Julia Vorholt Lecture 9 - ETH Zn.ethz.ch/~nielssi/download/3. Semester/Mikrobiologie/Unterlagen... · Brock Biology of Microorganisms, Twelfth Edition – Madigan / Martinko / Dunlap

Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Brock Biology of Microorganisms, Twelfth Edition – Madigan / Martinko / Dunlap / Clark

752-4001-00L Mikrobiologie

Julia Vorholt Lecture 9: Phototrophy and autotrophy Global carbon and nitrogen cycles Nov 19, 2012



1) Nutrients and microbial growth 2) Introduction to principles of metabolism 3) Chemoorganotrophy 4) Chemolithotrophy 5) Phototrophy 6) Autotrophy, nitrogen fixation 7) Global carbon, nitrogen, sulfur cycles


Photophosphorylation and ETP

ELQ = h c NA -1 = h v

ELQ, Free energy of light quanta h, Planck constant (6.6 x 10-34 J s) c, the speed of light (3 x 108 m s-1) NA, Avogadro‘s number (6 x 1023) v, frequency


Types of Photosynthesis

PS I and II PS I or II

Van Niel, 1930: Photosynthesis CO2 + 2 H2A -> [CH2O] + 2 A + H2O

Chap. 13.1 Fig. 13.2

Phototrophs

Anoxygenic Oxygenic

Purple and green bacteria Cyanobacteria, algae, green plants

Reducing power Carbon Energy Reducing power Carbon Energy

electrons Light Light


Groups of Phototrophs

GreenNonsulfur-bacteria

GreenSulfur-

bacteria

Cyanobacteria

Heliobacteria

Purple bacteria (Proteobacteria)

Purple Sulfur Bacteria

Purple Nonsulfur Bacteria

(Gram +)


Evolutionary Aspects

Sunlight represents the most important energy source on earth. Phototrophs use light as sole energy source. They are the starting point of the food chain. The oxygenic photosynthesis evolved rather early in evolution, 2.7 billion years ago. => major consequences in terms of primary biomass production (unlimited availability of H2O) and the presence of O2.

Fig. 16.6

Metabolic highlights

O2 level BYA Eon Organisms,

events

Phanaerozoic

Proterozoic

Archaean

Hadean

Cambrian

Precambrian

Anoxic

Extinction of the dinosaurs

Early animals

Multicellular eukaryotes

First eukaryotes with organelles

Ozone shield

Great oxidation event

Cyanobacteria

Purple and green bacteria

Bacteria/Archaea divergence

First cellular life; LUCA Formation of

crust and oceans Formation of Earth 4.5

4.0

3.5

3.0

2.5

2.0

1.5

1.0

0.5

0

20%

10%

1%

0.1%

Endosymbiosis?

Aerobic respiration

Oxygenic photosynthesis (2H2O O2 4H) Sulfate reduction

Fe3 reduction Anoxygenic photosynthesis

Acetogenesis

Methanogenesis

Sterile Earth


Chlorophylls and Bacteriochlorophylls

Organisms must produce some form of chlorophyll (or bacteriochlorophyll) to be photosynthetic

Chlorophyll is a porphyrin They are part of the reaction center (participate directly in the conversion of light

energy to ATP) Number of different types of chlorophyll exist with different absorption spectra

Chap. 13.2 Fig. 13.3


Carotenoids and Phycobilins

Phototrophic organisms have accessory pigments in addition to chlorophyll, including carotenoids

Carotenoids Always found in phototrophic organisms Typically yellow, red, brown, or green Energy absorbed by carotenoids can be transferred to a

reaction center Prevent photo-oxidative damage to cells

Chap. 13.3 Fig. 13.8

-carotene


Anoxygenic Photosynthesis

Anoxygenic photosynthesis is found in at least four phyla of Bacteria

Electron transport reactions occur in the reaction center of anoxygenic phototrophs

Reducing power for CO2 fixation comes from reductants present in the environment (i.e., H2S, Fe2+, or NO2

-)

