Seminar given at the Linnean Center for Plant Biology, Uppsala, Sweden, 30 November 2015

1. Sarracenia as a model system for
studying ecological regime shifts
Aaron M. Ellison
@AMaxEll17

4. Acknowledgments
• Raphael Contamin (École Normale Supérieure, Paris)
• Steve Carpenter (Wisconsin)
• Ben Baiser (Harvard Forest/Gainesville)
• Jennie Sirota (North Dakota State / HF REU)
• Bryan Ballif, Nick Gotelli, Amanda Northrop (Vermont)
• Ohio State Mathematical Biosciences Institute
• Santa Fe Institute
• Vermont Genetics Network
• NSF DBI 10-03938, DEB 11-44056

6. http://www.beringclimate.noaa.gov/reports/np_04.htm
From:IPCC[2001]Working
GroupIIreport)

7. Photo credit: Karen Scott

8. Photo : Karen ScottModel: Carpenter & Brock (2006)

9. cUHF
dt
dU
a 
))(( 2
dt
dW
rXMRbMsX
dt
dM

Annual time steps
36 within-year time steps
))(()()1( 21
dt
dW
rXMRXhs
dt
dW
cUHF
dt
dX
i  
Model modified from Carpenter & Brock 2006 by Contamin & Ellison 2009

10. Contamin & Ellison (2009) Ecological Applications

11. Includes both point-source and non-point-source inputs, “reasonable” levels of variance in the system,
intermediate (“politically acceptable”) rates of intervention and allowance of future inputs.
More aggressive
management and
intervention;
lower system variance;
“precautionary” principle
Slower, “conservative”
management; higher
system variance;
higher “consumer” risk
Contamin & Ellison (2009) Ecological Applications

13. Prey input (organic matter loading  prey mineralization)
A small change in nutrients
forces the system across
the bifurcation fold to a
new equilibrium
Away from the bifurcation
fold, the system remains in
its equilibriumSmall changes in the driver
lead to large, albeit
continuous changes in
response
Large changes in the driver
lead to proportionally large,
continuous changes in
response
Dissolvedoxygen

16. Sirota et al. (2013) PNAS

17. Sirota et al. (2013) PNAS

18. Sirota et al. (2013) PNAS

19. Sirota et al. (2013) PNAS

21. In-gel digest &
LC-MS/MS
Protein ID via search of custom
database
Metagenome
ortholog
designation
blastp
Blast2GO
Taxonomic analysis Protein entries
Functional analysis
Protein analysis
C E
Retinol metabolism
alpha Linolenic acid metabolism
C5 Branched dibasic acid metabolism
Glycine serine and threonine metabolism
Porphyrin and chlorophyll metabolism
Phenylalanine metabolism
Selenocompound metabolism
beta Alanine metabolism
Sulfur metabolism
Aflatoxin biosynthesis
Valine leucine and isoleucine biosynthesis
Toluene degradation
Tyrosine metabolism
Aminobenzoate degradation
Glutathione metabolism
Pantothenate and CoA biosynthesis
Alanine aspartate and glutamate metabolism
Oxidative phosphorylation
Limonene and pinene degradation
Butanoate metabolism
Lysine degradation
Arginine and proline metabolism
Phenylalanine tyrosine and tryptophan biosynthesis
Valine leucine and isoleucine degradation
Novobiocin biosynthesis
Pentose phosphate pathway
Carbon fixation in photosynthetic organisms
Pyruvate metabolism
Cysteine and methionine metabolism
Glyoxylate and dicarboxylate metabolism
Citrate cycle TCA cycle
Purine metabolism
Pyrimidine metabolism
0 0.02 0.04 0.06 0.08 0.1
Proportion of all peptides in pathway
Color Key
-elongation factor tu
-f0f1 atp synthase subunit beta
-molecular chaperone
-branched-chain amino acid abc transporter
substrate-binding protein
-porin
-f0f1 atp synthase subunit alpha
-phosphate abc transporter
substrate-binding protein
-heat shock protein 60
-dna-directed rna polymerase subunit beta
--dependent receptor plug
-glutamine synthetase
-malate dehydrogenase
-membrane protein
-rna polymerase sigma factor
-outer membrane protein
-polymerase
--dependent receptor
-abc transporter
substrate-binding protein
-atp synthase beta subunit
-60 kda partial
-not present
-elongation factor tu
-f0f1 atp synthase subunit beta
-molecular chaperone
-porin
-branched-chain amino acid abc transporter
substrate-binding protein
-atp synthase beta subunit
-dna-directed rna polymerase subunit beta
-abc transporter
substrate-binding protein
-outer membrane protein
-isocitrate lyase
-phosphate abc transporter
substrate-binding protein
-3-hydroxyacyl- dehydrogenase
-aldehyde dehydrogenase
-atp synthase alpha subunit
-glutamine synthetase
-phasin family protein
-ribosomal protein l1
-malate dehydrogenase
-rna polymerase sigma factor
-ribosomal l10 family protein
-not present
C E
155 15565
C E
Shared Proteins
Unmanipulated
control (C)
Detritus-
enriched (E)

