# Ecology/Ecosystems

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Chapter 13. Ecosystems
An ecosystem can be described simply as the collection of all living and non-living components in a particular area. The living components of the environment are known as biotic factors. Biotic factors include plants, animals, and micro-organisms. The non-living components of the environment are known as abiotic factors. Abiotic factors include things such as rocks,water,soil,light,etc.
The idea of the ecosystem relates to the idea that all organisms in the environment are engaged in relationships with every other aspect (like resources and other organisms) in that environment. Ecosystems deal with energy and nutrient flow through a system/community. For example, a household or a university could be described as an ecosystem, and a city or a state could be described as a larger ecosystem.
While ecosystems may be bound and individually discussed, they do not exist independently, but interact in a complex web. The ecological relationships connecting all ecosystems make up the biosphere. Because virtually no surface on the Earth is free of human contact, all ecosystems can be accurately classified as human ecosystems.
Ecosystems vary in diversity. Some ecosystems may be very diverse with many plants and animals; whereas other ecosystems may be less diverse with fewer animals and plants. For example, tropical rain forests could be classified as an ecosystem that has high diversity; whereas temperate rain forests could be classified as an ecosystem that has lower diversity as compared to tropical rain forests.

## Ecosystem Concept

    Living organisms and their nonliving (abiotic) environment are inseparably interrelated and interact upon each other. Any area of nature that includes living organisms and non-living substances interacting to produce an exchange of materials between the living and non-living parts is an ecological system or ecosystem - E. P. Odum, 1959 (emphasis added)
Thus, a Field Mouse (say a Meadow vole, Microtus pennsylvanicus) in its burrow in the soil is interacting with the non-living elements of that burrow as it breathes, taking in oxygen and expelling carbon dioxide$^1$. But that activity is but a moment in time and cannot, by itself, define an ecosystem. The mouse must leave the burrow for food, interacting with plants. Plants themselves interact and exchange materials with the soil and the atmosphere and are dependent on radiation from the sun and the activity of earthworms and fungi in the soil. The latter, in turn, feed upon organic molecules left behind from the death of former living plants (and field mice). Thus, the "ecosystem" of our field mouse includes plants, and soil, and soil organisms—and of course other field mice to insure that mice will always be a part of that ecosystem. And perhaps present are Bald eagles (Haliaeetus leucocephalus), dependent upon trees for nesting and roosting and a stream for water (and fish as an alternative food), feeding upon Field mice, recycling those that are caught into baby Bald eagles and droppings that are food for the plants and earthworms. Already, the "area" of this ecosystem is at least as large as that required to support a population of Bald eagles.
It is the inclusion of all the interrelationships within a functional system that make the concept of ecosystem so broad. And the seemingly endless networks of links and interactions that give geographical breadth to an ecosystem. Of course, an ecologist could study just the organisms, activities, and biotic/abiotic interactions within the local "soil ecosystem", treating mouse and eagle excrement as we described the sun above: external, but providing important input of energy and material to the soil ecosystem. In a sense, this is what we mean by calling "ecosystem" a concept rather than just a place. We may conceive of, for the purpose of study, ecosystems over a wide range of sizes or scale, from an aquarium to an ocean, and lots of places in between. Essential are certain components that we alluded to in our description of parts of the ecosystem supporting habitat for the Field mouse, and these we will next explore in detail.
In attempting to understand any interactive, complex system, especially one as elaborate as even a simple ecosystem, it is helpful to break the system down into various component parts. By this mental process we can arrive at some understanding of the specific system and can make comparisons with other systems to further our understanding of ecosystems in general. An ecosystem consists of many component structures and these function together in various ways, suggesting an initial approach to describe any ecosystem is to consider separately its structural and functional aspects.

