1. ACTIVITY 2: SIZE AND SCALE MATTER! Original drawings by John Tenniel

3. http://www.ca.gov/

4. Terrestrial environment: Soil Crumb Photo and Diagram from Brock Biology of Microorganisms, Madigan and Martinko

5. Aquatic Environment: Marine “snow” ‘Hot spots’ of bacterial concentration and activity, contributing to global cycling of carbon and nutrients Azam and Long, Nature, 2001

6. Sampling soil microbes in a relatively static soil community

8. Examples of microbial communities requiring different sampling considerations: 1.Small, isolated (non-interacting), moderate density, highly diverse (Drop-soda lakes, hypersaline mats)Small, isolated (non-interacting), moderate density, highly diverse (Drop-soda lakes, hypersaline mats) 2.Small, isolated but interacting, high density, moderately diverse (Gut, Ley)Small, isolated but interacting, high density, moderately diverse (Gut, Ley) 3.Small, isolated but interacting, low density, moderately diverse (Finlay and Fenchel)Small, isolated but interacting, low density, moderately diverse (Finlay and Fenchel) 4.Large, continuous, highly diverse????? What do you suggest?Large, continuous, highly diverse????? What do you suggest?

9. 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

10. Ley et al., 2006 GUT MICROBIAL COMMUNITY Back to list

11. BIOGEOGRAPHY: IS EVERYTHING EVERYWHERE??? Fenchel and Finlay’s work, as reported in Science, 2005 Back to list

12. PNAS, 2007

13. ACTIVITY #2: Let’s “sample” some diagrammatic representations of microbial communities!

15. STATISTICAL METHODS AND PRIMER, ENVIRONMENTAL APPLICATIONS: http://epa.gov/bioindicators/statprimer/ 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)

16. 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.

17. D A C B

18. v v C D

19. Site CSmall plot Large plot count: Transects: Species1234567891123 A0003001000000 B0005000000000 C0001000000000 D0001000000000 E 8000 F 18000 G 2000 H 1000 Site DSmall plot Large plot count: Transects: Species1234567891123 A8000001006110 B3210001025210 C2211102004000 D1300001001010 E1400000101000 F116010000512100 G2160000104301 H0140204001202 I0050020001511 J0000010000010 K0000020007020 L00501400008102 M003111000013003 SOME SAMPLE DATA

20. Findlay 1982: Both approaches yield similar estimates of abundance, but larger scale sampling tends to give poor representationof distribution/patchiness

21. 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

22. Desmarais 2002 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

23. 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!