Dynamic Energy Budget theory

1 Basic Concepts 2 Standard DEB model 3 Metabolism 4 Univariate DEB models 5 Multivariate DEB models 6 Effects of compounds 7 Extensions of DEB models 8 Co-variation of par values 9 Living together10 Evolution11 Evaluation

Taxa 10a

Carolus Linneus (1758) Systema Naturae, 10th edition

TribeSubtribe

Cladus

Taxon

CohortSubcohort

Series

Section

Group

SuperfamilyFamily

Subfamily

SuperkingdomKingdom

Subkingdom

DivisionSubdivision

PhylumSubphylum

SuperclassClass

SubclassInfraclass

SuperorderOrder

SuborderInfraorder

GenusSubgenus

SpeciesSubspecies

Race

Link between classification & evolutionEvolution is only partly understoodMany species still wait for description

Early ATP generation 10.1

FeS2

FeS

H2

2H+

H2SS0

S0

H2S

2OH-

2H+

ADPATP

Pi2e-

2H2O

FeS + S0 FeS2

ADP + Pi ATP• ATPase• hydrogenase• S-reductase

Madigan et al 1997

Ester vs Ether lipids 10.2

Eubacteria

Archaea

Nucleated prokaryotes 10.2a

Planktomycetes Poribacteria

Cellulose vs Chitine 10.2b

• Opisthokonts produce chitine, not cellulose Except 2 taxa via lateral gene transfer from -proteobacteria Urochordates (Matthysse et al (2004) PNAS 27:986-981)

Aspergillus fumigatus (Nobles et al Cellulose 11:437-448)

Deuterostomes don’t produce chitine

but CaCO3 and keratine in tetrapoda

• Amoebas (Dictyostelium) & bikonts got cellulose synthetase from cyanobacteria

• Some chlorophytes produce chitinase• Many fungi produce cellulase, no animals can (symbiosis)

n

Cellulose (C12H20O10)n Chitine (C16H26O10N2)n

Ciona

Aspergillus fumigatus

Giardia (Eopharyngia, Metamonada) 10.2c

Planctomyces

• eubacteria with nuclear membranes like eukaryotes

• some species can oxidize ammonia anaerobically they have ether lipids, like archaea

• some species have genes for formaldehyde detoxification that archaea use for methanogenesis & archaea & eubacteria for methanotrophy

• are abundant in stromatolites fossil stromatolites date from 3.5 Ga ago

• propagate by budding

• probably passed its 16 genes for C1-detoxification to archea for methane production/consumption

Planktomycetes 10.2d

Evolution of central metabolism 10.2.1

i = inverseACS = acetyl-CoA Synthase pathway PP = Pentose Phosphate cycleTCA = TriCarboxylic Acid cycle

RC = Respiratory Chain Gly = Glycolysis

Kooijman, Hengeveld 2005

in prokaryotes (= bacteria)3.8 Ga 2.7 Ga

Prokaryotic metabolic evolution 10.2.1a

Chemolithotrophy • acetyl-CoA pathway• inverse TCA cycle• inverse glycolysis

Phototrophy:• el. transport chain• PS I & PS II• Calvin cycle

Heterotrophy:• pentose phosph cycle• glycolysis• respiration chain

Survey of organisms 10.2.3

Bacteria

Opi

stho

kont

s

Chromista

Amoebozoa

Alveo-lates

Plantae

Excavates

Ret

aria

Cercozoa

Sizes of blobsdo not reflect

number of species

fungi

animals

forams

cort

ical

alv

eoli

Bik

ont

DH

FR

-TS

gen

e fu

sion

chlo

ropl

asts

mem

br. d

ynun

ikon

t

loss phagoc.gap junctions tissues (nervous)

bicentriolarmainly chitin

EF1 insertion

trip

le r

oots

mai

nly

celll

ose

Survey of organisms 10.2.3a

Bacillariophyceae(diatoms)

(brown algae)Phaeophyceae

Prymnesiophyceae

RaphidophyceaeXanthophyceae

EustigmatophyceaeDictyochophyceae

Pelagophyceae

ChrysophyceaeSynurophyceae

Cryptophyceae

(plants)Cormophyta

(green algae)Chlorophyceae

(red algae)Rhodophyceae

Glaucophyceae

Euglenozoa Dinozoa

Rhizopoda

Bicosoecia

Actinopoda

Pseudofungi

Labyrinthulomycota

MyxomycotaProtostelida Ciliophora

Sporozoa

Zygomycota

BasidiomycotaAscomycota

ArchaeprotistaKinetoplastida

Microsporidia

Chytridiomycota

Percolozoa

Parabasalia

Opalinata

Metamonada

Choanozoa

Diplonemida

GranuloreticulataXenophyophora

Loukozoa

PlasmodiophoromycotaChlorarachnida

Cercomonada

Apusozoa

Pedinellophyceae

Bolidophyceae

animals

Bacteria

mitochondriaprimary

chloroplast secondary

chloroplasttertiary

chloroplastphoto

symbionts

Survey of “algae 10.2.3b

Bacillariophyceae(diatoms)

(brown algae)Phaeophyceae

Prymnesiophyceae

RaphidophyceaeXanthophyceae

EustigmatophyceaeDictyochophyceae

Pelagophyceae

ChrysophyceaeSynurophyceae

Cryptophyceae

(plants)Cormophyta

(green algae)Chlorophyceae

(red algae)Rhodophyceae

Glaucophyceae

Euglenozoa Dinozoa

Rhizopoda

Bicosoecia

Actinopoda

Pseudofungi

Labyrinthulomycota

MyxomycotaProtostelida Ciliophora

Sporozoa

Bacteria

Zygomycota

BasidiomycotaAscomycota

ArchaeprotistaKinetoplastida

Microsporidia

Chytridiomycota

Percolozoa

Parabasalia

Opalinata

Metamonada

Choanozoa

Diplonemida

GranuloreticulataXenophyophora

Loukozoa

PlasmodiophoromycotaChlorarachnida

Cercomonada

Apusozoa

Pedinellophyceae

Bolidophyceae

animals

Algae: “little green things”

but many manyexceptions

The biggest organism is a “micro-organism”

(Endo)symbiosis 10.2.3c

Paramecium bursariaParamecium bursariaciliate with green algaeciliate with green algae

Ophrydium versatileOphrydium versatileciliate with green algaeciliate with green algae

PeltigeraPeltigeraascomycete with green algaeascomycete with green algae

Cladonia diversaCladonia diversaascomycete with green algaeascomycete with green algae

Please open DEB Ch10 Part II