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                            TOPIC 2.5: INVESTIGATING ECOSYSTEMS

To a large extent it is the physical (abiotic) conditions within any environment that controls the plant and thus the animal (biotic) community that develops. In terrestrial ecosystems physical conditions in the atmosphere, at the surface and  within the soils all interact to create the conditions that give rise to vegetation that develops. To make links between the physical environment and the biotic communities, ecologist and environmental scientist need to be able to measure the abiotic conditions.

Remember that biotic components of an ecosystems consists of all of the living organisms in the ecosystem.  Measuring the biotic component can be a challenge at times. Especially if the organism you are trying to sample is traveling over 50km per hour.  It can also be a challenge trying to find out how many anthills are in a 100 square kilometers.

In this unit you will learn how to make dichotomous keys to identify organisms and various sampling techniques. This unit is a minumum of 4.5 hours.

Significant ideas:

  • The description and investigation of ecosystems allows for comparisons to be made between different ecosystems and for them to be monitored, modelled and evaluate over time, measuring both natural change and human impacts.

  • Ecosystems can be better understood through the investigation and quantification of their components.


Knowledge & Understanding:

2.5.U1 The study of an ecosystem requires that it be named and located; for example, Deinikerwald in Baar, Switzerland—a mixed deciduous–coniferous managed woodland.

  • ​Demonstrate sound knowledge of named and located ecosystems.

Ecosystem ecology is the study of these and other questions about the living and nonliving components within the environment, how these factors interact with each other, and how both natural and human-induced changes affect how they function.

Understanding how ecosystems work begins with an understanding of how sunlight is converted into usable energy, the importance of nutrient cycling, and the impact mankind has on the environment. Plants convert sunlight into usable forms of energy that are carbon based. Primary and secondary production in populations can be used to determine energy flow in ecosystems. Studying the effects of atmospheric? CO2 will have future implications for agricultural production and food quality


2.5.U2 Organisms in an ecosystem can be identified using a variety of tools including keys, comparison to herbarium or specimen collections, technologies and scientific expertise.

  • Explain how to identify organisms using keys, technology and scientific expertise​

Proper identification of species is important to biologists if they want to compare their study area to other regions. Knowing the organisms that live in your region can help you to learn about their function within the ecosystem
and why it is important to protect them



2.5.U3 Sampling strategies may be used to measure biotic and abiotic factors and their change in space, along an environmental gradient, over time, through succession, or before and after a human impact (for example, as part of an EIA).

  • Explain sampling strategies and how they are applied to measuring changes in abiotic and biotic factors over time and space

Investigations in to ecosystems are very complicated since there are so many different factors that need to be considered. We can broadly group factors influencing ecosystems in to: biotic factors are living factors affecting an organism, such as food, competition or disease and abiotic factors, non-living factors.

If we want to know what kind of plants and animals are in a particular habitat, and how many there are of each species, it is usually impossible to go and count each and every one present. It would be like trying to count different sizes and colors of grains of sand on the beach.

This problem is usually solved by taking a number of samples from around the habitat, making the necessary assumption that these samples are representative of the habitat in general. In order to be reasonably sure that the results from the samples do represent the habitat as closely as possible, careful planning beforehand is essential.

Samples are usually taken using a standard sampling unit of some kind. This ensures that all of the samples represent the same area or volume (water) of the habitat each time.

Know the methods for measuring any three significant abiotic factors and how these may vary in a given ecosystem with depth, time or distance.

  • Marine—salinity, pH, temperature, dissolved oxygen, wave action

  • Freshwater—turbidity, flow velocity, pH, temperature, dissolved oxygen

  • Terrestrial—temperature, light intensity, wind speed, particle size, slope, soil moisture, drainage, mineral content.


There are three main ways of taking samples.

  1. Random Sampling - usually carried out when the area under study is fairly uniform, very large, and or there is limited time available

  2. Systematic Sampling (includes line transect and belt transect methods). - when samples are taken at fixed intervals, usually along a line.

  3. Stratified Sampling. - used to take into account different areas (or strata) which are identified within the main body of a habitat. These strata are sampled separately from the main part of the habitat

2.5.U4 Measurements should be repeated to increase reliability of data. The number of repetitions required depends on the factor being measured.

  • Explain why measurements need to be repeated.​


Reliability, like validity, is a way of assessing the quality of the measurement procedure used to collect data in a dissertation. In order for the results from a study to be considered valid, the measurement procedure must first be reliable. Reliability in research data refers to the degree to which an assessment consistently measures whatever it is measuring.

