological advice and describing many new example aquarium environments.

• Includes 16 page color insert with 57 color plates and 25% new photographs
• Offers 300 figures and 75 tables
• New chapter on Biogeography
• Over 50% new research in various chapters
• Significant updates in chapters include:
• The understanding of coral reef function especially the relationship between photosynthesis and calcification
• The use of living system models to solve problems of biogeography and the geographic dispersal and interaction of species populations
• The development of new techniques for global scale restoration of water and atmosphere
• The development of new techniques for closed system, sustainable aquaculture

• Language: English
• Publisher: Academic Press
• Release date: Aug 29, 2011
• ISBN: 9780080469102

Walter H. Adey

Walter Adey received his B.S. in Geophysics from MIT, performed graduate studies at MIT and Harvard in Paleontology and Biology, and obtained his Ph.D. in Marine Botany and Geology from the University of Michigan. Since 1977, he has been the Director of the Marine Systems Laboratory at the Museum of Natural History, Smithsonian Institution. Dr. Adey is an associate editor for Restoration Ecology and The Journal of Ecological Engineering. He has authored numerous publications, and has developed several exhibits and operational mesocosm systems.

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CHAPTER 1

Introduction

This book presents the process of building, managing, and restoring living aquatic ecosystems (in microcosms, mesocosms, and macrocosms) and its background, rationale, status, and future. We argue that there is no qualitative difference between a rationally constructed ecosystem in microcosm and mesocosm and that in a macrocosm. In this book, we use the term macrocosm for a wild ecosystem that has been altered or constrained by human endeavor. Human constraints are largely degrading in effect because they have mostly been performed with little concern for the continued function of the ecosystem. However, they can be constructive, such as a scientific or restorationist effort at repair, revitalization, and even optimization.

There has been a tendency on the part of some scientists to regard the modeling of living ecosystems as impossibly complex; that is, they view true ecosystems as beyond human construction. The tendency in mesocosm research today is to restrict efforts to a few species interactions, to keep control and limit the variables, but producing a result that most ecologists would hardly accept as an ecosystem. In the aquarium world, the feeling is widespread that total control over very limited diversity (gardening rather than ecology) is necessary to achieve anything but an explosion of weeds and parasites. Yet, as we shall discuss in this book, since the first edition was published, it has been possible for many years to operate in aquaria the most complex ecosystems in the sea, coral reefs; these microcosms of a few cubic meters, behave chemically as wild reefs, and have a biotic diversity per square meter exceeding that known for the wild. Similarly, we demonstrate the ability to produce whole estuaries, for periods of up to a decade, with much of their biotic complexity intact. These estuaries were first attempts and the future bodes well for those willing to move on to larger, more sophisticated, systems. We are not alone in these endeavors and concepts (e.g. Osmond et al., 2004). However, critically important at this juncture, Petersen et al. (2003) have had the resources to demonstrate a scaling rationale that demonstrates veracity thresholds. In general, as might be expected, larger models can more accurately depict the function of their analog. However, as Petersen et al. (2003) demonstrate, large microcosms and moderate-sized mesocosms have already begun to pass those thresholds; and we expand that concept by greatly increasing the biodiversity and ecosystem linkage of these models.

In our view, no longer are there aquatic ecosystems (including the oceans) on planet Earth that have not been significantly altered directly or indirectly by human activities. Many species have been driven to extinction, some as large as the Steller sea cow, and many more have had their ecological role greatly reduced and whole ecosystems altered (e.g. the North Atlantic codfish). Many fresh and coastal waters have been radically altered, some to a nearly dead state (e.g. upper Chesapeake Bay); even the open oceans have been degraded by food-chain concentrated toxic compounds that have rendered some organisms infertile and others subject to organ malfunction and cancers. Finally, simply to encompass what would be a very long list, a global girding biome, coral reefs, are facing drastic reduction, if not practical extinction. It has long been accepted by ecologists that ecosystem supports are critically important to the survival of human societies; the advent of concern for the effects of global warming, and the clearly impending collapse of our access to clean water has spread the ecosystem support concern far more widely. We feel that much of the ecosystem damage can be corrected, and our basic standard of living maintained if we greatly increase our efforts now. We have the tools, but time is running out for their application.