## Basic Structural Components

Consider first an ecosystem from a structural perspective: an ecosystem consists of living (biotic) and non-living (abiotic) components. Living components include populations of organisms and the living resources they use. Non-living components include non-living resources, such as space, and the non-living physical characteristics of habitats that differ by location, such as elevation, temperature, and humidity.
We know and can observe that the organisms living in almost any ecosystem are not all identical individuals, but can be categorized into species (discussed previously in Chapter 9); and each species has a unique set of morphological, physiological, and behavioral attributes (see Chapter 3) that will determine how each individual functions within the whole. The species present provide ways of considering their contribution to ecosystem structure. For examples: we could describe the number of species (species richness), or the number (or biomass) of individuals of each species (species diversity), or their distribution across the physical space of the ecosystem. These are a few ways an ecologist would approach describing ecosystem structure based upon the plants and animals (and others) present in it.
In addition to the organisms themselves, there are components utilized by the organisms that comprise the resources of the ecosystem. These are both biotic and abiotic, inorganic and organic, and are exchanged between organisms and between organisms and the environment (previously covered in part in Chapter 4). Resources are the materials cycled by the inhabitants of an ecosystem as they carry on with life processes. We say "cycled" because all living things have a finite existence, and the substances of their material composition remain after death to be utilized in other ways.
Finally, there are those factors that are the conditions under which the organisms live. The environment of a subarctic lake is vastly different from that of a forest in the wet tropics. But consider also that conditions within a pond (an aquatic environment) are very different from those just a few yards up from the shore (a terrestrial environment). While we might be describing mostly physical conditions, these need not be always abiotic. In many ecosystems there are organisms that provide or create the dominant physical structure of that ecosystem. Examples are a forest and a coral reef. In a forest ecosystem, the trees are both very prominent organisms and resources to many of the other species present; but they also have a substantial effect on the conditions—the microclimates—that prevail in the forest ecosystem by providing shade and physical structure for many other organisms that may not directly utilize the trees as a food resource.
It should be clear that when we speak of ecosystem structure, we are considering various aspects of an ecosystem from a perspective that need not—indeed does not—mesh exactly with other ways of categorizing ecosystem components. Consider the trees of a forest or the coral heads of a coral reef. Each is a living organism, a resource used by many other species, and a physical structure that determines the uniqueness of its particular ecosystem compared with the environment that would occupy the same space in the absence of either trees or corals. In describing ecosystem structure, we do not break down the components into divisions of abiotic vs. biotic, inorganic vs. organic, or by species. In the next section, we will consider components on the basis of their function in an ecosystem, creating yet another set of categories independent of the structural ones.

## Characteristics of Ecosystems

The complexity of an ecosystem will increase as the species diversity present in the ecosystem increases. Ecosystems that are not species rich (barren ecosystems) may appear to be physically complex but are actually considered functionally complex.
Even if few species live in an environment, often because it is an unfavorable environments, that ecosystem can be still functionally complex if it include species with remarkable biochemical specializations that allow them to survive. For instance some archaea live in environments that are 113-176° F. and some organisms can get energy from inorganic chemical sources, such as bacteria that break down crude oil.
A healthy ecosystem will have high species diversity and is not likely to be damaged by human interactions, natural disasters, and climate changes. Every species within an ecosystem has a niche, the unique way that a given species uses its environment. New species are discovered every day and the roles they play in their environment to keep it healthy. This idea behind the species within the environment using their niches to keep it healthy can clearly be illustrated in a lake ecosystem. In a lake ecosystem, the sun hits the water and helps the algae grow. Algae use carbon dioxide and water to make sugars and oxygen. The oxygen is useful for any eukaryote organism and the sugars provide food for the algae or anything that eats the algae, such as microscopic organisms. Small fish eat the microscopic animals, absorb oxygen with their gills and expel carbon dioxide, which plants then use to grow. If the algae disappeared, everything else would be impacted. Microscopic animals wouldn't have enough food, fish wouldn't have enough oxygen and plants would lose some of the carbon dioxide they need to grow.
Soil is also an important part of an ecosystem. It provides important nutrients for the plants in an ecosystem. It helps anchor the plants to keep them in place. Soil absorbs and holds water for plants and animals to use and provides a home for lots of living organisms. The atmosphere provides oxygen and carbon dioxide for the plants and animals in an ecosystem. The atmosphere is also part of the water cycle. Without the interactions among organisms and elements in the atmosphere, there would be no life at all.

## Basic Functional Components

We can recognize four functional components of an ecosystem: 1) abiotic factors, 2) producers, 3) consumers, and 4) decomposers. The latter three are living components, what Odum (1959) termed the three "functional kingdoms of nature", so important and universal is their presence in ecosystems.

