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ROOT PHYSIOLOGY: FROM GENE TO FUNCTION Plant Ecophysiology Volume 4 Series Editors: Luit J. De Kok and Ineke Stulen University of Groningen The Netherlands Aims & Scope: The Springer Handbook Series of Plant Ecophysiology comprises a series of books that deals with the impact of biotic and abiotic factors on plant functioning and physiological adaptation to the environment. The aim of the Plant Ecophysiology series is to review and integrate the present knowledge on the impact of the environment on plant functioning and adaptation at various levels of integration: from the molecular, biochemical, physiological to a whole plant level. This Handbook series is of interest to scientists who like to be informed of new developments and insights in plant ecophysiology, and can be used as advanced textbooks for biology students. Root Physiology: from Gene to Function Edited by HANS LAMBERS and TIMOTHY D. COLMER Reprinted from Plant and Soil, Volume 274 (2005). 123 DORDRECHT/BOSTON/LONDON Library of Congress Cataloging-in-Publication Data A C.I.P. Catalogue record for this book is available from the library of Congress. ISBN-10 1-4020-4098-9 (HB) ISBN-13 978-1-4020-4098-6 (HB) ISBN-10 1-4020-4099-7 (e-book) ISBN-13 978-1-4020-4099-3 (e-book) Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands Sold and distributed in North, Central and South America by Springer, 101 Philip Drive, Norwell, MA 02061, U.S.A. In all other countries, sold and distributed by Springer, P.O. Box 322, 3300 AH Dordrecht, The Netherlands Printed on acid-free paper All Rights reserved Ó 2005 Springer No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage and retrieval system, without written permission from the copyright owner. Printed in the Netherlands Contents ROOT PHYSIOLOGY: FROM GENE TO FUNCTION 1. Preface vii 2. Root nitrogen acquisition and assimilation A.J. Miller and M.D. Cramer 1 3. Phosphate acquisition K.G. Raghothama and A.S. Karthikeyan 37 4. Root-based N2-fixing symbioses: Legumes, actinorhizal plants, Parasponia sp. and cycads J.K. Vessey, K. Pawlowski and B. Bergman 51 5. Mycorrhizas: Gene to function J.H. Graham and R.M. Miller 79 6. Cluster roots: A curiosity in context M.W. Shane and H. Lambers 101 7. The roots of carnivorous plants W. Adlassnig, M. Peroutka, H. Lambers and I.K. Lichtscheidl 127 8. Roles of aquaporins in root responses to irrigation R. Vandeleur, C. Niemietz, J. Tilbrook and S.D. Tyerman 141 9. Mechanisms of plant resistance to metal and metalloid ions and potential biotechnological applications A.A. Meharg 163 10. The physiology, genetics and molecular biology of plant aluminum resistance and toxicity L.V. Kochian, M.A. Pieros and O.A. Hoekenga 175 11. Acclimation to soil flooding – sensing and signal-transduction E.J.W. Visser and L.A.C.J. Voesenek 197 12. Root defense responses to fungal pathogens: A molecular perspective P.A. Okubara and T.C. Paulitz 215 13. Soil microorganisms: An important determinant of allelopathic activity Inderjit 227 14. Facilitative root interactions in intercrops H. Hauggaard-Nielsen and E.S. Jensen 237 15. Root-to-shoot signalling: Assessing the roles of upÕ in the up and down world of long- distance signaling in planta I.C. Dodd 251 Cover Photo: Images of root cross sections taken from the flooding tolerant Rumex palustris (whole root system in background). R. palustris has been used by groups at Nijmegen University and Utrecht University as a model species for studies of submergence- and flooding-tolerance, at the molecular-to-ecological levels (see Chapter 11). Images of root cross sections from Ankie Ammerlaan (Utrecht University) and whole root system from Eric Visser (Nijmegen University). Cover designed by Ankie Ammerlaan. Plant and Soil (2005) 274:vii–xv Ó Springer 2005 DOI 10.1007/s11104-005-0964-x Root physiology – from gene to function Preface Introduction major breakthrough for understanding plant wa- ter relations, in particular water uptake (Vandel- In the last decade, enormous progress has been eur et al., 2005). Aquaporins are water-channel made on the physiology of plant roots, including proteins (Johansson et al., 2000; Maurel, 1997). on a wide range of molecular aspects. Much of Their name is somewhat unfortunate, since the that progress has been captured in the following term Ôporin’ is commonly used for proteins that papers, which highlight that the classical bound- allow the transport of large molecules in a fairly aries between physiology, biochemistry and unspecific manner, whereas we now know that molecular biology have vanished. Breakthroughs aquaporins, which belong to a class of proteins have been made possible through integration of termed MIPs (membrane-intrinsic proteins), are molecular and whole-plant aspects. There has rather specific. However, some can also transport been a strong focus