There are many forms of reliability, all of which will have an effect on the overall reliability of the instrument and therefore the data collected. Reliability is an essential pre-requisite for validity. It is possible to have a reliable measure that is not valid, however a valid measure must also be reliable.Below are some of the forms of reliability that the researcher will need to address

Inter-Rater or Inter-Observer Reliability
Used to assess the degree to which different raters/observers agree when measuring the same phenomenon simultaneously.

Test-Retest Reliability
Compares results from an initial test with repeated measures later on, the assumption being that the if instrument is reliable there will be close agreement over repeated tests if the variables being measured remain unchanged.

Parallel-Forms or Alternate-Forms Reliability
Used to assess the consistency of the results of two similar types of test used to measure the same variable at the same time.


2.5.U6 Methods for estimating the biomass and energy of trophic levels in a community include measurement of dry mass, controlled combustion and extrapolation from samples. Data from these methods can be used to construct ecological pyramids.

  • Explain methods for estimating biomass and energy in different trophic levels.

  • Explain how biomass and energy measurements can be used to construct ecological pyramids.

Primary productivity

As we saw in section 2.3.2, net primary productivity (NPP) is calculated using the following formula. Where GPP is gross primary productivity and R is respiration.

The method used to measure these components is partially direct and partially indirect. GPP is all the biomass that is produced before respiration and it is not possible to measure that. What we actually see in the plant is NPP – what is left after repair and respiration.

Dry weight measurements of quantitative samples could be extrapolated to estimate total biomass. Biomass is calculated to indicate the total energy within in a living being or trophic  level. The greater the mass of the living material the greater the amount of energy present.

​Secondary productivity
Given that it is unethical to kill animals, any measurements for secondary productivity will be inaccurate due to the variations in water content of different specimens.

The various elements of secondary productivity that need to me measured are gross secondary productivity (GSP) which is the food eaten – fecal loss. Net secondary productivity is GSP – R (respiration).


2.5.U7 Methods for estimating the abundance of non-motile organisms include the use of quadrats for making actual counts, measuring population density, percentage cover and percentage frequency.

  • Explain the use of quadrats for estimating the abundance of non-motile organisms through making actual counts, measuring population density, percentage cover and percentage frequency

Quadrat sampling is a classic tool for the study of ecology, especially biodiversity. In general, a series of squares (quadrats) of a set size are placed in a habitat of interest and the species within those quadrats are identified and recorded.

​A quadrat is usually a square made of wire. It may contain further wires to mark off smaller areas inside, such as 5 × 5 squares or 10 × 10 squares. The organisms underneath, usually plants, can be identified and counted. Quadrats may also be used for slow-moving animals, eg slugs and snails.



  • Number of species in an individual area

Population Density

  • The number of individuals per unit area

  • Once you know the number of individuals it is a simple calculation to establish the population density

  • D=ni/A (D = density; n = number of individuals in species, A = sampling area)

Percent Coverage

  • The proportion of ground that is occupied or area covered by the plant/species

  • Easily assessed if the quadrat is subdivided into 100 smaller squaresCi=ai/A​

Percent Frequency

  • The number of times a given event occurs

  • How often a particular species appears in an area.

  •  Best done with a gridded quadrat


2.5.U8 Direct and indirect methods for estimating the abundance of motile organisms can be described and evaluated. Direct methods include actual counts and sampling. Indirect methods include the use of capture–mark–recapture with the application of the Lincoln index.

  • Identify the types of direct and indirect methods

  • Apply the use of the Lincoln index


It is impossible for you to study every organism in an ecosystem. The number of organisms can be overwhelming. Limitations must be put on how many plants and animals you study. In order to study the animals there are trapping methods which help obtain more samples, like:

  • pitfall traps

  • small mammal traps

  • nets

  • pooter

  • light traps

  • kick sampling

  • tullgren funnels

  • aerial photography

It is important to take into consideration that the methods. It must be remembered that any method used to capture the animal must be as harmless as possible. Completely harmless capture is unlikely but there are some techniques that are less harmful. There are numerous humane techniques to catch animals for study then release them. 

Lincoln Index
The Lincoln Index is an indirect method by which the size of an animal population can be estimated. It is also called the capture/mark/release/recapture method

– n1 is the number caught in the first sample
– n2 is the number caught in the second sample
– nm is the number caught in the second sample that were marked

Assumptions of Lincoln Index:

  • The proportion of marked animals in the second sample is the same as the proportion of marked animals to unmarked animals in the whole population.