Chap. 13.4 Fig. 17.2 Fig. 17.6


Arrangement of Light-Harvesting Chlorophylls

RC, reaction center LH, light harvesting molecules

Chap. 13.2 Fig. 13.6


Structure of Reaction Center in Purple Bacteria

Arrangement of Pigment Molecules in Reaction Center

Molecular Model of the Protein Structure of the Reaction Center

Chap. 13.4 Fig. 13.13

1988, Nobel prize for the structure of the reaction center of Rhodopseudomonas viridis: J. Deisenhofer, H. Michel, and R. Huber


Electron Flow in Anoxygenic PS in a Purple Bacterium

Chap. 13.4

Fig. 13.14

Strong electron

donor

Poor electron

donor

1.0

0.75

0.5

0.25

0.0

0.25

0.5

(V) E0

Cyclic electron flow (generates proton motive

force)

Red or infrared light

External electron donors (H2S, S2O3

2-, S0, Fe2+)


Arrangement of Protein Complexes in Reaction Center

Chap. 13.4 Fig. 13.15

Photosynthetic membrane

Light Out (periplasm)

In (cytoplasm)

ATPase

Quinone pool


Electron Flow in Purple, Green, Sulfur and Heliobacteria

Chap. 13.4 Fig. 13.17

PSII PSI PSI

Purple bacteria Green sulfur bacteria Heliobacteria

Reverse electron

flow

Light Light Light

1.25

1.0

0.75

0.5

0.25

0

0.25

0.5

E0 (V)


Electron Flow in Oxygenic Photosynthesis

Chap. 13.5 Fig. 13.18 Photosystem II

Photosystem I

The Z Scheme:

Light

Light

PSII PSI

Cyclic electron flow (generates proton motive

force)

Noncyclic electron flow (generates

proton motive force)

1.25

1.0

0.75

0.5

0.25

0.0 E0 (V)

0.25

0.5

0.75

1.0


Oxygenic Photosynthesis

Oxygenic phototrophs use light to generate ATP and NADPH

The two light reactions are called photosystem I and photosystem II

“Z scheme” of photosynthesis Photosystem II transfers energy to photosystem I

ATP can also be produced by cyclic photophosphorylation

Chap. 13.5


Water blooms in lakes consisting of Cyanobacteria


Autotrophic CO2-fixation

6 different CO2 fixation pathways are known: 1. Calvin-Benson-Bassham cycle 2. Reductive citric acid cycle 3. Reductive acetyl-CoA pathway 4. 3-Hydroxypropionate/malyl-CoA cycle 5. 3-Hydroxypropionate/4-hydroxybutyrate cycle 6. Dicarboxylate/4-hydroxybutyrate cycle

CO2 + 4 [H] + n ATP -> (CH2O) + H2O + n ADP + n Pi

Chap. 13.12-13


The Calvin Cycle

Fixes CO2 into cellular material for autotrophic growth

Requires NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and phosphoribulokinase

6 molecules of CO2 are required to generate one molecule of glucose

Chap. 13.12 Fig. 13.30

3-Phospho-glycerate(36 carbons)

12

1,3-Bisphospho-glycerate(36 carbons)

12

Glyceraldehyde3-phosphate(36 carbons)

12

Glyceraldehyde3-phosphate(30 carbons)

10

Ribulose5-phosphate(30 carbons)

6

Ribulose1,5-bisphosphate(30 carbons)

6

Fructose6-phosphate(6 carbons)

To biosynthesis

RubisCO

Phosphoribulokinase

Sugarrearrangements

Overall stoichiometry:6 CO2 12 NADPH 18 ATP C6 H12 O6(PO3 H2) 12 NADP 18 ADP 17 Pi


Nitrogenase and Nitrogen Fixation

Only certain prokaryotes can fix nitrogen

Some nitrogen fixers are free living and others are symbiotic

Reaction is catalyzed by nitrogenase

Sensitive to the presence of oxygen

A wide variety of nitrogenases use different metal cofactors,

usually molybdenum

Pyruvate

Products

Flavodoxin(Oxidized)

Pyruvate flavodoxinoxidoreductase

CoA

Dinitrogenasereductase

(Reduced)