on a limited number of mod- other small molecules, e.g., glycerol (Zeuthen and el species, including Arabidopsis thaliana. That Klaerke, 1999) or CO2 (Uehlein et al., 2003). focus has allowed greater insight into the signifi- Knowledge on the regulation of aquaporins con- cance of specific genes for plant development and tributes to understanding plant responses to functioning. However, many species are very dif- some abiotic stresses and might help in the de- ferent from A. thaliana, in that they are mycor- sign of new irrigation techniques to improve use rhizal, develop a symbiosis with N2-fixing of scarce water resources. Aquaporins are in- microsymbionts, or have other specialised root volved in the adjustment of the hydraulic con- structures. Also, some have a much greater ductivity of roots, and therefore in adjustments capacity to resist extreme environments due to of the roots’ physiology during both phases of specific adaptations, for example aerenchyma in wet/dry cycles in natural communities and in the case of soil flooding, or are capable of toler- horticultural crops with irrigation management ating a wide range of soil chemical constraints, using partial root-zone drying (Vandeleur et al., such as acidity, salinity or heavy metal toxicities. 2005). Wider implications of the regulation of Research on species other than A. thaliana is aquaporins for acclimation during abiotic stress therefore pivotal, to develop new knowledge in include the recent finding that the well-known plant sciences in a comprehensive manner. This decrease in root hydraulic conductance during fundamental new knowledge can be the basis for flooding involves gating of a root aquaporin, due important applications in, e.g., agriculture and to cytosolic acidosis (Tournaire-Roux et al., plant conservation. Although significant progress 2003). Moreover, it can be speculated that aqu- has been made, much remains to be learnt, espe- aporins are important in hydraulic redistribution cially for many aspects of root physiology. It is of water in the root–soil system. Aquaporins envisaged, however, that discoveries made in the would allow a plant control over the exit of wa- recent past will likely lead to major break- ter from its roots into a soil with a more nega- throughs in the next decade. tive water potential than that of the roots themselves. This phenomenon, which was first described by Caldwell and Richards (1989) and Resource acquisition and carbon metabolism termed Ôhydraulic lift’, is quite common in desert species with access to deep water (Yoder and The discovery of the role of aquaporins in water Novak, 1999) and re-hydrates the rhizosphere of transport in both animals and plants has been a surface roots during the night. In contrast to viii Ôhydraulic lift’, for trees growing in a soil with a over 80% of applied phosphorus in fertilisers can low conductance between the top and deeper lay- be sorbed to soil particles, and hence, largely ers, water movement down the profile might rely unavailable for most crop plants. We will need on hydraulic redistribution via the taproot (Bur- crop species with the root traits of Proteaceae gess et al., 1998). So far, there are no data to and Cyperaceae to access that phosphorus bank. support any speculations on involvement of aqu- So far, only a limited number of species with aporins in hydraulic re-distribution, but it is ex- cluster roots have been used in agriculture and pected that such information will become horticulture, including Macadamia integrifo1ia available during the next decade. (to produce nuts) (Firth et al., 2003), Lupinus al- Major progress has been made on the physi- bus (as a source of protein) (Gardner et al., 1981) ology of uptake and metabolism of nitrogen and Aspalanthus linearis (to produce rooibos tea) (Miller and Cramer, 2005) and phosphorus (Rag- (Ratshitaka et al., 2001). Most Lupinus species hothama and Karthikeyan, 2005; Smith, 2003a). do not make cluster roots of the type produced Genes involved in the transport of these nutrients by L. albus, but they do make structures of a have been identified, and we are beginning to similar function (Hocking and Jeffery, 2004). learn when and where these are expressed. We Other Lupinus species that are used as crop spe- have also gained a much better understanding of cies, e.g., L. angustifolius make sand-binding the functioning of specialised roots involved in roots (pers. observation), which may well serve a nutrient acquisition, such as the ‘‘proteoid’’ or similar purpose. We are not aware of any species ‘‘cluster’’ roots of Proteaceae and Lupinus albus with dauciform roots being intentionally used in (Lambers et al., 2003; Shane and Lambers, managed systems, although, given the relatively 2005). These cluster roots produce and exude wide occurrence of dauciform roots in Cypera- vast amounts of carboxylates.