ADVANCES IN AGRONOMY Advisory Board PAUL M BERTSCH University of Kentucky RONALD L PHILLIPS University of Minnesota KATE M SCOW University of California, Davis LARRY P WILDING Texas A&M University Emeritus Advisory Board Members JOHN S BOYER University of Delaware KENNETH J FREY Iowa State University EUGENE J KAMPRATH North Carolina State, University MARTIN ALEXANDER Cornell University Prepared in cooperation with the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America Book and Multimedia Publishing Committee DAVID D BALTENSPERGER, CHAIR LISA K AL-AMOODI WARREN A DICK HARI B KRISHNAN SALLY D LOGSDON CRAIG A ROBERTS MARY C SAVIN APRIL L ULERY VOLUME ONE HUNDRED NINETEEN Advances in AGRONOMY Edited by DONALD L SPARKS Department of Plant and Soil Sciences University of Delaware Newark, Delaware, USA AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 525 B Street, Suite 1900, San Diego, CA 92101-4495, USA 225 Wyman Street, Waltham, MA 02451, USA 32 Jamestown Road, London, NW1 7BY, UK The Boulevard, Langford Lane, Kidlington, Oxford, OX51GB, UK Radarweg 29, PO Box 211, 1000 AE Amsterdam, The Netherlands First edition 2013 Copyright © 2013 Elsevier Inc All rights reserved No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights epartment in Oxford, UK: phone (+44) (0) 1865 843830; fax (+44) (0) 1865 853333; D email: permissions@elsevier.com Alternatively you can submit your request online by visiting the Elsevier web site at http://elsevier.com/locate/permissions, and selecting Obtaining permission to use Elsevier material Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made ISBN: 978-0-12-407247-3 ISSN: 0065-2113 (series) For information on all Academic Press publications visit our website at store.elsevier.com Printed and bound in USA 13 14 15 10 CONTRIBUTORS Barbara Amon Leibniz Institute for Agricultural Engineering, Department of Technology Assessment and Substance Cycles Max-Eyth-Allee 100, D-14469 Potsdam, Germany Melissa Arcand Department of Soil Science, University of Saskatchewan, Saskatoon, Canada Christel Baum Soil Science, University of Rostock, Rostock, Germany Nanthi S Bolan Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, Australia; Cooperative Research Centre for Contaminantion Assessment and Remediation of the Environment, Adelaide, Australia Nathan S Bryan Brown Foundation Institute of Molecular Medicine, Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA Piotr Burczyk Institute of Technology and Life Sciences (ITP), Westpomeranian Research Centre in Szczecin, Szczecin, Poland Kai-Uwe Eckhardt Soil Science, University of Rostock, Rostock, Germany Richard Farrell Department of Soil Science, University of Saskatchewan, Saskatchewan, Canada Nicholas Hutchings University of Aarhus, Dept of Agroecology, Tjele, Denmark M P Isaure LCABIE (Laboratoire de Chimie Analytique BioInorganique et Environement), Institut des Sciences Analytique et de Physico-chimie pour l’Environnement et les Matériaux, Université de Pau et des Pays de l’Adour, Pau cedex 09, France Satoru Ishikawa Soil Environmental Division, National Institute for Agro-Environmental Sciences, Tsukuba, Japan Gerald Jandl Soil Science, University of Rostock, Rostock, Germany Kristian Kiersch Soil Science, University of Rostock, Rostock, Germany Pil-Joo Kim Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea ix x Contributors Mary B Kirkham Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, USA J Diane Knight Department of Soil Science, University of Saskatchewan, Saskatchewan, Canada Jens Kruse Soil Science, University of Rostock, Rostock, Germany Anitha Kunhikrishnan Chemical Safety Division, Department of Agro-Food Safety, National Academy of Agricultural Science, Gyeonggi-do, Republic of Korea Peter Leinweber Soil Science, University of Rostock, Rostock, Germany Tomoyuki Makino Soil Environmental Division, National Institute for Agro-Environmental Sciences, Tsukuba, Japan H Castillo Michel European Synchrotron Radiation Facility (ESRF), Grenoble Cedex, France Masaharu Murakami Soil Environmental Division, National Institute for Agro-Environmental Sciences, Tsukuba, Japan Ravi Naidu Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, Australia; Cooperative Research Centre for Contaminantion Assessment and Remediation of the Environment, Adelaide, Australia Miriam Pinto NEIKER, Derio (Bizkaia), Spain Joanne Reid Ricard-AEA, Didcot, UK Lena Rodhe Swedish Institute of Agricultural and Environmental Engineering (JTI), Uppsala, Sweden Kenneth Sajwan Department of Natural Science, Savannah State University, Savannah, GA, USA Eva Salomon Swedish Institute of Agricultural and Environmental Engineering (JTI), Uppsala, Sweden G Sarret ISTerre, Institut des Sciences de la Terre, Université de Grenoble 1, CNRS, Grenoble, France H M Selim School of Plant, Environmental and Soil Science, Louisiana State University, Baton Rouge, Louisiana, USA Contributors xi Balaji