Synthesizing Units in Population Dynamics Bas Kooijman ept of Theoretical Biology rije Universiteit, Amsterdam ttp://www.bio.vu.nl/thb/deb/ Amsterdam, 2004/09/04 Aggregation & Perturbation Metho and Adaptive Dynamics adult embryo juvenile Dynamic Energy Budge theory for metabolic organisatio
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Synthesizing Units in Population Dynamics Bas Kooijman Dept of Theoretical Biology Vrije Universiteit, Amsterdam Amsterdam,
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When changing the space-time scale, new processes will become important other will become less importantIndividuals are special because of straightforward energy/mass balances
Each process has its characteristic domain of space-time scales
Research priorities
• Trophic interactions (nutrient recycling)
• Energetic implications of behaviour
• Simplification of individual-based models to small set of ode’s while preserving properties of individuals in populations
• Links between levels of organization separation of scales in time & space
individual system earth
Interactions of substrates
Kooijman, 2001Phil Trans R Soc B356: 331-349
Typical change in bounded fractions of SUs with
Flux of metabolite:
Mixtures of types:
Example of mixture between substitutable and complementary compounds:
SU dynamics
Trophic interactions
• Competition for same resources size/age-dependent diet choices
• Syntrophy on products faeces, leaves, dead biomass
• Parasitism (typically small, relative to host) biotrophy, milking, sometimes lethal (disease) interaction with immune system
• Predation (typical large, relative to prey) living individuals, preference for dead/weak specialization on particular life stages (eggs, juveniles) inducible defense systems; cannibalism
Tra
nsit
ions
bet
wee
n th
ese
type
s fr
eque
ntly
occ
ur
Symbiosis
product
substrate
Symbiosis
substrate substrate
Internalization
Structures merge Reserves merge
Free-living, clusteringFree-living, homogeneous
Steps in symbiogenesis
throughput rate
Chemostat Steady Statesbi
omas
s de
nsit
y
hostsymbiont
Free livingProducts substitutable
Free livingProducts complementary
EndosymbiosisExchange on conc-basis
Exchange on flux-basis Structures merged Reserves mergedHost uses 2 substrates
Symbiogenesis
• symbioses: fundamental organization of life based on syntrophy ranges from weak to strong interactions; basis of biodiversity• symbiogenesis: evolution of eukaryotes (mitochondria, plastids)• DEB model is closed under symbiogenesis: it is possible to model symbiogenesis of two initially independently living populations that follow the DEB rules by incremental changes of parameter values such that a single population emerges that again follows the DEB rules• essential property for models that apply to all organisms
Kooijman, Auger, Poggiale, Kooi 2003 Quantitative steps in symbiogenesis and the evolution of homeostasisBiological Reviews 78: 435 - 463
Resource dynamicsTypical approach
Usual form for densities prey x and predator y:
Problems:• Not clear how dynamics depends on properties of individuals, which change during life cycle• If i(x) depends on x: no conservation of mass; popular: i(x) x(1-x/K)• If yield Y is constant: no maintenance, no realism• If feeding function f(cx,cy) cf(x,y) and/or input function i(cx) ci(x) and/or output function o(cx) co(x) for any c>0: no spatial scaling (amount density)Conclusions:• include inert zero-th trophic level (substitutable by mass conservation)• need for mechanistic individual-based population models
Prey/predator dynamics
)(),(
),()(
yoyxfYydt
d
yxfxixdt
d
Resource dynamics
Nutrient
Effect of grazing
• rejuvenation of producers
• remobilization of nutrients via feces: fast, major flux
via dead consumers: slow, minor flux
Producers feed on feces and dead biomass: syntrophic aspects
Producer/consumer dynamics
PnCnNPm
ChrCdt
d
CjPrPdt
d
NPNCN
C
PAP
)(
PK
jj
my
kr PAm
PANNP
NP /1
;1
CNCPCNCPC rrrrr
1111
MNPANCNCNMPPACPCP kjmyrkjyr ;
producer
consumer
nutr reserveof producer
: total nutrient in closed system
N
h: hazard rate
CPCCN rry special case: consumer is not nutrient limited
• first preference for dead consumers enhanced remobilization of nutrients, which stimulates producers
• second preference for weak (non-productive) consumers most species have a post-reproductive stage reduction of competition productive non-productive consumers
• post-preference for strong (productive) consumers rejuvenation of consumers
Indirect syntrophic aspects via nutrients and producers
Resource dynamics
Nutrient
Producer/consumer/predator dynamicspr
oduc
erco
nsum
erpr
edat
or
total nutrient total nutrient
no p
refe
renc