(Oxidized)Dinitrogenase

Flavodoxin

Dinitrogenasereductase

(Reduced)

(Oxidized)

Dinitrogenase

(Reduced)

Acetyl-CoA CO2

Nitrogenaseenzyme

complex

Nitrogenasesubstrates

Overall reaction

Chap. 13.14


Symbiotic Nitrogen Fixation

Soy bean

without with Bradyrhizobium

(Alphaproteobacterium)

Root nodules

N2 NH3

Chap. 25.3 (Fig. 25.7)

Fig. 25.8


Symbiotic Nitrogen Fixation

The mutalistic relationship between leguminous plants and nitrogen-fixing bacteria is one of the most important symbioses known

Examples of legumes include soybeans, clover, alfalfa, beans, and peas

Rhizobia are the most well-known nitrogen-fixing bacteria engaging in these symbioses

Chap. 25.3


Key terms Metabolism - I

We need to distinguish between energy sources and carbon sources (both are usually identical for chemoorganotrophic organisms) Chemotrophy (energy from chemical substrates) > Chemoorganotrophy (organic substrates) > Chemolithotrophy (inorganic substrates)

Phototrophy (energy from light)

Autotrophy (CO2 as main carbon source) Heterotrophy (organic compounds as main carbon source)

Carbon sources

Energy sources


Key terms Metabolism - II

Aerobic: Growth of an organism using oxygen as electron acceptor Anaerobic: Growth of an organism not using oxygen as electron

acceptor Aerotolerant: Anaerobic organism whose growth is not inhibited by

oxygen and does not use it as electron acceptor

Oxic: Environmental condition where oxygen is present Anoxic: Environmental condition without oxygen

Oxygenic: Type of photosynthesis, oxygen is released from water Anoxygenic: Type of photosynthesis, without oxygen release


The Carbon Cycle and Major Carbon Reservoirs on Earth

Chap. 24.1 Fig. 24.1

Carbon is cycled through all of Earth’s major carbon reservoirs, i.e., atmosphere, land, oceans, sediments, rocks, and biomass

Humanactivities

Biological pump

Death andmineralization

Respiration

CO2

CO2

CO2

Landplants

Aquaticplants and

phyto-plankton

Animals andmicroorganisms

Fossilfuels

Humus

Soil formation

Earth’s crust Rock formation

Aquaticanimals


Methane hydrate

Pictures by K. Kvenvolden and GEOMAR

A methane hydrate is a cage-like lattice of ice, inside of which are trapped molecules of methane.



CO2

(CH2O)n

Oxisch

Anoxisch CH4

Aerobe Atmung (Chemolithotrophe)

Cyanobakterien Pflanzen

Tiere, verschiedene

Mikroorganismen (Paracoccus, E. coli)

Aerobe Methanoxidation

Anaerobe Methanoxidation

Oxygene Photosynthese

(CH2O)n

Anaerobe Atmung Anoxygene

Photosynthese

Purpurbakterien

E. coli Paracoccus denitrificans

Methanogenese

Chap. 24.1 (Fig. 24.2)

The Carbon Cycle



Assimilation/Baustoffwechsel

Aerober Prozess

Anaerober Prozess Dissimilation/

Energiestoffwechsel


The Carbon Cycle

Phototrophic organisms are the foundation of the carbon cycle CO2 is fixed primarily by photosynthetic land plants and marine

microbes CO2 is returned to the atmosphere by respiration of animals and

chemoorganotrophic microbes as well as anthropogenic activities Microbial decomposition is the largest source of CO2

released to the atmosphere The carbon and oxygen cycles are intimately linked Plants dominant phototrophic organisms of terrestrial

environments The two major end products of decomposition are CH4 and CO2

Chap. 24.1



NH3 N2

N2O

Org. N (NH2-Gruppen

N2-Fixierung Rhizobien Cyanobakterien

Nitrifikation Denitrifikation

Pseudomonas Paracoccus

Ammonifikation E. coli

The Nitrogen Carbon Cycle

NO3-

NO2-

NO Nitrosobakterien

(z.B. Nitrosomonas)