We start our discussion by demonstrating that the development and evolution of life is very likely an inevitable part of the chemistry of the universe. We demonstrate that the definition of an ecosystem becomes a functional reality given the right physical/chemical (i.e. ecologically engineered) framework, and an appropriately inserted, food web-based collection of species. In this scenario, inserted organisms self-organize into a community of species interacting to process energy and nutrients through a complex of food webs (i.e. an ecosystem). Since no ecosystem stands alone, the key element becomes understanding and re-creating the boundary conditions, the imports, and the exports. The ecosystem is the most complex end-point of biotic evolution, and when the experimental method is applied, and disassembly and reassembly utilized, progress in understanding is most rapid. Scaling becomes our primary difficulty in modeling, because almost by definition, some species are too big or wide ranging for microcosms and mesocosms and others have been fished out or otherwise damaged in macrocosms. We need to know enough about these ecosystems to interact with them to replace or provide the effects (e.g. grazing or predation) of the missing species; the process is continuously heuristic.

Because we are inextricably enmeshed in our biosphere and its ecosystems, and because we process global-scale quantities of energy and nutrients, human endeavors must seriously consider the effects those endeavors will have on our ecosystems and how they can be ameliorated. Microcosms and mesocosms are ideally suited for this task (see also Osmond et al., 2004).

THE ORIGIN OF LIFE: MICROCOSM EARTH

The four most abundant chemical elements (99%) of most living organisms, by number of atoms, are hydrogen, oxygen, carbon, and nitrogen. The elemental composition of the universe (Figure 1.1) compared to that of the crust of the Earth (Figure 3.6) suggests that living organisms have more in common with the universe as a whole than with the Earth alone. Even the relative proportions of these elements are about the same in living organisms as they are in the universe (although hydrogen is lower), but very different from that in the Earth’s crust. Including the oceans (which are one-sixteenth the mass of the crust) with the crust, in this elemental analysis, has very little effect on the relationship. In the Earth’s crust, by weight, oxygen, silica, aluminum, and iron, followed by sodium, magnesium, potassium, and calcium, are far above the very small percentages of hydrogen, carbon, nitrogen, and phosphorus. If the whole Earth is considered (as an estimate), the big four, at 93%, are iron, oxygen, silica, and magnesium.

FIGURE 1.1 Relative abundances of the chemical elements in the universe (based on silicon as 10⁴). Note that except for the very unreactive helium, the three most abundant elements of life are the same as those in the universe with the critical nutrient nitrogen next in line. From The Biological Chemistry of the Elements by Fraústo da Silva and Williams (1993). Reprinted by permission of John Wiley & Sons, Inc.

In addition to the millions of stars in our galaxy, composed mostly of hydrogen and helium, there are enormous masses of interstellar gas and dust. This interstellar gas and dust is enriched in the heavier elements formed in the cooling, nuclear furnaces of dying stars and then blown into space in supernovae. The prevailing chemistry in these interstellar regions has been called an organic cosmochemistry (Oró, 1994). It has been shown that the numerous hydrogen, carbon, nitrogen, and oxygen compounds, identified both in interstellar space and in the comets and meteorites that arrive on Earth, can be abiotically combined in the laboratory to provide water and a number of critical pre-biotic compounds (Table 1.1). A large proportion of cometary material is frozen water and some scientists have demonstrated that the volume of incoming comets has been more than sufficient to provide the Earth’s oceans (Frank and Huyghe, 1990). Furthermore, a large array of proteinic and nonproteinic amino acids, carboxylic acids, purines, pyrimidines, hydrocarbons, and other molecules has been found in the relatively primitive carbonaceous chondritic meteorites that have landed on Earth (Oró, 1994).

TABLE 1.1

Biomonomers, Biopolymers, and Chemical Properties That Can Be Derived from Interstellar and Cometary Molecules

*Detected in interplanetary dust particles of possible cometary origin and in meteorites. From Oró (1994).

