1. Quantitative symbiogenesis
Van Gogh NWO-exchange programme F-NL
on aggregation methods & time scale separation
Kooijman, Bas, VU-Amsterdam
Kooi, Bob, VU-Amsterdam
Auger, Pierre, Claude-Bernard Univ.-Lyon
Poggiale, Jean-Christophe, Centre d’Oceanol. -Marseilles
Dept of Theoretical Biology
Vrije Universiteit, Amsterdam

2. Contents of lecture symbiosis in context of DEB research
Internat Conf on Mathematics and Biology of the SMB
Knoxville, 2002/07/13-16
symbiosis in context of DEB research
elements of simplest DEB model
symbiosis in context of evolution
application of DEB theory to symbiogenesis
results

3. Dynamic Energy Budget theory
for metabolic organisation of all life on earth
first principles
quantitative
Biological equivalent of Theoretical Physics
Primary target: the individual with consequences for
sub-organismal organization
supra-organismal organization
Relationships between levels of organisation
Applications in
ecotoxicology
biotechnology
Direct link with empiry

4. DEB-ontogeny-IBM

5. DEB-ontogeny-IBM
Tom Hallam
visits Delft
1985/08/12

6. Reserve dynamics Increase: assimilation  surface area
Decrease: catabolism  reserve/structure
First order process on the basis of densities follows from
weak homeostatis of biomass = structure + reserve
partitionability of reserve dynamics
Mechanism: structural homeostasis
key feature: avoiding dilution by growth

7. Product Formation According to Dynamic Energy Budget theory:
Product formation rate =
wA . Assimilation rate +
wM . Maintenance rate +
wG . Growth rate
For pyruvate: wG<0
ethanol
pyruvate,m g/l
glycerol, ethanol, g/l
pyruvate
glycerol
throughput rate, 1/h
Glucose-limited growth of Saccharomyces

8. 1 Reserve – 1 Structure

9. 2 Reserves – 1 Structure

10. Simultaneous Substrate Processing
Flux of C:
Chemical reaction: 1A + 1B C
Poisson arrival events for molecules A and B
Standard enzyme kinetics:
Substrate Conc product flux (MM-kinetics)
Synthesizing Unit-concept: irreversible SU-substrate binding
Substrate conc substrate flux (transport module)
Substrate flux product flux + rejected substrate flux

11. Simultaneous Nutrient Limitation
B12 content,
10-21 mol/cell
P content, fmol/cell
Specific growth rate of Pavlova lutheri as function
of intracellular phosphorus and vitamin B12 at 20 ºC
Data from Droop 1974
Note the absence of high contents for both compounds
due to damming up of reserves, and
low contents in structure (at zero growth)

12. Reserve Capacity & Growth
low turnover rate: large reserve capacity
high turnover rate: small reserve capacity
DEBtool is freely downloadable from

13. Organism An organism converts substrates into products
and a bit more of itself

14. Symbiosis Major basis:
substrate
substrate
Major basis:
exchange of products between partners: syntrophy
with transitions to competition & parasitism & predation
Mutualism: not essential
“beneficial” involves an optimization criterion

15. Green animals corals Rotifera Platyhelminthes Cnidaria Dicranophorus
caudatus
Encentrum
saundersiae
Chlorohydra
viridissima
Itura
aurita
Rotifera
corals
Typhloplana
viridata
Dalyellia
viridis
Platyhelminthes
Cnidaria
From: Streble, H. & Krauter, D Das Leben im Wassertropfen. Komos, Stuttgart

16. Green fungi: lichenes
From: Nash, T. H Lichen biology, Cambridge UP

17. Green ciliates Ophrydium versatile Strongylidium crassum Strombidium
viride
Urostyla viridis
Stentor
polymorphus
Didinium
faurei
Paramecium
bursaria
Spathidium
opimum
Teuthophrys
trisulcata
Prorodon
viridis
From: Streble, H. & Krauter, D Das Leben im Wassertropfen. Komos, Stuttgart

18. Green protists Heliozoa Foraminifera Heterophrys myriepoda
Raphidiophrys
viridis
Heliozoa
Acanthocystis
mimetica
From:
Streble, H. & Krauter, D. 1973
Das Leben im Wassertropfen.
Komos, Stuttgart
Wolf-Gladrow, D. A., Bijma, J. &
Zeebe, R. E.1999
Mar. Chem 64:
Foraminifera
Globigerinoides
sacculifer

19. Choroplast evolution
Delwiche, C. F Tracing the thread of plastid diversity through the tapestry of life.
Am. Nat. 154, S164-S177

20. Survey of Organisms http://www.bio.vu.nl/thb/ “education”,”cycles”
many life cycle pictures
Basidiomycota
Eustigmatophyceae
Ascomycota
Raphidophyceae
Zygomycota
brown algae
Phaeophyceae
Xanthophyceae
Microsporidia
Plasmodiophoromycota
Chlorarachnida
Chytridiomycota
Cercomonada
Chrysophyceae
Labyrinthulomycota
Bicosoecia
animals
Synurophyceae
Percolozoa
Pseudofungi
Neomonada
Dictyochophyceae
Euglenozoa
Opalinata
Dinozoa
Kinetoplastida
Pelagophyceae
Sporozoa
Diplonemida
diatoms
Bacillariophyceae
Ciliophora
Myxomycota
plants
Cormophyta
Protostelida
Some parts of the classification are well-settled, other parts
are more speculative
protist classification is based on a combination of
Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. and Doolittle,
W. F A kingdom-level phylogeny of eukaryotes based on
combined protein data. Science 290:
Cavelier-Smith, T A revised six-kingdom system of
life. Biol. Rev. 73:
Lee, R. E Phycology, Cambidge University Press
Patterson, D. J The diversity of eukaryotes, Am. Nat. 154:
S96-S124
flagella fundamentally different from bacteria with usually a
[9(2)+2] structure of microtubules; are also named undulipodia
nuclear envelope usually present
Prymnesiophyceae
Rhizopoda
Cryptophyceae
green algae
Chlorophyceae
Archaeprotista
Glaucophyceae
Actinopoda
Bacteria
red algae
Rhodophyceae
Xenophyophora
Trichozoa
Granuloreticulata
Metamonada

21. Steps in symbiogenesis
Free-living, clustering
Internalization
Free-living, homogeneous
Structures merge
Reserves merge

22. Steps in symbiogenesis
in the context of the DEB theory
2 populations, substrates, products
from substitutable to complementary products
spatial clustering
internalization
weak homeostasis for structure
from concentrations to fluxes of internal prod.
strong homeostasis for structure
coupling of assimilation fluxes
coupling of reserve dynamics
weak homeostasis for reserves
strong homeostasis for reserves

23. Chemostat Steady States
Free living
Products substitutable
Free living
Products complementary
Endosymbiosis
Exchange on conc-basis
biomass density
Exchange on flux-basis
Structures merged
Reserves merged
Host uses 2 substrates
throughput rate
symbiont
host

24. Results It is possible to merge partners smoothly
through incremental changes of parameter values
Homeostasis can be achieved gradually
range of ratio of structures reduces
Partitionability argument for reserve kinetics
can be reformulated in a mergebility argument
If partners follow DEB rules,
symbiogenesis can be such that
symbiosis again follows DEB rules
We made some progress in understanding
the modular organization of cell’s metabolism
in an evolutionary context

25. Thank you for your attention
Free internet course on DEB theory
February-April 2003 (part time)
Tom: congratulations !