Seshadri Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, South Australia, Australia; Cooperative Research Centre for Contaminants Assessment and Remediation of the Environment (CRC CARE), University of South Australia, South Australia, Australia E.A.H Pilon Smits Biology Department, Colorado State University, Fort Collins, CO, USA Peter Sørensen University of Aarhus, Dept of Agroecology, Tjele, Denmark R Tappero Photon Sciences Department, NSLS, Brookhaven National Laboratory, Upton, NY, USA Hans van Grinsven PBL Netherlands Environmental Assessment Agency, Department of Water, Agriculture and Food, Bilthoven, The Netherlands Gerard Velthof Alterra, Wageningen, The Netherlands Hailong Wang School of Environmental and Resource Sciences, Zhejiang A & F University, Hangzhou, Zhejiang, China J Webb Ricard-AEA, Didcot, UK F J Zhao College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China; Rothamsted Research, Harpenden, Hertfordshire, UK PREFACE Volume 119 contains seven timely and thought provoking reviews that deal with three of the defining challenges of our time- environment, energy, and human health The reviews not only contain cutting-edge science but provide insights into policy and technology applications Chapter is a comprehensive chapter on the use of novel synchrotron- based molecular scale techniques to understand metal uptake and metabolism in plants Chapter also provides advances in the use of synchrotron as well as other state-of-the-art tools to understand nitrogen chemistry in soils Chapter addresses the role of nitrate in human health Chapters and and address various aspects of trace metal transport, contamination, and risk assessment Chapter covers cadmium contamination and risk assessment in rice ecosystems while Chapter provides a thorough review on the competitive sorption effects on transport and retention of heavy metals in soils Chapter is a review on clean coal technology combustion products and aspects of their agricultural and environmental applications as well as risk assessment considerations Chapter discusses the variability of manure nitrogen efficiency in Europe and ways to increase efficiency I am grateful to the authors for their outstanding reviews Donald L Sparks Newark, Delaware, USA xiii CHAPTER ONE Use of Synchrotron-Based Techniques to Elucidate Metal Uptake and Metabolism in Plants G Sarret*,1, E A H Pilon Smits, H Castillo Michel, M P IsaureĐ, F J Zhaoả,**, R Tappero†† *ISTerre, Institut des Sciences de la Terre, Université de Grenoble 1, CNRS, Grenoble, France †Biology Department, Colorado State University, Fort Collins, CO, USA ‡European Synchrotron Radiation Facility (ESRF), Grenoble Cedex, France §LCABIE (Laboratoire de Chimie Analytique BioInorganique et Environement), Institut des Sciences Analytique et de Physico-chimie pour l’Environnement et les Matériaux, Université de Pau et des pays de l’Adour, CNRS, Pau cedex 09, France ¶College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China **Rothamsted Research, Harpenden, Hertfordshire, UK ††Photon Sciences Department, NSLS, Brookhaven National Laboratory, Upton, NY, USA 1Corresponding author: E-mail: geraldine.sarret@ujf-grenoble.fr Contents Introduction P resentation of the Techniques 2.1 Introduction to X-ray Fluorescence Microprobe 2.2 M icro X-ray Fluorescence Imaging 2.2.1 V isualization of µXRF Data 2.2.2 Quantification of µXRF Images 2.3 C omputed Microtomography: Full-Field and Microfocused Beam Modes 2.4 X -ray Absorption Spectroscopy (Bulk and Microanalyses) 2.4.1 A natomy of XAS Spectrum 2.4.2 Data Analysis for Complex, Mixed-Component Systems 2.4.3 Self-Absorption 3 13 14 18 19 20 21 2.5 S ynchrotron-Based µFTIR S ample Preparation and Possible Artifacts R esults Obtained 4.1 N ickel 4.2 Z inc 4.3 C admium 4.4 S elenium 4.5 A rsenic 4.6 C opper 4.7 M anganese 4.8 O ther Elements 22 25 27 27 32 34 36 41 46 47 48 © 2013 Elsevier Inc Advances in Agronomy, Volume 119 ISSN 0065-2113, http://dx.doi.org/10.1016/B978-0-12-407247-3.00001-9 All rights reserved G Sarret et al 4.9 N anoparticles 4.9.1 M etal-Oxide NPs 4.9.2 Elemental Nanoparticles C omplementary Techniques 5.1 H istochemical Techniques 5.2 E lectron Microscopy 5.3 T echniques Using Ion Beams (PIXE, SIMS) 5.4 L aser Ablation Coupled with ICP-MS C onclusions and Perspectives Acknowledgments References 51 52 55 56 56 57 60 62 63 65 65 Abstract Synchrotron techniques have become key components of the toolbox for studying the mechanisms involved in metal(loid) uptake and metabolism in plants Most widely used techniques in this field include micro-X-ray fluorescence (µXRF) for imaging the distribution of elements in plant tissues and cells and quantifying them, and X-ray absorption spectroscopy (XAS) for determining their chemical forms Recent advances in terms of spatial resolution, sensitivity and versatility of the sample environment have opened new perspectives for the study of trace elements at the micro- and nanoscale with a minimal