geomicrobiology

G
E
O
MI
C
R
O
BI
O
L
OG
Y
Fif
t
h

Edi
t
i
o
n
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G
E
O
MI
C
R
O
BI
O
L
OG
Y
Fif
t
h

Edi
t
i
o
n
H
enry Lutz Ehrlic
h
D
ianne K. Newman
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CRC_7906_FM.indd viCRC_7906_FM.indd vi 11/11/2008 5:11:59 PM11/11/2008 5:11:59 PM
vii
C

ontents
P
re
f
ace
.
xix
A
ut
h
or
s

x
x
i
1
Chapter Introduction

1
R
eferences

3
2
Chapter
Earth as a Microbial Habitat

t
5

2.1 Geolo
g
icall
y
Important Features

5
2.2 Bios
p
here
.
1
0
2
.
3

S
ummary

1
1
Re
f
e
r
e
n
ces

1
1
3
Chapter
O
ri
g
in of Life and Its Earl
y
Histor
y


1
5
3
.1 Be
g
innin
gs

1
5
3
.1.1 Or
i
g
i
n o
f

L
if
e on Eart
h
: Pansperm
ia

.
1
5
3
.1.2 Or
igi
n o
f
L
if
e on Eart
h
:
d
e novo
A
ppearance

1
6
3
.1.3 Life from Abioticall
y

Formed Or
g
anic Molecules in Aqueou
s
So
l
ut
i
on (Organ
i
c Soup T
h
eory
)

.
1
6
3
.1.4 Sur
f
ace Meta
b
o
li
sm T
h
eor
y

1
8
3
.1.
5
Ori
g
in of Life throu
g
h Iron Monosul de Bubbles in Hadean
O
cean at t
h
e Inter
f
ace o
f
Su
l

d
e-Bear
i
ng Hy
d
rot
h
erma
l

Solution and Iron-Bearing Ocean Water

r
1
9
3
.2 Evolution of Life throu
g
h the Precambrian: Biolo
g
ical
an
d
B
i
oc
h
em
i
ca
l
Benc
h
mar
ks

.
2
0
3

.2.1 Ear
ly
Evo
l
ut
i
on Accor
di
n
g
to Or
g
an
i
c Soup Scenar
io


2
1
3
.2.2 Earl
y
Evolution Accordin
g
to Surface Metabolist Scenari
o

2
7

3
.
3
E
vid
ence
.
2
8
3
.
4

S
ummar
y

3
1
Re
f
e
r
e
n
ces

3
2
4

Cha
p
ter
Lithosphere as Microbial Habitat

t
3
7
4
.
1 Rock and Minerals

3
7
4.2 M
i
nera
l

S
o
il

.
3
9
4.2.1 Or
igi
n o
f

M
i
nera
l
So
il


3
9
4.2.2 Some Structural Features of Mineral Soil

4
0
4.2.
3
E
ff
ects o
f
P
l
ants an
d
An
i
ma
l
s on
S

o
il
E
v
o
l
ut
i
o
n

.
4
2
4.2.4 E
ff
ects o
f
M
i
cro
b
es on
S
o
il
E
v
o
l

ut
i
on

4
2
4.2.
5
Effects of Water on Soil Erosion

4
3
4.2.
6
Water Distribution in Mineral
S
oi
l

.
4
3
4.2.7 Nutr
i
ent Ava
il
a
bili
t
y

i
n M
i
nera
l
So
il

4
4
4.2.8 Some Ma
j
or Soil T
y
pe
s

4
5
4.2.9 Types o
f
M
i
cro
b
es an
d
T
h

e
i
r D
i
str
ib
ut
i
on
i
n M
i
nera
l
So
il

.
4
7
CRC_7906_FM.indd viiCRC_7906_FM.indd vii 11/11/2008 5:11:59 PM11/11/2008 5:11:59 PM
v
iii

C
ontent
s
4.3 Or
g
anic Soil

s

4
9
4.4 The Dee
p
Subsurface

5
0
4.5 Summary
.
5
1
R
eferences

5
2
5
Chapter
T
h
e
Hydrosphere as Microbial Habitat

t
5
7
5

.1 The Ocean
s

5
7
5
.1.1 Physical Attribute
s

.
5
7
5
.1.2
O
cean in Motion

5
9
5.1.3 Chemical and Physical Properties of Seawater

r
6
2
5
.1.4 Microbial Distribution in Water Column and Sediments
.
6
8
5.1.5 Effects of Temperature, Hydrostatic Pressure, and Salinity

on Microbial Distribution in Ocean
s

7
0
5
.1.6 Dominant Phytoplankters and Zooplankters in Oceans
.
7
1
5.1.7 Plankters of Geomicrobial Interest

t
7
2
5
.1.8 Bacterial Flora in Oceans

7
2
5
.2 Freshwater Lake
s

.
7
3
5.2.1 Some Physical and Chemical Features of Lakes

7

4
5
.2.2 Lake Bottom
s

7
6
5
.2.3 Lake Fertilit
y

.
7
7
5
.2.4 Lake E
v
olutio
n

7
7
5
.2.
5
Microbial Po
p
ulations in Lake
s

7
7
5
.3 River
s

.
7
8
5
.4
G
round
w
aters

7
9
5
.
5
Summar
y

8
2
Re
f
e

r
e
n
ces
.

.
8
3
6
Chapter
G
eomicrobial Processes: Ph
y
siolo
g
ical and Biochemical Overview

8
9
6
.1 T
y
pes of Geomicrobial A
g
ents

8
9
6

.2 Geomicrobiall
y
Important Ph
y
siolo
g
ical Groups of Prokar
y
otes

9
0
6
.3 Role of Microbes in Inorganic Conversions in Lithosphere
and H
y
drospher
e


9
1
6
.4 T
y
pes of Microbial Activities In uencin
g
Geolo
g
ical Processes

9
2
6
.5 Microbes as Catalysts of Geochemical Processes
.
9
3
6
.5.1 Catabolic Reactions: Aerobic Res
p
iratio
n


9
4
6
.
5
.2 Catabolic Reactions: Anaerobic Res
p
iratio
n

9
6
6
.5.3 Catabolic Reactions: Respiration Involving Insolubl
e

Inor
g
anic Substrates as Electron Donors or Acceptors

9
8
6
.
5
.4 Catabolic Reactions: Fermentation

1
0
0
6
.5.5 How Energy Is Generated by Aerobic and
A
naero
bic
Respirers and Fermenters Durin
g
Catabolism

10
1
6
.
5
.6 How Chemolithoautotro
p

hic Bacteria (Chemos
y
ntheti
c
Autotrop
h
s) Generate Re
d
uc
i
ng Powe
r

f
or Ass
i
m
il
at
i
n
g
CO
2
and Convertin
g
It into Or
g
anic Carbon

10
3
6
.
5
.7 How Photos
y
nthetic Microbes Generate Ener
gy
and Reducing Power

r
1
0
3
6
.5.8 Anabolism: How Microbes Use Ener
gy
Trapped in Hi
g
h-Ener
gy
Bonds to Drive Ener
gy
-Consumin
g
Reaction
s

10

5
6
.5.9 Carbon Assimilation by Mixotrophs, Photoheterotrophs,
and Heterotro
p
hs

10
8
CRC_7906_FM.indd viiiCRC_7906_FM.indd viii 11/11/2008 5:11:59 PM11/11/2008 5:11:59 PM
C
ontents
i
x
6.6 Microbial Mineralization of Organic Matter

r
10
8
6
.7 Microbial Products of Metabolism That Can Caus
e
G
eom
i
cro
bi
a
l
Trans

f
ormat
i
on
s

11
0
6
.8 Ph
y
sical Parameters That In uence Geomicrobial Activit
y


11
0
6
.9 Summar
y

11
2
R
e
f
erences
.
11
3

7
C
ha
p
ter Nonmo
l
ecu
l
ar Met
h
o
d
s
i
n Geom
i
cro
bi
o
l
ogy

11
7
7.1 Intro
d
uct
i
on

11
7
7.2 Detection, Isolation, and Identi cation of Geomicrobiall
y
Active
O
rganism
s

11
8
7.
2
.
1
In
S
itu O
b
servat
i
on o
f
Geom
i
cro
bi
a
l
Agents

11
8
7.2.2 Identi cation b
y
Application of Molecular Biolo
g
ical Technique
s

12
0
7.3 Sampling
12
0
7.3.1 Terrestr
i
a
l
Sur
f
ace/Su
b
sur
f
ace Samp
li
n
g

12
1
7.3.2 Aquatic Samplin
g

12
1
7.3.3 Sample Storag
e

12
2
7.3.4 Cu
l
ture Iso
l
at
i
on an
d
C
h
aracter
i
zat
i
on o
f
Act
i

ve Agents
from Environmental Sam
p
les

12
4
7.4
I
n
S
it
u
S
tudy of Past Geomicrobial Activity
12
5
7.
5
In
S
it
u
Stu
d
y o
f
Ongo
i
ng Geom

i
cro
bi
a
l
Act
i
v
i
ty

12
6
7.6 Laborator
y
Reconstruction of Geomicrobial Processes in Nature

12
8
7.7 Quantitative Study of Growth on Surfaces 13
2
7.8 Test
f
or D
i
st
i
ngu
i
s

hi
ng
b
etween Enzymat
i
c an
d
Nonenzymat
ic
Geomicrobial Activit
y

13
4
7.9 Study of Reaction Products of Geomicrobial Transformatio
n

1
3
4
7.
10

S
ummary

13
5
Re
f

e
r
e
n
ces

13
5
8
C
ha
p
ter Mo
l
ecu
l
ar Met
h
o
d
s
i
n Geom
i
cro
bi
o
l
og
y

1
3
9
8
.1 Intro
d
uct
i
on 1
3
9
8.2 Who Is There? Identi cation of Geomicrobial Or
g
anisms

