Chapter 23

Ecology is the name given to the study of the relationship between organisms and their environment. An ecosystem is made up of all the living organisms that interact with one and another in a defined area, and also the physical factors present in that region. The boundaries of a particular ecosystem are defined by the team carrying the study. All ecosystems are dynamic meaning they are constantly changing which is a result of the living organisms present and the envirobnmental conditions, which can be divided into two groups:

• Biotic factors - the living factors, for example the presence of species and the size of their populations, along with competition between different populations for food, space and breeding partners, they often refer to interactions between organisms that are living or have once lived
• Abiotic factors - the non living factors, which include the amount of rainfall recieved and the yearly temperature range of the ecosystem. The main abiotic factors are:
• Light - Most plants are directly affected by loght availibility as light is required for photosynthesis, the greater the availibility of light, the greater the success of the plant species. Plants also develop strategies to cope with different light intensities, for example in areas of low light they might have larger leaves, or may develop photosynthetic pigments that require less light, or reproductive systems which only operate at optimum light availibility.

• Temperature - The greatest effect of temperature is on the enzymes controlling metabolic reactions. Plants will develop more rapidly in warmer temperatures as will ectothermic animals. Changes in the temperature of an ecosystem due to changing  seasons can trigger migration or domancy of animals. In plant species it can trigger leaf fall, dormancy and flowering.
• Water availability - In most plant and animal populations, a lack of water leads to water stress, which can lead to death. A lack of water will cause most plants to wilt as water is required to keep plant cells turgid and keep the plant upright and is also required for photosynthesis.
• Oxygen availability - In aqautic ecosystems it is beneficial to have fast flowing cold water as it contains high concentrations of oxygen. If water becomes too warm or the flow rate too slow, the resulting drop in oxygen concentration can lead to the suffocation of aquatic organisms. In waterlogged soil the spaces between soil particles are filled with water, reducing the oxygen available for plants.
• Edaphic (soil) factors - Different soils have different particle sizes which affects the organisms able to survive in them. Clay has fine particles and is easily waterlogged, forming clumps when wet, loam has different sized particles, retains water but does not become waterlogged. Sandy soil has coarse well seperated particle that allow free draining, but do not retain water and is easily eroded.

All organisms within an ecosystem require a source of energy which is transferred from producers to consumers in a food web, a diagram used to show the trasfer of biomass and therefore energy through an ecosystem. Each stage in the chain is known as a trophic level. The first trophic level is always a producer which is an organism that converts light energy into chemical energy by the process of photosynthesis. The subsequent trophic levels are all consumers which are organisms which obtain their energy by feeding on other organisms. The second trophic level occupied by a primary consumer - an animal that eats a producer. The following trophic levels are labelled successively as secondary, tertiary and quaternary consumers. Food chains rarely gace more trophic levels than this as there is not sufficient biomass and stored energy left to supprot any further organisms. Decomposers are also important comopnents of food webs, they break down dead organisms releasing nutrients back into the ecosystem. Food chains can also be represented pyramidically with each level representign the number of organisms at each trophic level which producers at the bottom and subsequent consumers added above.

 Biomass is the mass of living material present in a partocular plcae or in particular organisms. It is an important measure as it can be eqquated to energy content. To calculate the biomas at each trophic level, you multiply the biomass present by the total number of organisms in that trophic level, this represents the biomass at a particular moment in time and does not take into account seasonal changes. The easiest way to measure biomass is to measure rhe mass of fresh material present. However water content must be discounted and the presence of varying amounts of water in different organisms makes the technique unreliable unless very large samples are used. Scientists therefore calculate the dry mass of an organism which means they have to be killed and dried to evapourate all the water present. To minimise the destruction of organisms only a small sample is taken. However it may not be representatuve of the population as a whole. Biomass is measured in grams per sqaure metre of areas of land. The biomass at each trophic level is nearly always less than the trophic level below because biomass consists of all the the cells and tissues of the organisms present, including carbohydrates and other carbon compounds the organism contains. As carbon compounds are a store of energy biomass can be equated to energy. When animals eat only a small proportion of the food they ingest is converted into new tissue, which is available fot the next trophic level to eat. As biomass is transferred between trophic levels, so the energy contained is transferred. The efficiency with which biomass is transferred from one trophic level to the next is called ecological efficiency.

