Transcript Slide 1

ACTIVITY 2:
SIZE
AND
SCALE
MATTER!
Original drawings by John Tenniel
http://www.ca.gov/
Terrestrial environment: Soil Crumb
Photo and Diagram from Brock Biology of Microorganisms, Madigan and Martinko
Aquatic Environment:
Marine “snow”
‘Hot spots’ of bacterial
concentration and activity,
contributing to global cycling of
carbon and nutrients
Azam and Long, Nature, 2001
Sampling soil microbes in a
relatively static soil
community
Location of Proposed Phytormediation Cells
th
N or
Stre
et
59.70 ft
L ow M e r c ur y I s opltth (1-20 ppm)
Isopleth - A
Low Mercury Concentration
A1
A3
Ctl
mer A
High M e r c ur y I s opltth (96-320 ppm)
200 cm
100 cm
115.22 ft
200 cm
A6
W
ate
r
Ctl
wt
B ro
A5
ok
Di
rec
tio
A7
A8
A9
wt
Ctl
Barnum C
o
urt
n
mer A
Plot Key (Enlarged to show detail)
Plot ID
A1
Approximate soil sampling location
A1-1
mer A = presence of mer A gene
Ctl = No Plants
}
Di
rec
tio
n
53.13 ft
A1-2

Populus deltoides type
wt = Wild Ty pe
W
ate
r
187.46 ft
(Isopleth areas are approximate)
nz a
A4
mer A
a
Koh
wt
I nte r me diate M e r c ur y I s opltth (29-50 ppm)
A2
Reference Position
WT
A1-3
A1-4
43.58 ft
17.91 ft
80.60 ft
20.30 ft
81.19 ft
Examples of microbial communities requiring
different sampling considerations:
1. Small, isolated (non-interacting), moderate density, highly
diverse (Drop-soda lakes, hypersaline mats)
2. Small, isolated but interacting, high density, moderately
diverse (Gut, Ley)
3. Small, isolated but interacting, low density, moderately
diverse (Finlay and Fenchel)
4. Large, continuous, highly diverse????? What do you suggest?
Drop-size soda lakes (Qvit-Raz , Genetics, 2008)
This is an amzing study showing actual differences in complex communities that go
through successional stages in tiny drops that form from dew and exudates of the
Tamarax tree which releases salty compounds.
Back to list
GUT MICROBIAL COMMUNITY
Ley et al., 2006
Back to list
BIOGEOGRAPHY:
IS EVERYTHING
EVERYWHERE???
Fenchel and Finlay’s work, as
reported in Science, 2005
Back to list
PNAS, 2007
ACTIVITY #2:
Let’s “sample” some diagrammatic representations
of microbial communities!
BRAINSTORM: HOW DOES ONE MAKE
DECISIONS ABOUT SAMPLING?
1. Size of population, community or system, area of interest
2. Scope of study?
3. Budget?
4. Variability (standard deviation, error)? depends on heterogeneity,
abundance, distribution, both spatial and temporal, method, etc.
5. Technological ability (Can one directly observe organisms or cells? Can one
target individuals or groups with specificity? How precise are the units of
measurement?)
6. Experimental approach
7. SCALE! (many issues)
STATISTICAL METHODS AND PRIMER, ENVIRONMENTAL APPLICATIONS:
http://epa.gov/bioindicators/statprimer/
EXAMINE YOUR BACTERIAL “COMMUNITY “ and answer
the following questions:
1. Would it be more appropriate to sample a large number of small plots, or fewer large
plots? Considering the scale, how many large plots would be feasible to measure? Would
sampling a larger number of smaller plots be less or more costly or time consuming?
2. Would using a line transect approach be appropriate? What would be the advantages or
disadvantages to using this method, compared to plot sampling?
3. Describe a microbial ecosystem or community that you feel most
closely matches the hypothetical “community” that your diagram
represents.
A
B
C
D
v
v
v
C
D
SOME SAMPLE DATA
Site C
Small plot
count:
Species
1
2
A
0
0
B
0
0
C
0
0
D
0
0
E
F
G
H
Small plot
count:
Species
1
2
A
8
0
B
3
2
C
2
2
D
1
3
E
1
4
F
1 16
G
2
1
H
0
1
I
0
0
J
0
0
K
0
0
L
0
0
M
0
0
3
0
0
0
0
4
3
5
1
1
5
0
0
0
0
6
0
0
0
0
7
1
0
0
0
8
0
0
0
0
Site D
3
0
1
1
0
0
0
6
4
5
0
0
5
3
4
0
0
1
0
0
1
0
0
0
0
0
0
11
5
0
0
1
0
0
0
0
2
0
0
0
14
10
6
0
0
0
0
0
0
0
0
2
1
2
0
0
7
1
1
2
1
0
0
0
4
0
0
0
0
0
8
0
0
0
0
1
0
1
0
0
0
0
0
0
Large plot
count:
Transects:
9
1
1
0
0
0
0
0
0
0
0
0
0
0
0
8
0
18
0
2
0
1
0
Large plot
count:
Transects:
9
1
1
0
6
1
2
5
2
0
4
0
0
1
0
0
1
0
5
12
1
0
4
3
0
1
2
0
1
5
0
0
0
0
7
0
0
8
1
1
3
0
2
0
0
0
0
0
0
0
0
2
1
1
0
1
0
0
0
0
1
1
2
0
0
3
0
0
0
0
0
0
0
0
3
0
0
0
0
0
0
1
2
1
0
0
2
3
Findlay 1982:
Both approaches yield similar estimates
of abundance, but larger scale sampling
tends to give poor representationof
distribution/patchiness
WHAT ABOUT MICROBIAL COMMUNITIES?
Ranjard et al. 2003 tested effect of SIZE of soil sample used in molecular
community analysis.
For bacteria, SIZE OF SAMPLE did not affect ability to distinguish unique
communities from one another. For fungi, samples <1g may not be adequate.
HOWEVER, in larger samples, technique of DNA extraction is biased toward
dominant organisms and may not accurately assess diversity.
FOR BACTERIA: Many subsamples are often taken, and it is the selection of
the sampling location that will give best indicator of larger scale abundance
and diversity
When is use of transect appropriate?
•One example: when one hypothesizes a gradient relationship and wishes to
test it using regression analysis, see below!
•In this study, researchers looked for change in numbers of fecal indicator
organisms across various transects in relation to water’s edge.
•Keep in mind, most aquatic depth sampling is, in effect – transect sampling
Desmarais 2002
FINAL THOUGHTS:
•The question being asked drives the experimental design.
•The practical limitations of sampling limit the type of question that
can be asked – and answered!
•Pilot sampling is always essential to assess the nature of the
system!!
Students will better understand scientific process when
they appreciate the considerations that go into every
scientist’s sampling and measurement plan!