Ecological aspects of nitrogen metabolism in plants 9780813816494, 9780470959381, 9780470959404, 9780470959398, 0813816491, 0470959398

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Contents Contributors Preface Section 1 The Nitrogen Cycle 1 The New Global Nitrogen Cycle Jan Willem Erisman Section 2 Plant-Soil Microbe Interactions 2 Plant Associations with Mycorrhizae and Rhizobium—Evolutionary Origins and Divergence of Strategies in Recruiting Soil Microbes Gerben Bijl, Stéphane De Mita, and René Geurts 3 Arbuscular Mycorrhizas and N Acquisition by Plants Luisa Lanfranco, Mike Guether, and Paola Bonfante 4 Ectomycorrhiza and Nitrogen Provision to the Host Tree Michel Chalot and Claude Plassard 5 Proteins in the Rhizosphere: Another Example of Plant-Microbe Exchange Clelia De-la-Peña and Jorge M. Vivanco 6 Actinorhizal Symbioses Katharina Pawlowski

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7 Two in the Far North: The Alder-Frankia Symbiosis, with an Alaskan Case Study Mike Anderson 8 The Path of Rhizobia: From a Free-Living Soil Bacterium to Root Nodulation Pedro F. Mateos, Raúl Rivas, Marta Robledo, Encarna Velázquez, Eustoquio Martínez-Molina, and David W. Emerich 9 Exploiting Mycorrhizae and Rhizobium Symbioses to Recover Seriously Degraded Soils Sérgio Miana de Faria, Alexander S. Resende, Orivaldo J. Saggin Júnior, and Robert M. Boddey Section 3 Epi- and Endo-Phytic Microbes 10 Nitrogen: Give and Take from Phylloplane Microbes Mark A. Holland 11 N2-Fixing Endophytes of Grasses and Cereals Veronica Massena Reis, Jos Vanderleyden, and Stijn Spaepen Section 4 Arthropods 12 Effects of Insect Herbivores on the Nitrogen Economy of Plants Leiling Tao and Mark D. Hunter 13 Plant Defense Proteins that Inhibit Insect Peptidases Carlos Peres Silva and Richard Ian Samuels

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14 Nutrient Acquisition and Concentration by Ant Symbionts: The Incidence and Importance of Biological Interactions to Plant Nutrition Cynthia L. Sagers Section 5 Environmental Signalling in N Acquisition 15 The Functions of Flavonoids in Legume-Rhizobia Interactions Oliver Yu and Yechun Wang 16 Plant Hormones and Initiation of Legume Nodulation and Arbuscular Mycorrhization Arijit Mukherjee and Jean-Michel Ané 17 Nitric Oxide as a Signal Molecule in Intracellular and Extracellular Bacteria-plant Interactions Andrés Arruebarrena Di Palma, Lorenzo Lamattina, and Cecilia M. Creus Index

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Ecological Aspects of Nitrogen Metabolism in Plants

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This edition first published 2011 © 2011 by John Wiley & Sons, Inc. Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical and Medical business with Blackwell Publishing. Registered office John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial offices 2121 State Avenue, Ames, Iowa 50014-8300, USA The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 9600 Garsington Road, Oxford, OX4 2DQ, UK For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book, please see our website at www.wiley.com/wiley-blackwell. Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Blackwell Publishing, provided that the base fee is paid directly to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923. For those organizations that have been granted a photocopy license by CCC, a separate system of payments has been arranged. The fee codes for users of the Transactional Reporting Service are ISBN-13: 978-0-8138-1649-4/2011.

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Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks, or registered trademarks of their respective owners. The publisher is not associated with any product or vendor mentioned in this book. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold on the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Library of Congress Cataloging-in-Publication Data Ecological Aspects of Nitrogen Metabolism in Plants / Editors, Joe C. Polacco, Christopher D. Todd. p. cm Includes bibliographical references and index. ISBN 978-0-8138-1649-4 (hardback) 1. Plants–Effect of nitrogen on. 2. Plant ecology. 3. Plants–Metabolism. 4. Plant-microbe relationships. 5. Plant-soil relationships. 6. Nitrogen cycle. I. Polacco, Joe C. (Joe Carmine), 1944– II. Todd, Christopher D. QK898.N6E28 2012 572′.5442–dc22

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2010052572 A catalogue record for this book is available from the British Library. This book is published in the following electronic formats: ePDF 9780470959381; Wiley Online Library 9780470959404; ePub 9780470959398

