Molecular Geomicrobiology

308 Pages·2005·7.792 MB·English

by  Jillian F Banfield, Javiera Cervini-Silva, Kenneth H Nealson, Eds.

REVIEWS MINERALOGY
in
GEOchEMIStRY
and
Volume 59 2005
Molec u l a r
GeoM ic robiolo G y
EDITORS:
Jillian F. Banfield University of California, Berkeley
Berkeley, California
Javiera Cervini-Silva University of California, Berkeley
Berkeley, California
Kenneth H. Nealson University of Southern California
Los Angeles, California
FRONT COVER: Dinitrogen (N) bound at the molybdenum-iron-sulfur
2
active site of the nitrogenase enzyme complex, where it is ultimately reduced
to biologically-useful ammonia. Nitrogenase is the only enzyme known to
catalyze such a transformation, and is found only in prokaryotes, representing
a crucial shunt between the inorganic and organic worlds. Created by Jason
Raymond and Jill Banfield.
Series Editor: Jodi J. Rosso
MINERALOGIcAL SOcIEtY of AMERIcA
GEOchEMIcAL SOcIEtY
Copyright 2005
Mineralogical Society of aMerica
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r M
eviewS in ineralogy
g
and eocheMiStry
( Formerly: reviews in Mineralogy )
iSSn 1529-6466
volume 59
Molecular Geomicrobiology
iSBn 093995071-5
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DeDication
Dr. William C. Luth has had a long and distinguished career in research,
education and in the government. He was a leader in experimental
petrology and in training graduate students at Stanford University. His
efforts at Sandia National Laboratory and at the Department of Energy’s
headquarters resulted in the initiation and long-term support of many of
the cutting edge research projects whose results form the foundations of
these short courses. Bill’s broad interest in understanding fundamental
geochemical processes and their applications to national problems is a
continuous thread through both his university and government career.
He retired in 1996, but his efforts to foster excellent basic research, and to
promote the development of advanced analytical capabilities gave a unique
focus to the basic research portfolio in Geosciences at the Department of
Energy. He has been, and continues to be, a friend and mentor to many of
us. It is appropriate to celebrate his career in education and government
service with this series of courses in cutting-edge geochemistry that have
particular focus on Department of Energy-related science, at a time when
he can still enjoy the recognition of his contributions.
This page is blank.
M o l e c u l a r
G e oM i c r o b i o l oGy
59 Reviews in Mineralogy and Geochemistry 59
From the SerieS editor
This volume was prepared in advance of a short course entitled “Molecular
Geomicrobiology.” The short course, sponsored by the Mineralogical Society of America,
the Geochemical Society, the US Department of Energy, and NASA Astrobiology Institute,
was held at the University of California, Berkeley, December 3-4, 2005 prior to the fall
AGU meeting in San Francisco, California. Errata (if any) can be found at the MSA website
www.minsocam.org.
Jodi J. Rosso, Series Editor
West Richland, Washington
October 2005
PreFace
As geomicrobiologists, we seek to understand how some of nature’s most complex
systems work, yet the very complexity we seek to understand has placed many of the
insights out of reach. Recent advances in cultivation methodologies, the development
of ultrahigh throughput DNA sequencing capabilities, and new methods to assay gene
expression and protein function open the way for rapid progress. In the eight years since
the first Geomicrobiology volume (Geomicrobiology: Interactions between microbes and
minerals; volume 35 in this series) we have transformed into scientists working hand in hand
with biochemists, molecular biologists, genome scientists, analytical chemists, and even
physicists to reveal the most fundamental molecular-scale underpinnings of biogeochemical
systems. Through synthesis achieved by integration of diverse perspectives, skills, and
interests, we have begun to learn how organisms mediate chemical transformations, the
ways in which the environment determines the architecture of microbial communities, and
the interplay between evolution and selection that shapes the biodiversity of the planet.
This volume presents chapters written by leaders in the rapidly maturing field we refer to
as molecular geomicrobiology. Most of them are relatively young researchers who share
their approaches and insights and provide pointers to exciting areas ripe for new advances.
This volume ties together themes common to environmental microbiology, earth science,
and astrobiology. The resesarch presented here, the associated short course, and the volume
production were supported by funding from many sources, notably the Mineralogical Society of
America, the Geochemical Society, the US Department of Energy Chemical Sciences Program
and the NASA Astrobiology Institute. We thank Jodi Rosso for her editorial contributions.