Nitrobakterien (z.B. Nitrobacter)

Chap. 24.3 (Fig. 24.7)


The Nitrogen Cycle

Chap. 24.3 Fig. 24.7


The Nitrogen Cycle

N2 is the most stable form of nitrogen and is a major reservoir The ability to use N2 as a cellular nitrogen source

(nitrogen fixation) is limited to only a few prokaryotes Denitrification is the reduction of nitrate to gaseous nitrogen

products and is the primary mechanism by which N2 is produced biologically

Ammonia produced by nitrogen fixation or ammonification can be assimilated into organic matter or oxidized to nitrate

Denitrification and anammox result in losses of nitrogen from the biosphere

Chap. 24.3



Chemolithotrophe S-Oxidation

Dissimilatorische Sulfatreduktion

Desulfovibrio

Photolithotrophe

Beggiatoa

Schwefel- Purpurbakterien

Schwefel- Grüne Bakterien

The Sulfur Cycle Org. S

H2S

Assimilatorische Sulfatreduktion

Diss. S0 reduktion

S0

SO42-

Chap. 24.4 (Fig. 24.8)


The Sulfur Cycle

Hydrogen sulfide is a major volatile sulfur gas that is produced by bacteria via sulfate reduction or emitted from geochemical sources

Sulfide is toxic to many plants and animals and reacts with numerous metals

Sulfur-oxidizing chemolithotrophs can oxidize sulfide and elemental sulfur at oxic/anoxic interfaces

Chap. 24.4


Catabolic Diversity

Fig. 4.22 Chap. 4.12

Fermentation Carbon flowOrganic compound

Carbon flow inrespirations Electron transport/

generation of pmf

Aerobic respiration

Biosynthesis

Biosynthesis

BiosynthesisBiosynthesis

Organiccompound

Electronacceptors

Anaerobic respirationChemoorganotrophy

Chemolithotrophy

Phototrophy

Electron transport/generation of pmf

Anaerobic respiration

Electronacceptors

Aerobic respiration

LightPhotoheterotrophy Photoautotrophy

Electrontransport

Generation of pmfand reducing power

e

donor

Che

mot

roph

sPh

otot

roph

s


Fermentation Carbon flowOrganic compoundCarbon flow inrespirations Electron transport/

generation of pmf

Aerobic respiration

Biosynthesis

Electronacceptors

Anaerobic respirationChemoorganotrophy

Che

mot

roph

s

Chemoorganotrophy

Anaerobic respiration, alternative electron acceptors (not O2) Energy generating process: Electron transport phosphorylation (and SLP) Catabolic end product: CO2 (exception: methanogenesis -> CH4) Example: Escherichia coli with nitrate

Aerobic respiration, O2 as electron acceptor Energy generating process: Electron transport phosphorylation (and SLP) Catabolic end product: CO2 Example 1: Paracoccus Example 2: Escherichia coli

Fermentation, anaerobic process without external electron acceptors Energy generating process: Substrate-level-phosphorylation (SLP) Example: Lactic acid fermentation Catabolic end product: lactic acid (homofermentative)

Chemoorganotrophy Energy and carbon source: organic compound(s)


Chemolithotrophy

Energy source: reduced inorganic compound Electron acceptor, mostly O2 Energy generating process: Electron transport phosphorylation Catabolic end product: oxidized inorganic compound Example: Nitrification of Nitro(so)bacteria Carbon source: CO2 (in most bacteria/archaea)

Biosynthesis Electron transport/ generation of pmf

Anaerobic respiration

Electron acceptors

Aerobic respiration


Phototrophy

Energy source: Light Energy generating process: Electron transport phosphorylation Carbon source: CO2 (in most bacteria)

Biosynthesis Biosynthesis

Organic compound

Light Photoheterotrophy Photoautotrophy

Electron transport

Generation of pmf and reducing power

e donor

Documents

Julia Vorholt Lecture 9 - ETH Zn.ethz.ch/~nielssi/download/3. Semester/Mikrobiologie/Unterlagen... · Brock Biology of Microorganisms, Twelfth Edition – Madigan / Martinko / Dunlap