  • Enough time has elapsed to allow full mixing of marked and unmarked animals.

  • All animals are just as easily caught – that is unlikely as some animals may be more easily caught in both samples giving a biased sample.

  • The population is closed and that there is no immigration or emigration.


Issues Associated with Lincoln Index

  • Capturing the animals may injure them or alter behavior

  • The mark may be toxic to some animals but not others – you may not know until it is tested on the organism under study.

  • Marks may rub off between release and recapture.

  • Marks may make the animal more or less attractive to predators.

  • Some animals become trap happy (causing an overestimation of numbers) whilst others become trap shy (causing an under-estimation).


2.5.U9 Species richness is the number of species in a community and is a useful comparative measure.

  • Interpret species richness data.

Biological diversity can be quantified in many different ways. The two main factors taken into account when measuring diversity are richness and evenness. Richness is a measure of the number of different kinds of organisms present in a particular area.

​For example, species richness is the number of different species present. However, diversity depends not only on richness, but also on evenness. Evenness compares the similarity of the population size of each of the species present.


2.5.U10 Species diversity is a function of the number of species and their relative abundance and can be compared using an index. There are many versions of diversity indices, but students are only expected to be able to apply and evaluate the result of the Simpson diversity index as shown below. Using this formula, the higher the result (D), the greater the species diversity. This indication of diversity is only useful when comparing two similar habitats, or the same habitat over time.

  •  Apply the Simpsons diversity index.

  • Discuss the use of species richness to evaluate the status of an ecosystem.

D is the Simpson diversity index
– N is the total number of organisms of all species found
– n is the number of individuals of a particular species


Diversity is often considered as a function of two components: 

  • the number of different species 

  • the relative numbers of individuals of each species.

When we consider ecosystems, diversity is sometimes used to mean how may different species there are in a community.

Species diversity is best describe as  a combination of richness and evenness. Ecologists have developed various formula to measure species diversity.

When using the Simpson's diversity index, D is a measure of species richness. A high value of D suggests a stable and ancient site, and a low value of D could suggest pollution, recent urbanization or agricultural activity. The index is normally used in studies of vegetation but can also be applied to comparisons of animal or species diversity.

One of the most common indices of species diversity is the Simpson’s index. In Environmental Systems and Society we use a derivative of the index with the formula


Applications and skills:

2.5.A1 Evaluate sampling strategies.

The aim of sampling is to select a sample which is representative of the population. There are three techniques:

  • Random sampling

  • Stratified sampling

  • Systematic sampling


Random sampling is where each member of the population is equally likely to be included. ​For taking random samples of an area, use a random number table or random number generator to select numbers

Evaluation of random sampling


Stratified sampling is where a proportionate number of observations is taken from each part of the population. ​Divide a habitat into zones which appear different and take samples from each zone

Evaluation of Stratified Sampling


Systematic sampling is used where the study area includes an environmental gradient. A transect is used to sample systematically along the environmental gradient.

Evaluation of Systematic Sampling


2.5.A2 Evaluate methods to measure at least three abiotic factors in an ecosystem

​There are many abiotic factors that can be investigated in an ecosystem depending on the type of ecosystem. These factors can be measured in variations ways depending on the type of ecosystem

Evaluation of probes

​Evaluation of Secchi disk.

Evaluation of flow velocity meters

Evaluation of anemometer

Evaluation of clinometer


2.5.A3 Evaluate methods to investigate the change along an environmental gradient and the effect of a human impact in an ecosystem

The distribution of organisms in a habitat may be affected by physical factors, such as temperature and light. Transects and quadrats are used to collect quantitative data.

An environmental gradient is the gradual change in the biotic factors through space. An environmental gradient is present as you move up a mountain, away from a stream or a road. These changes in the abiotic factors will cause changes in the biotic factors and these can all be measured.

When measuring these changes, all parts of the gradient needs to be sampled. A transect is usually used. The simplest one is when a line of tape is laid down across the area wanted to be measured then to take samples of all the organisms touching the tape. Many transects should be taken to obtain quantitative data.

A belt transect is used for bigger samples


2.5.A4 Evaluate methods for estimating biomass at different trophic levels in an ecosystem

A food chain is made of various trophic levels. It is possible to investigate the amount of biomass and energy in each level. The major problem is that biomass is measured as dry weight and the measurements can be very destructive.

The energy in a trophic level is measured as productivity. It is easier and more ethical to take the productivity of plants than it is animals due to the dry weight problem.