Producers only convery 1-3% of the sunlight (solar energy) they recieve into energy and hence biomass. This is because:

• Not all the solar energy availible is used for photosynthesis - approximately 90% is reflected, some is transmitted through the leaf and some is of an unusuable wavelength.
• Other factors may limit photosynthesis such as water availability.
• A proportion of energy is lost as it is used for photosynthetic reactions.

The total solar energy tha plants convert to organic matter is called the gross production. However plants use 20-50% of this energy in respiration. The remaining energy is converted into biomass and is the energy available to the next trophic level and is known as the net production. The energy available to the next trophic level can be calculated using the following formula:

Net production = gross production  - respiratory losses

Note that this calculation can be applied equally to the biomass or energy production within an organism. The generation of biomass in a producer is referred to as primary production and in a consumer is known as secondary production.

Consumers at each trophic level convert at most 10% of the biomass in their food to their own organic tissue. This is because:

• Not all of the biomass of an organism is eaten, for example plant roots or animal bones ,ay not be consumed.
• Some parts of an organism are eaten but are indigestible - these parts (and their energy content) are egested as faeces.
• Some energy is lost from the animal in excretory materials such as urine.

Only around 0.0001% of the total energy originally present in the incident sunlight is finally embodied as biomass in a tertiary consumer. You can use the following formula to calculate the efficiency of the energy transfer (approximately equivalent to biomass transfer) between each trophic level of a food chain:

Ecological efficiency  = (energy or biomass available after the transfer)/(energy or biomass available before the transfer) x 100

Human civilisation depends on agriculture, which involves manupulating the environment to favour plant species that we can eat (crops) and rear animals for food or their produce. Plants and animals are provided with the abiotic conditions they require to thrive such as adequate watering and warmth. Competition from other species is removed for example through the use of presticides along with the threat of predators for example through creating barriers such as fences. In a natural ecosystem humans woulc occupy the second, third or eve fourth trophic level. At each trophoc level only a small proportion of energy at the start of the food chain is turned into biomass for consumption at third and fourth trophic levels as a result of considerable energy losses. Agriculture creates very simple food chains. In farming animals or animal produce for human consumption only 3 levels are present, producers (animal feed), primary consumers (livestock) and secondary consumers (humans). In ciltivating plants for human consumption there are onlt two trophic levels - producers (crops) and orimary consumers (humans). This means that minimum energy is lost since there are fewer trophic levels present than in the natural ecosystem. This ensures that as much energy as possible is transferred into biomass than can be eaten by humans.

Sea urchins are marine invertebrates that feed on kelp. In regions where sea urhcins are abundant kelp forest ecosystems can be disrupted. The urhcins eat the kelps' holdfasts, which are strong structures which anchor the kelp to the sea bed. The remainder of the plant floats away resulting in a ecosystem thta is known as an 'urchin barren' ecosystem, which contains so little biomassof seaweeds that few species are able to live in this region. The presence or absence of kelp beds therefore has a major influence on the structure of the marine community. In many areas, sea otters feed on urchins, keeping their levels low and therefore the kelp forests intact. During the 19th century this ecological balance was destroyed when populations of sea otters were almost wiped out by excessive hunting for otter fur. This balance has since been restored by the cessation of the hunting of sea otters, allowing them to again gain control of the abundance of sea urchins and in turn the productive kelp forests have been able to redevelop.

Nutrients have to be constantly recycled through an ecosystem in order for plants and animlas to grow, as they are used up by organisms and there is no large external source constantly replenishing nutrients in the way the sun supplies energy. Decomposition is a chemical proces in which a compound is broken down into smaller molecules or its constituent elements. Often an essential element such as nitrogen or carbon cannot be used directly by an organism in the organic matter it is in, in dead or waste matter. This organic material must be processed into inorganic elements and compounds which are a more usuable form, and returned to the environment. A decomposer is an organism that feeds on and breaks down dead plant or animal matter, thus turning organic compounds into inorganic ones (nutrients) available to photosynthetic producers in the ecosystem. Decomposers are primarily microscopic fungi and bacteria. Decomposers are saprotrophs because they obtain their energy from dead or waste organic material (saprobiotic nutrition). They digest their food externally by secreting enxymes onto dead organisms or organic waste matter. The enzymes break down complex organic molecules into simpler soluble ones which the decomposers then absorb, releasing stored inorganic compounds back into the environment. Detrivires are another class of organism involved in decomposition, they help to speed up the decomposition process by feeding on detritus. They break it down into smaller pieces of organic material, increasing the surface area for decomposers to work on. Examples include woodlice or earthworms. Detrivores perform internal digestion.

