P6 - Bottle Microcosm

BI201 – General Ecology
Weeks 10-12 Practical: Bottle Microcosm
This week you will be creating a mini-ecosystem or a ‘microcosm’ that explores biogeochemical cycles
and environmental change. The microcosm has three basic components (i.e., soil, water and plants) and
you will observe changes to this system over 15-21 day period. Background information on “Bottle
biology” can be found here http://bottlebiology.org/investigations/terraqua_main.html.
In lectures in the next three weeks of the course you will be learning about global ecosystem patterns
and factor, in particular primary productivity and cycling of nutrients (biogeochemical cycles) and lastly,
looking at human-induced environmental change. By creating a microcosm in a bottle, we have the
opportunity to study these topics at a much smaller and more easily manipulated scale. The learning
points for this home-based practical are manifold but the main objectives are:
 To learn about primary productivity and how it is related to nutrient cycles.

 To understand how decomposition is related to nutrient flows in an ecosystem.
 To practically demonstrate the effect of decomposition and nutrient cycling on primary
productivity in the form of plant growth.
 To demonstrate the effect of human-induced environmental change on our microcosm
by simulating environmental pollution.
Materials Required
You will need to gather these items from around your home before beginning the experiment:
1. A 1.5L water bottle (for Fiji based students I recommend the Aquasafe bottle)
2. A cotton wick (such as the wicks used in kerosene or benzene lamps) ~ 3 inches long
3. 1.5L of freshwater (I recommend collecting rainwater prior to creating your bottle microcosm)
4. Soil (loamy soil from your garden; if your garden soil is too sandy or red, use potting mix or add
an equal portion of organic compost to the garden soil)
5. Seeds of a quick growing vegetable such as beans, cabbage, okra (if you do not have seeds or
are unable to buy seeds use small seedlings of any plant species that you may find growing in
your garden [these must be young,
small and still growing])
6. Ingredients to make a soapy mixture
(soap, dish detergent, laundry
detergent or washing powder and
freshwater)
7. A standard ruler (a clear plastic one
is recommended but you may use
any that you have)
Experimental Protocol
Part A: Making your bottle microcosm
1. Remove the label from the water bottle. Cut around the shoulder or just below the part of the
bottle that curves toward the mouth (just above the upper edge of the label). When this upper part
of the bottle is fully cut off, removed and turned upside down it should resemble the upper part of a
‘vintage’ wine glass.
2. Using a heated skewer or simply a sharp knife, make a small opening approx. 3-4 mm across, in the
centre of the bottle cap.
3. Insert a cotton wick (used for kerosene or Benzine lamps) in through the hole so that about an inch
lies above the cap (with the top half of the bottle you have cut up standing in an upturned position)
and the rest of the wick will hang down into the bottom half of the bottle.
4. Fill the upturned half of the bottle to the cut edge, with soil from your garden. The amount of soil
should cover the wick completely.
5. Stand the bottom half of the bottle on a flat surface, in an upright position and sit the soil-filled top
half of the bottle into the open bottom half.
6. Mark on the side of the lower half of the bottle, the