e
pref
eren
ce f
or d
ead
and
wea
k
Effects of parasites/pathogensOn individuals: Many parasites • increase (chemical manipulation)• harvest (all) allocation to dev./reprod.Results• larger body size higher food intake• reduced reproduction
On populations: Many small parasites• convert healthy (susceptible) individuals to affected ones on contact• convert affected individuals into unsusceptible one
Predation in combination with parasitism:• predators protect consumers against pathogens via preference for weak individuals• weak individuals are more susceptible than strong ones
Resource dynamics
Nutrient
Co-metabolismConsider coupled transformations A C and B DBinding probability of B to free SU differs from that to SU-A complex
Co-metabolismCo-metabolic degradation of 3-chloroaniline by Rhodococcus with glucose as primary substrateData from Schukat et al, 1983
Brandt et al, 2003Water Research37, 4843-4854
Co-metabolismCo-metabolic anearobic degradation of citrate by E. coli with glucose as primary substrateData from Lütgens and Gottschalk, 1980
Brandt et al, 2003Water Research37, 4843-4854
Adaptation
glucose, mg/l glucose, mg/l
spec
ific
grow
th r
ate,
h-1
“wild type”Schulze & Lipe, 1964
glucose-adaptedSenn, 1989
Glucose-limited growth of Escherichia coli
70 mg/l 0.06 mg/l
max
.5 max
many types of carriers only carriers for glucose
Aggressive competition
V structure; E reserve; M maintenance substrate priority E M; posteriority V MJE flux mobilized from reserve specified by DEB theoryJV flux mobilized from structure amount of structure (part of maint.) excess returns to structurekV dissociation rate SU-V complex kE dissociation rate SU-E complex kV kE depend on such that kM = yMEkE(E. + EV)+yMVkV .V is constant
Main driving force behind evolution:• Darwin: Survival of the fittest (internal forces) involves out-competition argument• Wallace: Selection by environment (external forces) consistent with observed biodiversity
Mean life span of typical species: 5 - 10 Ma
Sub-optimal rare species: not going extinct soon (“sleeping pool of potential response”) environmental changes can turn rare into abundant species
1-species mixotroph community
Mixotrophs areproducers, which live off light and nutrientsas well asdecomposers, which live off organic compounds which they produce by aging
Simplest community with full material cycling
1-species mixotroph communityCumulative amounts in a closed community as function of total C, N, light
E: reserveV: structureDE: reserve-detritusDV: structure-detritusrest: DIC or DIN
Note: absolute amountof detritus is constant
Canonical communityShort time scale:Mass recycling in a community closed for mass open for energy
Long time scale:Nutrients leaks and influxes
Memory is controlled by life span (links to body size)Spatial coherence is controlled by transport (links to body size)
1-spec. vs canon. community
Total nitrogenTotal carbon
Tot
al n
itrog
enT
otal
nitr
ogen
1-species:mixotroph community
3-species:canonicalcommunity
biomass
nutrient
detritus
biomass
detritus
nutrient
nutrient
consumer
producerdecomposer
decomposer
producer
consumerT
otal
car
bon
Tot
al c
arbo
n
Self organisation of ecosystems• homogeneous environment, closed for mass • start from mono-species community of mixotrophs• parameters constant for each individual• allow incremental deviations across generations link extensive parameters (body size segregation) • study speciation using adaptive dynamics• allow cannibalism/carnivory• study trophic food web/piramid: coupling of structure & function• study co-evolution of life, geochemical dynamics , climate
Kooijman, Dijkstra, Kooi 2002 Light-induced mass turnover in a mono-species community of mixotrophsJ. Theor. Biol. 214: 233-254
Organic carbon pumpWind: weak moderate strong
light + CO2
“warm”no nutrients
coldnutrientsno light
readily degradable
poorly degradable
no growth growth poor growthbloom
producersbind CO2
from atmosphereand transport
organic carbonto deep ocean
recovery ofnutrients tophoto-zone
controls pump
Rhizosolenia Phaeocystis
Chlorophyll
Methane hydrates
Methane food chain
methane-ice worm Hesiocoeca with methanothrophic symbionts
Photosynthesis: CO2 + H2O + NO3 + h CHON + O2
Decomposition: CHON + O2 CO2 + H2O + NO3 Fermentation: CHON + H2O CO2 + H2 + NO3 Methanogenesis: CO2 + H2 H2O + CH4 Methanotrophy: CH4 + CO2 + H2O + O2 + NH3 CHON M-host: CHON + O2 CO2 + H2O + NH3
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Rock cycle
SiO2 + CaCO3
CO2 + CaSiO3H4SiO4 + 2 HCO3
- + Ca++
2 CO2 + 3 H2O
weathering
burialsedimentation
out gassing
Photosynthesis: H2O + CO2 + light CH2O + O2
Fossilisation: CH2O C + H2OMethanogenesis: 4 H2+ H+ + HCO3