October 2005
Jillian F. Banfield
Javiera Cervini-Silva
Kenneth H. Nealson
1529-6466/05/0059-0000$05.00 DOI: 10.2138/rmg.2005.59.0
tABLE Of cONtENtS

1
The Search for a Molecular-Level Understanding
of the Processes that Underpin the Earth’s Biogeochemical Cycles
Jillian F. Banfield, Gene W. Tyson,
Eric E. Allen, Rachel J. Whitaker
ChArACTerIzIng bIOgeOCheMICAL SySTeMS .....................................................1
MOLeCULAr geOMICrObIOLOgy: OppOrTUnITIeS AnD ChALLengeS .........3
COnCLUDIng COMMenTS .............................................................................................5
ACknOwLeDgMenTS .....................................................................................................5
reFerenCeS ......................................................................................................................6
2
What Genetics Offers Geobiology
Dianne K. Newman, Jeffrey A. Gralnick
InTrODUCTIOn .................................................................................................................9
DeFInITIOnS .....................................................................................................................10
what is genetics? .........................................................................................................10
how is genetics different from molecular biology and genomics? .............................10
what is a mutant? .......................................................................................................11
what is mutagenesis? ..................................................................................................11
TypeS OF geObIOLOgICAL prObLeMS ThAT geneTICS CAn SOLVe .............11
prACTICAL COnSIDerATIOnS FOr CreATIng geneTIC SySTeMS ..................15
Step 1: Isolation and growth ........................................................................................15
Step 2: Methods of mutagenesis ..................................................................................17
genetic polarity in bacteria .........................................................................................20
Step 3: Identifying mutants .........................................................................................20
Step 4: Mutant verification ..........................................................................................22
A brief note on phage ..................................................................................................22
Step 5: Mutant analysis ...............................................................................................23
COnCLUSIOnS..................................................................................................................23
ACknOwLeDgMenTS ...................................................................................................24
reFerenCeS ....................................................................................................................24
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Molecular Geomicrobiology ‒ Table of Contents
3
Enzymology of Electron Transport:
Energy Generation With Geochemical Consequences
Thomas J. DiChristina,
Jim K. Fredrickson, John M. Zachara
InTrODUCTIOn ...............................................................................................................27
enzyMATIC bASIS OF IrOn AnD MAngAneSe reDUCTIOn..............................27
Direct enzymatic reduction at the outer membrane .....................................................29
electron shuttling pathways ........................................................................................32
Fe(III) solubilization by exogenous or bacterially-produced organic
ligands followed by reduction of soluble organic-Fe(III) ....................................34
enzyMATIC bASIS OF UrAnIUM reDUCTIOn ........................................................35
Involvement of c-type cytochromes in enzymatic U(VI) reduction ............................35
effect of U(VI) chemical speciation on enzymatic U(VI) reduction activity .............36
electron donors and competing electron acceptors .....................................................37
Subcellular location of enzymatic U(VI) reduction activity .......................................38
enzyMATIC MeChAnISM OF TeChneTIUM reDUCTIOn ....................................39
Involvement of hydrogenases in Tc(VII) reduction ....................................................39
Subcellular location of enzymatic Tc(VII) reduction activity .....................................39
MICrObIAL reDUCTIOn-InDUCeD ChAngeS In
MeTAL bIOgeOCheMISTry ....................................................................................41
Direct enzymatic effects of dissimilatory metal-reducing bacteria
(DMrb) on metal solubility .................................................................................41
Indirect effects of DMrb on metal solubility .............................................................42
reDUCTIVe TrAnSFOrMATIOn OF Fe- AnD Mn-COnTAInIng MInerALS .....43
Laboratory studies .......................................................................................................43
Field studies .................................................................................................................44
rOLe OF MICrObIAL MeTAL reDUCTIOn In reDOX CyCLIng ........................45
redox cycling in chemically stratified environments .................................................45
Microscale redox cycling ............................................................................................46
SUMMAry .........................................................................................................................46
ACknOwLeDgMenTS ...................................................................................................47
reFerenCeS ....................................................................................................................47
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Molecular Geomicrobiology ‒ Table of Contents
4
Siderophores and the Dissolution of
Iron-Bearing Minerals in Marine Systems
Stephan M. Kraemer, Alison Butler,
Paul Borer, Javiera Cervini-Silva
InTrODUCTIOn ...............................................................................................................53
Scope of this review ...................................................................................................53
The iron limitation hypothesis ....................................................................................54
bIOLOgICAL IrOn ACqUISITIOn STrATegIeS .......................................................54
Iron acquisition by bacteria .........................................................................................54
Iron acquisition by eukaryotic phytoplankton .............................................................55
role of protozoan grazers in the cycling of iron ........................................................56
SOUrCeS OF IrOn In hnLC OCeAn regIOnS .......................................................56
Atmospheric dust as a source of iron ..........................................................................57
Iron mineralogy of atmospheric dust ...........................................................................57
Transformation of iron-bearing minerals during atmospheric transport .....................57
COnCenTrATIOnS, SpeCIATIOn AnD SOLUbILITy OF IrOn In SeAwATer ...58
Iron concentrations as a function of depth in hnLC regions ......................................58
Inorganic iron species ..................................................................................................58
Solubility of iron in the presence of iron oxides .........................................................59
Colloidal iron in marine systems .................................................................................62
photochemistry and redox speciation of iron ..............................................................62
OrgAnIC LIgAnDS AnD IrOn SOLUbILITy AnD SpeCIATIOn ...........................63
Speciation of soluble iron in the presence of organic ligands .....................................63
Marine siderophores ....................................................................................................64
photo reduction of iron and redox cycling in the presence of siderophores ...............65