Most theories of the origin of the solar system (e.g. Brown et al., 1992) start with condensation out of a solar nebula. In these models, the inner planets (including Earth) had all of their volatiles (including the principal elements and molecules of life) blasted out of them by the sun as they formed. Newer concepts of the formation of the Earth–Moon system (e.g. Redfern, 2001), mostly evolve around the impact of a Mars-sized object with the early Earth, resulting in the Moon being ejected with many of the planetary dynamic characteristics (orbit, spin, and wobble) formed or altered by the impact. In either case, the Earth started as a rocky cinder (like the planet Mercury today). It became revitalized with oceans and gases, most likely, from cometary and meteorite introduction. We now know that at the outer margins of the solar system, there are a large number of ice objects that form the Oort Cloud. These provide the comets that are sometimes perturbed into the inner solar system, where they can impact the planets bringing water and organic compounds (Redfern, 2001). The key to the next step was a planetary mass and temperature environment in which the already omnipresent water components could be present in their liquid phase. While this may have happened on Mars and Venus as well as on planet Earth, it is only on Earth that the conditions for life have remained for 4 billion years. Later cometary and asteroid impacts snuffed out some of that life when they impacted, but so far none have reset the life clock.

Chemically, water is a most unusual material. By accepted physical/chemical rules, under normal pressures, one would expect this ubiquitous compound to exist only as a solid or as a gas, depending on temperature. However, due largely to the polarization of individual water molecules and the tendency of this compound to form a semicrystalline liquid at moderate temperatures, water appears in its most familiar liquid form over a relatively wide temperature range. At the same time, it becomes a universal solvent. Almost every chemical element that occurs in the Earth’s crust dissolves in water, ultimately finding its way into the sea. Water also has one of the highest capacities of any compound for storing and exchanging heat, and it has great surface tension. Thus, this almost miraculous material is a basic stabilizing element, resisting temperature variations.

Most of the above are debated only in the details by scientists today. The critical step, from simple organic molecules, abundant in the colder parts of the universe, to life is where the debate lies. Indeed, this may have not been a step, but rather a flickering, on-and-off process, happening millions of times before taking hold. Was it enough that physical energy inputs, whether from lighting at the surface of the sea or hydrothermal energy at ocean spreading centers (van Dover, 2000), into the primitive ocean soup (water plus simple inorganic compounds) created the next level of complexity of organic compounds? This has been repeatedly accomplished in the laboratory. It may be that anywhere in the universe, except near stars, when the temperature is right and water is liquid, then the organic soup is ready to brew.

Water has a tendency, because of its surface tension, to create membranes and bubble structures. Lipids, present among the universal, simple, organic compounds, spontaneously accumulate on these bubbles to form membranes and cellular structures. This can be abiotically accomplished in the laboratory (Hanczyc and Szostak, 2004). Membranes can isolate, structure, and locate organic reactions making them more efficient than they would be in the greater soup.

Thus, while it seems that cellular structures with simple organic compounds would be just everyday chemistry in a pre-biotic world, is there an external information component required to kick-start life from there? Very long polymers, strings of smaller organic molecules, are the everyday magic of organic chemists and industrial plants today, but they are also part of the critical stuff of life. Some scientists would have it that the ordered, endlessly replicating structure of inorganic clay minerals could provide a template against which many simple organic compounds could become polymers. This can be done in the laboratory, and it is an intriguing idea that in the pre-biotic world this is where carbon and silicon chemistry come together. Carbon and silicon are chemically similar, as elements: they form multiple bonds with themselves and many other elements – silicon, one step up on the periodic table, is roughly twice as heavy as carbon.

Could it be that silicon, the key chemical element in the crust of cinder Earth, and carbon, coming with water from the cold outer solar system to bring potential life to a later, temperature-moderated Earth, provided the next step up the ladder to full-blown life? In the contact between the primordial water, rich in a wide variety of simple organics and cellular bubbles, and abundant clay minerals formed from erosion of rocks, polymers could have formed from all the types of simpler organics, including nucleic acids. Possibly formed in much the same way, RNA is the basic message carrier of life today, and could well have preceded DNA. This is the so-called RNA world that some researchers see as an essential phase (Orgel, 2004).