perturbation of the sample Sample conditioning remains a key issue for the study of metals in plants Cryogenic sample environments allow work on hydrated systems, with a limited risk of metal remobilization and changes in speciation Still, radiation damage should be monitored carefully, especially for high-flux spectrometers In addition, progress in software for data analysis has facilitated data mining and integration of results from various techniques This chapter presents the principle and the basics of data analysis for µXRF imaging and tomography, XAS and micro-Fourier transform infrared spectromicroscopy (µFTIR) Major results obtained on Ni, Cd, Zn, Se, As, Cu, Mn and nanoparticles in hyperaccumulating and nonaccumulating plants are presented Complementary approaches including histochemical techniques, micro and nanoscopic techniques using electron- or ion beams, and laser ablation coupled with inductively coupled plasma mass spectrometry (ICP-MS) are also presented, and key results reviewed Finally, there is also great interest in coupling synchrotron techniques, which is possible on more and more beamlines, and also in coupling synchrotron techniques with other approaches such as the ones mentioned above; perspectives in this area are discussed INTRODUCTION The status of metals in plants and the mechanisms controlling metal homeostasis in plants are still intensively studied as key processes for metal hyperaccumulation, detoxification, and prevention against nutrient deficiency Applications of these research areas include phytoremediation and food safety in the case of metal-contaminated media, and biofortification of crops in the Use of Synchrotron-Based Techniques to Elucidate Metal Uptake and Metabolism in Plants case of low-nutrient soils Key steps for metal homeostasis include mobilization from the soil, root uptake, xylem loading and unloading, storage/sequestration in the different plant parts, and, in some cases, exudation Classical methods to assess gene functions and physiological processes in plants involve molecular biology and molecular genetics, and UV, visible light and electron microscopy Synchrotron techniques have emerged as powerful and highly complementary techniques, particularly to study the distribution and the speciation of metals in plants.The major advantages of these techniques are their high sensitivity and lateral or spatial resolution, the limited sample preparation and nondestructive character, and the possibility to work on hydrated samples, in vivo in some cases Another major advantage of this technology is the capacity to analyze several elements simultaneously and to combine different and complementary techniques, as discussed in this chapter The application of synchrotron techniques in plant sciences has been the subject of several reviews (Donner et al., 2012; Gardea-Torresdey et al., 2005; Lombi et al., 2011b; Lombi and Susini, 2009; Punshon et al., 2009; Salt et al., 2002) This chapter not only presents the principles of the techniques and data analysis but also emphasizes the results obtained for metals or metalloids of interest in plant sciences Also, it compares synchrotron techniques with other imaging techniques that have undergone recent developments and can be combined with synchrotron techniques PRESENTATION OF THE TECHNIQUES 2.1 Introduction to X-ray Fluorescence Microprobe X-ray fluorescence (XRF) as an elemental analysis technique, using characteristic X-rays emitted from atoms excited by an external source, is likely to be familiar to many scientists X-ray tubes, scanning electron microscopes, proton and other particle beams have all been used as XRF sources Utilizing synchrotron X-rays as the excitation source, materials can be analyzed with little or no pretreatment and with no requirement for analysis in vacuum The low power deposition of the technique provides a practical means of analyzing materials in their natural state, even liquid, wet, or moist samples The high-intensity photons that these facilities provide are up to 11 orders of magnitude brighter than can be generated using more conventional X-ray tube sources It is the high brightness and brilliance of these sources, the extreme collimation of the synchrotron light, and the polarized nature of the X-ray beams, which makes them so amendable to building X-ray probes with high spatial resolution and sensitivity ... operation of any methods, products, instructions or ideas contained in the material herein Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses... in Bleuet et al (2008) and Lanzirotti et al (2010) In recent years, there has been a growing interest in the use of phase-contrast imaging and phase-contrast tomography to obtain structural information,... primary vein) showing the region of the spectrum representing the XANES and EXAFS Inset: k2-weighted χ(k) EXAFS spectrum (left) and corresponding Fourier transform (including real and imaginary parts)