Nitrogen is am essential element for making amino acids and consequently proteins. Animals obtain nitrogen from the food they eat, but plants need to have to take in nitrogen from their environment. Nitrogen is abundant in the atmosphere, but this form cannot be taken up by plants, and needs to be combined with oxyegn or hydrogen, and bacteria play a very important role in converting nitrogen into a form useable by plants. The processes of nitrogen fixation, nitrification, denitrification and ammonification all form part of the nitrogen cycle.

Nitrogen fixing bacteria such as Azobacter and Rhizobium contain the enzyme nitrogenase which combines atmospheric nitrogen with hydrogen to produce ammonia. This process is known as nitrogen fixation. Azobacter is a free living soil bacterium, however many nitrgen-fixing bacteria such as Rhizobium live inside root nodules, and has a symbiotic mutualistic relationship with the plant as the plant gains amino acids from Rhizobium produced by fixing nitrogen gas into ammonia, and the bacteria gain carbohydrates produced by the plant during photosynthesis, which they use as an energy source. Recent studies suggest that plants 'select' Rhizobium colonies that provide the most nitrates by cutting off nodules that contain less productive bacteria by cutting off the supply of carbohydrates. This is a form of natural selection which maximises the benefit to the plant. 

Nitrification is the process by which ammonium compounds in the soil are converted into nitrogen containing molecules that can be used by plants. Free living bacteria in the soil called nitrifying bacteria are involved. Nitrification is an oxidation reaction and so only occurs in well aerated soil and takes place in 2 steps:

• Nitrifying bacteria (such as Nitrosomonas) oxidise ammonium compounds into nitrites (NO2-)
• Nitrobacter oxidise nitrites into nitrates (NO3-) which are highly soluble and therefore the form in which most nitrogen enters a plant.

In the absence of oxygen, for example in waterlogged soils, denitrifying bacteria in the soil back into nitrogen gas. This process is known as denitrification and only happens under aerobic conditions. The bacteria use the nitrates as a source of energy for respiration.

Ammonification is the name given to the process by which decomposers convert nitrogen containing molecules in dead organisms, faeces, and urine into ammonium compounds.

Carbon is a component of all major organic molecules present in living organisms such as lipids, proteins and carbohydrates. The main source of carbon for land living organisms is the atmosphere. Although carbon dioxide only makes up 0.04% of the atmosphere, there is a constant cycling of carbon between the atmosphere, the land and living organisms. 

Carbon dioxide is present in the atmosphere and dissolved in the seas and oceans. It is converted into small carbon containing molecules by photosynthesis in plants and algae and the carbon is used in the production of complex macromolecules. These are passed from producers into primary consumers when they are eaten and are passed up the food chain via feeding. Respiration of producers and consumers releases carbon dioxide into the atmosphere. When living organisms die the carbon compounds in their bodies are released by decomposition. The carbon is released into the atmosphere as carbon dioxide when the decomposers respire. If dead organic matter accumulates in areas where decomposers are not present such as the bottom of the ocean or in bogs, the carbon they contain may become 'trapped'. Over millions of years these remains form fossil fules, which released carbon dioxide back into the atmosphere via combustion.

Carbon dioxide levels fluctuate throughout the day as photosynthesis only takes place in the light, and so during the day photosynthesis removes carbon dioxide from the atmosphere. Respiration however is carried out by all living organisms thriugh the day and night, releasing carbon dioxide at a relatively constant rate into the atmosphere. Therefore atmospheric carbon dioxide levels are higher at night than in the day. Localised levels also fluctuate seasonally and are lower in summer than in winter as photosynthesis rates are higher. Over the past 200 years global atmospheric carbon dioxide levels have increased significantly, mainly due to:

• The combustion of fossil fuels - which has released carbon dioxide back into the atmosphere which had been previously trapped for millions of years below the Earth;s surface.
• Deforestation - which has removed significant quantities of photosynthesising biomass form Earth and as a result less carbon dioxide is removed from the atmosphere.

The amount of carbon dioxide dissolved in seas and oceas is affected by the temperature of the water (higher temperatures lead to less gas being dissolved), so global warming reduces the carbon bank in the oceans resulting in a positive feedback loop. Increased levels of carbon dioxide trap more thermal energy in the atmosphere and human activites is contributing to global warming.