Such RNA in the ammonia, carbon dioxide rich and anaerobic early world, could theoretically exist and replicate itself, becoming more complex, based on natural selection. Eventually, the RNA molecules would have found themselves inside developing cellular bubbles, where they could have co-opted those structures, to spontaneously produce what one would have to call life. This very basic life probably began soaking up the organic chemicals of the soup. However, until regular energy sources and a means of synthesizing carbon and nitrogen compounds from CO2 and NH3 (and eventually N2) were tapped to bring reproduction and growth together, the future of this life had to be uncertain, and perhaps frequently snuffed out. Eventually, several pathways for fixation of carbon and nitrogen evolved in what could be called primitive bacteria, leading to the highly successful Calvin cycle of cyanobacteria (Raymond, 2005). Tied to solar energy capture by the early photosynthetic bacteria, some 3.5 billion years ago, life became firmly established on Earth. From there, with occasional disruptions, as large comets and asteroids continued to arrive, life was on its way to creating the modern, complex Earth, so fully integrated, at least from its crust to the atmosphere, with life.

Today, the overwhelming geochemical evidence is that cellular life formed very quickly in the pre-biotic soup (at 3.6–3.8 billion years ago) within at most a few hundred million years of the formation of a liquid ocean on Earth (Gedulin and Arrhenius, 1994). Furthermore, it is difficult not to conclude that life will form quickly (on a geological scale) anywhere in the universe where the physical conditions for liquid water develop (National Research Council, 1990).

The Gaia concept was popular several decades ago and has now faded. The basic premise of Gaia, that some life made more life easier, even possible for more advanced life, is certainly correct. The primordial soup was necessary for the development of cellular systems and the earliest molecular complexes that could be called life. The early bacteria that survived on the soup were a necessary condition for photosynthesis and eventually the symbiotic incorporation of photosynthetic bacteria into early protists to greatly expand the process of pulling CO2 out of the atmosphere and replacing it with oxygen. And so on it went to life on land, eventually to primates and humans.

Whatever is to be made of these arguments about the development and expansion of early life, one thing is very clear: photosynthesis eventually came to be the key to most life on Earth. Also, it is likely that the Earth’s crust, biosphere, oceans, and atmosphere together hold more carbon than ever before because of continual outgassing of CO2 from the Earth’s mantle over the last 3 billion years. Photosynthesis invented by early life has kept the Earth from the fate of Venus – a boiling, runaway greenhouse – by continually locking a large part of this carbon into semi-permanent storage. By releasing carbon from geological burial to the atmosphere, we are courting both human and biosphere disasters every bit as much as we were (and are) with our nuclear arsenals. Many scientists are more immediately concerned with a global warming that will disrupt many human societies creating global friction. Photosynthesis may be somewhat more effective with higher levels of CO2 (there is still much debate on this point). However, most scientists have concluded that this natural increase of photosynthesis cannot keep up with our destruction of forests and tundra and the release of fossil fuels carbon. Desertification and the reduction of more efficient land photosynthesis by rising sea level, with human societies putting more and more CO2 into the atmosphere in a struggle to obtain energy to survive the harsher conditions, could push us to the high temperatures and sea levels of the Cretaceous with far less land area. Perhaps then modern human societies would collapse (Diamond, 2005) and save the biosphere from a runaway greenhouse tumble.

Today, all the Earth is a microcosm, or at least the concepts of microcosm, mesocosm, macrocosm, and biosphere lie a spectrum of overlapping scale. No one doubts any longer that we can affect our Earth on a global scale. The principles that we describe in this book for microcosms and mesocosms are very much the same as what we would use for macrocosms and the oceans. We cannot return to a more simple state where the biosphere can be counted on to cover up for us. We must quickly learn to properly manage the biosphere.

MICROCOSMS AND MESOCOSMS OF AQUATIC ECOSYSTEMS

Over the last third of the 20th century, scientists in a variety of laboratories around the world have been making significant advances in keeping marine, estuarine, and freshwater organisms in aquaria-like simulations of wild environments; they have generally been referred to as model ecosystems or microcosms. Some of these become quite large, and when they exceed a few thousand gallons in water volume, they are sometimes called mesocosms. There is no sharp line between the microcosm and the aquarium. Perhaps it is best to draw the line at the point where the desire for strict ecosystem simulation is relaxed because of size, cost, or interest. The older literature on ecological microcosms or controlled ecologies was reviewed byAdey (1987; 1995), Adey and Loveland (1998), and Kangas and Adey (1996). Petersen et al. (2003) point out that mesocosms have become as numerous as field studies and they provide citations that would allow an extensive review of recent literature. Osmond et al. (2004) discuss the use of a very large mesocosm (Biosphere II) in the context of global climate change, and argue for the much wider use of mesocosms to understand and solve our global change problems.

