1. The Darwin Project at MIT: Modeling Marine Microbes from Cellular to Global Scales.
What is the Darwin Project?
Goals
Investigators
Funding
Modeling global phytoplankton biogeography
Prochlorococcus ecotypes
Some future directions

2. What is the Darwin Project?
An inter-disciplinary, inter-departmental effort at MIT to develop and apply novel models of marine microbes and microbial communities
from molecular and cellular scales that regulate an individual’s response to its environment
to the large scale environmental influences
What regulates observed community structure?
What are feedbacks on the environment?
How might structure and feedbacks vary with climate?

3. Ecosystem structure and function Physical and Chemical Environment
Genomes
Proteins
Metabolism
Growth and reproduction
Physical and Chemical Environment
competition
predation
natural selection
community
self-assembly
Ecosystem structure
and function

4. The Darwin Project at MIT
Genomes
Proteins
Metabolism
Growth and reproduction
Physical and Chemical Environment
competition
predation
natural selection
community
self-assembly
Earth, Atmospheric
and Planetary
Sciences
Computational and
Systems Biology
Civil and
Environmental
Engineering
Ecosystem structure
and function

5. Who are the Darwin Project Investigators?
Microbial ecologists, microbiologists, climate scientists, biogeochemists, computer scientists across the campus at MIT:
PI’s: Follows, Chisholm, Marshall, Tidor, Mastudaira, Hill, Delong, Polz
Investigators: Stephanie Dutkiewicz, Jason Bragg…
Matt Gardner
Links to the wider community: CAMERA, C-MORE, …

6. How is the Darwin Project Funded
How is the Darwin Project Funded? The Moore Foundation Marine Microbiology Initiative
Personnel:
Mick and Steph
2 post-docs, programmer
2 grad students
Computational Infrastructure:
128 node compute cluster
512 terabyte storage facility
64 panel visualization wall
National Lambda Rail link

7. What have we been doing?
Pursuing a “self-organizing” approach to modeling the phytoplankton community structure of the global ocean
The emergent biogeography and physiological characteristics of model analogs of Prochlorococcus provide a proof-of-concept.

8. Prochlorococcus ecotype habitats along AMT13
(Johnson et al., Science, 2006)
Genetically distinct ecotypes
Correlated physiological differences
Expressed as different habitats

9. What sets ecosystem structure?
physical and
chemical
environment
genetics and
physiology
competition
predation
selection
ecosystem structure
and function

10. physical and genetics and chemical physiology environment competition
Empirical physiological descriptions
MITgcm – simulated environment
physical and
chemical
environment
genetics and
physiology
O(100) cell types
competition
predation
selection
ecosystem structure
and function
Emergent ecosystem

11. Emergent biogeography – 16 most abundant phytoplankton types
Prochlorococcus analogs
Synechococcus & small eukaryotes .
Diatoms
In these runs 15 – 20 “phytoplankton functional types” are “fit” i.e. maintain a population above some threshold value
KEY:
1 – 4, top row: The four most abundant Prochlorococcus analogues (small phyto, cannot assimilate NO3)
5 – 9, second row + 1: Small phyto, can consume NO3 (Synchococcus and small eukaryote analogues)
10 – 12, rest of third row: Diatom analogues (large phyto, need Si)
13 – 16, bottom row: Other large phyto
Other large eukaryotes

12. Prochlorococcus ecotypes
Plausible emergent analogs of Prochlorococcus ecotypes
Model ecotype physiologies are also consistent with real-world counterparts.
Prochlorococcus ecotypes
AMT13 (Johnson et al., 2006)
Emergent
model-ecotypes

13. What next?
Examine emergent microbial community structure in the light of ecological theory (Steph and Jason)
Examine the role of unresolved ocean eddies in shaping community structure (Andrew)
Model and interpret variations of community structure and relationship to climate
Address genomic and metagenomic data sets
Mechanistic cellular scale parameterizations:
systems biology
Address a broader range of organism types: heterotrophs, mixotrophs, grazers, virus
Adaptive organisms, mutation, natural selection

14. Addressing metagenomic data
DeLong Lab
Mapping microbial communities by function
CAMERA – metagenomic storehouse and analysis facility
C-MORE

15. Climate Variations and Community Structure
Continuous Plankton Recorder – Sir Alister Hardy Foundation
Continuous sampling of ~250 planktonic taxa in North Atlantic since 1930’s
Can we simulate changes? Response to climate variations?
Diatom abundance,
NE/SE regions

16. Systems Biology
Develop mechanistic descriptions of environmental sensitivities
Replace/enhance empirical parameterizations

17. The Darwin Project at MIT
Genomes
Proteins
Metabolism
Growth and reproduction
Physical and Chemical Environment
competition
predation
natural selection
community
self-assembly
Ecosystem structure
and function

19. P P Self-organizing ecosystem model:
initialize many organism types
fittest organisms selected for by interactions of organisms and environment, reflecting real world organization P P
Complex initialized food web self-organized state

20. Simulation of Prochlorococcus ecotypes provides
Proof of concept for the approach
Test-bed for ecological theory and interpretation (e.g. Tilman, 1977; Steph and Jason)
Basis for Darwin Projects flagship, regional and global simulations
examining broader spectrum of organisms and biogeographical controls
Investigating links to biogeochemical cycles and climate change