Systems Microbiology
Weds Sept 20 - Ch 5 & Ch 17 (p 533-555)
Bioenergetics & Metab.Diversity
• BASIC MODES OF ENERGY GENERATION
• THERMODYNAMICS OF GROWTH -cont’d
• APPLICATIONS of MICROBIAL
CHEMOLITHOTROPHY & ANAEROBIC RESP.
Phototrophs
(Use Light as Energy Source )
Photoautotrophs
(Use CO2)
Photoheterotrophs
(Use Organic Carbon)
Figure by MIT OCW.
Cyclic Photophosphorylation
ATP
Electron
transport
chain
Excited
electrons
(2 e-)
Light
Chlorophyll
Energy for
production
of ATP
Electron carrier
Figure by MIT OCW.
Anoxygenic photoautotrophs utilize cyclic
photophosphorylation
LOTS OF DIVERSITY IN BACTERIAL ANOXYGENIC PHOTOTROPHS !
Purple Bacteria
Green Sulfur Bacteria
-1.25
-1.0
P840
P870
-0.75
E 0'
(V)
Chl a-OH
Chl a
BChl
BPh
-0.25
+0.5
P870
Cyt
c2
Q
Cyt
bc1
Light
Reverse
electron
P840
flow
Fd
Fd
NADH
+0.25
FeS
FeS
-0.5
0
Heliobacteria
P798
Cyt
c553
Cyt
bc1
Light
Cyt
bc1
Q
P798
Q
Cyt
c553
Light
Figure by MIT OCW.
P700*
-1.25
Chl a0
-1.0
-0.75
QA
P680*
-0.5
Ph
0
+0.25
+0.5
Fp
NAD(P)H
Q pool
Cyt bf
Noncyclic
electron flow
(generates proton
motive force)
+0.75
e+1.0
Fd
QB
0.0
(V)
FeS
NAD(P)+
QA
-0.25
E'
Cyclic electron flow
(generates proton
motive force)
H2O
P680
Photosystem II
1 O + 2H
2 2
Light
Pc
P700
Light
Photosystem I
The Z Scheme
PSII
PSI
Figure by MIT OCW.
HALOARCHAEA
Live in hypersaline habitats
Aerial photograph of haloarchaea changing the colors of their saltwater habitats removed due to copyright restrictions.
H+
Asp-96
Asp-85
Retinal
Arg-82
Glu-204
Glu-194
H+
Figure by MIT OCW.
Microbial rhodopsins fall into two main functional classes
Sensory rhodopsins
Light-driven ion pumps
Rhodopsin Functional Diversity
H+
BR
HR
SRl
SRll
Htrl
Htrll
Cl-
Cytoplasm
Methylation helices
Bacteriorhodpsin
His-kinase
Regulator
His-kinase
P
Regulator
P
Regulator
Flagellar motor
Figure by MIT OCW.
Bacteriorhodopsin and proteorhodospin
Light driven proton pumps
Cell interior
H+
High H+ concentration
2
H+
Asp-96
Outside cell
H+
}
Electron transport
chain (includes
proton pumps)
Asp-85
Retinal
1
Arg-82
Glu-204
ATP
synthase
3
Glu-194
ADP+ Pi
Electrons from
NADH or chlorophyll
H+
Cell exterior
Inside cell
Membrane
ATP
Low H+ concentration
Figure by MIT OCW.
Figure by MIT OCW.
Images and diagrams of various rhodopsins removed due to copyright restrictions.
See Science 289 (September 15, 2000). www.sciencemag.org.
Venter et al., Environmental Genome Shotgun
Sequencing of the Sargasso Sea,
Science 394:66-74 (2004)
Diagram removed due to copyright restrictions.
Many new bacterial
proteorhodopsins discovered
in environmetnal shotgun
sequencing
Images of a hybrid automobile, hydrocarbons, and electricity removed due to copyright restrictions.
Where do organisms get their energy?
ALL ORGANISMS
chemotrophs
phototrophs
Derive energy from light
chemolithotrophs
Oxidize inorganic compounds
chemoorganotrophs
Oxidize organic compounds
Relative Voltage
Relative Voltage
REDUCTANTS (EAT)
MICROBIAL
METABOLIC
DIVERSITY
Microbes can
eat & breathe just
about anything !
