Microbial Processing of Metal Sulfides

Microbial Processing of Metal Sulfides

Microbial Processing of Metal Sulfides edited by

Edgardo R. Donati University of La Plata, Argentina

and

Wolfgang Sand University of Duisburg-Essen, Germany

A C.I.P. Catalogue record for this book is available from the Library of Congress.

ISBN 978-1-4020-5588-1 (HB) ISBN 978-1-4020-5589-8 (e-book) Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. www.springer.com

Printed on acid-free paper

All Rights Reserved © 2007 Springer No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work.

TABLE OF CONTENTS

List of Contributors

vii

Preface

xi

Section I – Fundamentals, microorganisms and mechanisms

1

1.

2.

3.

4.

Microorganisms involved in bioleaching and nucleic acid-based molecular methods for their identification and quantification Axel Schippers Mechanisms and biochemical fundamentals of bacterial metal sulfide oxidation Thore Rohwerder and Wolfgang Sand Electrochemical techniques used to study bacterial-metal sulfides interactions in acidic environments Denise Bevilaqua, Heloisa A. Acciari, Assis V. Benedetti and Oswaldo Garcia Jr Catalytic role of silver and other ions on the mechanism of chemical and biological leaching Antonio Ballester, María Luisa Blázquez, Felisa González and Jesús A. Muñoz

3

35

59

77

5.

Recovery of zinc, nickel, cobalt and other metals by bioleaching Marisa Viera, Cristina Pogliani, Edgardo Donati

103

6.

Bioleaching of metals in neutral and slightly alkaline environment Aleksandra Sklodowska and Renata Matlakowska

121

v

vi

TABLE OF CONTENTS

Section II – Bioreactors and Bioheaps

131

7.

Bioleaching of sulfide minerals in continuous stirred tanks Dominique Henri Roger Morin

133

8.

Bioreactor design fundamentals and their application to gold mining Fernando Acevedo and Juan Carlos Gentina

151

9.

Airlift reactors: characterization and applications in biohydrometallurgy Alejandra Giaveno, Laura Lavalle, Patricia Chiacchiarini and Edgardo Donati

10.

Principles, mechanisms and dynamics of chalcocite heap bioleaching Jochen Petersen and David G. Dixon

Section III – Genetics and Molecular Biology 11.

12.

13.

The use of bioinformatics and genome biology to advance our understanding of bioleaching microorganisms Raquel Quatrini, Jorge Valdés, Eugenia Jedlicki and David S. Holmes Proteomics and metaproteomics applied to biomining microorganisms Carlos A. Jerez Cell-cell communication in bacteria: A promising new approach to improve bioleaching efficiency? Susana Valenzuela, Alvaro Banderas, Carlos A. Jerez and Nicolas Guiliani

Section IV – Other Applications 14.

15.

Index

Bioflotation and bioflocculation of relevance to minerals bioprocessing K. Hanumantha Rao and S. Subramanian Hydrogen sulfide removal from gaseous effluents José Manuel Gómez and Domingo Cantero

169

193

219

221

241

253

265

267

287

311

LIST OF CONTRIBUTORS

Heloisa A. Acciari Universidade Estadual Paulista, Instituto de Química, Departamento de Bioquímica e Tecnologia Química, Araraquara-SP, Brazil. Fernando Acevedo School of Biochemical Engineering, Pontifical Catholic University of Valparaiso, Valparaiso, Chile. Antonio Ballester Departamento de Ciencia de Materiales e Ingeniería Metalúrgica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain. Assis V. Benedetti Universidade Estadual Paulista, Instituto de Química, Departamento de Fisico-Química, Araraquara-SP, Brazil. María Luisa Blázquez Departamento de Ciencia de Materiales e Ingeniería Metalúrgica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain. Alvaro Banderas Unit of Bacterial Cell Communication, Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile. Denise Bevilaqua Universidade Estadual Paulista, Instituto de Química, Departamento de Bioquímica e Tecnologia Química, Araraquara-SP, Brazil Domingo Cantero Universidad de Cádiz, Cádiz, Spain. Patricia Chiacchiarini Facultad de Ingeniería, Universidad Nacional del Comahue, Neuquén, Argentina. David G. Dixon Department of Materials Engineering, University of British Columbia, Vancouver, Canada. Edgardo Donati Cindefi (CONICET-UNLP), Universidad Nacional de La Plata, La Plata, Argentina. vii

