Systems: V Microorganisms in the Natural Environment
Human metabolism relies on
C6 H12 O6  O2  CO2
1.
2.
3.
4.
Oxidation state of carbon in glucose is zero
Oxidation state of carbon in CO2 is +4
Energy is obtained with glucose as an electron donor
The energy source also serves as the carbon sources
In natural environments a variety of other oxidation/reduction reactions take
place altering the solubility of minerals:
1.
Uranium
2.
acid mine tailings
3.
Bio mining
At the end of this module we will see how these systems might be harnessed
For fuel cells.
C6
Typical redox “ladder” (order of reduction)
O2
H2O
NO3NO2N2
Mn4+
Mn2+
Fe3+
Fe2+
Fe2+
SO42SO
S2O3
C2H4O4 (fumarate)
CH4
- CO2
methanogenesis
Depth of sediment (lack of oxygen)
Patricia A. Maurice and Lesley A. Warren,Introduction to Geomicrobioloyg: Microbial Interactions with Minerals
CMS Workshop Lectures, Vol 14
Iron oxides are very reactive surfaces and serve as an electron source/donor
For a large variety of environmental electron transfer reactions.
The most common electron acceptors in the environment are
(in order of activity)
O2> NO3->MnO2,s>Fe(OH)3s>SO42->CO2
Most reactions occur by
Organic + electron
acceptor
oxidized organic + reduced
electron
acceptor
Some types of interesting organic “eating” “bugs”
Psuedomonas denitrificans

3

2
CH3OH  NO  NO  NO  N 2
Electron donor
methanol
C3 H6 O3  Mn
4
 Mn
Electron donor
lactate
CH3 COO   Mn 4   Mn 2   CO2
U (VI )
NO3
Geobactermetallireducens
2
 CO2
Degrade explosives: RDX
Geobactermetallireducens
pyruvate   2 Fe( III )  2 H 2O  acetate   HCO3   2 Fe( II )  3H 
acetate   8 Fe( III )  4 H 20  2 HCO3   8 Fe( II )  9 H 
Can uses acetate,
Ethanol, propionate, butyrate
Valerate, pyruvate, propanol
And toluene
The Impact of Fe(III)-reducing acterium on uraniu mobility, Biogeochemistry 2006
125-150, Michael J. Wilkins, Francis R. Livens, David j. Vaughan,
Jonathan R. Lloyd.
Ferrihydrite is present in less quantity in rock-forming minerals but is the most
Bioavailable. – fine grained with surface area of several hunded m2/g
Present as coatings on other materials (including clays).
Thermodynamically unstable (ripens to hematite or goethtie).
Enzymatic reduction of hematite/goethite phases
Hansel, C.M., Benner, Nico P. and Fendorf, S., 2004, Geochim. Cosmochim Acta
68, 3217-3229: Structural constrainst of ferric hydroxoides on dissimilatory iron
Reduction and the fate of Fe(II)
Appears to be altered by the deposition of Fe(II) coating – passification occurs.
Natural minerals easier to reduce due to greater crystalline disorder and defects
Between the natural and syntheic s oxides.
The Impact of Fe(III)-reducing acterium on uraniu mobility, Biogeochemistry 2006
125-150, Michael J. Wilkins, Francis R. Livens, David j. Vaughan,
Jonathan R. Lloyd.
Oxidized uranium is soluble UVIO22Reduced uranium is insoluble UIVO2
Therefore of interest in containing uranium contamination in
Groundwater.
Principle microorganisms
D. Vulgaris
G. Sulfurreducens
Shewanella putrefacians
Remainder of the review discusses in site injection of microorganisms
lactate  Fe( III )  CO2  Fe( II )
Shewanellaputrifaciens
Shewanellaoneidensis