### Abiotic Factors

Abiotic factors can increase or decrease the amount of environmental stress on an ecosystem and therefore can also affect the stability of that ecosystem. We studied many of these in detail in (Chapter 4). Do not forget that physical (essentially geological) structure can influence ecological function: the nature of interactions of species in the sea can be very different from those in the atmosphere directly as a consequence of difference in physical properties of air and water.
The intertidal zone is the shore area that is submerged at high tide and exposed at low tide. It is rich in oxygen and nutrients and provides a home for many different species. The organisms that live in this area are constantly exposed to a high stress, less stable environment. However, they have adapted to huge daily changes in moisture, temperature, turbulence (from the water), and salinity. They have to be used to living in both wet and dry conditions continually. Water is a very powerful substance and the constant impact from the moving water can have drastic impacts on both living and non-living things. Intertidal organisms are forced to bury into the sand, hide under rocks and/or attach themselves to larger structures to avoid being carried away by the waves. Also, the constant flux of the environmental temperature is enough to make any creature uncomfortable. Since this area is exposed to both water and land, the organisms here must compete with predators that hunt at both areas.
Jungles or rainforests are an example of a low stress, more stable environment that are vital to maintaining the ecosystems of the earth. Unlike the intertidal zone, this environment has more subtle changes that occur at a much slower rate. Jungles are very stable environments that possess some 40% of all species. It is also a very diverse environment consisting of several layers of organisms using different parts of the ecosystem. As well as increasing biodiversity, jungles are beneficial to increasing our knowledge of medicinal plants and increasing oxygen output. Since the rainforest is literally a smörgåsbord a plants and animals, discoveries are continually made of the beneficial nature of these organisms.
Read: Intertidal Zones

## Food Webs

A food web is a series of interacting food chains. Food chains show the order in which animals consume food. Food chains and food webs are made up of Producers, Consumers, and Decomposers. Producers are Autotrophic Organisms. "Autotrophic" means self-nourishing. The most conspicuous group of autotrophs are the photolithoautotrophs, organisms such as algae and flowering plants that have cells containing chlorophyll and are thus capable of fixing light energy ("photo-") to build complex organic substances from simple inorganic substances ("litho-"). In the next chapter we are going to study the energetics of this process; now, we are mostly interested in how producers "create" organic matter utilizing energy and inorganic matter. The organic compounds that are created may be used structurally within the organism or may be latter broken down into inorganic matter and energy extracted by the process.
Consumers are [Heterotrophic Organisms], which are also termed macroconsumers. A simple definition of a heterotrophic organism is a species that is dependent on organic matter for food. Decomposers are heterotrophic organisms. These are also termed microconsumers, saprobes, or saprophytes. Decomposers are scavengers that break down dead plants and animals.
Decomposers are vital to the food web because they break down and recycle nutrients back into the soil. These nutrients are then used by producers to sustain life. Without the enzymes that decomposers provide to breakdown organic material into inorganic material, phosphorous(P) and nitrogen(N), Producers would eventually die out and the main part of food webs would cease to exist and therefore life would cease to exist. Decomposers recycle material but they do not recycle energy. Solar irradiation still provides the energy that drives the life cycle.
Decomposition is a natural process but decomposers speed up the process of decomposition. Bacteria, fungi and actinomycetes are three main types of decomposers. Bacteria make up about 90% of all microorganisms and are the most abundant of decomposers. They can eat anything from dead trees, dead animals and oil slicks on the surface of the ocean. Fungi and actinomycetes work on harder substances like cellulose, bark, paper and stems. These decomposers usually only work to a certain stage in decomposition then bacteria will finish the process, similar to primary and secondary succession.
A study conducted in a California river by Mary Power showed the impact that fish had on the river food wed. The main fish studied in the experiment were the steelhead and roach, these fish at a juvenile stage consume insects and fish fry, which consume chironomid larvae. These larvae reduce the algae biomass in the river. She found that when the larger adult fish species were absent, smaller more abundant predators thrived and decrease the chironomid larvae population significantly, which allowed the algae biomass to increase. This results in more cyanobacteria and diatoms to flourish on the algal turfs. This study showed a good example of how consumers and producers interact, and also showed that when one trophic level is disrupted it has a domino effect on the other trophic levels involved in the food web.
With Food Webs there are a few calculations that we can use to help us better understand the system. Chain Length is essentially the number of links between trophic levels. But when we calculate this we use the mean length. So to calculate Chain Length(CL) the equation is CL=(# of links/T-1) where T is equal to the number of trophic levels. We can also calculate link density(LD). LD=(# of Links/n) where n is the number of species in the web. And finally we can calculate Web Connectance(C). C=(actual links/potential links(N)) Where N=n(n-1)/2.
Food webs do pose some problems for ecological studies. Identifying trophic levels is very difficult in nature. Ecosystem boundaries are also tough to determine. Identifying all of the species in a community can be difficult. Quantifying and identifying the strengths of interactions is hard. In most cases it is very hard to determine what the eliminating nutrients are.