viii

LIST OF CONTRIBUTORS

Oswaldo Garcia Jr. Universidade Estadual Paulista, Instituto de Química, Departamento de Bioquímica e Tecnologia Química, Araraquara-SP, Brazil. Juan Carlos Gentina School of Biochemical Engineering, Pontifical Catholic University of Valparaiso, Valparaiso, Chile. Alejandra Giaveno Facultad de Ingeniería, Universidad Nacional del Comahue, Neuquén, Argentina. Nicolas Guiliani Unit of Bacterial Cell Communication, Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile. Jose Manuel Gómez Montes de Oca Universidad de Cádiz, Cádiz, Spain. Felisa González Departamento de Ciencia de Materiales e Ingeniería Metalúrgica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain. K. Hanumantha Rao Division of Mineral Processing, Luleå University of Technology, Luleå, Sweden. David S. Holmes Center of Bioinformatics and Genome Biology, Andrés Bello University (UNAB), Life Science Foundation and Millennium Institute of Fundamental and Applied Biology, Santiago, Chile. Eugenia Jedlicki Program of Cellular and Molecular Biology, I.C.B.M., Faculty of Medicine, University of Chile, Santiago, Chile. Carlos A. Jerez Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile. Laura Lavalle Facultad de Ingeniería, Universidad Nacional del Comahue, Neuquén, Argentina. Renata Matlakowska

Warsaw University, Faculty of Biology, Warsaw, Poland.

Dominique Henri Roger Morin BRGM, Orléans, France. Jesús A. Muñoz Departamento de Ciencia de Materiales e Ingeniería Metalúrgica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain.

LIST OF CONTRIBUTORS

ix

Jochen Petersen Department of Chemical Engineering, University of Cape Town, South Africa. Cristina Pogliani Cindefi (CONICET-UNLP), Universidad Nacional de La Plata, La Plata, Argentina. Raquel Quatrini Center of Bioinformatics and Genome Biology, Andrés Bello University (UNAB), Life Science Foundation and Millennium Institute of Fundamental and Applied Biology, Santiago, Chile. Thore Rohwerder University of Duisburg-Essen, Biofilm Centre, Aquatic Biotechnology, Duisburg, Germany. Wolfgang Sand University of Duisburg-Essen, Biofilm Centre, Aquatic Biotechnology, Duisburg, Germany. Axel Schippers Geomicrobiology, Federal Institute for Geosciences and Natural Resources, Hannover, Germany. Aleksandra Sklodowska Warsaw University, Faculty of Biology, Warsaw, Poland. S. Subramanian Bangalore, India.

Department of Metallurgy, Indian Institute of Science,

Jorge Valdés Center of Bioinformatics and Genome Biology, Andrés Bello University (UNAB), Life Science Foundation and Millennium Institute of Fundamental and Applied Biology, Santiago, Chile. Susana Valenzuela Unit of Bacterial Cell Communication, Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile. Marisa Viera Cindefi (CONICET-UNLP), Universidad Nacional de La Plata, La Plata, Argentina.

PREFACE

In the last years, the application of microbiological methods to the extraction of metals from minerals has definitely gained a prominent role supported by the several bioleaching and biooxidation processes operating in different sites over the world. This may be an important reason why fundamental research has received a new powerful stimulus with fascinating discoveries and in addition it surely will become the cause of future development in the field. In 1997 Springer published an excellent book entitled ‘Biomining’ (edited by D. E. Rawlings) which not only provided critical discussion of microbial and physicochemical aspects of bioleaching processes (written by prestigious experts in biohydrometallurgical field) but also it concentrated many contributions by people employed in industries. During the last years since the publication of ‘Biomining’, the advances in molecular biology methods have been applied extensively to the study of microorganisms involved in bioleaching processes. In addition recent studies about proteomic and bioinformatics are bringing a new perspective on the microbial processes. Furthermore, there is a growing agreement about the mechanisms of bioleaching and the role played by exopolymers substances in the interfacial degradation of metal sulfides. Additionally new evidence has been supplied by new techniques (electrochemical techniques, atomic force microscope). Due to the growing literature in these and other aspects, we think a new book could be opportune to organize partially this new information. However, it is clear that covering the range of subject areas in depth would require several volumes of specialist text. That is why, it has been necessary to be selective. Since the book ‘Biomining’ is still a large reference to the applied technology, we hope that this new book could go some way towards introducing undergraduate and postgraduate students as well as interested industrialists to the main subjects of microbial processing with special emphasis to the last contributions of the chemical and microbial aspects of bioleaching process and use of microorganisms in the treatment of complex ores and concentrates. Our sincere thanks all the contributors whose efforts made this book possible and the editorial staff of Springer for their help in readying the manuscript for publication. We wish to express our grateful recognition to Giovanni Rossi, Corale Brierley, James Brierley, Violaine Bonnefoy, Franz Glombitza, David Holmes, Jacco Huisman, Barrie Johnson, Douglas Rawlings, Erika Kalman, Halit Kuyumcu and Axel Schippers for their generous contribution with the peer review of the chapters. Wolfgang Sand and Edgardo Donati xi

SECTION I FUNDAMENTALS, MICROORGANISMS AND MECHANISMS

CHAPTER 1 MICROORGANISMS INVOLVED IN BIOLEACHING AND NUCLEIC ACID-BASED MOLECULAR METHODS FOR THEIR IDENTIFICATION AND QUANTIFICATION

AXEL SCHIPPERS Geomicrobiology, Federal Institute for Geosciences and Natural Resources, Stilleweg 2, D-30655 Hannover, Germany. E-mail: [email protected]

1.

