1. Molecular Ecology of Alpine Lake
Microbial Communities
Ashwani Kumar, Dinesh Hariraju, Owen Patterson,
Shreya Srivastava

2. Alpine lakes
Black canyon lake – BC
Lady of the lake – LL
Becker lake – BL
Beartooth lake – BT
Island lake – IL

3. Question ?
What is the variation in diversity among
different lakes at different depth?
Idea: Diversity variation depends on the
biogeochemical parameters.

4. Comparison of alpha diversity of alpine lakes
Fig. Comparison of dominant phyla of alpine lakes
Table : Total OTUs for dominant phyla

5. Comparison of alpha diversity at different depth
Fig. Comparison of dominant phyla of alpine lakes at
different depth
Table : Total OTUs for dominant phyla
at different depth

6. Questions
• Question being addressed
How diverse is the microbial community across different depths
in all lakes?

7. Methodology
Lake samples from depth 3 m
Mothur
Jaccard similarity, rarefaction curve,
distribution of taxons

8. Results…

9. Similarity coefficient
• Jaccard similarity
• Jabund, based on abundance of OTUs
• Jclass, based on presence or absence of species.
• Lady of lake was found to share similar OTUs with all other
lakes.

10. Jabund
Jclass
Jaccard similarity coefficient

11. Rarefaction curve

16. Venn diagram Samples-BT-BL-IL-LL

17. Phylogenetic tree

18. Samples- BL-BC-BT-LL

19. Phylogenetic tree

21. Questions
• Question being addressed
How diverse is the microbial community across different depths
in all lakes?
Conclusion:
1) Lady of lake(LL) and BL are the most diverse.
2) The species found in BL, BT and IL are closely related and
share similar OUT’s.
3) The species found in LL is found to be evolutionarily distant

22. Depth – 7 to 12 m
Alpha and Beta Diversity

23. Alpha Diversity
Group Sobs (observed
OTUs)
Shannon Index Coverage
BC 12 252 4.5137 0.8238
BT8 340 4.8988 0.7507
IL9 353 5.0541 0.7375
LL8 350 4.8546 0.7285
LL12 318 4.7294 0.7526

24. Rarefaction Curve
0
50
100
150
200
250
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350
400
0 200 400 600 800 1000 1200
OTU (0.03)
Number of Samples
Rarefaction Curve
0.03-BC12A
0.03- BT8
0.03- IL9
0.03-LL12
0.03-LL8

25. Beta Diversity
Samples – LL8,
BT8, IL9, BC12

26. Samples-
BT8, IL9, BC12, LL12

27. Jaccard Similarity
BC 12
BT8 0.8637
IL9 0.8754 0.8174
LL12 0.8712 0.8456 0.8568
LL8 0.8789 0.8557 0.8679 0.8176
BC12
BT8 0.4157
IL9 0.5257 0.3468
LL12 0.6114 0.3944 0.5177
LL8 0.6061 0.4197 0.5394 0.3427
Jaccard similarity based on Presence
Jaccard similarity based on Abundance

28. Phylogenetic Tree

29. Conclusion
• Island Lake and Lady of the Lake are the most
diverse with 353 and 350 species respectively.
• Island Lake and Beartooth Lake are the most
similar at depth 8-12 m.
• Black Canyon Lake is the most phylogenetically
distant.

30. Depths >12m

31. Depths >12 m

32. Similarity
Jaccards Index
(Abundance) BL17 BL20 BT20
BL17
BL20 0.249352
BT20 0.683578 0.694027
Jaccards Index
(Presence) BL17 BL20 BT20
BL17
BL20 0.733656
BT20 0.883239 0.871094

33. 0
50
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200
250
300
350
0 100 200 300 400 500 600 700 800 900 1000
UniqueOTUs
Samples Examined
Rarefaction Curves
0.03-BL20 0.03-BL17 0.03-BT20
Coverage:
BL17: 0.82
BL20: 0.76
BT20: 0.83

34. Relative Abundance
0
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RelativeAbundance
Observations
Phyla
Becker Lake: 17m
0
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RelativeAbundance
Observations
Phyla
Becker Lake: 20m

35. Relative Abundance
0
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RelativeAbundance
Observations
Phyla
Becker Lake: 17m
0
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RelativeAbundance
Observations
Phyla
Becker Lake: 20m

36. Relative Abundance
0
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RelativeAbundance
Observations
Phyla
Becker Lake: 17m
0
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RelativeAbundance
Observations
Phyla
Becker Lake: 20m

37. Relative Abundance
0
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RelativeAbundance
Observations
Phyla
Beartooth: 20m

38. Relative Abundance
0
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RelativeAbundance
Observations
Phyla
Beartooth: 20m

39. Relative Abundance
0
0.05
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0.15
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0.25
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0.35
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RelativeAbundance
Observations
Phyla
Grouped Relative Abundance
Depths >12 m

40. 0
0.1
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0.5
0.6
BL17 BL20 BT20
RelativeAbundance
Sampling Location
Comparison of Phyla
Cyanobacteria Actinobacteria Proteobacteria

41. Depths > 12 m
• Dominant phyla differ between sites
• Similarity in abundance differs within BL,
between depths
• Similarity (presence) is relatively high between
samples

42. Similarity
Jaccards Index
(Abundance) BL17 BL20 BT20
BL17
BL20 0.249352
BT20 0.683578 0.694027
Jaccards Index
(Presence) BL17 BL20 BT20
BL17
BL20 0.733656
BT20 0.883239 0.871094

43. Depths > 12 m
• Dominant phyla differ between sites
• Similarity in abundance differs within BL,
between depths
• Similarity (presence) is relatively high between
samples