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 Photoheterotrophs
(Use CO2) (Use Organic Carbon)

Figure by MIT OCW.

 Cyclic Photophosphorylation

ATP
Electron
transport
chain
Excited
electrons Energy for
(2 e-) production
of ATP

Light Chlorophyll Electron carrier

Figure by MIT OCW.

Anoxygenic photoautotrophs utilize cyclic

photophosphorylation
 LOTS OF DIVERSITY IN BACTERIAL ANOXYGENIC PHOTOTROPHS !

Purple Bacteria Green Sulfur Bacteria Heliobacteria

P798
-1.25 P840
Chl a-OH
-1.0 Chl a
P870
BChl
-0.75 FeS FeS
BPh
-0.5
E 0' Fd Fd
NADH
(V) -0.25
Cyt Q
0 Q Cyt Q bc1
Reverse bc1
Cyt electron Cyt Cyt
+0.25 bc1 P840 c553 P798 c553
Cyt flow
c2
+0.5 P870
Light Light
Light

Figure by MIT OCW.

 -1.25 P700*

Chl a0
-1.0
QA
P680* FeS
-0.75 Cyclic electron flow
(generates proton Fd
-0.5 motive force) Fp
Ph NAD(P)+
NAD(P)H
QA
-0.25
QB
Q pool
E'
0
0.0
Cyt bf
(V)
Noncyclic
+0.25 electron flow Pc
(generates proton P700
motive force) Light
+0.5 Photosystem I

+0.75 H2O The Z Scheme

e-
1 O + 2H
+1.0 P680 2 2 PSI
PSII
Light
Photosystem II

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-194
Glu-204

H+

Figure by MIT OCW.

 Microbial rhodopsins fall into two main functional classes

Light-driven ion pumps Sensory rhodopsins

Rhodopsin Functional Diversity

H+

BR HR SRl SRll Htrll

Htrl

Cl-
Cytoplasm
Methylation helices

Bacteriorhodpsin His-kinase His-kinase

P
Regulator Regulator
P
Regulator

Flagellar motor

Figure by MIT OCW.

 Bacteriorhodopsin and proteorhodospin
Light driven proton pumps
Cell interior

H+

High H+ concentration
2 H+ H+
Outside cell
Asp-96

Electron transport
chain (includes
proton pumps) } Membrane

Asp-85 Retinal
1 ATP
Inside cell synthase
Arg-82
3
Glu-194
Glu-204
ADP+ Pi
Electrons from
NADH or chlorophyll ATP
H+

Low H+ concentration
Cell exterior 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)

Many new bacterial

Diagram removed due to copyright restrictions.
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 chemoorganotrophs
Oxidize inorganic compounds Oxidize organic compounds
 Relative Voltage Relative Voltage

MICROBIAL REDUCTANTS (EAT) OXIDANTS (BREATHE)

-10 -10
METABOLIC
-8 Photoreductants
DIVERSITY Organic H2
-8
-6 -6
Carbon A
H2S CO2
-4 -4
Microbes can So SO4=
-2 AsO43- -2
eat & breathe just FeOOH
0 Fe(II) B 0
about anything !
+2 +2
+4 SeO3 +4
+6 NH4+ NO2- +6
NO3-
+8 +8
Mn(II)
MnO2
+ 10 + 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
Periplasm
NH2OH N + 5H+
+ H2O O- Oxidation of
hydroxylamine
2H+
4e- Cyt c 2e- H+
HAO
Cyt c
2e-
2e- 2e-
AMO Q
Cyt aa3

1 O + 4H+
2 2
NH2OH + H2O NH3 + O2+ 2H+ H2O ADP ATP
+ Pi
Oxidation of Reduction
ammonia of oxygen 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 Photograph removed due to copyright restrictions
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.
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- Fe3+

Image of geobacter growing on iron oxides removed due to copyright restrictions.

e-

CO2 Fe2+
 Complex Organic Matter

Hydrolysis

Fermentable Substrates

Fermentation

H2 Acetate Other low molecular

weight organic acids
}
}
NO3- reducers
Microbial Competition Mn(IV) reducers
for Substrates Fe(III) reducers
SO42- reducers
Methanogens

Figure by MIT OCW.

Organic Matter Degradation In Anaerobic Environments
Diagram removed due to copyright restrictions.
Energetic explains order: not all e- 25
acceptors 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
 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 Source

Low O2 Methanogenic

SO42 reduction

Fe(III) reduction

Mn(IV) reduction
- reduction Aerobic
NO 3 (IV)

High O2
Groundwater flow

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

Photograph removed due to copyright restrictions.
Acetate + U (VI) U (IV)s + CO2
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

Nature. 2005 Jun 23;435(7045):1098-101.
a conducting probe atomic force microscope (CP-AFM).
HOPG, highly oriented pyrolytic graphite.
‘Good’ electron acceptors

‘Good’ electron donors

Photograph removed due to copyright restrictions
 SO42- Seawater
Sea Floor

SO42- Diffusion
Sulfate Reduction Zone

DNS
C

B
A

DNS

METHANE FLUX

Figure by MIT OCW.

 ANAEROBIC METHANE OXIDATION
Geochemical Observations:
CH4 + SO42- HCO3- + HS- + H2O

Microbiologically ???
CH4 + 2H2O CO2 + 4H2 “Reverse Methanogenesis” ΔGo’ = +131 kJ/mol
HSO4- + 4H2 HS- + 4H2O Sulfate reduction ΔGo’ = -156 kJ/mol

CH4 + HSO42- CO2 + HS- + 2H2O 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.