The method used to measure these components is partially direct and partially indirect. Gross Primary Productivity (GPP) is all the biomass that is produced before respiration. This is not possible to measure. What we actually measure in the plant is Net Primary Productivity (NPP) – what is left after repair and respiration.

Given that it is unethical to kill animals, any measurements for Secondary Productivity (SP) will be inaccurate due to the variations in water content of different organisms. The various elements of secondary productivity that need to be measured are gross secondary productivity (GSP) which is the food eaten – fecal loss and ​Net secondary productivity (NSP) which is GSP – R (respiration).

​Evaluation of measuring biomass.

Evaluation of measuring secondary productivity

2.5.A5 Evaluate methods for measuring or estimating populations of motile and non-motile organisms

Measuring non motile species will  ​include the use of quadrats for making actual counts, measuring population density, percentage cover and percentage frequency. Motile species can be sampled using the capture-mark-release-recapture method (with estimates based on the Lincoln index)


​Evaluation of quadrats for assessing number of individuals, percentage frequency and population density.

Evaluation of quadrats for assessing percentage coverage.


2.5.A6 Calculate and interpret data for species richness and diversity

Species diversity is a function of the number of different species and their relative abundance and it is calculated using the Simpsons diversity index and is discussed fully in section

Richness is the number of species per sample. The more species present in a sample, the 'richer' the sample. Species richness as a measure on its own takes no account of the number of individuals of each species present. It gives as much weight to those species which have very few individuals as to those which have many individuals.

If you are investigating an environmental gradient you could measure the change in species diversity as you move away form the river. To calculate the Simpsons diversity index you would need to record the number of individuals of each species in every sample quadrate

High D Value Indicates:

  • Stable and ancient site

  • More diversity

  • Healthy habitat

Low D Value Indicates:

  • Dominance by one species

  • Environmental stress

  • Pollution, colonization, agriculture

Kite Diagrams
Kite diagrams are a great tool to show the spatial changes in species along a transect. They are a very effective way to show spatial changes in species diversity


2.5.S1 Design and carry out ecological investigations.


Methods of Investigation

  • The Scientific Method

  • Planning an Investigation

  • Stages of an Investigation

  • Making Investigations


Collection and Analysis

  • Transformations

  • Constructing Tables and Graphs

  • Descriptive Statistics

  • Frequency Distributions

Sampling and Data Collection

  • Direct Methods

  • Point Sampling

  • Quadrat Sampling

  • Transect Sampling

  • Mark and Recapture


Sampling Animal Populations

  • Indirect Methods

  • Equipment and Sampling Methods

  • Keying Out Species


2.5.S2 Construct simple identification keys for up to eight species.

Keys called dichotomous keys are used to identify species. The key is written so that the identification is done in steps. At each step two options are given based on different possible characteristics of the organism you are looking at.  You go through all the steps until the name of the species is discovered.

This is a key that divides macroinvertebrates into four categories.

For the exams you need to have at least eight species in the key you construct. This can also be shown graphically.

Evaluation of dichotomous key


2.5.S3 Draw graphs to illustrate species diversity in a community over time, or between communities.

Classroom Materials
Quadrat Method Samping worksheet
Quadrate Method investigation
Quadrate Sampling Lab Simulation​
A line transect
Measuring abundance
Capture / Mark / Release / Recapture practice
Lincoln Index Internal Assessment

Abiotic Systems Links
Marine Ecosystem
Woodland Ecosystem
Freshwater Ecosystem
Grassland Ecosystem

Useful Links
2.5 Practical field work Part 1​ - Niche Science
2.5 Practical Field Work Part 2 - Niche Science
How to Measure Abiotic Factors - eHow
Sampling and Measuring Abiotic and Biotic Factors from BBC
Abiotic Factors of Ecosystems - BBC Bitesize
Abiotic Tools - Educational Media Learning Centre
How to Measure Wind Speed - eHow
Ecological Sampling Methods - Offwell Woodland and Forest Trust
Measuring Biomass PDF Booklet - UN Food and Agriculture Organisation
Measuring Biomass - Global Greenhouse Warming
Cropland Capture - GeoWiki
Quadrat Sampling - Science Aid
All About Transects - PB Works
This Example from New Zealand is the model we use for the courtyard transect
Dichotomous Keys - Biology Junction
The Broads - Biology Junction
Using Dichotomous Keys - Oregon State University
Another Macro-Invertebrate Key - CVRB
Benthic Macro-invertebrates - EPA
Fieldguide to Freshwater Macro Organisms
Pond Organisms - Microscopy UK
Interactive Plant Key - Web World Wonders
Interactive Insect Key -
Interactive Tree Key - Key Nature
All Kinds of Sampling Techniques - Field Studies Counsel
Terrestrial Measuring Techniques - Oregon State University
Ecological Surveys - Offwell Woodland and Forest Trust
Lincoln Index - Offwell Woodland and Forest Trust
Biotic Index - Water Action Volunteers
Simpson's index - Offwell Woodland and Forest Trust
Simpson's Diversity  Index - Offwell Woodland and Forest Trust
Screencast of Simpson's index - Tiger Tube
Simpson Index Calculator - Al Young Studios