INTRODUCTION

Bioleaching is the biological conversion of an insoluble metal compound into a water soluble form. In case of metal sulfide bioleaching, metal sulfides are oxidized to metal ions and sulfate by aerobic, acidophilic Fe(II) and/or sulfurcompound oxidizing Bacteria or Archaea. Bioleaching involves chemical and biological reactions. Despite molecular oxygen being the final electron acceptor for the overall metal sulfide bioleaching process, Fe(III) ions are the relevant oxidizing agent for the metal sulfides. The metal sulfide oxidation itself is a chemical process in which Fe(III) ions are reduced to Fe(II) ions and the sulfur moiety of the metal sulfide is oxidized to sulfate, and various intermediate sulfur compounds, e.g. elemental sulfur, polysulfide, thiosulfate, and polythionates. For example the oxidation of sphalerite (ZnS) to elemental sulfur is given in the following equation: (1)

ZnS + 2Fe3+ → Zn2+ + 0125S8 + 2Fe2+

Because of two different groups of metal sulfides exist, two different metal sulfide oxidation mechanisms have been proposed, namely the thiosulfate mechanism (for acid-insoluble metal sulfides, such as pyrite) and the polysulfide mechanism (for acid-soluble metal sulfides, e.g. sphalerite or chalcopyrite, CuFeS2 . These mechanisms explain the occurrence of all inorganic sulfur compounds which have been detected in the course of metal sulfide oxidation (for review see: Sand et al., 2001; Rohwerder et al., 2003; Schippers, 2004; Chapter 2). The role of the microorganisms in the bioleaching process is to oxidize the products of the chemical metal sulfide oxidation (Fe(II) ions and sulfur- compounds) in order to provide Fe(III) and protons, the metal sulfide attacking agents. In addition, proton production keeps the pH low and thus, the Fe ions in solution. 3 E.R. Donati and W. Sand (eds.), Microbial Processing of Metal Sulfides, 3–33. © 2007 Springer.

4

SCHIPPERS

Aerobic, acidophilic Fe(II) oxidizing Bacteria or Archaea provide Fe(III) by the following equation: (2)

2Fe2+ + 05O2 + 2H+ → 2Fe3+ + H2 O

Aerobic, acidophilic sulfur-compound oxidizing Bacteria or Archaea oxidize intermediate sulfur compounds to sulfate and protons (sulfuric acid). Most relevant is the oxidation of elemental sulfur to sulfuric acid since elemental sulfur can only be biologically oxidized under bioleaching conditions: (3)

+ 0125S8 + 15O2 + H2 O → SO2− 4 + 2H

The sulfur-compound oxidizing Bacteria or Archaea produce protons which dissolve metal sulfides besides pyrite which is not acid-soluble. Pyrite is only attacked by Fe(III) ions (not by protons) and therefore only dissolved by Fe(II) oxidizing Bacteria or Archaea. This book chapter gives an update of previous excellent reviews on microorganisms involved in bioleaching (e.g. Harrison, 1984; Rossi, 1990; Rawlings, 1997, 2002; Johnson, 1998; Hallberg & Johnson, 2001). In the first part of this chapter, the metal sulfide oxidizing microorganisms are described. In the second part, acidophilic microorganisms which do not oxidize metal sulfides and their importance for bioleaching are reviewed. In the third part, nucleic-acid based methods for the identification and quantification of these microorganisms are introduced. 2.

METAL SULFIDE OXIDIZING MICROORGANISMS

The most described acidophilic metal sulfide oxidizing microorganisms belong to the mesophilic and moderately thermophilic Bacteria. The Archaea are usually extremely thermophilic (besides the genus Ferroplasma). Most industrial heap and tank bioleaching operations run below 40 ˚C but operations at higher temperatures promise higher reaction rates (Olson et al., 2003; Batty & Rorke, 2006). All acidophilic metal sulfide oxidizing microorganisms oxidize Fe(II) and/or sulfur compounds. Most of these microorganisms fix CO2 and grow chemolithoautotrophically. A list of the metal sulfide oxidizing Bacteria or Archaea, their phylogeny and some of their physiological properties is given in the Tables 1–3. The organisms can be separated in three groups according to their temperature optimum for growth: Mesophiles up to ∼ 40 ˚C, moderate themophiles between ∼40 – ∼55 ˚C, and extreme thermophiles between ∼55 – ∼80 ˚C. 2.1. 2.1.1.