U ( IV ) 
lactate U (VI ) 
H 2  SO42    S 2  
Disulfovibrio desulfuricans
methanogenicbacteria
2Corg  2 H2 O  CO2  CH4
Surface structure effects on direct reduction of iron oxides by Shewanella oneidensis, Geochimica et
Cosmochimica Acta, 67, 23, 4489, Andrew L. Neal, Kevin M. Rosso, Gill G. Geesey, Yuri A. Gorby,
Brenda J. Little.
Shewanell Oneidensis is a bacteria that terminates its respiration by donating electrons
to Fe3+. How it does this is of general interest to environmental chemists, geochemists,
and for possible application to biofuel cell development.
Shewanella on hematite
Developing biofilm of Shewanella oneidensis MR-1. The
three-dimensional structure of biofilms is revealed by live
imaging using confocal microscopy. Red color indicates
cellular DNA and green color indicates extracellular
polysaccharides, which play a structural role in the biofilm
and may actively and passively sequester metals and
radionuclides from the environment. Each unit represents
40 microns.
http://www.eurekalert.org/multimedia/pub/589.php
http://www.sysbio.org/sysbio/biofilms.stm
Acid mine reactions
Pyrite reactions
2 FeS 2  7O2  2 H2 O  2 Fe 2   4 SO42   4 H 
4 Fe 2   O2  4 H   4 Fe 3  2 H2 O
RDS
4 Fe 3  12 H2 O  4 Fe OH  3  12 H 
ferrihydrite
FeS 2  14 Fe 3  8 H2 O  15Fe 2   2 SO42   16 H 
3FeS 2  8O2  20 H2 O  14 Fe 3  13Fe 2   6SO42   4 Fe OH  3  28 H 
ferrihydrite
6 H 2 SO4
Thiobcillus ferrooxidans
Acid loving creatures found at acid mine waste sites
Oxidize iron and sulfur and alter the solubility of the minerals facilitating
Formation of soluble metals (helps mining) and formation of sulfates (increases
Acid discharge)
Fe 2  21 O2  2 H   Fe 3  H2 O
2 FeS 2  2 H2 O  7O2  2 FeSO4  2 H2 SO4
Acid Mine Waste
http://technology.infomine.com/enviromine/ard/Microorganisms/roleof.htm
3
Fe 2  21 O2  2 H  


Fe
 H2 O
thiobacillus ferrooxidans
MS  2 Fe 3  M 2   2 Fe 2   S
Catalytic cycle results in mobile or soluble metal M ions
Cu,
Zn
Pb,
Cd
Electron transfer kinetics iron mineral
reductions
1.
2.
3.
4.
Reactivity of Edges
Effect of Size (role of clays)
Structural implications of reduction
Calculated and measured e.t.
Surface Complexation of Ferrous Iron and Carbonate on Ferrihydrite and the
Mobilization of Arsenic, Appelo et al EST 2002 36 3096
Arsenic water poisoning major issue in Bangladesh where irrigation dropped
Water table resulting in one of the following
1. Dissolution of iron oxides containing As
2. Reduction of sorbed As and desorption of arsenite
3. Oxidation of arsenic containing pyrite.
4. Author’s proposal: Displacement of sorbed As by carbonates
Behaviour of Fe-oxides relevant to cntaminant uptake in the environment,
Chemical Gegology, 190, 2002, 321-337, Stipp et al
Iron-oxides with their high surface area andstrong affinity, sequester cations
Such as the transitin metals and radionucleides in proportions that are storngly
A funciton of oslution composition and pH.
Also strong adsorbers of anionic complexes
Persson, P.; Nilsson, N.; Sjoberg, S., 1996, Strucuture and obnding of orthophosphate ions at the iron oxideaqueous surface, J. Colloic InterfaceSci, 177, 263-275
Randall, S. R.,Sherman, D. M., Ragnarsdottir, K. V., 2001, Sorption of As(V) ongreeen rust
(Fe4(II)Fe2(III)(OH)12SO403H2O) and lepidocrocite (gamma-FeOOH): surface complexes from EXAFS
spectroscopy,Geochim Cosmochim Acta 65, 1015-1023
CrO42- Ding, M., B.H.W. S. de JOng, S. J. Roosendall, Bredenberg, A. Geochemica Cosmochimica Acta 65,
2000, 1209-1219
XPS studies on the electronic structure of fonbing between oslid and solutes: adsorption of arsenate, chromate,
phsophate, Pb2+and Zn2_ on amorphous black ferric oxyhydroxide.
Mix iron oxides with contaminated sources (water, ash from incinerators etc),
Precipitate and bind as an oxidie. Use as a reactive barrier.
Behaviour of Fe-oxides relevant to cntaminant uptake in the environment,
Chemical Gegology, 190, 2002, 321-337, Stipp et al
Many contaminants (ash) dissolve and are precipitated with iron to prevent
Motion.
Irreversible sorption implies localization within the changing crystal as
opposed to surface complexation – depends on rate of transformation
1. Adsorb to surface (precipitation)
2. Transformation to a more stable phase
3. Dissolve again or exsolve incorporated components
Figure 2 shows that only 40% of material is released – suggesting transformation
Should depend on
mineral morphology
particle size
Figure 8 shows that ferrihydrite minerals “age”into larger sized hematite and
goethite
Iron redox cycling in the with iron oxides
Reduction of POlyhalogenated Methanes by Surface-BoundFe(II) in Aqueous Suspensions of Iron Oxides, Env. Sci.
Tech. 36, 2002 36 1734-1741 K. Pecher et al.
Iron cycling known to control reductive transformaiton of organic and inorganic
Pollutants in soils and groundwater
In nearly all cases: Fe(II)-surface is more reactive than Fe(II) aqueous
Study use of Fe(II)-iron oxide on reduction of polyhalogenated methanes
Highest reactivity found at pH consistent with precipitation of hydrous oxides
Color of species was blue-green suggests mixed valence iron phases as the acti
Possible green rust, green rust is a powerful reductant for CCl4
+e
CX4
-X.CX3
-R.
:CX3-
+2e
-2X:CX2
-X-
+R-H
+H2O -2HX
HCOO-
+H+
HCX3
CO
+OH-
Not well understood what controlls the 1e vs either 2e or ee halves
Eng. Life Sci 007 7 1 2-60, Masih, Izumi, Aika, Seida, Optimation of an Iron
Intercalated Montmorillonite Preparation for theRemoval of Arsenic at Low
Concentrations
The most active iron species for arsenic adsorption was prepared by ion
exchange
Converts arsenite to arsentate
IN order to determine the mechanism of reaction the authors compare
Fe  OX  CX 4 12 products
k
They do
NOTstate,
But it is
k12
Implicit in
The application
Of the comparison