OXIDANTS (BREATHE)
-10
-10
Photoreductants
-8
-6
-4
Organic
Carbon
H2
H2S
So
A
-2
0
-8
Fe(II)
B
-6
CO2
SO4=
AsO43FeOOH
+2
+8
+ 10
-2
0
+2
+4
+6
-4
NH4+
Mn(II)
SeO3
NO2NO3MnO2
+4
+6
+8
+ 10
+ 12
NO3-/N2
+ 12
+ 14
O2
+ 14
Diagrams removed due to copyright restrictions.
See Figures 5-22a, 5-20, and 5-23 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.
11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
METABOLIC DIVERSITY - Continued ….
Chemolithoautotroph (chemo [chemical], litho [rock], auto[self], troph [feeding])
Energy source: inorganic substrates (H2, NH3, NO2-, H2S, Fe2+)
Carbon source: CO2
e- acceptor: O2(aerobes), or S(some anaerobes), Fe3+, NO3, SO4
Chemolithoautotrophs can be grouped according to the inorganic
compounds that they oxidize for energy:
Nitrifiers - Oxidize reduced Nitrogen compounds such as NH4+
Sulfur Oxidizers- Oxidize reduced Sulfur compounds such as H2S, S0, and S2O-
Iron Oxidizers- Oxidize reduced Iron-Fe2+ (ferrous iron)
Hydrogen Oxidizers-Oxidize Hydrogen gas-H2
Table of energy yields from the oxidation of various inorganic electron donors removed due to copyright restrictions.
See Table 17-1 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed.
Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
METABOLIC DIVERSITY
CHEMOLITHOAUTOTROPHS - Examples
CHEMOLITHOTROPHIC AMMONIA OXIDATION - AEROBIC
NH4+ + 3/2O2 --> NO2- + H2O + 2H+
O
N + 5H+
NH2OH
+ H2O
O- Oxidation of
hydroxylamine
4e- Cyt c 2eHAO
Cyt c
2eAMO
2e-
Q
Periplasm
2H+
H+
2eCyt aa3
1 O + 4H+
2 2
NH2OH + H2O
NH3 + O2+ 2H+
Oxidation of
ammonia
H2O
Reduction
of oxygen
ADP ATP
+ Pi
H+
Figure by MIT OCW.
CHEMOLITHOTROPHIC
AMMONIA OXIDATION ANAEROBIC
Anammox means "anaerobic ammonium oxidation". Anammox is both a new low-cost method of
N-removal in wastewater treatment, and a spectacular microbial way of life - woo - woo !
Courtesy of the Department of Microbiology at Radboud University Nijmegen. Used with permission.
2NH4+/N2 half reaction (6e-) Eo = -0.277 V
2NO2-/N2 half reaction (6e-) Eo = +0.956 V
ΔEo= Eo (electron acceptor) - Eo (electron donor) = 1233 mV
ΔGo=-nF ΔEo= -(3) (96.5 kJ/Vmol)(1.233V) = - 357 kJ/mol
Broda predicted, based solely on the thermodynamics, that such
microorganisms should exist. (And also the fact that if a
bioenergetically favorable niche exists, a microbe will evolve
to fill it !).
About a decade later, the ’ bugs’ were discovered in bioreactors
started from waste water treatment plants.
Diagram removed due to copyright restrictions.
Compared to conventional
nitrification/denitrification, this
method saves 100% of the carbon
source, & 50% of the required
oxygen. This leads to a reduction of
operational costs of 90%, a decrease
in CO2 emissions of more than 100%
(the process actually consumes CO2),
and a decrease in energy demand.
Photograph removed due to copyright restrictions
Anaerobic ammonium oxidation by anammox bacteria in the Black Sea
Marcel M. M. Kuypers, A. Olav Sliekers, Gaute Lavik, Markus Schmid, Bo Barker Jørgensen, J. Gijs Kuenen,
Jaap S. Sinninghe Damsté, Marc Strous and Mike S. M. Jetten. Nature 422, 608-611 (10 April 2003)
Graphs removed due to copyright restrictions.
ANAEROBIC RESPIRATION =
Dumping your electrons on something other than oxygen
Denitrification = Use of NO3- as terminal electron acceptor, that results
in complete conversion to N2 gas.
Diagrams removed due to copyright restrictions.
See Figures 17-35 and 17-37 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed.
Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
Geobacter growing on iron oxides
Anaerobic
respiration
CH3COO-
Image of geobacter growing on iron oxides removed due to copyright restrictions.
CO2
Fe3+
e-
Fe2+
Complex Organic Matter
Hydrolysis
Fermentable Substrates
Fermentation
H2
Other low molecular
weight organic acids
Acetate
}
Microbial Competition
for Substrates
}
NO3- reducers
Mn(IV) reducers
Fe(III) reducers
SO42- reducers
Methanogens
Organic Matter Degradation In Anaerobic Environments
Figure by MIT OCW.
Diagram removed due to copyright restrictions.
Energetic explains order: not all eacceptors are equal!
E- acceptor
ΔGo’ (using glucose)
Oxygen
-3190 kJ/mol
NO3-
-3030
Mn (IV)
-3090
Fe(III)
-1410
Sulfate
-380
CO2
-350
From Nealson and Saffarini 1994
25
Complex Assemblage of Organic Matter
Hydrolysis into Constituents
Fermentable Sugars and Amino Acids
Fermentation by a Fermentative Microbial
Consortium
Long-Chain Fatty Acid
Acetate and Minor Products
Aromatic Compounds
Fe3+ Oxide
Geobacter spp.
Fe2+
CO2
Generalized pathway for the anaerobic oxidation of organic matter to carbon dioxide with Fe3+ oxide
serving as an electron acceptor in temperate, freshwater and sedimentary environments. The process is
mediated by a consortium of fermentative microorganisms and Geobacter species.
Figure by MIT OCW.
High
organics
Low O2
Source
Methanogenic
SO42 reduction
Fe(III) reduction
Mn(IV) reduction
reduction
NO 3 (IV)
Groundwater flow
Aerobic
High O2
Figure by MIT OCW.
The distribution of terminal electron-accepting processes (TEAPs) observed within anaerobic portions of aquifers
contaminated with organic compounds.
Images removed due to copyright restrictions.
See Lovley, D. R., E. J. P. Phillips, Y. A. Gorby, and E. R. Landa. "Microbial Reduction of Uranium." Nature 350 (1991): 413-416.
Anaerobic respiration to “clean up” of uranium pollution
Soluble= mobile
Insoluble, immobile
Acetate + U (VI) U (IV)s + CO2
Photograph removed due to copyright restrictions.
CH3C00- + 4 U(VI)U (IV)s + 2HCO3- + 9H+
Carried out by Geobacter
Example of “bioremediation”
Lovley DR, Phillips EJP, Gorby YA, Landa ER. Microbial Reduction of Uranium, 1991, Nature.
350(6317): 413-6.
Diagram removed due to copyright restrictions.
Diagram removed due to copyright restrictions.
See Bond, Holmes, Tender, and Lovley. Science 295 (2002): 483-485.
Diagram and photograph of a sediment microbial fuel cell removed due to copyright restrictions.
V=IR
Atomic force microscope stage
Correspondence between pilus current and applied voltage demonstrating
the linear, ohmic, response characteristic of a true conductor.
Extracellular electron transfer via
microbial nanowires.
Schematic of the electronic connection of the AFM tip in
a conducting probe atomic force microscope (CP-AFM).
HOPG, highly oriented pyrolytic graphite.
Nature. 2005 Jun 23;435(7045):1098-101.
‘Good’ electron acceptors
‘Good’ electron donors
Photograph removed due to copyright restrictions
Sulfate Reduction Zone
SO42-
Seawater
Sea Floor
SO42- Diffusion
C
DNS
B
A
DNS
METHANE FLUX
Figure by MIT OCW.
ANAEROBIC METHANE OXIDATION
Geochemical Observations:
CH4 + SO42-
HCO3- + HS- + H2O
Microbiologically ???
CH4 + 2H2O
HSO4- + 4H2
CO2 + 4H2 “Reverse Methanogenesis” ΔGo’ = +131 kJ/mol
HS- + 4H2O Sulfate reduction
CH4 + HSO42-
CO2 + HS- + 2H2O
ΔGo’ = -156 kJ/mol
ΔGo’ = -25 kJ/mol
SO4
-2
CH4
H2
HS
CO2
World maps showing global methane distribution removed due to
copyright restrictions. See D’Hondt et al. Science 295 (2002): 2067.