13
9
8.2.1 Culture-Inde
p
endent Methods

1
3
9
8.2.2 New Cu
l
tur
i
ng Tec
h

n
i
que
s

14
1
8.3 W
h
at Are T
h
e
y
Do
i
n
g
? De
d
uc
i
n
g
Act
i
v
i
t
i
es

of

G
eom
i
cro
bi
a
l
Or
g
anisms

14
1
8.3.1 S
i
ng
l
e-Ce
ll
Isotop
i
c Tec
h
n
i
que
s
14

2
8.3.2 S
i
n
gl
e-Ce
ll
Meta
b
o
li
te Tec
h
n
i
que
s

14
4
8.3.3 Communit
y
Techniques Involvin
g
Isotopes

14
5
8.3.4 Commun
i

ty Tec
h
n
i
ques Invo
l
v
i
ng Genom
i
c
s

1
4
6
8.3.5 Probin
g
for Expression of Metabolic Gene
s
or Their Gene Pr
oducts


14
7
8.4 How Are T
h
ey Do
i

ng It? Unrave
li
ng t
h
e Mec
h
an
i
sms
o
f
Geom
i
cro
bi
a
l
Or
g
an
i
sms

14
7
8.4.1 Genetic A
pp
roaches

14

8
8.4.2 B
i
o
i
n
f
ormat
i
c Approac
h
e
s

15
1
8.4.3 Fo
ll
ow-Up Stu
di
e
s

15
1
8.
5
Summar
y

1
5
2
R
e
f
erences
.
1
5
2
CRC_7906_FM.indd ixCRC_7906_FM.indd ix 11/11/2008 5:11:59 PM11/11/2008 5:11:59 PM
x

C
ontents
9
Chapter Microbial Formation and De
g
radation of Carbonates

1
5
7
9.1 Distribution of Carbon in Earth’s Crust

t
1
5
7

9.2 Biolo
g
ical Carbonate Depositio
n

1
5
7
9.2.1 H
i
stor
i
ca
l
Perspect
i
ve o
f
Stu
d
y o
f
Car
b
onate Depos
i
t
i
o
n

1
5
8
9.2.2 Basis for Microbial Carbonate Depositio
n


1
6
1
9.2.3 Conditions for Extracellular Microbial Carbonate Preci
p
itatio
n


16
4
9.2.4 Car
b
onate Depos
i
t
i
on
b
y Cyano
b
acter
ia

16
7
9
.2.5 Possible Model for Oolite Formation

16
8
9.2.6 Structural or Intracellular Carbonate Deposition b
y
Microbes

16
8
9.2.7 Mo
d
e
l
s
f
or S
k
e
l
eta
l
Car
b
onate Format
i

on 1
7
1
9
.2.8 Microbial Formation of Carbonates
O
ther Than
Those of Calcium

1
7
3
9
.2.8.1 So
di
um Car
b
onate 1
7
3
9
.2.8.2 Man
g
anous Carbonat
e


1
7
4

9
.2.8.3 Ferrous Carbonat
e


1
7
6
9
.2.8.4 Stront
i
um Car
b
onat
e
1
7
7
9
.2.8.5 Ma
g
nesium Carbonate

1
7
7
9.3 Biode
g
radation of Carbonates

1
7
8
9.3.1 B
i
o
d
egra
d
at
i
on o
f
L
i
mestone 1
7
8
9.3.2 C
y
ano
b
acter
i
a, A
lg
ae, an
d
Fun
gi

T
h
at Bore
i
nto L
i
meston
e


18
0
9.4 Biolo
g
ical Carbonate Formation and De
g
radation and the Carbon C
y
cle

1
8
3
9.5 Summary 1
8
4
Refe
r
e
n

ces

18
4
1
C
ha
p
ter
0
G
eom
i
cro
bi
a
l
Interact
i
ons w
i
t
h
S
ili
co
n
1
9
1

10.1 D
i
str
ib
ut
i
on an
d
Some C
h
em
i
ca
l
Propert
i
e
s
1
9
1
10.2 B
i
o
l
og
i
ca
ll
y Important Propert

i
es o
f
S
ili
con an
d
Its Compoun
ds


19
2
10.3 Bioconcentration of Silico
n

19
3
10.3.1 Bacter
i
a 19
3
10.3.2 Fung
i

19
5
10.3.3 Diatom
s

19
5
10.4 B
i
omo
bili
zat
i
on o
f
S
ili
con an
d
Ot
h
er Const
i
tuents o
f
S
ili
cates
(B
i
oweat
h
er
i
ng

)


19
8
10.4.1 Solubilization b
y
Li
g
and
s

19
8
10.4.2 So
l
u
bili
zat
i
on
b
y Ac
ids
20
0
10.4.3 So
l
u
bili

zat
i
on
b
y A
lk
a
li

20
1
10.4.4 Solubilization b
y
Extracellular Pol
y
saccharide

20
2
10.4.5 Depolymerization of Polysilicates 2
0
2
10.5 Role of Microbes in the Silica C
y
cle

20
2
10.6 Summar
y

20
3
R
e
f
erences
.
2
0
4
1
C
ha
p
ter
1
G
eom
i
cro
bi
o
l
ogy o
f
A
l
um

i
num: M
i
cro
b
es an
d
Baux
i
te
20
9
11.1 Intro
d
uct
i
on
20
9
11
.
2 M
i
cro
bi
a
l
Ro
l
e

i
n Baux
i
te Format
i
on

21
0
11
.
2
.
1
N
ature of Bauxit
e


21
0
11.2.2 B
i
o
l
og
i
ca
l
Ro

l
e
i
n Weat
h
er
i
ng o
f
t
h
e Parent Roc
k
Mater
i
a
l

21
0
11.2.3 Weat
h
er
i
n
g
P
h
as
e

21
1
11
.
2
.
4 Bauxite Maturation Phas
e


21
1
CRC_7906_FM.indd xCRC_7906_FM.indd x 11/11/2008 5:11:59 PM11/11/2008 5:11:59 PM
C
ontents
xi
11.2.5 Bacterial Reduction of Fe(III) in Bauxites from Differen
t

L
ocat
i
o
n
s


21
4

11.2.
6

O
ther
O
bser
v
ations of Bacterial Interaction
w
ith Bauxite
21
4
11
.
3

S
ummar
y


21
5
Re
f
e
r
e
n

ces

21
5
1
Chapter
2
G
eomicrobial Interactions with Phos
p
horus

21
9
12.1 Biolo
g
ical Importance of Phosphoru
s


21
9
12.2 Occurrence in Earth’s Crust

t
21
9
12.3 Convers
i
on o

f
Organ
i
c
i
nto Inorgan
i
c P
h
osp
h
orus an
d
Synt
h
es
is
of Phos
p
hate Ester
s

22
0
12.4 Ass
i
m
il
at
i

on o
f
P
h
osp
h
orus
22
1
12.5 Microbial Solubilization of Phosphate Minerals

22
2
12.6 Microbial Phos
p
hate Immobilization

22
3
12.6.1 Phosphorite Deposition
22
3
12.
6
.1.1 Authigenic Formation
s

22
4
12.6.1.2 Dia

g
enetic Formatio
n

22
6
12.6.2 Occurrences of Phosphorite Deposit
s

22
6
12.
6
.3 Deposition of Other Phosphate Minerals

22
6
12.7 Microbial Reduction of Oxidized Forms of Phos
p
horu
s


22
7
12.8 M
i
cro
bi
a

l
Ox
id
at
i
on o
f
Re
d
uce
d
Forms o
f
P
h
osp
h
oru
s

22
8
12.9 M
i
cro
bi
a
l
Ro
l

e
i
n t
h
e P
h
osp
h
orus Cyc
le


22
9
12
.
10

S
ummar
y


22
9
R
e
f
erences
.

22
9
1
C
ha
p
ter
3
G
eomicrobially Important Interactions with Nitrogen 2
3
3
13.1 Nitrogen in Biosphere 2
3
3
13.2 M
i
cro
bi
a
l
Interact
i
ons w
i
t
h
N
i

troge
n

23
3
13.2.1 Ammoni catio
n

23
3
13.2.2 Nitri cation
2
3
5
1
3
.2.
3
Ammon
i
a
O
x
id
at
i
on

23
5

13.2.4 Nitrite Oxidation

23
6
13.2.
5
Heterotro
p
hic Nitri catio
n

2
3
6
13.2.
6
Anaerobic Ammonia Oxidation
(
Anammox
)

23
6
13.2.7 Denitri catio
n


23
7
13.2.8 Nitrogen Fixation

2
3
8
13.3 M
i
cro
bi
a
l
Ro
l
e
i
n t
h
e N
i
trogen Cyc
l
e

23
9
13
.
4

S
ummar
y

24
0
Re
f
e
r
e
n
ces
.

