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 The appearance of the code at the bottom of the first page of each chapter in this volume indicates the copyright owner’s consent that copies of the article can be made for personal use or internal use or for the personal use or internal use of specific clients, provided the original publication is cited. The consent is given on the condition, however, that the copier pay the stated per-copy fee through the Copyright Clearance Center, Inc. for copying beyond that permitted by Sections 107 or 108 of the U.S. Copyright Law. This consent does not extend to other types of copying for general distribution, for advertising or promotional purposes, for creating new collective works, or for resale. For permission to reprint entire articles in these cases and the like, consult the Administrator of the Mineralogical Society of America as to the royalty due to the Society. r M eviewS in ineralogy g and eocheMiStry ( Formerly: reviews in Mineralogy ) iSSn 1529-6466 volume 59 Molecular Geomicrobiology iSBn 093995071-5 Additional copies of this volume as well as others in this series may be obtained at moderate cost from: the MineralogiCal soCiety of aMeriCa 3635 ConCorde parkway, suite 500 Chantilly, virginia, 20151-1125, u.s.a. www.MinsoCaM.org 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 vi 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 vii 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 viii 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 ix 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