effect of organic ligands on the solubility of iron oxides ...........................................67
DISSOLUTIOn OF AerOSOLS AnD DeFIneD IrOn OXIDeS In SeAwATer .......70
Dissolution mechanisms ..............................................................................................70
experimentally observed dissolution rates of aerosol and defined minerals ...............72
photo-reductive dissolution in seawater ......................................................................72
OrgAnIC LIgAnDS AnD IrOn OXIDe DISSOLUTIOn In SeAwATer .................73
Siderophore-promoted dissolution mechanisms..........................................................73
photo-reductive dissolution mechanisms in the presence of siderophores .................75
Amphiphilic siderophores ...........................................................................................75
COnCLUSIOnS .................................................................................................................76
reFerenCeS ....................................................................................................................76
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Molecular Geomicrobiology ‒ Table of Contents
5
Geomicrobiological Cycling of Iron
Andreas Kappler, Kristina L. Straub
InTrODUCTIOn ..............................................................................................................85
general aspects of the iron cycle .................................................................................85
Solubility and chemical transformation of Fe(II) and Fe(III) minerals .......................85
Surface area and reactivity of ferric iron oxides .........................................................87
Ferrihydrite ..................................................................................................................87
Forms of iron present in the environment ..................................................................88
role of iron for microbial energy metabolism ............................................................88
MICrObIAL OXIDATIOn OF Fe(II) ................................................................................89
Competition between chemical and microbial oxidation of Fe(II) .............................89
Aerobic acidophilic Fe(II)-oxidizing microorganisms ................................................89
Aerobic neutrophilic Fe(II)-oxidizing microorganisms ..............................................90
Anaerobic Fe(II)-oxidizing phototrophic bacteria.......................................................91
Anaerobic Fe(II)-oxidizing nitrate-reducing bacteria .................................................92
Mechanisms of microbial Fe(II) oxidation .................................................................93
Formation of Fe(III) minerals by microbial Fe(II) oxidation ......................................95
MICrObIAL DISSIMILATOry reDUCTIOn OF Fe(III) ..............................................95
Acidophilic Fe(III)-reducing microorganisms ............................................................96
Microbial reduction of Fe(III) at neutral ph ...............................................................96
Methods to study mechanisms of microbial Fe(III) reduction ....................................97
Microbial mechanisms of Fe(III) reduction at neutral ph...........................................98
MICrObIAL IrOn CyCLIng ..........................................................................................99
Microbial iron cycling under acidic conditions ...........................................................99
Microbial iron cycling at neutral ph ...........................................................................99
prerequisites for microbial iron cycling at neutral ph ..............................................100
Oxygen-dependent microbial cycling of iron ............................................................100
Oxygen-independent microbial cycling of iron .........................................................101
enVIrOnMenTAL IMpLICATIOnS .............................................................................101
Degradation of organic compounds coupled to dissimilatory Fe(III) reduction .......101
Iron minerals as adsorbents .......................................................................................102
Immobilization of toxic metal ions by microbial Fe(II) oxidation and
Fe(III) reduction .................................................................................................102
Formation of reactive iron minerals .........................................................................102
SOMe TASkS FOr FUTUre InVeSTIgATIOnS ........................................................103
ACknOwLeDgMenTS .................................................................................................103
reFerenCeS ..................................................................................................................104
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Molecular Geomicrobiology ‒ Table of Contents
6
Molecular-Scale Processes Involving
Nanoparticulate Minerals in Biogeochemical Systems
Benjamin Gilbert, Jillian F. Banfield
InTrODUCTIOn .............................................................................................................109
Sources of nanoparticles in the environment.............................................................111
Impacts of nanoparticles on their surroundings.........................................................112
nanoparticles—special properties and implications .................................................112
Overview of small size effects in minerals ................................................................113
phySICAL STrUCTUre AnD COMpOSITIOn OF nAnOSCALe MInerALS .....113
Thermodynamic constraints on the structure of nanoparticles ..................................113
The nature of the initial precipitates and subsequent aging ......................................114
Size dependence of mineral solubility .......................................................................114
Characterization studies of biogenic nanoparticles ...................................................115
The effects of water and other surface-bound molecules on nanoparticle structure .118
Incorporation of impurity atoms ................................................................................119
The surfaces of nanoscale minerals ...........................................................................120
eLeCTrOnIC STrUCTUre OF nAnOSCALe MInerALS......................................121
Introduction to electronic structure of solids .............................................................121
energy levels in semiconductor minerals ..................................................................123
electronic structure of nanoparticles .........................................................................125
reDOX behAVIOr OF nAnOpArTICLeS .................................................................132
Size effects on nanoparticle redox behavior ..............................................................132
examples of nanoparticle redox behavior .................................................................134
phOTOCheMISTry........................................................................................................137
Size effects on nanoparticle photochemistry ............................................................137
nanoparticle interactions with biomolecules ............................................................138
examples of nanoparticle photochemistry ................................................................140
The stability of nanoparticles during redox chemistry and photochemistry .............142
nanoparticle interactions with microorganisms .......................................................143
nanoparticle aggregation and its consequences ........................................................144
COnCLUSIOnS................................................................................................................146
ACknOwLeDgMenTS .................................................................................................146
reFerenCeS ..................................................................................................................146
x