Vary CX4
=change in K12
k11 k 22 K12 f
But same reaction
Mechanism (
Reorganization energies)
With the reaction of
12
Fe  porphyrin  CX 4 
 products
1e
k
12
hydroquinone mercapto  juglone  CX 4 
 products
2e k
Should get a slope close to 1 in comparing the two types of reactions
If they are similar. They find a slope of 0.86 in comparing the
Rates of reactions of Fe-O-X to juglone so they conclude the reaction is
Most likely could involve 2 e
Compared 1 vs 2 e products as a function of surface coverage by Fe(II) and
Conclude that the relative importantce of 2e transfer increases with Fe(II)
Coverage (provides adjacent sites)
At higher pH the 1e pathway increaseswhich they suggest is due tote
prsence of green rust precipitates which have both Fe(II) and Fe(III)
centers thus reducing the concentration of Fe(II) adjacent sites.
T2g d orbitals on the
Central metal lie
Somewhat out of
The path of the
Incoming octahedrally
Oriented ligands
Eg d orbitals on central metal
lie in the path
Of incoming octahedrally
Oriented ligands
Image: A Van der Ven and G. Ceder, p 47 in Lithium Batteries Science and
Technology, Nazri and Pistoia, eds., Kluwer, 2004
An extreme example of the inner sphere work required is to reduce an iron
containing crystal
Charge transport in micas: The kinetics of FeII/III electron transfer in the octahedral
sheet, Keven M. Rosso and Eugene S. Ilton, . J of Chemical Physics, 119, 17, 9207
Hydroxyl group at “waist” (cis)
Hydroxyl group at apex (trans)
Calculate the self exchange
Of FeII to FeIII from the M1
And M2 sites using a cluster
Anschtz, amy J. and R. Lee Pnn, Reduction of crystalline iron(III) oxyghydroxides
Uisng hydroquinone: influence of phase and particle size, Geochemical
Transacations, 2005, 6,3, 60-66
Prepare
ferrihdrite 6 nm
nanorod goethite
microrod goethite
Characterize the surface area by TEM, and calculation of edge area
Characeerize the cyrstallinity of the mineral surfaces
2
2 Fe5 HO8  4 H2 Os  5H2 Q  20 H  
 5Q  10 Feaq  24 H 2 O
ferrihydrite
2
10 FeOOH s  5H2 Q  20 H  
 10 Feaq  5Q  20 H 2 O
goethite
Stoichiometry checked; initial rates measured by the production of Q as a function
Of H2Q concentration holding the total iron constant
Anschtz, amy J. and R. Lee Pnn, Reduction of crystalline iron(III) oxyghydroxides
Uisng hydroquinone: influence of phase and particle size, Geochemical
Transacations, 2005, 6,3, 60-66
Prepare
ferrihdrite 6 nm
nanorod goethite
microrod goethite
Characterize the surface area by TEM, and calculation of edge area
Characeerize the cyrstallinity of the mineral surfaces
Table 2 here
Reactivity of ferrihydrite was two orders higher – suggested
Related to cyrstallinity and greater surface area/unit iron.
To account for possilbe diffusion through different void shapes the data for
Ferrihydrite was compared for two different particle sizes to determine an
Area dependent rate and the relative reaction orders
Suggest that it is not area per se but thenumber of kinks and atomic steps
Present resulting in greater surface energy and reativity also showing differnet
Reaction orders with the larger size ferrihydrite showing
Anschtz, amy J. and R. Lee Pnn, Reduction of crystalline iron(III) oxyghydroxides
Uisng hydroquinone: influence of phase and particle size, Geochemical
Transacations, 2005, 6,3, 60-66
Reactivity of ferrihydrite was two orders higher – suggested
Related to cyrstallinity and greater surface area/unit iron.
To account for possilbe diffusion through different void shapes the data for
Ferrihydrite was compared for two different particle sizes to determine an
Area dependent rate and the relative reaction orders
Suggest that it is not area per se but thenumber of kinks and atomic steps
Present resulting in greater surface energy and reativity also showing differnet
Reaction orders with the larger size ferrihydrite showing
d Q
m
n
 k H2 Q  S 
dt