Mesophilic and Moderately Thermophilic Bacteria Proteobacteria

Acidithiobacillus spp. The genus Acidithiobacillus was proposed by Kelly & Wood (2000) after reclassification of some species of the genus Thiobacillus. The affiliation of the genus Acidithiobacillus to the - or -Proteobacteria is not clearly

5

MICROORGANISMS INVOLVED IN BIOLEACHING Table 1. Phylogeny of metal sulfide oxidizing, acidophilic microorganisms Species#

Phylum

G+C (mol%)

Mesophilic and moderately thermophilic Bacteria Acidimicrobium ferrooxidans Acidithiobacillus albertensis Acidithiobacillus caldus Acidithiobacillus ferrooxidans Acidithiobacillus thiooxidans Alicyclobacillus disulfidooxidans Alicyclobacillus tolerans “Caldibacillus ferrivorus” “Ferrimicrobium acidiphilum” Leptospirillum ferriphilum “Leptospirillum ferrodiazotrophum” Leptospirillum ferrooxidans Sulfobacillus acidophilus “Sulfobacillus montserratensis” Sulfobacillus sibiricus Sulfobacillus thermosulfidooxidans Sulfobacillus thermotolerans “Thiobacillus plumbophilus” “Thiobacillus prosperus” Thiomonas cuprina

Actinobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Firmicutes Firmicutes Firmicutes Actinobacteria Nitrospira Nitrospira Nitrospira Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Proteobacteria Proteobacteria Proteobacteria

67-69 61.5 63-64 58-59 52 53 49 51 51-55 55-58 na 52 55-57 52 48 48-50 48 66 64 66-69

Mesophilic and moderately thermophilic Archaea “Ferroplasma acidarmanus” Ferroplasma acidiphilum “Ferroplasma cupricumulans”

Euryarchaeota Euryarchaeota Euryarchaeota

37 36.5 na

Extremely thermophilic Archaea Acidianus brierleyi Acidianus infernus Metallosphaera hakonensis Metallosphaera prunae Metallosphaera sedula Sulfolobus metallicus Sulfolobus yangmingensis Sulfurococcus mirabilis Sulfurococcus yellowstonensis

Crenarchaeota Crenarchaeota Crenarchaeota Crenarchaeota Crenarchaeota Crenarchaeota Crenarchaeota Crenarchaeota Crenarchaeota

31 31 46 46 45 38 42 ∼ 44 45

#

Listed in alphabetical order; G + C = mole% guanine+cytosine content of genomic DNA; na = data not available; species without standing in nomenclature (http://www.bacterio.cict.fr/) are given in quotation marks

defined in the literature (Lane et al., 1992; McDonald et al., 1997; Kelly & Wood, 2000; Hallberg & Johnson, 2001). Species of the genus Acidithiobacillus are obligately acidophilic (pH < 4.0), Gram-negative, motile rods. CO2 is fixed by means of the Benson-Calvin Cycle. The genus comprises the following species: At. ferrooxidans, At. thiooxidans, At. caldus, and At. albertensis.

6

SCHIPPERS

Table 2. Optimum and range of growth for pH and temperature of metal sulfide oxidizing, acidophilic microorganisms Species#

pH pH Temperature Temperature optimum minimum- optimum minimummaximum (˚C) maximum (˚C)

Mesophilic and moderately thermophilic Bacteria Acidimicrobium ferrooxidans ∼2 Acidithiobacillus albertensis 3.5-4.0 Acidithiobacillus caldus 2.0-2.5 Acidithiobacillus ferrooxidans 2.5 Acidithiobacillus thiooxidans 2.0-3.0 Alicyclobacillus disulfidooxidans 1.5-2.5 Alicyclobacillus tolerans 2.5-2.7 “Caldibacillus ferrivorus” 1.8 “Ferrimicrobium acidiphilum” 2-2.5 Leptospirillum ferriphilum 1.3-1.8 “Leptospirillum ferrodiazotrophum” na Leptospirillum ferrooxidans 1.5-3.0 Sulfobacillus acidophilus ∼2 “Sulfobacillus montserratensis” 1.6 Sulfobacillus sibiricus 2.2-2.5 Sulfobacillus thermosulfidooxidans ∼2 Sulfobacillus thermotolerans 2-2.5 “Thiobacillus plumbophilus” na “Thiobacillus prosperus” ∼2 Thiomonas cuprina 3.5-4

na 2.0-4.5 1.0-3.5 1.3-4.5 0.5-5.5 0.5-6.0 1.5-5 na 1.3-4.8 na 2 1.1-3.5 1.5-5.5 1.2-5 4.0-6.5 1.0-4.5 1.5-7.2

45-50 25-30 45 30-35 28-30 35 37-42 45 37 30-37 na 28-30 45-50 37 55 45-48 40 27 33-37 30-36