24
0
1
Chapter
4
G
eomicrobial Interactions with Arsenic and Antimon
y

24
3
14
.
1 Introduction

24
3

14.2 Arsen
ic
.

2
4
3
14
.
2
.
1 D
i
str
ib
ut
i
on

24
3
14.2.2 Some Chemical Characteristics

24
3
14.2.3 Tox
i
c
i
t

y

24
4
14.2.4 M
i
cro
bi
a
l

O
x
id
at
i
on o
f
Re
d
uce
d
Forms o
f
Arsen
i
c

24
5

14.2.4.1 Aerobic Oxidation of Dissolved Arseni
c


24
5
14.2.4.2 Anaero
bi
c
O
x
id
at
i
on o
f
D
i
sso
lv
e
d
Arsen
ic
2
4
7
CRC_7906_FM.indd xiCRC_7906_FM.indd xi 11/11/2008 5:12:00 PM11/11/2008 5:12:00 PM
x
ii

C
ontents
14.2.5 Interaction with Arsenic-Containin
g
Minerals

24
7
14.2.6 Microbial Reduction of Oxidized Arsenic S
p
ecie
s

25
0
14.2.7 Arsen
i
c Resp
i
rat
i
on
25
1
14.2.
8
Direct
O
bser

v
ations of Arsenite
O
xidation and Arsenate
Reduct
i
o
n In
S
it
u

2
5
4
14.3 Ant
i
mon
y

25
6
14.3.1 Antimony Distribution in Earth’s Crust

t
25
6
14.3.2 Microbial Oxidation of Antimon
y
Compound

s

25
6
14.3.3 M
i
cro
bi
a
l
Re
d
uct
i
on o
f
Ox
idi
ze
d
Ant
i
mony M
i
nera
l
s 2
5
7
14

.
4

S
ummar
y


2
5
7
Re
f
e
r
e
n
ces

2
5
8
1
C
ha
p
ter
5
G
eomicrobiology

o
f Mercury
2
6
5
1
5
.1 Introduction
2
6
5
15.2 Distribution of Mercury in Earth’s Crust

t
26
5
1
5
.3 Anthropo
g
enic Mercur
y


26
6
15.4 Mercury in Environment

t
26

6
15.5 Speci c Microbial Interactions with Mercury

2
6
7
1
5
.
5
.1 Nonenz
y
matic Meth
y
lation of Mercur
y
b
y
Microbe
s

2
6
7
1
5
.
5
.2 Enzymatic Methylation of Mercury by Microbe
s

26
8
15.5.3 Microbial Diphenylmercury Formation

2
6
9
1
5
.
5
.4 Microbial Reduction of Mercuric Ion

26
9
1
5
.
5
.
5
Formation of Meta-Cinnabar (
ß
-HgS) from Hg(II
)
b
y Cyano
b
acter

i
a

27
0
1
5
.
5
.6 Microbial Decomposition of Or
g
anomercurials

27
0
1
5
.
5
.7 Oxidation of Metallic Mercury
27
0
15.6 Genetic Control of Mercury Transformation
s

27
1
1
5
.7 Environmental Si

g
ni cance of Microbial Mercur
y
Tr
a
n
s
f
o
rm
at
i
o
n
s
2
7
2
15.8 Mercury Cycl
e

27
2
1
5
.9 Summar
y


2

7
3
Re
f
e
r
e
n
ces
.
2
7
4
1
C
ha
p
ter
6
G
eom
i
cro
bi
o
l
ogy o
f
Iron

27
9
16.1 Iron Distribution in Earth’s Crust

t
27
9
1
6
.2 Geochemicall
y
Important Properties

27
9
16.3 Biological Importance of Iron
28
0
1
6
.
3
.1 Function of Iron in
C
ell
s

28
0
16.3.2 Iron Assimilation b

y
Microbes

28
0
16.4 Iron as Energy Source for Bacteria 2
8
2
1
6
.4.1 Acidophile
s

28
2
16.4.2 Domain Bacteria: Meso
p
hile
s


28
2
16.4.2.1
A
cidithiobacillu
s
(
Formerly
Thiobacillus

)
s
f
errooxi
d
ans

28
2
16.4.2.2
T
hiobacillus prosperu
s

29
4
16.4.2.3 Leptospirillum
f
errooxidan
s
2
9
4
1
6
.4.2.4 Meta
ll
ogenium

29

5
16.4.2.
5
Ferromicrobium acidophilum

29
5
16.4.2.6 Strain CCH
7

2
9
5
CRC_7906_FM.indd xiiCRC_7906_FM.indd xii 11/11/2008 5:12:00 PM11/11/2008 5:12:00 PM
C
ontents
xiii
1
6
.4.3 Domain Bacteria: Thermophiles

29
5
16.4.3.1 Sul
f
obacillus thermosul

dooxidan
s

2
9
5
1
6
.4.
3
.2 Su
l
fo
b
aci
ll
us aci
d
op
h
i
l
u
s
.
2
9
6
1
6
.4.
3
.

3
A
cidimicrobium ferrooxidans

29
6
16.4.4 Domain Archaea: Meso
p
hiles

2
9
6
1
6
.4.4.1 Ferro
pl
asma aci
d
i
ph
i
l
um 2
9
6
1
6
.4.4.2 Ferroplasma acidarmanus

29
6
16.4.
5
Domain Archaea: Thermo
p
hiles

2
9
6
1
6
.4.
5
.1
A
ci
d
ianus
b
rier
l
e
yi
2
9
6
1
6

.4.
5
.2 Sulfolobus acidocaldarius

29
8
16.4.6 Domain Bacteria: Neutro
p
hilic Iron Oxidizers

29
8
1
6
.4.
6
.1
U
nicellular Bacteri
a
29
8
1
6
.4.7 Appenda
g
ed Bacteri
a

29
8
16.4.7.1
G
allionella
f
errugine
a

29
8
1
6
.4.7.2 Sheathed, Encapsulated, and Wall-Less Iron Bacteri
a

30
1
1
6
.
5
Anaerobic
O
xidation of Ferrous Iron

30
2
16.
5

.1
P
hototro
p
hic Oxidation

3
0
2
16.5.2 Chemotrophic Oxidatio
n

30
3
1
6
.
6
Iron(III) as Terminal Electron Acceptor in Bacterial Respiration

30
4
16.6.1 Bacterial Ferric Iron Reduction Accompan
y
in
g
Fermentation

3
0

4
1
6
.
6
.2 Ferric Iron Respiration: Early Histor
y

30
6
1
6
.
6
.3 Metabolic Evidence for Enz
y
matic Ferric Iron Reductio
n

30
8
16.6.4 Ferric Iron Res
p
iration: Current Status

3
0
9
16.6.5 Electron Transfer from Cell Surface of a Dissimilator
y

Fe(III) Re
d
ucer to Ferr
i
c Ox
id
e Sur
f
ac
e


31
3
16.6.6 Bioener
g
etics of Dissimilator
y
Iron Reduction

3
1
4
16.6.7 Ferric Iron Reduction as Electron Sink

k
31
4
1
6

.
6
.8 Reduction of Ferric Iron b
y
Fun
gi


31
5
16.6.9 T
y
pes of Ferric Compounds Attacked b
y
Dissimilator
y
I
ron
(
III
)
Re
d
uct
i
o
n

3
1

5
1
6
.7 Nonenz
y
matic Oxidation of Ferrous Iron and Reduction
of Ferric Iron b
y
Microbe
s

3
1
6
1
6
.7.1 Nonenzymatic Oxidatio
n

31
6
1
6
.7.2 Nonenz
y
matic Reduction

31
7
16.8 Microbial Preci

p
itation of Iro
n


3
1
8
1
6
.8.1 Enzymatic Processe
s

31
8
1
6
.8.2 Nonenz
y
matic Processe
s

31
9
16.8.3 Bioaccumulation of Iro
n


32
0

1
6
.9 Concept of Iron Bacteria
32
0
1
6
.10 Sedimentar
y
Iron Deposits of Putative Bio
g
enic Ori
g
in

32
2
16.11 Microbial Mobilization of Iron from Minerals in Ore, Soil
,
an
d

S
e
di
ment
s

3
2

5
1
6
.12 Microbes and Iron C
y
cle

32
6
16.13 Summar
y


32
7
R
e
f
erences
.

