The Effect of Different Soil Samples on Microbial Diversity
Bacterial diversity in a soil sample refers to the amount of different bacteria present in
that particular sample of soil. The type of soil and the plants that are grown in the soil where the
sample was taken are the key factors that determine soil microbial diversity (2). Since soil types
and plants differ from place to place, the diversity and abundance of bacterial communities
would also differ. Generally, different ecosystems produce different numbers and different types
of bacterial communities.
Bacteria are one-celled organisms that are extremely small, most 4/100000 inch long (4).
Although their size seems insignificant, they make up for their size by numbers, millions of
individual bacteria living in a small sample of soil. Bacteria falls into four functional groups:
decomposers that help break down organic matter into more useable forms, mutualists that form
relationships with plants, pathogens that cause gall formation in plants, and chemoautotrophs that
obtain energy through compounds other than carbon (4). The bacterial diversity of soil is so
important that it can alter the soil environment, causing the soil to favor certain plants over
others (4). After the bacterial colonies establish themselves in the soil, they change the structure
of the soil and the type of environment for the plants, meaning that the amount and types of
bacteria determines the types of plants growing in the soil.
In 2005, Noah Fierer and Robert B. Jackson performed an experiment where they
collected 98 soil samples from different areas in North and South America. They found that
bacterial diversity was unrelated to the site’s temperature, latitude, and other such variables used
to determine plant and animal diversity (1). In their experiment, the difference in bacterial
diversity was due to the soil’s pH: neutral soils (pH of around 7) produced the greatest amount of
diversity while acidic soils (pH of 1-6) produced low levels of bacterial diversity (1). Fierer and
Jackson further concluded that particular soil conditions such as texture and moisture determined
microbial diversity.
We, the first period Research Design class, decided to perform a pilot study of dirt,
particularly dirt from the greenhouse, and the different microbial diversities of soil samples. Our
purpose in conducting this experiment was to analyze the microbial diversity of different soil
samples. Our normal hypothesis was that there would be a significant difference in diversity in
the different soil samples. Our null hypothesis was that there would be no difference in diversity
in the different soil samples.
Materials and Methods
All of us in the first period Research Design class (Jenny Chen, Deanna Myer, Elea
Simpson, Claire McWhite, Timo Chung, and David Wang) performed the experiment in the
greenhouse at Wootton High School in Rockville, Maryland on Friday, November 20, 2009. Our
different soil samples were: the soil from the trash can, dark soil from the sink, a negative/ soil
from an empty pot, light soil from the sink, soil taken from Deanna’s house, and soil taken from
my garden. In my paper, these samples will be known as Sample 1, Sample 2, Sample 3, Sample
4, Sample 5, and Sample 6 respectively. Our materials were: six soil samples, six funnels, six
coffee filters, six beakers, six pipettes, six petri dishes, tape, six black sharpies, Dixie cups, and
six spreading tools. Each of us chose one soil sample to perform the experiment on, Timo taking
Sample 1, Elea taking Sample 2, Claire taking Sample 3, David taking Sample 4, myself taking
Sample 5, and Deanna taking Sample 6. The size of our soil sample was a limiting factor because
we did not have enough samples so as to see whether our data was significant. Therefore, in
order to accurately calculate whether the data is statistically significant, the data is multiplied by
5, meaning that there were five trials per individual sample, each of the five trials having the
same bacterial diversity as the original sample. Doing this may have changed our results
significantly; however, this is a pilot study, not a real experiment.
In order to perform our procedure, we took all of our materials up to the Wootton High
School greenhouse. We separated the materials so we got one of each individual item, except for
the Dixie cups, which we took two each. When each of us had all of our materials, we found a
place in the greenhouse where we set up our materials. The first step was to measure out a Dixiecup full of the soil (all the way up to the top). In this first step, we were limited by the fact that
each of us was doing one sample each and that our measurements were not as accurate as it
would have been if only one person did each soil sample. Next, we put the coffee filter in the
funnel and put the funnel with the coffee filter in it on top of the empty beaker. We made sure
that each of the beakers was clean before performing the experiment. We then dumped the Dixiecup full of soil into the funnel.
To allow the bacteria to pass through the filter, we went over to the sink in the
greenhouse and measured out approximately half a Dixie cup of water. Again, measuring out the
water without being precise limited us. However, we had time restraints and had nothing else to
measure our water out with. The inaccuracy of measuring the water may have meant that more or
less bacteria may have passed through the filter paper into the beaker below it; but since our
experiment is looking at the microbial diversity of different soil samples rather than the amount
of bacteria present, that did not make a difference.