In the Earth’s biosphere no ecosystem stands alone. Indeed, as we noted above, the primary energy source for the biosphere itself is derived externally from the sun; the remainder internally, from the Earth’s heat. Most of the original biotic materials came from outside the Earth and, to some extent, are still arriving; the remainder derive by erosion from the Earth’s crust. External solar and lunar cycles are also important sources of information. The boundaries of an ecosystem are entirely arbitrary. However, whether carrying out pure field research or drawing boundaries for modeling purposes, drawing those boundaries so that cross-boundary interchanges can be known and measured or estimated is a key to success. All ecosystems have cross-boundary interchanges, and the microcosm builder must know what those interchanges are and simulate them accordingly or the model ecosystem will have little relationship with the wild analog.

When modeling boundaries are established for most aquatic ecosystems, water inflow and outflow are important parameters. In many cases (e.g. coral reefs and rocky shores), where local biomass exceeds diurnal recycling capabilities, incoming water quality is crucial to ecosystem function, and when it is not possible to provide that flow from an undamaged wild source ecosystem, a water quality management system is established. There are three basic approaches to the management of water quality in aquatic models (i.e. to match the lack of high-quality incoming water). One approach is abiological, in which chemical methods such as ozonation and physical methods such as physical filtration, protein skimming, and ultraviolet radiation are used to offset the effects of a poor water quality. These methods are almost always used with the second, more generalized, approach of bacteriological filtration, which is employed in various forms and has been used in virtually all aquarium systems (and sewage systems) of the past 50 years.

The bacteriological (or biological) filter is a device of almost infinite variety used to maximize surfaces with bacterial cultures (i.e. bacterial films) in close contact with flowing water of the system being managed. The purpose is threefold: (1) the trapping and breakdown of organic particulates; (2) the degradation of the universal waste products urea and highly toxic ammonia to the less toxic nitrite and thence to the least toxic nitrate; and more recently (3) either in special anaerobic chambers, or in open-aerated trickle systems, the denitrification of nitrate nitrogen to atmospheric gas nitrogen. Either separately or in conjunction with the above systems, oxygen input into the aquarium and carbon dioxide release from the aquarium are maximized to support not only the organisms being maintained, but also the essential respiration activity of the bacteria. The respiration of the bacteria in these filters releases considerable carbon dioxide, which can significantly acidify the culture. Thus, buffering with calcium carbonate in a wide variety of forms is often used. Hendal (2006) and Delbeek and Sprung (2005) provide recent reviews of these methods for aquaria. In most cases, these methods are sufficient to maintain many organisms. However, they rarely achieve the quality of unpolluted wild waters.

The basic principles of bacteriological filtration (and sewage treatment) lie in the assumption that microbes have been the dominant force controlling water quality in the wild. However, this is likely to be incorrect, since far more organic material is stored in soils and geological sediments than exists in the biosphere. In addition, the Earth’s atmosphere is rich in oxygen and, prior to human involvement, was very poor in carbon dioxide. Higher plants and algae have created far more organic matter than microbes have degraded, with a concomitant production of oxygen and removal of carbon dioxide from the biosphere. Thus, plants have been and (until humans started burning coal and oil and using rivers to dump their wastes) remain the dominant force controlling Earth’s water and atmospheric chemistry and particularly the needs of higher animals. Humans assume that lack of raw materials to maximize production is a basic need that must be managed; thus, the primary requirement is rapid breakdown of all organics to basic mineral elements (carbon, nitrogen, phosphorus, sulfur, silica, etc.). We disagree with this concept. Primary productivity in the wild is sometimes limited by the lack of nutrients. On the other hand, excess nutrients usually result in unstable (bloom) conditions. Farming and aquaculture almost invariably add nutrients to drive productivity of a single organism. However, the result is either unstable or semistable, requiring continuous careful management to avoid a variety of crash scenarios. Biospheric, and ultimately ecosystem, stability lies not in the rapid breakdown of organics but rather in emphasis on their storage as either plant biomass or geological materials. Stability in the biosphere, in most wild ecosystems, and in microcosms and mesocosms must lie in competition for scarce resources including carbon and nutrients. In aquaculture systems designed to produce food, these requirements are reduced locally to maximize growth, but must be managed in a broader context, or they will be passed onto wild ecosystems where degradation is inevitable. It is probably best to recycle all human organic wastes, but the next best approach would be to pump them into sealed oil wells or deep mines (geological storage). Had that been done for the last century, we would be faced with neither global warming nor polluted rivers and coasts and could perhaps tap the resulting methane gas for energy. We have not taken that approach and, at this stage, we need to quickly organize to emphasize the locking up of nutrients, including carbon in plant (including algal) biomass.