3
2
9
1
C
ha
p
ter
7

G
eom
i
cro
bi
o
l
ogy o
f
Manganese

34
7
17.1 Occurrence of Manganese in Earth’s Crust

t
34
7
17.2 Geochemicall
y
Important Properties of Man
g
anese

34
7
17.3 Biological Importance of Manganese
3
4
8

CRC_7906_FM.indd xiiiCRC_7906_FM.indd xiii 11/11/2008 5:12:00 PM11/11/2008 5:12:00 PM
x
i
v
C
ontent
s
17.4 Man
g
anese-Oxidizin
g
and Man
g
anese-Reducin
g
Bacteri
a
and Fun
g
i

3
4
8
17.4.1 Manganese-Ox
idi
z
i
ng Bacter
i

a an
d
Fung
i

3
4
8
17.4.2 Man
g
anese-Reducin
g
Bacteria and Fun
g
i

35
1
17.
5
Biooxidation of Man
g
anese

35
2
17.5.1 Enzymatic Manganese Oxidatio
n

35

2
17.5.2 Group I Man
g
anese Oxidizer
s

35
4
17.
5
.2.1 Sub
g
roup I
a


35
4
17.5.2.2 Subgroup Ib
35
7
17.5.2.3 Sub
g
roup I
c

35
7
17.
5

.2.4 Sub
g
roup Id

35
8
17.5.2.5 Uncertain Subgroup Af liations
35
9
17.5.3 Group II Man
g
anese Oxidizers

35
9
17.
5
.4 Group III Man
g
anese Oxidizer
s


3
6
2
17.5.5 Nonenzymatic Manganese Oxidatio
n

36

2
17.
6
Bioreduction of Man
g
anes
e


36
3
17.6.1 Or
g
anisms Capable of Reducin
g
Man
g
anese Oxides
On
l
y Anaero
bi
ca
ll
y
36
4
17.
6
.2 Reduction of Man

g
anese Oxides b
y
Or
g
anisms Capabl
e
of Reducin
g
Man
g
anese Oxides Aerobicall
y
an
d
Anaero
bi
ca
lly

36
5
17.
6
.3 Bacterial Reduction of Man
g
anese(III
)

37

0
17.6.4 Nonenz
y
matic Reduction of Man
g
anese Oxide
s

37
1
17.7 B
i
oaccumu
l
at
i
on o
f
Manganes
e

3
7
2
17.8 M
i
cro
bi
a
l

Man
g
anese Depos
i
t
i
on
i
n So
il
an
d
on Roc
ks

37
5
17.8.1 Soi
l

37
5
17.
8
.2 Roc
k
s
3
7
7

1
7.
8
.
3

O
res

3
7
8
17.9 Microbial Man
g
anese Deposition in Freshwater Environment
s

37
9
17.9.1 Bacter
i
a
l
Manganese Ox
id
at
i
on
i
n Spr

i
ngs
3
7
9
17.9.2 Bacterial Man
g
anese Oxidation in Lake
s

3
7
9
17.9.3 Bacterial Man
g
anese Oxidation in Wate
r
Di
str
ib
ut
i
on Systems
.

38
3
17.10 Microbial Man
g
anese Deposition in Marine Environments

38
4
17.10.1 Microbial Man
g
anese Oxidations in Ba
y
s, Estuaries
,
I
n
l
ets
,
t
h
e B
l
ac
k
Sea
,
etc.
.

38
5
17.10.2 Man
g
anese Ox

id
at
i
on
i
n M
i
xe
d
La
y
er o
f
Ocean

38
6
17.10.3 Manganese Oxidation on Ocean Floor

r
3
8
7
17.10.4 Manganese Ox
id
at
i
on aroun
d
Hy

d
rot
h
erma
l
Vent
s

3
9
2
17.10.5 Bacterial Man
g
anese Precipitation in Seawater Column

39
6
17.11 Microbial Mobilization of Man
g
anese in Soils and Ores

39
7
17.11.1
S
o
il
s
39
7

1
7.
11
.
2

O
res

3
9
8
17.12 Microbial Mobilization of Man
g
anese in Freshwater Environments

39
9
17.13 M
i
cro
bi
a
l
Mo
bili
zat
i
on o
f

Manganese
i
n Mar
i
ne Env
i
ronment
s

40
0
17.14 M
i
cro
bi
a
l
Man
g
anese Re
d
uct
i
on an
d
M
i
nera
li
zat

i
on
of Organic Matter

r
4
0
1
17.15 Microbial Role in Manganese Cycle in Natur
e
4
0
2
17.1
6
Summar
y


40
5
Re
f
e
r
e
n
ces

40

6
CRC_7906_FM.indd xivCRC_7906_FM.indd xiv 11/11/2008 5:12:00 PM11/11/2008 5:12:00 PM
C
ontents
xv
1
Chapter
8
G
eomicrobial Interactions with Chromium, Mol
y
bdenum, Vanadium,
U
ranium, Polonium, and Plutoniu
m

42
1
18.1 Microbial Interaction with Chromium

42
1
1
8
.1.1
O
ccurrence o
f

Ch

rom
i
um 4
2
1
18.1.2 Chemicall
y
and Biolo
g
icall
y
Important Propertie
s


42
1
18.1.3 Mobilization of Chromium with Microbiall
y
G
enerate
d
L
i
x
ivi
ant
s
42
2

18.1.4 Biooxidation of Chromium(III
)


42
2
18.1.
5
Bioreduction of Chromium(VI)

42
2
1
8
.1.
6
In Situ C
h
romate Re
d
uc
i
ng Act
i
v
i
t
y
4
2

6
18.1.7 A
pp
lied As
p
ects of Chromium(VI) Reduction

42
7
18.2 Microbial Interaction with Mol
y
bdenum

42
7
18.2.1 Occurrence an
d
Propert
i
es o
f
Mo
l
y
bd
enum 4
2
7
1
8

.2.2 Microbial
O
xidation and Reductio
n

42
7
18.3 Microbial Interaction with Vanadiu
m

42
8
1
8
.
3
.1 Bacter
i
a
l

O
x
id
at
i
on o
f
Vana
di

u
m

4
2
8
1
8
.4 M
i
cro
bi
a
l
Interact
i
on
wi
t
h

U
ran
i
um

42
9
18.4.1 Occurrence and Pro
p

erties of Uranium

42
9
18.4.2 M
i
cro
bi
a
l
Ox
id
at
i
on o
f
U
(
IV
)

4
2
9
18.4.3 M
i
cro
bi
a
l

Re
d
uct
i
on o
f
U(IV
)


43
0
18.4.4 Bioremediation of Uranium Pollution

4
3
1
1
8
.
5
Bacterial Interaction
w
ith Polonium 4
3
2
1
8
.
6

Bacterial Interaction
w
ith Plutonium

43
2
18.7 Summar
y


4
3
2
R
e
f
erences
.
4
3
3
1
Chapter
9
Geomicrobiology of Sulfur

r
4
3
9

19.1 Occurrence of Sulfur in Earth’s Crust

t
4
3
9
19.2 Geochemically Important Properties of Sulfur

r
4
3
9
19.3 Biological Importance of Sulfur

r
44
0
19.4 Mineralization of Or
g
anic Sulfur Compounds

44
0
1
9
.5 Sulfur Assimilation 4
4
1
19.
6

Geomicrobiall
y
Important T
y
pes of Bacteria That React with Sulfur
and Sulfur Com
p
ound
s

44
2
19.6.1 Oxidizers of Reduced Sulfur

r
4
4
2
19.6.2 Reducers of Oxidized Forms of Sulfur

r
44
6
19.6.2.1 Sulfate Reductio
n

44
6
1
9

.
6
.2.2 Sul te Reduction 44
8
19.6.2.3 Reduction of Elemental Sulfur

r
44
8
19.7 Ph
y
siolo
gy
and Biochemistr
y
of Microbial Oxidation of Reduce
d
Forms of Sulfur

r
44
9
1
9
.7.1 Su
l

d
e

44
9
19.7.1.1 Aerobic Attack

k
44
9
19.7.1.2 Anaerobic Attack

k
45
0
19.7.1.3 Ox
id
at
i
on o
f
Su
l

d
e
by
Heterotrop
h
s an
d
M
i

xotrop
hs

4
5
1
19.7.2 Elemental Su lfu r

r
4
5
1
19.7.2.1 Aerobic Attack

k
4
5
1
19.7.2.2 Anaerobic Oxidation of Elemental Sulfur

r
4
5
1
19.7.2.3 Dis
p
ro
p
ortionation of Sulfu
r

4
5
1
CRC_7906_FM.indd xvCRC_7906_FM.indd xv 11/11/2008 5:12:00 PM11/11/2008 5:12:00 PM
xv
i

C
ontent
s
1
9
.7.3 Su l te Oxidatio
n


4
5
2
19.7.3.1 Oxidation b
y
Aerobe
s

4
5
2
19.7.3.2 Ox
id

at
i
on
b
y Anaero
b
e
s

45
3
1
9
.7.4 Thiosulfate Oxidatio
n

45
3
19.7.4.1 Dis
p
ro
p
ortionation of Thiosulfat
e

4
5
5
19.7.5 Tetrathionate Oxidatio
n

45
6
19.7.
6
Common Mechanism for Oxidizin
g
Reduced Inor
g
ani
c
Sulfur Com
p
ounds in Domain Bacteri
a


45
6
19.8 Autotrophic and Mixotrophic Growth on Reduced Forms of Sulfur

r
45
6
19.8.1 Ener
gy
Couplin
g
in Bacterial Sulfur Oxidation

45
6
19.8.2 Reduced Forms of Sulfur as Sources of Reducin
g
Power

f
or
CO
2
F
i
xat
i
on
b
y Autotrop
hs

45
7
19.8.2.1 Chemos
y
nthetic Autotrophs

45
7
19.8.2.2 Photos
y
nthetic Autotroph

s

45
7
19.8.3 C
O
2
F
i
xat
i
on
b
y Autotrop
h
s
45
7
19.8.3.1
C
hemos
y
nthetic Autotrophs

45
7
19
.
8
.