Then, we dumped the water into the filter. So as to push the water through the filter faster,
we used the bottom of our used Dixie cups to push the water through the filer, allowing the
liquid to collect in the beaker. After most all of the water had dripped into the beaker, we remove
the funnel and threw away the filter paper and soil. Using a small pipette, we measured out one
pipette-full of the liquid from the beaker. By using the same pipette, we were able to somewhat
control for the amount of liquid that would be put into the petri dish. At the same time, how
strong the pipette was squeezed could have resulted in different amounts of liquid in the pipette.
We then opened the clean and empty petri dishes to the side, just large enough to squeeze the
liquid into the petri dishes. This was done so as to not allow bacteria from the air to get into the
petri dish.
Using a clean spreading tool, we spread the liquid all around the dish. When that was
done, we taped the dish closed and labeled the lid of the dish with a black sharpie, writing down
where we got the sample from. Then, we flipped the petri dishes over so that the lid was facing
downwards. Finally, we took the petri dishes down to room 208 in Wootton High School and set
the petri dishes on the heater to allow the bacteria to grow for a weekend (Saturday, November
21, 2009- Sunday, November 22, 2009). Here, the limiting factor was that the amount of heat to
which the petri dishes were exposed to was different since they were placed on different areas on
the heater. Also, we do not know if the heater was left on over the entire weekend and whether it
was on for the full 48 hours. However, we were able to control for that by placing all of the petri
dishes on the same heater at the same time and placing them quite close to one another. On
Monday, November 23, 2009, we observed our data.
Pictures of Procedure Being Done
1)
2)
4)
6)
3)
5)
To analyze the different soil samples’ bacterial diversity, we counted the different
bacteria we saw. If the bacterium was a different size, shape, or texture, it would count as a
separate bacterium. Since we were only looking for bacterial diversity, we did not count multiple
bacteria of the same type more than once. The bacterium was very difficult to see, we tried
multiple ways to increase our view of the bacteria. Eventually, we decided that we would
primarily put each petri dish on the overhead, turn on the overhead light, and look at the
projection screen to count the bacteria. If that was ineffective and the bacterium was too small to
be seen on the overhead, we held the petri dish up to the fluorescent lights on the ceiling and
counted the bacteria that way.
The bacterial diversity count was done mainly by Elea Simpson and Claire McWhite and
the rest of us re-counted their bacteria count to make sure that no other bacteria were missed.
Since our methods were not very high-tech, our bacteria count may not have been very accurate
since there were probably bacteria that we could not see without a microscope; however, a very
rough count was good enough for our analysis. Below, I will provide photographs of all the petri
dishes with the bacteria in it. In two of the soil samples, Sample 5 and Sample 6, the bacterium
was too small to be seen on the overhead. Therefore, I had to hand-draw the bacteria that we saw
for Sample 5 and Sample 6.
Photographs of Petri Dishes
Sample 1
Sample 3
Sample 5
Sample 2
Sample 4
Sample 6
Data Analysis
Data Table
Soil Sample
Sample 1
Sample 2
Sample 3
Sample 4
Sample 5
Sample 6
Bacterial Diversity (# of
different bacteria)
2
5
2
3
2
2
Total Bacterial Diversity in
the 5 samples
10
25
10
15
10
10
Graph
The statistical analysis that I will be using is ANOVA (Analysis of Variance). I will use
this test because our experiment wants to measure the differences between the means of more
than two samples, six to be exact. We will look at the F ratio (test statistic) and the F value. If the
F ratio is greater than the F value, than we can reject the null hypothesis and accept our normal
hypothesis.
Since the F ratio is infinite and is greater than the F value, I rejected my null hypothesis
and accepted my normal hypothesis that there is a significant difference in the bacterial diversity
of the different soil samples. Another question to investigate might be other factors that
contribute to bacterial growth such as temperature, moisture, and plant growth. One such testable
question might be: How does temperature affect bacterial diversity? The hypothesis could be:
Bacterial diversity will decrease steadily as temperature increases.
Bibliography
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626.full>.
2. Garbeva, P., J. A. Van Veen, and J. D. Van Elsas. “MICROBIAL DIVERSITY IN SOIL:
Selection of Microbial Populations by Plant and Soil Type and Implications for Disease
Suppressiveness.” Annual Reviews. N.p., 2 Apr. 2004. Web. 24 Nov. 2009.
<http://arjournals.annualreviews.org/doi/abs/10.1146/
annurev.phyto.42.012604.135455?select23=Choose&cookieSet=1&journalCode=phyto>.
3. Kennedy, A. C., and K. L. Smith. “Soil microbial diversity and the sustainability of
agricultural soils .” SpringerLink. N.p., 20 Sept. 2005. Web. 24 Nov. 2009.
<http://www.springerlink.com/content/x60450v25036102j
4. Ingham, Elaine R. "Soil Biology." NRCS. United States Department of Agriculture,
n.d. Web. 28 Nov. 2009. <http://soils.usda.gov/sqi/concepts/soil_biology/
bacteria.html>.