22. 155 15565
C E
Shared Proteins

24. a
b

25. -elongation factor tu
-f0f1 atp synthase subunit beta
-molecular chaperone
-branched-chain amino acid abc transporter
substrate-binding protein
-porin
-f0f1 atp synthase subunit alpha
-phosphate abc transporter
substrate-binding protein
-heat shock protein 60
-dna-directed rna polymerase subunit beta
--dependent receptor plug
-glutamine synthetase
-malate dehydrogenase
-membrane protein
-rna polymerase sigma factor
-outer membrane protein
-polymerase
--dependent receptor
-abc transporter
substrate-binding protein
-atp synthase beta subunit
-60 kda partial
-not present
-elongation factor tu
-f0f1 atp synthase subunit beta
-molecular chaperone
-porin
-branched-chain amino acid abc transporter
substrate-binding protein
-atp synthase beta subunit
-dna-directed rna polymerase subunit beta
-abc transporter
substrate-binding protein
-outer membrane protein
-isocitrate lyase
-phosphate abc transporter
substrate-binding protein
-3-hydroxyacyl- dehydrogenase
-aldehyde dehydrogenase
-atp synthase alpha subunit
-glutamine synthetase
-phasin family protein
-ribosomal protein l1
-malate dehydrogenase
-rna polymerase sigma factor
-ribosomal l10 family protein
-not present
C E

26. C E
Retinol metabolism
alpha Linolenic acid metabolism
C5 Branched dibasic acid metabolism
Glycine serine and threonine metabolism
Porphyrin and chlorophyll metabolism
Phenylalanine metabolism
Selenocompound metabolism
beta Alanine metabolism
Sulfur metabolism
Aflatoxin biosynthesis
Valine leucine and isoleucine biosynthesis
Toluene degradation
Tyrosine metabolism
Aminobenzoate degradation
Glutathione metabolism
Pantothenate and CoA biosynthesis
Alanine aspartate and glutamate metabolism
Oxidative phosphorylation
Limonene and pinene degradation
Butanoate metabolism
Lysine degradation
Arginine and proline metabolism
Phenylalanine tyrosine and tryptophan biosynthesis
Valine leucine and isoleucine degradation
Novobiocin biosynthesis
Pentose phosphate pathway
Carbon fixation in photosynthetic organisms
Pyruvate metabolism
Cysteine and methionine metabolism
Glyoxylate and dicarboxylate metabolism
Citrate cycle TCA cycle
Purine metabolism
Pyrimidine metabolism
es in pathway
C E
Retinol metabolism
alpha Linolenic acid metabolism
C5 Branched dibasic acid metab
Glycine serine and threonine me
Porphyrin and chlorophyll metab
Phenylalanine metabolism
Selenocompound metabolism
beta Alanine metabolism
Sulfur metabolism
Aflatoxin biosynthesis
Valine leucine and isoleucine bi
Toluene degradation
Tyrosine metabolism
Aminobenzoate degradation
Glutathione metabolism
Pantothenate and CoA biosynth
Alanine aspartate and glutamate
Oxidative phosphorylation
Limonene and pinene degradati
Butanoate metabolism
Lysine degradation
Arginine and proline metabolism
Phenylalanine tyrosine and tryp
Valine leucine and isoleucine de
Novobiocin biosynthesis
Pentose phosphate pathway
Carbon fixation in photosyntheti
Pyruvate metabolism
Cysteine and methionine metab
Glyoxylate and dicarboxylate me
Citrate cycle TCA cycle
Purine metabolism
Pyrimidine metabolism
0 0.02 0.04 0.06 0.08 0.1
Proportion of all peptides in pathway
Color Key