### Biological Magnification

The focus of this chapter is trophic levels and nutrient transfer between trophic levels and the food webs. Not all transfers between trophic levels are positive. Biological Magnification is the tendency of pollutants to concentrate in successive trophic levels. The pollutants are usually toxic and cause death to the organism.
The first step in Biomagnification is when a producer takes up nutrients in the soil that it stores by accident as an essential nutrient. Producers will try to store massive amounts of nutrients, when "mistaken" nutrients are absorbed, i.e. DDT and Mercury, The concentration levels in the producers are greater than the levels in the surrounding environment. When the producer is eaten by the herbivore or omnivore the pollutants are transferred to the next trophic level. Since energy transfer between trophic levels is approximately ten percent, the next chain in the trophic level must try to consume large amounts of the previous trophic level to sustain life and the pollutant, once again, is concentrated in the next trophic level.
The pollutants, once absorbed, are stored in the bodies of the consumers. DDT and PCB's are fat soluble and when one trophic level is consumed by the other the fat moves from one consumer to the next. Water soluble pollutants usually cannot concentrate because they would easily dissolve in the organism. Polluted water leaves an organism rather easily whereas fat does not leave the body.
Three main criteria must be met for a pollutant to biomagnify:
* The pollutant must be long lived.
* The pollutant must be concentrated by the producers.
* The pollutant must be fat-soluble.

### Guild

Species competing for the same resources in similar fashion are known as guilds. They are classified according to how they acquire their nutrients, their state of mobility, and their mode of feeding. Some examples of guilds are forbs, geophytes, graminoids, shrubs, trees and vines. A guild is much more stable than a single species, since more than one species can balance out the system. In a study of feeding patterns on polychaetes, Fauchald and Jumars (1979) utilized feeding guilds as a method of generalization and determining phylogenetic relationships, indeed claiming that guilds were very useful in summarizing data into patterns .
In a 2009 study, a guild approach was used to evaluate the roles of foraging habitats and exposure timing, as well as tropic position on Mercury (Hg) bioaccumulation. Five species of waterbirds forming three distinct foraging guilds in the San Francisco Bay (SFB) estuary were used in this investigation. Because estuarine waterbirds form well-documented, distinct guilds distinguished by their feeding method and habitat use and because the SFB estuary has a legacy of Hg contamination from historic mining in the Sierra Nevada Coast Mountain Range, Hg exposure was able to be evaluated on both large-scale foraging strategies (such as tropic position) occurring among guilds and small-scale strategies (such as foraging micro-habitats) that occur within guilds. As indicated by this study, SFB waterbirds accumulated alarming Hg concentrations. Concentrations that place them at considerable risk to deleterious reproductive effects. Such exposure was shown to vary as a function of micro-habitat, region, trophic level, and time spent in the estuary. These results have raised quite a bit of concern because the SFB estuary is among the most important sites for wintering, migrating, and breeding waterbird populations along the Pacific Flyaway .