Ecosystems are dynamic, and are constantly changing over time, on reason this occurs is due to succession, which occurs as a resut of changes to the environment which cause the animal and plant species present to change. There are twp types of succession:

• Primary succession - this occurs on an area of land that has been newly formed or exposed such as bare rock, and there is no soil or organic material present to begin with. It can occur when volcanoes erupt creating igneous rock, by sand being blown by wind to create new sand dunes, by silt and mud being deposited at river estuaries, or when glaciers retreat depositing rubble and exposing rock.
• Secondary succession - this occurs on areas of land where soil is present, but it contains no animal or plant species, for example the earth that remains after a forest fire.

Succession takes place in a number of stages, each known as a seral stage. At each seral stage key species can be identified that change the abiotic factors such as the soil to make it more suitable for the subsequent existence of other species. The main seral stages are pionerr community, indermediate community and climax community.

Primary succession begins with the colonisation of an inhospitable environment, by organisms known as pioneer species which represent the first seral stage. These species arrive as spores or seeds carried by the wind from nearby land masses or by the droppings of birds. Examples include algae and lichen. Pioneer species have a number of adaptations that enable them to colonise a bare environment such as:

• The ability to produce large quantities of seeds or spores which can be blown by the wind and deposited on the 'new land'.
• Seeds germinate rapidly.
• The ability to photosynthesise and to produce their own energy - light, rainfall and air (and so carbon dioxide) are often the only abiotic factors present.
• Tolerance to extreme environments.
• The abaility to fix nitrogen from the atmosphere, so adding to the mineral content of the soil.

Over time weathering of the bare rock produces particles that form the basis of a soil. On its own this cannot support other species. However when organisms of the pioneer species die and decompose small organic compounds are released into the soil. This organic component of soil is known as humus. The soil becomes able to support the growth of new species of plant, known as secondary colonisers, as it contains minerals such as nitrates and has an ability to retain some water. These secondary colonisers arrive as spores or seeds. Mosses are an example of secondary colonisers. In some cases pioneer species also provide a food source for consumers so some animal species will start to colonise the area. As the environmental conditions continue to include new species of plant arrive which are known as tertiary consumers, these plants have a waxy cuticle that protects them from water loss. These species can survive in conditions without an abundance of water, but need to obtain most of their water and mineral salts from the soil. At each stage the rock continues to be eroded and the mass of organic matter increases. When an organism decompose they contribute to more nutrient-rich soil which retains more water making the abiotic conditions more favourable initially for small flowering plants like grasses. This period of succession is known as the intermediate community and in often multiple seral stages evolve during this period until climax conditions are attained. At each seral stage different plant and animal species are better adapted to the current conditions in the ecosystem, these organisms outcompete many of the  species that were previously present and become the dominant species.

The final setal stage is called the climax community. The community is then in a stable state and will show very little change over time. there are normally a few dominant plant and animal species, which are the most abundant species (by mass) present in the ecosystem at a given time. Which species make up the climax community deoends in the climate. For example in climates where the temperature is mild and there is plenty of water, large trees will usually form the climax community. By comparision in a sub-artic climate ferbs or shrubs make up the climax community as temperature and water availibility are low. Although biodiversity generally increases as succession takes place, the climax community is often not the biodiverse. Biodiversitytends to reach peak in mid-succession and then tends to decrease due to the dominant species out-competing pioneer and other species, resulting in their elimimation. The more successful the dominant species, the less the biodiversity in a given ecosystem. 

Alongside the succession of plant species, animal species undergo similar progression. Primary consumers such as insects are first to colonise an area as they consume and shelter in the mosses/lichens present. They must move in from neighbouring areas so animal succession is slower, especially if the new area is geographically isolated. Secondary consumers arrive once a suitable food source is established and the existing plant cover will provide them with suitable habitats. Eventually larger animals will colonise the area when abiotic factors are favourable.

Human activites can halt the natural flow off succession and prevent the ecosystem from reaching a climax community. When succession is stopped artificially, the final stage that is formed is known as a plagioclimax. Agriculture is one of the main reasons this occurs, for example:

• Grazing and trampling of vegetation by domesticated animals resulting in large areas remaining as grassland. 
• Removing existing vegetation (shrub land) to plant crops which become the final community.
• Burning as a means of forest clearance - this often leads to an increase in biodiversity as it provides space and nutrient-rich ash for other species to grow such as shrubs.