Model
1D
1D
2D
2D

Particle
4nm-6LF
6nm-6LF
Nanorod
Microrod
Accounting for diffusion as either 1D on the surface
Or two dimensional for the nanoand micro rods
m
0.55
0.79
0.92
0.82
n
0.51
1.29
1.61
1.74
kBET
1.29x108 /h-m2
0.35x108/h-m2
7.2x
3.6x
Only one possible literature comparison
Andrew G. Stack, Kevin M. Rosso, Dale M. A. Smith, and Carrick M. Eggleston, Reaction of hydroquinone
with hematite. II. Calculated electron-transfer rates and comparison to the reductive dissolution rate,
Journal of Colloid and Interface Science 2004, 274-442-450.

Fe x Oy 
 Fe x Oy  e
Fe x Oy  Q H  2  Fe x Oy  QH2
k12
K
Stack, EC-STM
Measured 1.1 Q/nm2
McBride and Wesselink mesured QH2 on boehmite (AlOOH) of 0.2QH2/nm2
Find that they have no correlation with the rate of dissolution
Suggest that the mechanism genealized as
1. H2Q adsorption
2. Et to form a semiquinone and reduced iron
3. Desorption of the semiquinone
4. Dissolution of the reduced iron
5. Adsorption of the semiquinone
6. ET to form a quinone and reduced iron
7. Desorption of Q
8. Dissolution of reduced iron
NOT RDS et large
not likely
NOT RDS et large
could be RDS
not likely
For microbial rates would indicate that should be very high et dependent
Primarily on the orientaiton of the active enzyme site to the surface
Enzyem aticle on hemtatie and goethite here
Direct et
Cell attachment
Cell cyt c orientation
distance
Calculate
The electrostatic surface of the iron
oxides
The electrostatic of the heme
Calculate inner sphere bond length
changes
Calculate the work to bring cytochrome
and hematite together from the charges
Calculate activation energy and the rate of
electron transfer as a function of cyt c
distance from the iron oxide surface
k et  Ae


f
4

F  E  E o   wo  wr 
 Grxo 
  
     1 

  1 



i  o
4




 i  o  
G  


 rnn  ro 
2
2
Compares the calculated
e.t. Rates with cell density
Measurements of colonies
Assuming growth limited by
e.t.
External


f
F  E  E o   wo  wr 
 Grxo 
  
     1 

  1 



i  o
4




 i  o  
G  

4
2
Suggest:
Larger internal reorganization energies
associated with the iron oxide surfaces as
opposed to the internal bulk mineral
internal
3.43
5.34
4.303
Rate of cell density increase (104/cm2)/min
Results are not consistent suggesting that …….
More
work
2
Microbial driven reduction
1.
Direct contact by dissimilatory iron reducing bacteria (DIRB
Assumes pili of the baceria could either attach and/or reduce
the iron. Suggest the possibility of nanowires to shuttle electrons
(Reguera, G., McCarthy, K. D., Mehta, T., Nicoll, J. S.Tu
2.
Chelators to enhance solubility
3.
Existing electron mediators
humic acids (functional groups are quinones) (analog
is 2,6-anthraquinone disulfonate (AQDS)
4.
Production of electron mediators