3
.
2
P
hotos
y
nthetic Autotroph
s

4
5
8
19.8.
4
Mixotroph
y


4
5
8
19
.
8
.
4
.
1
Free-L
i

v
i
n
g
Bacter
i
a

4
5
8
19.8.
5
Unusual Consorti
a


4
5
8
19.9 Anaero
bi
c Resp
i
rat
i
on Us
i
ng Ox
idi

ze
d
Forms o
f
Su
lf
ur as Term
i
na
l
E
l
ectron Acceptor
s


4
5
9
19.9.1
Reduction of Fully or Partially Oxidized Sulfur

r
4
5
9
1
9
.
9

.2
Bi
oc
h
em
i
stry o
f
D
i
ss
i
m
il
atory Su
lf
ate Re
d
uct
i
o
n
4
5
9
19
.
9
.
3

S
u
lf
ur Isotope Fract
i
onat
i
on

4
6
1
19.9.4
Reduction of Elemental Sulfur

r
4
6
2
1
9
.
9
.5
R
e
d
uct
i
on o

f
T
hi
osu
lf
at
e

46
3
1
9
.
9
.
6

T
erminal Electron Acceptors Other Than Sulfate, Sul te,
TT
Thiosulfate, or Sulfur

r
4
6
3
1
9
.
9

.7
O
xygen To
l
erance o
f
Su
lf
ate-Re
d
ucers 4
6
4
19.10 Autotrop
hy
, M
i
xotrop
hy
, an
d
Heterotrop
hy
amon
g
Su
lf
ate-Re
d
uc

i
n
g
B
acte
ri
a


4
6
4
1
9
.10.1
A
utotrop
h
y 4
6
4
19
.
10
.
2
M
i
xotrop
hy

46
5
19.10.
3
H
eterotroph
y


4
6
5
19.11 Biodeposition of Native Sulfur

r
46
6
19
.
11
.
1
Ty
pes o
f
Depos
i
t

s


46
6
19.11.
2
Examples of S
y
n
g
enetic Sulfur Deposition

46
6
19
.
11
.
2
.
1
Cy
renaican Lakes, Lib
y
a, North Afric
a


46

6
1
9
.11.2.2 La
k
e Senoye
46
9
19.11.2.3 Lake E
y
re

4
6
9
19
.
11
.
2
.
4
S
o
l
ar La
k
e

47

0
19.11.2.5
Th
erma
l
La
k
es an
d
Spr
i
ngs
47
0
19
.
11
.
3
Examples of Epi
g
enetic Sulfur Deposit
s

47
2
1
9
.11.3.
1

S
i
c
ili
an Su
lf
ur Depos
i
t
s

47
2
19.11.3.
2
Salt Dome
s

47
2
19
.
11
.
3
.
3
Gaurdak Sulfur Deposit

t

4
7
4
19.11.3.
4
Shor-Su Sulfur Deposit

t
4
7
4
19.11.3.
5
Kara Kum Sulfur Deposit

t
47
5
CRC_7906_FM.indd xviCRC_7906_FM.indd xvi 11/11/2008 5:12:00 PM11/11/2008 5:12:00 PM
C
ontents
x
v
ii
19.12 Microbial Role in Sulfur C
y
cle

47
5

19.13 Summar
y


4
7
6
R
e
f
erences
.
4
7
7
2
C
ha
p
ter
0
Bi
ogenes
i
s an
d
B
i
o
d

egra
d
at
i
on o
f
Su
l

d
e M
i
nera
l
s at Eart
h
’s Sur
f
ace 4
9
1
2
0
.1 Intro
d
uct
i
on 4
9
1

20.2 Natural Ori
g
in of Metal Sul des

49
1
20.2.1
Hy
drothermal Ori
g
in (Abiotic
)

4
9
1
2
0
.2.2
S
e
di
mentary Meta
l
Su
l

d
es o
f

B
i
ogen
i
c Or
i
g
in

4
9
3
20.3 Principles of Metal Sul de Formation

49
4
20.4 Laborator
y
Evidence in Support of Bio
g
enesis of Metal Sul des

4
9
5
2
0
.4.1
B
atc

h

C
u
l
ture
s

4
9
5
20
.
4
.
2
Column Experiment: Model for Bio
g
enesis of Sedimentar
y

Metal Sul de
s

4
9
7
2
0
.

5
Biooxidation of Metal
S
ul de
s
49
8
2
0
.
5
.
1
O
r
g
an
i
sms Invo
l
ve
d

i
n B
i
oox
id
at
i

on o
f
Meta
l
Su
l

d
es

49
8
20.
5
.
2
D
irect Oxidation

49
9
2
0
.
5
.
3
I
n
di

rect
O
x
id
at
i
o
n

50
3
2
0
.
5
.
4
Py
r
i
te Ox
id
at
i
on

50
4
20.6 Bioleachin
g

of Metal Sul de and Uraninite Ores

50
7
2
0
.
6
.
1
Meta
l

S
u
l

d
e
O
re
s

50
7
2
0
.
6
.

2
Uran
i
n
i
te Leac
hi
n
g


51
1
20.6.
3
Mobilization of Uranium in Granitic Rocks b
y
Heterotrophs

5
1
2
2
0
.
6
.
4
S
tu

d
y o
f
B
i
o
l
eac
hi
ng K
i
net
i
cs
5
1
3
2
0
.
6
.
5
I
n
d
ustr
i
a
l

versus Natura
l
B
i
o
l
eac
hi
n
g

5
1
3
20.7 Bioextraction of Metal Sul de Ores b
y
Complexation

5
1
3
20.8 Format
i
on o
f
Ac
id
Coa
l
M

i
ne Dra
i
nag
e

51
4
20
.
8
.
1
New Discoveries Relatin
g
to Acid Mine Draina
g
e

5
1
5
20.9 Summar
y

51
7
R
e
f

erences
.

51
8
2
C
ha
p
ter
1
G
eom
i
cro
bi
o
l
ogy o
f
Se
l
en
i
um an
d
Te
ll
ur
i

u
m

52
7
21.1 Occurrence in Earth’s Crust

t
52
7
21.2 Biolo
g
ical Importance

52
7
21.3 Toxicit
y
of Selenium and Telluriu
m

5
2
8
21.4 B
i
oox
id
at
i

on o
f
Re
d
uce
d
Forms o
f

S
e
l
en
i
um
.

5
2
8
21.5 Bioreduction of Oxidized Selenium Compounds

5
2
8
21.
5
.1
O
ther Products of Selenate and Selenite Reductio

n

53
0
21.
5
.2
Selenium Reduction in the Environment

t
53
1
21.
6
Selenium C
y
cl
e


53
2
21
.
7 Biooxidation of Reduced Forms of Tellurium

5
3
2
21.

8
B
i
ore
d
uct
i
on o
f

O
x
idi
ze
d
Forms o
f
Te
ll
ur
i
u
m

53
3
21
.
9

S
ummar
y


53
3
Re
f
e
r
e
n
ces

5
3
4
2
Chapter
2
G
eom
i
cro
bi
o
l
o
gy

o
f
Foss
il
Fue
l
s

53
7
22
.
1 Intro
d
uct
i
o
n


53
7
22
.
2
N
atural Abundance of Fossil Fuels

5
3

7
CRC_7906_FM.indd xviiCRC_7906_FM.indd xvii 11/11/2008 5:12:01 PM11/11/2008 5:12:01 PM
xv
iii

C
ontent
s
22.
3
Methane

53
7
22.3.1 Methano
g
ens

53
9
22.
3
.2 Met
h
anogenes
i
s an
d
Car
b

on Ass
i
m
il
at
i
on
b
y Met
h
anogens
54
1
22.3.2.1
M
ethano
g
enesis

54
1
22.
3
.
3
Bi
oenerget
i
cs o
f

Met
h
anogenes
is

54
4
22
.
3
.
4
Carbon Fixation b
y
Methano
g
en
s

54
4
22.3.
5
Microbial Methane Oxidation

54
5
22.
3
.

5
.
1
Aerobic Methanotroph
y


54
5
22.
3
.
5
.
2
Anaero
bi
c Met
h
anotrop
hy

54
7
22.
3
.
6
Bi
oc

h
em
i
str
y
o
f
Met
h
ane Ox
id
at
i
on
i
n Aero
bi
c Met
h
anotrop
hs

5
4
8
22.3.7 Carbon Assimilation b
y
Aerobic Methanotroph
s

54
9
22.
3
.
8
P
os
i
t
i
on o
f
Met
h
ane
i
n Car
b
on Cyc
le

55
0
22.4
Peat

55
0

22
.
4
.1
Nature of Peat

t
55
0
22.4.2
R
o
l
es o
f
M
i
cro
b
es
i
n Peat Format
i
o
n

55
2
22.
5

C
oal

55
2
22.
5
.1 Nature of Coal

55
2
22.
5
.2
R
o
l
e o
f
M
i
cro
b
es
i
n
C
oa
l

Format
i
on
55
3
22.
5
.
3
C
oa
l
as M
i
cro
bi
a
l

S
u
b
strate

55
4
22.
5
.4 Microbial Desulfurization of Coal

55
5
22.
6
Petroleum
55
6
22.
6
.1
N
ature o
f
Petro
l
eum

55
6
22.6.2
Ro
l
e

o
f Mi
c
r
obes
in P

et
r
o
l
eu
m F
o
rm
at
i
o
n

55
6
22.
6
.
3
Role of Microbes in Petroleum Migration in Reservoir Rock

k
55
7
22.
6
.4 M
i
cro
b

es
i
n Secon
d
ar
y
an
d
Tert
i
ar
y
O
il
Recover
y

55
8
22.6.
5
R
emoval of Or
g
anic Sulfur from Petroleu
m

55
9
22.