Deflected succession is an important conservation technique. To ensure the survival of certain species it is important to preserve their habitat in its current form, which may require ecological management to prevent further succession from occuring, so measures such as mimicking controlled grazing or removing successional species are used to maintain a current state of an environment, such as in the maintennance of heathland and its community.

One of the few examples where all the stages of succession can be seen clearly in one place is when a series of sand dunes form on a beach with the youngest dunes being found closest to the shore and the oldest being furthest away. Seeds are blown onto the dunes or washed onto the sand by the sea. At this stage the rooting conditions are poor due to drought, strong winds, and salty seawater immersion, The presence of a large number of shells also makes the environment very alkaline. As the wind blows across the dunes it moves the sand constantly changing the profile of the dunes and allowing rainwater to soak through rapidly. However, some of the species such as sea couch grass are able to survive these harsh conditions.

Marram grass becomes the next dominant species. As these plants grow sand is trapped between the roots helping to stabilise the dunes, and the formation of soil begins. Minerals released from decaying pioneer plants create more fertile growing conditions and the soil becomes less alkaline as pioneer plants grow and trap rainwater. The grasses also reduce salt spray into the hind dunes and act as a partial wind barrier. Less resistant plants can now grow and over time they start to shade out the pioneers. As more species of plant colonise the dunes the sand gradually disappers. Finally taller or more complex plant species can grown and plants from earlier stages are no longer present. When the water table reaches or nearly reaches the suface, dune slacks occur and plants that are specially adapted to be water-tolerant can grow here adding to the biodiversity of the sand dunes.

The distribution of organisms refers to where individual organisms are found within an ecosystem, and it is usually uneven throughout an ecosystem. Organisms are generally found where abiotic and biotic factors favour them, and therfore their survival rate is high as all the resources they need to live are presnet and predation/pressure from consumers is low. To measure the distribution of organisms within an ecosystem, a line or belt transect is normally used. A line transect involves laying a line or surveyor's tape along the ground and taking samples are regular intervals. A belt transect provides more information - two parallel lines are marked and samples are taken of the area between these specified points. Belt and line transects are a form of systematic sampling, a type of non-random sampling. In systematic sampling different areas within an overall habitat are identified, which are then sampled seperately. This cna have advanatgea over random sampling as it allows scientists to study how the differing abiotic factors in differing areas of the habitat affect the distribution of a species. For example systematic sampling may used to study how plant species change as you move inland from the sea. This would therefore be used to stud the successional changes that take place along a series of sand dunes.  

The abundance of organisms refers to the number of individuals of a species present in an area at any given time. This number may fluctaute daily, it can increase due to immigration and births increasing the number of individuals, and can decrease due to emigration and deaths decreasing the number of individuals. A population is a group of similar organisms living in an area at a given time. Populations can rarely be counted accurately, for example because some animals elude capture, it may be too time consuming to count all members of a population, or the counting process could damage the environment. Populations are therefore estimated using sampling techniques. A sample, however, is never entirely representative of the organisms present in a habitat. To increase accuracy you should use as large a sample size as possible as the greater the number of individuals studied, the lower the probability that chance will influence the result. ou should also use random sampling to reduce the effects of sampling bias. 

Measuring plant abundance: to measure the abundance of plants, qiuadrats are placed randomly in an area. The abundance of organisms in that area is done by countinf the number of individual plants contained within a quadrat, and then abundance can be estimated using the following formula: Estimated number in population (per square metre) =

Number of individuals in sample/Area of sample (metres squared)

Measuring animal abundance: Quadrtaes cannot be used to measure the abundance of animals (unless they are very slow moving, such as barnacles or mussles) so the capture-mark-release-recapture technique is often used to estimate population size. The techniques is carred out as follows:

• Capture as many individuals as possible in a sample area and mark or tag each individual.
• Release the marked animals back into the sample area and allow time for them to redistribute themselves throughout the habitat.
• Recapture as many individuals as possible in the original sample area.
• Record the number of marked and unmarked individuals present in the sample and release all individuals back into their habitat.
• Use the Lincoln index to estimate the population size where Estimated population size = 

(number of individuals in first sample) x (number of individuals in second sample/number of recaptured marked individuals.

Once the abundance of all the organisms present in a habitat has been determined you can then calculate the biodiversity present in a habitat using Simpson's Index of Diversity (D).