The third approach, which we describe in this volume, is to match an undegraded analog wild ecosystem as closely as possible with the microcosm or mesocosm of interest, in terms of physical and chemical characteristics, cross-boundary exchanges, and as many organisms, with their food webs, as possible. In some cases, especially for smaller systems, human manipulation must account for the cross-boundary exchanges of organisms that have a significantly larger territory in the wild than is available in the model. Water quality control of high biomass of benthic systems usually involves open water exchange with phytoplankton-dominated communities in the wild. We simulate this process with algal photosynthetic systems, allowing production and export or recycling of biomass (and nutrients) as appropriate. Foam fractionation, filtration, and engineered bacterial systems are not generally employed because they remove plankton and swimming or floating larvae on the one hand and unbalance water chemistry on the other.

In Chapter 25, we describe several large-scale systems for the closed or semi-closed aquaculture of food fish. These systems use the same Algal Turf Scrubber (ATS™) systems described in this book for controlling water quality in microcosms and mesocosms. Technically these aquaculture operations are quite successful, and indeed one system is still operating as a commercial endeavor after 10 years. However, until truly sustainable wild fisheries, without habitat degradation, can become the rule, and a cost is levied on nutrient release from aquaculture, it will be difficult for these sustainable methods to be truly cost competitive.

The hobby aquarium industry, in its public education effects, can have an incalculable positive effect on the need for public understanding of biology and ecology. Since it is hands on per unit effort it is probably far more effective than text book/lecture education. However, as practiced today, there are enormous losses of organisms in the commercial aquarium trade. The suffering of the animals is deplorable, and there exists the very real possibility that intensive collection will deplete the environment and upset the balance of natural communities. While large numbers of plants and animals may die in the wild during environmental extremes, in general, human impacts are becoming severe enough to shift the delicate survival balance negatively for many species and even for ecosystems. For recreation and education purposes, we cannot accept subjecting organisms to stressful conditions beyond their normal environmental range. Even for research purposes, it is crucial that scientists be sensitive to the health of the organisms involved and to the potential negative impacts of collecting.

Open water culture can help in some situations, and are increasingly important in coral reef culture. However, through the use of ecosystem techniques, culture systems can produce most of the organisms (and live rock) used in the aquarium trade, and distributors, dealers, and hobbyists can maintain functioning systems and reduce losses dramatically. Indeed, experimental ecosystems and their organisms can be maintained separately from wild ecosystems and endangered organisms can be nurtured for return to the wild. Zoological parks have made a strong entrance into this arena in recent decades, and now public aquaria, with sufficient financial and scientific expertise, can do likewise. Many freshwater fish have been bred in aquaria, and in the past decade increasing numbers of marine species of fish have been also. Because of our success in breeding hundreds of species of marine invertebrates and plants in our ecosystem tanks, the prognosis for greatly reducing wild collecting is encouraging, and we describe systems for accomplishing this objective. We also describe culture systems that can be used for identifying organisms that have potential for the production of pharmaceutical drugs and for initial harvest culture until the synthetic equivalents can be produced.