position or level where the cap sits on the inside. Life the
top half out carefully so as not spill the soil and place this
somewhere it won’t spill (you can place this into a mug or
cup or have someone hold onto it until you are done with
step 8).
7. In the lower half of the bottle pour fresh water (rain water
would be best), to just below the cap (the water level must
not reach the cap).
8. Place the top half of the bottle filled with soil back into the bottom half, taking care to ensure the
wick hangs down into the water.
9. Plant 5 seeds of a fast growing vegetable (like cabbage or okra or beans) into the soil (bury them just
below the surface of the soil; not too deep or they will not germinate).
10. Every one or two days check the bottle(s) and replenish the water level back to the original level
(only when necessary; replace with fresh water only). Keep doing so until the seeds germinate.
11. It would be a good idea to create three replicate microcosm bottles to ensure you have sufficient
data to analyse. Another good idea would be to have a fourth bottle as an experimental control,
where there is no addition of organic compost and the pollutant (in Part B and Part C). If you have
more than one replicate try to ensure that all have exactly the same components (types of water
bottles, water source, volume of water, wicking, amount and type of soil, number and type seeds
planted) so that it is only the addition of the nutrients (organic compost) and then pollutant that
influences seed growth).
Part B: Measuring plant growth
12. Once germinated, establish a set routine whereby each day at the same time or thereabouts, you
measure the height of the seedlings by gently holding the seedling upright and stretched out against
a standard ruler. Best to wait until the seedlings are at least 1 cm tall before you begin taking
measurements. In your records, record the date and time too. After measuring the seedlings, top up
the water to the original level before replacing the upper half into the lower half of the bottle.
13. Take seedling height measurements daily for at least one week after the seeds have germinated. Be
sure to use the same ruler and method of measuring height, each time you take measurements.
Record these values in the datasheet overleaf.
14. After 5-7 days of growth, add ½ a cup of organic compost (which you can make by placing vegetable
peelings and/or garden clippings in a container from the first day you start preparing for the
experiment) to the soil being careful to place the compost around the seedlings and not smother
the seedlings.
15. Take seedling height measurements daily for at least one week after the seeds have germinated. Be
sure to use the same ruler and method of measuring height, each time. Record these values in the
datasheet overleaf.
Part C: Measuring the effect of pollution
16. Create a soap or detergent mixture using tap water and soap, or dish detergent, or laundry
detergent. Try to mimic the consistency of soapy water that would go into your kitchen drain after
the dishes are washed, or soapy water discharge from your washing machine.
17. Add the soapy water (the pollutant or toxin) to the water in the bottle on day 14 of your experiment
(on this day you do not have to add the daily water refill).
18. The day after the toxin is applied, begin taking seedling height measurements again using the same
ruler. Record these values in the datasheet overleaf.
Notes:
 You must document this process using photographs and record your measurements as immediately
as possible to prevent data loss.
 You may share data amongst your group members but need to generate your own datasets and
gallery of images as evidence of individual experiments. If you share data be mindful that unless you
prepared your microcosms using the exact same materials then the seedling growth is not
comparable (as differences between your experimental set ups may affect the seedling growth; e.g.
differences in soil types, freshwater vs tapwater, types of seeds used, amount and nutrient content
of the organic compose used, etc.).
 The discussion will relate to concepts covered in the lectures from weeks 11-13.
Lab Write-up
For this lab the key concepts to consider are:

 To undertake interesting research, think about what you’re going to do and why you’re going to
do it
 Good scientific method requires consistent conditions are maintainede throughout the duration
of the experiment, monitored consistently, and measurements are taken accurately
 Display the results in an easily understandable format (i.e. a clear and well labelled graph or a
summary table).
In your lab write-up, include the following:

- What is your research question? Why is this interesting? What did you expect to find prior to
taking any measurements?
- What are your reasons and support for choosing this research question?
- Methods
o What did you measure?
o How often did you make these measurements?
o How did you record and document these measurements?
o How did you ensure that conditions were kept consistent throughout the duration of
the experiment?
- Results
o Excellent documentation of what you observed over the course of the experiment. You
may choose to use tables, images, graphs, drawings etc.
o Write 1 – 2 paragraphs that summarize the key findings of the changes and observations
you made. Any assertions you make in your findings must be supported by your results.
- Summary
o Provide 1 paragraph on how your observations relate to your research question. Were
your results expected or different?
o Provide 1 paragraph on how your study could have been improved or strengthened. For
example, were there other factors that could have been measured if you’d had
appropriate equipment (and limitless budget?)?
Marking criteria
Item An excellent submission will include the following:

Introduction Brief background or rationale for the experiment. Should
(4 marks) include the overall aim, objectives, and a null and alternate
hypothesis. At least 2 peer-reviewed scientific publications
used to support the research hypothesis (HA).
Methods A simple statement of “As per guidelines”. If there are any
(0.5 mark) differences in your set up and the one described in the
guidelines you need to state briefly and clearly what the
differences were.
Results Clear and concise summary of the observations made during
(4 marks) the full duration of the experiment (in words); raw data table
and/or graph of seedling height graphed against time.
Photographs or images showing experimental set up over the
observation period.
Discussion Valid and appropriate discussion of the experiment as well as
(3 marks) directions and/or recommendations for future studies.
Originality Clear and convincing evidence that you conducted an original
(2 mark) and independent experiment.
Formatting and style (1) Scientific, logical and well-thought out; graphics easy to read
and understand; proper referencing with in text citations
correctly formatted.
Grammar and spelling (0.5) Less than 5 grammar or spelling mistakes.
TOTAL = 15 marks

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BI201 – General Ecology

Weeks 10-12 Practical: Bottle Microcosm

 To learn about primary productivity and how it is related to nutrient cycles.

Part A: Making your bottle microcosm

6. Mark on the side of the lower half of the bottle, the

Part B: Measuring plant growth

Part C: Measuring the effect of pollution

For this lab the key concepts to consider are:

In your lab write-up, include the following:

Item An excellent submission will include the following:

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