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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
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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
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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
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Ester vs Ether lipids 10.2
Eubacteria
Archaea
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Nucleated prokaryotes 10.2a
Planktomycetes Poribacteria
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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
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Giardia (Eopharyngia, Metamonada) 10.2c
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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
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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
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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
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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
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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
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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”
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(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
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Please open DEB Ch10 Part II