As we have pointed out, there is already a large applied world that uses microcosms as tools for testing the fates of pollutants in wild ecosystems and hopefully developing standards for lessening pollutant loads as a result. These testing procedures use either highly simplified ecosystems or a few species without a real ecology. However, the results derived would be more applicable to the real world if the models used were the more complex systems that we describe in this book. Of equal interest, it has long been known that up to a certain level, ecosystems have a considerable capability for accepting polluting elements and degrading or detoxifying and storing them. We have much to learn from ecosystems in this respect, as we detail in Part V. However, what is most relevant in the real world, where efficiency counts, is that knowledge gained, through models, of ecosystem processes can lead to more economic means of handling large quantities of pollutants and keeping those pollutants from degrading wild ecosystems.

RESTORATION OF DAMAGED ECOLOGICAL SYSTEMS

We have used the term macrocosm for wild ecosystems that have come under the significant influence of human activities and are in need of restoration to prevent loss of biodiversity and the degraded provision of ecological services to human society. It may be that most ecosystems on Earth are now macrocosms, but there is certainly a broad gradient between those in great need of repair and those minimally affected.

There is no lack of understanding of the current, serious nature of our loss of ecosystem function and support. We cite two recent authors: Jared Diamond (2005) calling notice to the global level of ecosystem degradation that can lead to social collapse, and Robert Livingston (2006) calling notice specifically to serious aquatic ecosystem degradation. There is considerable scientific consensus that human society, in its alteration of the biosphere, is approaching a number of thresholds beyond which ecosystem supports will begin to fail and potentially cause social collapse. There are many dimensions to the loss of ecosystem supports: for example Diamond (2005) lists 12 key problems. As we discuss in Chapter 25, a number of these relate to a need to restrict human population growth and human demand for continued resources as well as the increasing number of invasive species caused by globalization (see also Ruiz and Carlton, 2003). However, better than half of the basic problems relate to water and atmospheric quality control and to fisheries. We describe in Chapter 25 how in working with numerous microcosms and mesocosms, we have identified a practical methodology for solving these problems using large-scale solar energy capture through algal photosynthesis. These ATS™ systems have already been scaled up to a module size of up to 5 acres and 40Mgpd by HydroMentia, Inc. of Ocala, Florida. HydroMentia offers nutrient, toxics, and atmospheric carbon removal with water oxygenation and bioenergy supply as by-products at the scale of large rivers (formal designs for ATS™ systems up to 1500 acres, processing billions of gallons per day, have been developed). There are numerous other approaches to bioenergy, which are also carbon neutral, but they either add to nutrient problems (e.g. corn, soy, and switchgrass) or are monocultural in their solution (microalgae). The ATS™ was derived from mesocosm R&D, and is itself a biodiverse ecosystem that provides multi-solutions. It demonstrates the great potential of microcosm and mesocosm research, but in the solution of grave problems of mankind.

SUMMARY

It is quite reasonable that we wish to understand in depth the complex ecosystem processes in which we are enmeshed. It may well be essential to our continued existence as a species. To develop ecosystems in microcosms, mesocosms, and aquaria, and to control their relationship to the rest of the world is simply the experimental method of science at the most complex scale of biology. The ecosystem is the exquisite potential of the universe, and we can capture it and look at it logically for understanding or for its intrinsic beauty. To build and control ecosystem models and to use the knowledge and techniques gained to restore damaged ecosystems is an essential endeavor.

TAXONOMIC NOTES

As we have noted, the biological world is far more complex than the chemical world. While the core chemical elements and compounds have a standard terminology that has long existed for chemistry, the biological world remains in flux. The Linnean system has been backed up by a formal, international system for the standardization and stabilization of nomenclature, but the result is hardly stable. Some of these changes are reflected in advances in our understanding of organismic evolution, prodded on by a rapidly advancing knowledge of what is called molecular biology, the documentation of genetic coding. Unfortunately, some change also comes from nomenclatural wrestling. For basic reference we provide a modern tree of life (Figure 1.2) from Knoll (2003); the volumes of Parker (1982) can continue to fill in that framework down to family and genus. In our descriptions of microcosms and mesocosms, as one part of the demonstration of success or veracity of modeling of an analog wild ecosystem, we provide species lists. Since these lists were accomplished, some genus and species names have changed. In this edition, we have not updated these changes because it would have meant returning to the specialists that identified the flora and fauna in the first place, or in some cases finding new specialists, and this would have changed the basic function of the volume very little. In most situations, field guides will provide the older names along with their newer versions.