6
.
6
M
i
cro
b
es
i
n Petro
l
eum Degra
d
at
i
o
n

55
9
22.
6
.7 Current State o
f
Know
l
e
dg
e o
f

Aero
bi
c an
d
An
ae
r
obic
P
etroleum De
g
radation b
y
Microbes

56
0
22.
6
.
8
Use o
f
M
i
cro
b
es
i
n Prospect

i
ng
f
or Petro
l
eum
56
3
22.
6
.
9
M
i
cro
b
es an
d

Sh
a
l
e
Oil


56
3
22
.

7
S
ummar
y


56
4
R
e
f
erences
.

56
5
G
lossar
y

5
77
In
dex

5
8
9
CRC_7906_FM.indd xviiiCRC_7906_FM.indd xviii 11/11/2008 5:12:01 PM11/11/2008 5:12:01 PM
xix

Pr
e
fa
ce
S
evera
l

i
mportant a
d
vances
h
ave occurre
d

i
n t
h
e

e
ld
o
f
geom
i
cro
bi
o

l
ogy s
i
nce t
h
e
l
ast e
di
t
i
on
o
f
t
hi
s
b
oo
k
,
i
nc
l
u
di
ng a num
b
er o
f

o
b
servat
i
ons ma
d
e poss
ibl
e
b
y t
h
e
i
ntro
d
uct
i
on o
f
genet
i
c
and molecular biolo
g
ical techniques that make revision and updatin
g
of the previous edition of
G
eomicro

b
io
l
o
gy
t
i
me
l
y
.
Henry Lutz E
h
r
li
c
h
, aut
h
or o
f
t
h
e ear
li
er
f
our e
di
t

i
ons,
h
as
b
een
j
o
i
ne
d

b
y D
i
anne K. Newman
f
o
r

this  fth edition to lend her expertise in the area of molecular
g
eomicrobiolo
gy
. This has resulted in a
n
ew c
h
apter (C
h

apter 8)
i
n t
hi
s e
di
t
i
on, w
hi
c
h

i
s ent
i
t
l
e
d
“Mo
l
ecu
l
ar Met
h
o
d
s
i

n Geom
i
cro
bi
o
l
ogy.”
Th
e tec
h
n
i
ques
d
escr
ib
e
d

i
n t
hi
s c
h
apter
ill
um
i
nate t
h

e processes
b
y w
hi
c
h

b
acter
i
a cata
l
yze
i
mpor-
tant
g
eomicrobial reactions. For example, we are be
g
innin
g
to understand the molecular details
w
h
ere
b
y some gram-negat
i
ve
b

acter
i
a export e
l
ectrons to m
i
nera
l
ox
id
es w
i
t
h
w
hi
c
h
t
h
ey are
i
n
ph
ys
i
ca
l
contact
i

n t
h
e
i
r resp
i
ratory meta
b
o
li
sm. Suc
h
e
l
ectron trans
f
er
i
s ena
bl
e
d

b
y resp
i
ratory
e
nz
y

mes in the outer membrane and periplasm of such or
g
anisms. Molecular techniques have also
d
emonstrate
d
t
h
at at
l
east one gram-negat
i
ve
b
acter
i
um can
i
mport e
l
ectrons
d
onate
d

b
y an e
l
ec-
tron

d
onor,
f
errous
i
ron,
i
n contact w
i
t
h
t
h
e outer sur
f
ace o
f
t
h
e outer mem
b
rane o
f
t
hi
s or
g
an
i
sm.

In some cases, electron shuttles have been shown to facilitate electron transfer. Further im
p
ortan
t

a
d
vances
i
n t
hi
s area are ant
i
c
i
pate
d
. Co
ll
ect
i
ve
l
y, t
h
ese mec
h
an
i
st

i
c o
b
servat
i
ons ma
k
e c
l
ear t
h
a
t

mi
cro
b
es p
l
a
y
a muc
h
more
di
rect ro
l
e
i
n t

h
e trans
f
ormat
i
on o
f
ox
idi
za
bl
e an
d
re
d
uc
ibl
e m
i
nera
l
s
than had been previousl
y
believed b
y
man
y
researchers in this  eld. We anticipate that as mechanis-
t

i
c mo
l
ecu
l
ar approac
h
es are
i
ncreas
i
ng
l
y app
li
e
d
to
di
verse pro
bl
ems
i
n geom
i
cro
bi
o
l
ogy, exc

i
t
i
ng
di
scover
i
es w
ill

b
e ma
d
e a
b
out
h
ow
lif
e susta
i
ns
i
tse
lf
even
i
n seem
i
n

gly

i
n
h
osp
i
ta
bl
e env
i
ronments
s
uch as the dee
p
subsurface
.
Just as
i
n t
h
e case o
f
t
h
e prev
i
ous e
di
t

i
ons o
f
Geomicro
b
io
l
o
gy
,
t
h
e c
hi
e
f
a
i
m o
f
t
h
e


f
t
h
e
di

t
i
on
i
s to serve as an
i
ntro
d
uct
i
on to t
h
e su
bj
ect an
d
an up-to-
d
ate re
f
erence. To cont
i
nue to prov
id
e a
broad
p
ers
p
ective of the develo

p
ment of the  eld, discussion of the older literature that a
pp
eared
i
n ear
li
er e
di
t
i
ons o
f
t
hi
s
b
oo
k

h
as
b
een reta
i
ne
d
. C
h
anges

i
n un
d
erstan
di
ng an
d
v
i
ewpo
i
nts are
p
o
i
nte
d
out w
h
ere necessar
y
. A
l
t
h
ou
gh
we
d
o not c

l
a
i
m t
h
at t
h
e re
f
erence c
i
tat
i
ons at t
h
e en
d
o
f

e
ach chapter are exhaustive, cross-referencin
g
should reveal other pertinent literature. As before, a
g
l
ossary o
f
terms t
h

at may
b
e un
f
am
ili
ar to some rea
d
ers
h
as
b
een a
dd
e
d
. A
ll
c
h
apters
h
ave
b
een
up
d
ate
d
w

h
ere necessar
y

by

i
ntro
d
uc
i
n
g
t
h
e

n
di
n
g
s o
f
recent researc
h.
W
e are continuin
g
to retain some of the drawin
g

s prepared b
y
Stephen Chian
g
for the  rs
t

edi
t
i
on. Ot
h
er
ill
ustrat
i
ons
f
rom t
h
e
f
ourt
h
e
di
t
i
on
h

ave
b
een reta
i
ne
d

i
n t
h
e current e
di
t
i
on
,
w
i
t
h
appropr
i
ate ac
k
now
l
e
dg
ments to t
h

e
i
r source w
h
en not or
igi
nat
i
n
g

f
rom us, an
d
some new
ill
ustra-
tions have been added. We are ver
y

g
rateful to Andreas Kappler for allowin
g
us to use the photomi-
c
rograp
h
o
f
C

hl
oro
b
ium
f
errooxi
d
an
s
f
or t
h
e
b
oo
k
co
v
er
ill
ustrat
i
on o
f
t
hi
s e
di
t
i

on
.
W
e owe spec
i
a
l
t
h
an
k
s to Mart
i
n Po
l
z, V
i
ctor
i
a Orp
h
an, an
d
A
l
ex Sess
i
ons
f
or st

i
mu
l
at
i
n
g

di
s-
c
ussions that shaped the content of Chapter 8; and we
g
ratefull
y
acknowled
g
e Alexandre Poulain
f
or
hi
s
h
e
l
p
i
n prepar
i
ng t

h
e

gures
f
or t
hi
s c
h
apter. We a
l
so owe s
i
ncere t
h
an
k
s to Jon Pr
i
ce
f
or
hi
s
ass
i
stance
i
n o
b

ta
i
n
i
n
g
t
h
e p
h
oto
g
rap
h
o
f
t
h
e samp
l
e o
f

b
asa
l
t
f
rom t
h

e roc
k
co
ll
ect
i
on at Rensse
l
ae
r

P
ol
y
technic Institute.
W
e apprec
i
ate t
h
e encouragement an
d
e
di
tor
i
a
l
ass
i

stance o
f
Ju
di
t
h
Sp
i
ege
l
, Bar
b
ara Norw
i
tz,
an
d
Patr
i
c
i
a Ro
b
erson o
f
Ta
yl
or & Franc
i
s Group LLC.