### Keystone Species

A keystone species is a species having a disproportionate effect on the ecosystem. They provide stability to an ecosystem. Normally they are not the dominant species but are required for a community to have stability. Many times, keystone species are predators that keep some type of herbivore from consuming all of the dominant plant species. One interesting aspect of keystone species is that, since they normally feed on predators that consume small numbers of prey, they can effectively control a system without actually needing to have a large population size.
J. Brown and E. Heske studied the effects of the removal of Dipodomys spp. (Kangaroo rats) from the Chihuahuan Desert shrub habitat in southeastern Arizona. Twelve years after the removal of three species of kangaroo rats, the controlled plots in the habitat went from shrubland to grassland. The density of perennial and annual grasses increased considerably, and other rodent species in the area colonized. These major changes in the ecosystem showed that the Dipodomys spp. have a significant effect on the diversity and biogeochemical processes, which led the researchers to believe that the kangaroo rats are a keystone species . Some other examples of keystone species would include Starfish, Sea Otters, Bears, Beavers and Domestic Cats.
* Read: Keystone Species
All the examples of keystone species mentioned above are animals. However, this isn't always the case. Pinus chiapensis is an early successional, neotropical pine species found in warm, humid, mid-elevation Mesoamercian areas such as in the tropical montane areas of southern Mexico and western Guatemala. It has been discovered that forests dominated by P. chiapensis are the first to appear after disturbance, modifying drastically the environment by shading the forest floor, favoring soil development, increasing the rate of soil carbon sequestration, acidifying the soil, releasing nutrient cations by weathering the bed rock, and providing a source of food for birds and mammals. P. chiapensis trees inhibit their own development while facilitating the growth of broadleaved species typical of tropical montane cloud forests. Ultimately, P. chiapensisis a keystone species because of its crucial impacts in tropical montane cloud forest regeneration and its effect on ecosystem processes .

### Hypotheses of Food Web Control

Each food web contains N numbers of trophic levels and with each number the cycle of dependence flip-flops according to the Oksanen's Model. There are two hypotheses involved in this model one is known as the Bottom-up Control hypothesis. The bottom-up control hypothesis states that both the top and the bottom trophic levels are controlled by resource limitations For example in a three tiered food web (three trophic levels), the bottom trophic level would contain a species of plants, which of course are dependent on the resources available to it. The next trophic level would be some species of herbivore, these herbivores are limited and controlled by a species of predator which is also the third trophic level. The predator or top trophic level is then limited by the plant resources keeping the herbivores alive and reproducing.
If we were to now add a trophic level, such as a secondary predator (the original predator being the primary predator), the cycle of dependence would then flip-flop, and the Top-bottom Control hypothesis would apply. The top-bottom control hypothesis states that the food web cycle is predator limited. We now have our plant species ==> the herbivore ==> the primary predator ==> and the secondary predator. The plants that were resource limited are now predator limited by the herbivores. The herbivores are now resource limited by the plants abundance. The primary predator is now limited by the secondary predator and the secondary predator is now limited by the resources of the primary predator, herbivore, and plants.
This cycle repeats itself and with each additional trophic level added, the limitation of the lower trophic levels changes from either resource limited or predator limited to the other. The relationships of two trophic levels when the bottom is resource limited and the top is predator limited gives a positive slope. The more of the lower trophic level the more there is of the upper trophic level. The inverse is true when the lower trophic level is predator limited and the upper trophic level is resource limited, it creates a negative slope the more are of the upper trophic level the less there will be of the lower trophic level.
For more detailed information on this trophic cascade idea and for examples read:Trophic cascade

## References

* ^ Fauchald, Kristian, and Peter A. Jumars. "The Diet of Worms: a Study of Polychaete Feeding Guilds." Oceanogr. Mar. Biol. Ann. Rev. 17 (1979): 193-284.
* ^ Brown, J.,Heske,E. 1990.Control of a Desert-Grassland Transition by a Keystone Rodent Guild. Science, New Series, Vol 250. 1705-1707.
* ^ Power, Mary E. 1990. Effects of Fish in River Food Webs. Science, Vol. 250 811-814.
* ^ Eagles-Smith, Collins A. et al. 2009. Mercury Bioaccumulation and the Risk to Three Waterbird Foraging Guilds is Influenced by Foraging Ecology and Breeding Stage. Environmental Pollution. Article in Press, corrected proof.
* ^ Castillo, Rafael F. del et al. 10 May 2009. Pinus chiapensis, a Keystone Species: Genetics, Ecology, and Conservation. Forest Ecology and Management, Vol. 257, Issue 11, pgs. 2201-2208.
* Footnote:$^1$ Breathing is an activity at the organism level of biological complexity. The actual use of oxygen molecules and production of carbon dioxide molecules takes place at the cellular and subcellular levels. The exchange process within the vole involves tissue and organ level activities (lungs and circulatory system).