FIGURE 1.2 Family tree of eukaryotes and ancestral bacteria (there are other, more distantly related bacteria, such as the Archaea, that are minimally shown). All of the major lines of eukaryotes, including the five major groups, had already formed well back in the pre-Cambrian, probably before the major animal groups evolved. After Knoll (2003).

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CHAPTER 2

The Envelope

Physical Parameters and Energy State

The shape and size of an aquatic ecosystem relative to its controlling physical and energy parameters can determine the basic character of the system. This is especially true of the thickness of the water mass and its relationship to the bottom. A 100-meter-deep lake of several square kilometer surface dimensions, all other factors aside, would be dominated by true plankters, normally living most of their lives suspended in mid and surface waters, with little benthic (or bottom) influence, whereas the shallow stream or narrow lagoon of a few meters in depth is very much benthic dominated. Light enters only through the air–water interface of a water ecosystem, and the shape of the containing body of water relative to depth, as well as water turbidity, determines the basic photosynthetic vs heterotrophic (nonphotosynthetic feeding) character of the ecosystem. The direction of current flow and wave action through an aquatic system relative to the position and orientation of the communities present is critical to simulate in any ecosystem model, or else the character of the communities and the abundance of its various species will change in the microcosm or mesocosm.

The all-glass aquarium, ranging from about 40 liters (10 gallons) to 1000 liters (250 gallons) is a standard and highly reliable piece of equipment in the aquarium industry (Color Plates 1 and 2). Likewise, because of its low cost and availability, every effort is generally made to use all-glass aquaria for microcosm work. Indeed, by drilling holes to attach pipes and linking all glass tanks in complex arrays, many aspects of wild ecosystems can be modeled with reasonable accuracy.

We talk about the issue of scaling later, but anyone wishing to simulate the planktonic aspects of an ecosystem, not overwhelmed by the benthic communities, is likely to be seeking tanks with radii greater than 1–2 meters. The construction of molded fiberglass tanks or poured concrete or concrete block tanks sealed with a wide variety of commercially available sealants has considerable advantages for systems larger than about a thousand liters. This is also true when the mesocosm modeler departs from the purely aquatic systems and enters the realm of wetlands, marshes, and swamps, where the key species are either large individuals or the very nature of the community (e.g. a marshland) requires a large area compared to water and sediment volume.

Each of the aquaria, microcosms, and mesocosms described in Chapters 20–23 illustrates the process of designing envelope (tank) shapes to fit the functional requirements of the enclosed ecosystems. Whether they are fully successful or not is limited only by the ingenuity and financial resources of the human builders (Figure 2.1).

FIGURE 2.1 Diagrammatic illustrations of two very different types of ecosystem models (a coral reef and a mangrove/swamp sandy shore) showing spatial configurations, water movement, controls, and energy supply as well as the basic materials used in construction. Both of these models are streated in considerably more detail in Chapters 20 and 22.

Ideally, the microcosm or mesocosm envelope would be like that of the boundary of the mathematical modeler, a theoretical boundary controlling access but not having any inherent characteristics. Of course, that is not possible, for two primary reasons. First, walls, whatever their nature (unless rather esoteric measures are used to prevent organisms and organic molecules from using their surfaces) are effectively hard bottoms. In an aquatic model of an ecosystem dominated by hard bottom communities that may not make a difference (remembering however, that especially in marine and estuarine systems that some species have larvae that must escape into the plankton for the early part of their lives). The important of the walls is less, as is often the case in an all-glass system, if the walls are frequently scraped. However, for a small model of a planktonic system, the presence of uncleaned walls may prevent the system from being plankton dominated. Second, walls of living models consist of real materials. To some degree, they interact with the water of the ecosystem they contain. For most purposes, glass and many plastics are ideal in this respect. There are few aquatic systems in which the slow leaching of silica into the water column would be a problem, and barring the significant presence of ultraviolet radiation, most plastics that one might use for walls (polyester, polyvinyl chloride (PVC), polyethylene) are characterized environmentally by their long-term stability and a lack of leachable