Responsibilit
y
for the presentation and interpretation of the sub
j
ect matter in this edition rests
e
nt
i
re
l
y w
i
t
h
t
h
e aut
h
ors
.
H
enry Lutz Ehrlich
Di
anne K.
N
ewma
n
CRC_7906_FM.indd xixCRC_7906_FM.indd xix 11/11/2008 5:12:01 PM11/11/2008 5:12:01 PM
CRC_7906_FM.indd xxCRC_7906_FM.indd xx 11/11/2008 5:12:01 PM11/11/2008 5:12:01 PM
xxi

Aut
h
or
s
D
r. Henr
y
Lutz Ehrl
i
ch earne
d
a BS
d
egree
f
rom Harvar
d
Co
ll
ege (ma
j
or:
bi
oc
h
em
i
ca
l
sc

i
ences)
i
n 1948, an MS degree in 1949 (major: agricultural bacteriology), and a PhD degree in 1951 (major:
a
g
ricultural bacteriolo
gy
; minor: biochemistr
y
); both of the latter de
g
rees from the Universit
y
of
Wi
scons
i
n, Ma
di
son. He
j
o
i
ne
d
t
h
e
f

acu
l
ty o
f
t
h
e B
i
o
l
ogy Department o
f
Rensse
l
aer Po
l
ytec
h
n
i
c
Institute as an assistant professor in the fall of 1951, attaining the rank of full professor in 1964.
D
r. Ehrlich became
p
rofessor emeritus in 1994 but continues to be active in the de
p
artment in
p
ursuit of

s
ome scholarly work. He began teaching a course in geomicrobiology in the spring semester of 1966.
Dr. E
h
r
li
c
h

i
s a
f
e
ll
ow o
f
t
h
e Amer
i
can Aca
d
emy o
f
M
i
cro
bi
o
l

ogy, Amer
i
can Assoc
i
at
i
on
f
or t
h
e
A
dvancement of Science, the International Union of Pure and Applied Chemistr
y
, and the Inter-
n
at
i
ona
l
Sympos
i
a on Env
i
ronmenta
l
B
i
ogeoc
h

em
i
stry. He
i
s a mem
b
er o
f
t
h
e Inter
di
sc
i
p
li
nary
Comm
i
ttee o
f
t
h
e Wor
ld
Cu
l
tura
l
Counc

il
(Conse
j
o Cu
l
tura
l
Mun
di
a
l
) an
d
an
h
onoree o
f
t
h
e 11t
h

International S
y
mposium on Water/Rock held in 1994 in Sarato
g
a Sprin
g
s, New York. Dr. Ehrlich
h

as
b
een a consu
l
tant at var
i
ous t
i
mes
f
or a num
b
er o
f

diff
erent compan
i
es. He was e
di
tor-
i
n-c
hi
e
f
o
f

Geomicrobiology Journal

(1983–1995) and has since continued as co-editor-in-chief. He is a mem-
l
be
r
o
f
t
h
e

ed
i
to
ri
a
l
boa
r
ds

of

A
pplied and Environmental Microbiology
a
n
d
Applied Microbiology
a
n

d
Biotec
h
no
l
o
gy
.
He
i
s a
l
so emer
i
tus mem
b
er o
f
Amer
i
can Assoc
i
at
i
on
f
or t
h
e A
dv

ancement o
f

S
c
i
ence, Amer
i
can Inst
i
tute o
f
B
i
o
l
o
gi
ca
l
Sc
i
ences, Amer
i
can Soc
i
et
y

f

or M
i
cro
bi
o
l
o
gy
, an
d
t
h
e
S
ociet
y
of Industrial Microbiolo
gy
.
Dr. E
h
r
li
c
h
’s researc
h

i
nterests

h
ave res
id
e
d

i
n
b
acter
i
a
l
ox
id
at
i
on o
f
Mn
(
II
)
an
d
re
d
uct
i
on o

f

Mn(IV) assoc
i
ate
d
w
i
t
h
mar
i
ne
f
erroman
g
anese concret
i
ons, mar
i
ne
hyd
rot
h
erma
l
vent commun
i
t
i

es,
and some freshwater environments; bacterial oxidation of arsenic(III); bacterial reduction of Cr(VI);
b
acter
i
a
l

i
nteract
i
on w
i
t
h

b
aux
i
te; an
d

bi
o
l
eac
hi
ng o
f
ores

i
nc
l
u
di
ng meta
l
su
l

d
es,
b
aux
i
te, an
d
ot
h
ers.
He
i
s aut
h
or or coaut
h
or o
f
more t
h

an 100 art
i
c
l
es
d
ea
li
n
g
w
i
t
h
var
i
ous top
i
cs
i
n
g
eom
i
cro
bi
o
l
o
gy

.
D
r. Dianne K. Newman earne
d
a BA
d
e
g
ree
f
rom Stan
f
or
d
Un
i
vers
i
t
y
(ma
j
or: German stu
di
es)
i
n 1993, and a PhD de
g
ree in 1997 (ma
j

or: environmental en
g
ineerin
g
with an emphasis on micro-
bi
o
l
ogy)
f
rom t
h
e Massac
h
usetts Inst
i
tute o
f
Tec
h
no
l
ogy (MIT). S
h
e spent two years as an exc
h
ange
s
cholar at Princeton Universit
y

in the Geosciences department from 1995 to 1997. Dr. Newman was
a postdoctoral fellow in the Department of Microbiolo
gy
and Molecular Genetics at Harvard Medical
S
c
h
oo
l

f
rom 1998 to 2000. S
h
e
j
o
i
ne
d
t
h
e
f
acu
l
ty o
f
t
h
e Ca

lif
orn
i
a Inst
i
tute o
f
Tec
h
no
l
ogy
i
n 2000,
w
h
ere s
h
e was
j
o
i
nt
ly
appo
i
nte
d

i

n t
h
e
di
v
i
s
i
ons o
f
Geo
l
o
gi
ca
l
an
d
P
l
anetar
y
Sc
i
ences an
d
B
i
o
l

o
gy
. In
2007, she returned to MIT, where she is currentl
y
the John and Doroth
y
Wilson Professor of Biolo
gy

an
d
Geo
bi
o
l
ogy, w
i
t
h
a
j
o
i
nt appo
i
ntment
i
n t
h

e
d
epartments o
f
B
i
o
l
ogy an
d
Eart
h
, Atmosp
h
er
i
c an
d

Pl
anetary Sc
i
ences. Dr. Newman
i
s a
l
so an Invest
i
gator o
f

t
h
e Howar
d
Hug
h
es Me
di
ca
l
Inst
i
tute
.
Dr. Newman’s honors include bein
g
a Clare Boothe Luce assistant professor, an Of ce of Naval
R
esearc
h
young
i
nvest
i
gator, a Dav
id
an
d
Luc
ill

e Pac
k
ar
d
Fe
ll
ow
i
n sc
i
ence an
d
eng
i
neer
i
ng, an
Invest
ig
ator o
f
t
h
e Howar
d
Hu
gh
es Me
di
ca

l
Inst
i
tute, an
d
a
f
e
ll
ow o
f
t
h
e Amer
i
can Aca
d
em
y
o
f

Microbiolo
gy
. She was the 2008 recipient of the Eli Lil
y
and Compan
y
Research Award from the
A

mer
i
can Soc
i
ety
f
or M
i
cro
bi
o
l
ogy. S
h
e
i
s an e
di
tor o
f
t
h
e Geo
b
io
l
o
gy
Journa
l

,
an
d

i
s on t
h
e e
di
to-
ri
a
l

b
oar
d
o
f
t
h
e
A
nnua
l
Review of Eart
h
an
d
P

l
anetary Scienc
e
. S
h
e
i
s on t
h
e sc
i
ent
i
c a
d
v
i
sor
y

board of Mascoma Corporation, and is a member of the American Societ
y
of Microbiolo
gy
and the
A
mer
i
can Geop
h

ys
i
ca
l
Un
i
on
.
Dr. Newman’s
l
a
b
orator
y
see
k
s to
g
a
i
n
i
ns
igh
ts
i
nto t
h
e evo
l

ut
i
on o
f
meta
b
o
li
sm as recor
d
e
d

i
n ancient rocks b
y
stud
y
in
g
how modern bacteria catal
y
ze
g
eochemicall
y
si
g
ni cant reactions.
S

pec
i
ca
ll
y, s
h
e
f
ocuses on putat
i
ve
l
y anc
i
ent
f
orms o
f
p
h
otosynt
h
es
i
s an
d
resp
i
rat
i

on, w
i
t
h
a spe-
ci
c
i
nterest
i
n t
h
e ce
ll
u
l
ar mec
h
an
i
sms t
h
at ena
bl
e t
h
ese comp
l
ex processes to wor
k

.
CRC_7906_FM.indd xxiCRC_7906_FM.indd xxi 11/11/2008 5:12:01 PM11/11/2008 5:12:01 PM
CRC_7906_FM.indd xxiiCRC_7906_FM.indd xxii 11/11/2008 5:12:01 PM11/11/2008 5:12:01 PM
1
1
I
ntr
od
ucti
on
G
eom
i
cro
bi
o
l
ogy
d
ea
l
s w
i
t
h
t
h
e ro
l
e t

h
at m
i
cro
b
es p
l
ay at present on Eart
h

i
n a num
b
er o
f

f
un
d
a-
m
ental
g
eolo
g
ic processes and have pla
y
ed in the past since the be
g
innin

g
of life. These processes
i
nclude the cycling of organic and some forms of inorganic matter at the surface and in the sub-
s
ur
f
ace o
f
Eart
h
, t
h
e weat
h
er
i
ng o
f
roc
k
s, so
il
an
d
se
di
ment
f
ormat

i
on an
d
trans
f
ormat
i
on, an
d
t
h
e
g
enesis and de
g
radation of various minerals and fossil fuels.
G
eomicrobiology should not be equated with microbial ecology or microbial biogeochemistry.
Micro
b
ia
l
eco
l
og
y

i
s t
h

e stu
d
y o
f

i
nterre
l
at
i
ons
hi
ps
b
etween
diff
erent m
i
croorgan
i
sms; among m
i
cro-
or
g
anisms, plants, and animals; and between microor
g
anisms and their environment.
Mic
r