In The News
Biodiversity Articles from the Guardian
Biodiversity Articles from Earth Times
Terrestrial  Primary Production: Fuel For Life from Knowledge Project
Secondary productivity from Knowledge Project


  • How does the role of instrumentation circumvent the limitations of perception? Can environmental investigations and measurements be as precise or reliable as those in the physical sciences? Why is this, and how does this affect the validity of the knowledge? Applying similarly rigorous standards as are used in physics, for example, would leave environmentalists with very little they could claim as knowledge. But, by insisting on high degrees of objectivity, would we miss out on a useful understanding of the environment? Is a pragmatic or correspondence test of truth most appropriate in this subject area?

Video Clips

This video describes five common methods of sampling in data collection. Each has a helpful diagrammatic representation


















Line transects are used when you wish to illustrate a linear pattern along which plant or animl communities change. They are especially good for showing zonation. In this video I show you how to do both a continuous line transect and an interrupted line transect

















































his chapter explains the concept of line transect sampling for estimating prey populations

































































































































​Seining is the method of using a long net, with weights and floats, to capture fish and invertebrates. Learn how Smithsonian scientists are using this sampling method to look at the health of populations of nearshore fish and invertebrates in the Chesapeake Bay.

On June 30, 2010 a Harbor Porpoise (10-012) underwent satellite tagging at the University of New England's Marine Animal Rehabilitation Center and was released shortly after, a couple of miles off-shore in Biddeford, Maine.

Dr. Chris Jenkins of The Orianne Society demonstrates how to place an electronic transponder inside a live snake in order to track its movements in the wild over time. Data recovered from the electronic tracking device, called a PIT tag, are used by scientists in their efforts to save rare and endangered reptiles in their native habitats.

Paul Andersen explains the importance of biodiversity. He starts by describing how biodiversity can be species, genetic or ecosystem diversity. He explains the importance of keystone species in an environment and gives two examples; the jaguar and the sea otter. He finishes with a quote from the father of biodiversity, E.O. Wilson

Madagascar, the 4th largest island in the world and home to 5% of its plant and animal species, is designated as a "biodiversity hot spot." Hot spots are areas that are directly threatened by an expanding human population.

Wildlife biology students Brandon Davis, James Goerz and Tucker Seitz talk about their snowshoe hare research projects

This video clip shows how to use excel to calculate both Shannon-Wiener and Simpson Index for biodiversity. Only need to focus on Simpson Index

Ecosystem Investigation Techniques (2.5)

Abiotic Factors

Importance of Abiotic Factors in an Ecosystem
Abiotic Factor Procedures- how to measure (student written)


Dichotomous Keys 

​Understanding Scientific Names
Dichotomous Key Practice
How a Dichotomous Key works


Sampling Techniques

Determining what method to use


Quadrant Sampling

Quadrats can be used in conjunction with the transcet method
Sampling methodology
Random Number Generator
Quadrant sampling method - video
Using a Quadrat- video (useage of percentage vs #)
Estimation of Plant Coverage- video


Transect Sampling

There are two types of Transect Sampling: Line and Belt line. They are very similar, difference is Belt line uses wider width than just the line 
Belt Line Transect
Density Measurements using Belt line transects
​Transects, Quadrants, and Percent coverage- video
How to do a line transect- video
Random Number Generator


Diversity Indexes

 Simpson's Diversity Index
Comparison of types of Simpson's Indicies
​Diversity Indexes
Simpson's vs Shannon-Weiner Index
Calculation comparisons for Simpsons vs Weiner- includes comparison index (note: the Simpson's here uses a different


calculation than the ESS book)

Non-Motile Organism

Measuring Frequency of plants/ non motile organisms 
Population size and density

Measuring Motile Organisms

Mark Capture Release (bees)
Population size using Lincoln Index 

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