obial

bio-
g
eochemistr
y
is the study of microbially in uenced geochemical reactions, enzymatically catalyzed
or not, an
d
t
h
e
i
r
ki
net
i
cs. T
h
ese react
i
ons are o
f
ten stu
di
e
d

i
n t

h
e context o
f
cyc
li
ng o
f

i
norgan
i
c an
d

or
g
anic matter with an emphasis on environmental mass transfer and ener
gy
 ow. These sub
j
ects
overlap to some degree, as shown in Figure 1.1.
It
i
s unc
l
ear as to
wh
en t
h

e term geomicro
b
io
l
ogy
w
as

rst
i
ntro
d
uce
d

i
nto t
h
e sc
i
ent
i
c
v
oca
b
u-
lar
y
. This term is obviousl

y
derived from the term
g
eological microbiology. Beerstecher (19
5
4)
de ned geomicrobiology as “the study of the relationship between the history of the Earth and
m
icrobial life upon it.” Kuznetsov et al. (19
6
3) de ned it as “the study of microbial processes cur-
r
entl
y
takin
g
place in the modern sediments of various bodies of water, in
g
round waters circulatin
g

through sedimentary and igneous rocks, and in weathered Earth crust [and also] the physiology
o
f
spec
i
c m
i
croorgan
i

sms ta
ki
ng part
i
n present
l
y occurr
i
ng geoc
h
em
i
ca
l
processes.” Ne
i
t
h
e
r

author traced the histor
y
of the term, but the
y
pointed to the important roles that scientists such a
s
S
. Winogradsky, S. A. Waksman, and C. E. ZoBell played in the development of the  eld.
G

eom
i
cro
bi
o
l
ogy
i
s not a new sc
i
ent
i
c
di
sc
i
p
li
ne, a
l
t
h
oug
h
unt
il
t
h
e 1980s
i

t
did
not rece
i
ve
m
uch specialized attention. A uni ed concept of
g
eomicrobiolo
gy
and the biosphere can be said
to have been pioneered in Russia under the leadership of V. I. Vernadsky (1863–194
5
) (see Ivanov,
19
6
7; Lapo, 1987; Bailes, 1990; Vernadsky, 1998, for insights and discussions of early Russian
g
eomicrobiolo
gy
and its practitioners)
.
Certain early investigators in soil and aquatic microbiology may not have thought of themselves
as geom
i
cro
bi
o
l
og

i
sts,
b
ut t
h
ey nevert
h
e
l
ess exerte
d
an
i
mportant
i
n

uence on t
h
e su
bj
ect. One o
f
t
h
e
 rst contributors to
g
eomicrobiolo
gy

was Ehrenber
g
(1836, 1838), who discovered the association
o
f Gallionella
f
erruginea with ochreous deposits of bog iron in the second quarter of the nineteenth
c
entury. He
b
e
li
eve
d
t
h
at t
hi
s organ
i
sm, w
hi
c
h

h
e c
l
ass
i

e
d
as an
i
n
f
usor
i
an (protozoan),
b
ut w
hi
c
h

we now reco
g
nize as a stalked bacterium (see Chapter 16), pla
y
ed a role in the formation of such
deposits. Another important early contributor to geomicrobiology was S. Winogradsky, who discov-
e
re
d
t
h
at Beggiato
a
,
a



l
amentous
b
acter
i
um (see C
h
apter 19), cou
ld
ox
idi
ze
H
2
S
to e
l
ementa
l
su
lf
u
r

(Wino
g
radsk
y

, 1887) and tha
t
Leptothrix ochrace
a
,
a sheathed bacterium (see Cha
p
ter 1
6
),
p
romoted
oxidation of FeCO
3
to ferric oxide (Winogradsky, 1888). He believed that each of these organisms
ga
i
ne
d
energy
f
rom t
h
e correspon
di
ng processes. St
ill
ot
h
er

i
mportant ear
l
y contr
ib
utors to geom
i
cro-
biolo
gy
were Harder (1919), a researcher trained as a
g
eolo
g
ist and microbiolo
g
ist, who studied the
s
igni cance of microbial iron oxidation and precipitation in relation to the formation of sedimentary
i
ron
d
epos
i
ts, an
d
Stutzer (1912) an
d
ot
h

ers, w
h
ose stu
di
es
l
e
d
to t
h
e recogn
i
t
i
on o
f
t
h
e s
i
gn
i
cance
o
f mi
c
r
ob
i
a

l
o
xi
dat
i
o
n
o
f H
2
S
to elemental sulfur in the formation of sedimentar
y
sulfur deposits. Ou
r

e
arly understanding of the role of bacteria in sulfur deposition in nature received a further boost from
the discovery of bacterial sulfate reduction by Beijerinck (1895) and van Delden (1903)
.
CRC_7906_Ch001.indd 1CRC_7906_Ch001.indd 1 11/5/2008 5:11:45 PM11/5/2008 5:11:45 PM
2
Geomicro
b
io
l
og
y
Startin
g

with the Russian investi
g
ator Nadson (1903, 1928) at the end of the nineteenth centur
y
,
and continuing with such investigators as Bavendamm (1932), the important role of microbes in
s
ome
f
orms o
f

C
a
CO
3
prec
i
p
i
tat
i
on
b
egan to
b
e note
d
. M
i

cro
bi
a
l
part
i
c
i
pat
i
on
i
n manganese ox
id
a-
tion and precipitation in nature was  rst reco
g
nized b
y
Bei
j
erinck (1913), Soehn
g
en (1914), Lieske
(1919), and Thiel (192
5
). Zappfe (1931) later related this activity to the formation of sedimentary
m
anganese ore (see C
h

apter 17). A m
i
cro
bi
a
l
ro
l
e
i
n met
h
ane
f
ormat
i
on (met
h
anogenes
i
s)
b
ecame
apparent throu
g
h the observations and studies of Béchamp (1868), Tappeiner (1882), Popoff (187
5
),
Hoppe-Seyler (1886), Omeliansky (1906), Soehngen (1906), and Barker (19
5

6). The role of bacte-
r
ia in rock weathering was  rst suggested by Muentz (1890) and Merrill (1895). Later, the involve-
m
ent of acid-producin
g
microor
g
anisms, such as nitri ers, and crustose lichens and fun
g
i in such
weathering was suggested (see Waksman, 1932). Thus by the beginning of the twentieth century,
m
any
i
mportant areas o
f
stu
d
y o
f
geom
i
cro
bi
a
l
processes
h
a

d

b
egun to rece
i
ve ser
i
ous attent
i
on
from microbiolo
g
ists. In
g
eneral it ma
y
be said that most of the earl
y

g
eomicrobiall
y
importan
t

discoveries were made through physiological studies in the laboratory, which revealed the capacity
o
f
spec
i

c organ
i
sms to promote geom
i
cro
bi
a
ll
y
i
mportant trans
f
ormat
i
ons, caus
i
ng
l
ater wor
k
ers
to stud
y
the extent of the occurrence of such processes in nature.
In the United States, geomicrobiology can be said to have begun with the work on iron-depositing
b
acter
i
a
b

y Har
d
er (1919). Ot
h
er ear
l
y Amer
i
can
i
nvest
i
gators o
f
geom
i
cro
bi
a
l
p
h
enomena
i
nc
l
u
d
e
J. Lipman, S. A. Waksman, R. L. Starke

y
, and H. O. Halvorson, all prominent in soil microbiolo
gy
,
and G. A. Thiel, C. Zappfe, and C. E. ZoBell, all prominent in aquatic microbiology. ZoBell was a
pi
oneer
i
n mar
i
ne m
i
cro
bi
o
l
ogy (see E
h
r
li
c
h
, 2000).
Ve r
y
fundamental discoveries in
g
eomicrobiolo
gy
continue to be made, some havin

g
been made
as the twentieth century progressed and others very recently. For instance, the concept of environ-
m
enta
l

li
m
i
ts o
f
pH an
d
E
h
for microbes in natural habitats was  rst introduced by Baas-Becking
h
e
t al. (1960) (see Cha
p
ter 6). The
p
H limits as these authors de ned them have since been extended
at both the acidic and alkaline ends of the pH range (pH 0 and 13) as a result of new observations.
L
if
e at
hi
g

h
temperature was systemat
i
ca
ll
y stu
di
e
d

f
or t
h
e

rst t
i
me
i
n t
h
e 1970s
b
y Broc
k

(1978) and associates in Yellowstone National Park in the United States. A s
p
eci c acido
p

hilic, iron-
oxidizing bacterium, originally name
d
Thiobacillus
f
errooxidan
s
a
n
d
l
ate
r r
e
n
a
m
ed

A
cidithiobacillus
f
errooxi
d
an
s
,
was discovered by Colmer et al. (1950) in acid coal mine drainage in the late 1940s
and thou
g

ht b
y
these investi
g
ators and others to be directl
y
involved in its formation b
y
promotin
g

oxidation of pyrite occurring as inclusions in bituminous coal seams (see also Chapters 16 and 20)
.
Biogeochemistry
biogeochemistry
Microbial
Microbial
ecology
Geomicrobiology
FI
GU
RE 1
.
1
I
nterrelationships between
g
eomicrobiolo
gy
, microbial ecolo

gy
, microbial bio
g
eochemistr
y
,
and bio
g
eochemistr
y
.
CRC_7906_Ch001.indd 2CRC_7906_Ch001.indd 2 11/5/2008 5:11:45 PM11/5/2008 5:11:45 PM