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Contributors Mike Anderson, Department of Biology, MacAlester College, Saint Paul, MN, USA Jean-Michel Ané, Department of Agronomy, University of Wisconsin, Madison WI, USA Andrés Arruebarrena Di Palma, Unidad Integrada Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata—EEA INTA Balcarce, Balcarce, Argentina Gerben Bijl, Wageningen University, Wageningen, The Netherlands Robert M. Boddey, Embrapa Agrobiologia, Seropédica, Rio de Janeiro, Brazil Paola Bonfante, Department of Plant Biology, University of Torino, IPP-CNR, Torino, Italy Michel Chalot, Nancy-Université, Faculté des Sciences et Techniques, Vandoeuvre cedex, France Cecilia M. Creus, Unidad Integrada Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata—EEA INTA Balcarce, Balcarce, Argentina Clelia de-la-Peña, Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA

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Stéphane De Mita, Wageningen University, Wageningen, The Netherlands David W. Emerich, Department of Biochemistry, University of Missouri, Columbia, MO, USA Jan Willem Erisman, Energy Research Center of the Netherlands, ECN Petten, The Netherlands René Geurts, Wageningen University, Wageningen, The Netherlands Mike Guether, Department of Plant Biology, University of Torino, Torino, Italy Mark A. Holland, Department of Biological Sciences, School of Science and Technology, Salisbury University, Salisbury, MD, USA Mark D. Hunter, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA Lorenzo Lamattina, Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina Luisa Lanfranco, Department University of Torino, Torino, Italy

of

Plant

Biology,

Eustoquio Martínez-Molina, Departamento de Microbiología y Genética and Centro Hispano Luso de

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Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain Veronica Massena Reis, Embrapa Seropédica, Rio de Janeiro, Brazil

Agrobiologia,

Pedro F. Mateos, Departamento de Microbiología y Genética and Centro Hispano Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain Sérgio Miana de Faria, Embrapa Seropédica, Rio de Janeiro, Brazil

Agrobiologia,

Arijit Mukherjee, Department of Agronomy, University of Wisconsin, Madison, WI, USA Claude Plassard, Nancy-Université, Faculté des Sciences et Techniques, Vandoeuvre cedex, France Katharina Pawlowski, Department of Botany, Stockholm University, Stockholm, Sweden Carlos Peres Silva, Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil Joe C. Polacco, Department of Biochemistry, University of Missouri, Columbia, MO, USA and Visiting Professor, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil Alexander S. Resende, Embrapa Seropédica, Rio de Janeiro, Brazil

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Agrobiologia,

Raúl Rivas, Departamento de Microbiología y Genética and Centro Hispano Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain Marta Robledo, Departamento de Microbiología y Genética and Centro Hispano Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain Cynthia L. Sagers, Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA Orivaldo J. Saggin Júnior, Embrapa Agrobiologia, Seropédica, Rio de Janeiro, Brazil Stijn Spaepen, Center of Microbial and Plant Genetics, K. U. Leuven, Belgium Richard Ian Samuels, Department of Entomology and Plant Pathology, Universidade Estadual do Norte Fluminense, Campos Dos Goytacazes, Rio de Janeiro, Brazil Leiling Tao, University of Michigan, Department of Ecology & Evolutionary Biology, Kraus Natural Sciences Building, Ann Arbor, MI, USA Christopher D. Todd, Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada Jos Vanderleyden, Center of Microbial and Plant Genetics, K. U. Leuven, Belgium

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Encarna Velázquez, Departamento de Microbiología y Genética and Centro Hispano Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain Jorge M. Vivanco, Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA Oliver Yu, Donald Danforth Plant Science Center, Saint Louis, MO, USA Yechun Wang, Donald Danforth Plant Science Center, Saint Louis, MO, USA

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Preface Nitrogen: Too Much and Too Little of a Good Thing Joe C. Polacco and Christopher D. Todd Nitrogen, plants, and the environment, the three intertwined themes of this volume, are not only of interest in their own right but also can be viewed from an anthropocentric perspective: Humans and plants interact with environmental nitrogen (N) from opposite poles. We, as all terrestrial vertebrates, ingest a daily excess so that our average excretion of urinary N (16 g/d) is the equivalent of the protein N in 1000 soybeans (~250 g)—protein that the plant dedicated the major portion of its “lifetime N” to deposit. We hunt, gather, cultivate, and industrially fix our N, whereas plants are usually N-limited. N presents a challenge to plants as arguably the major limiting environmental mineral nutrient. However, anthropogenic excesses of N (e.g., in artificial fertilizer, combustion of bio- and fossil fuels, and in poorly treated waste), present other environmental challenges to plants and to the biosphere in general. The proper stewardship of plants can lead to amelioration of many environmental problems, including those brought on by too much, or too little, N. Stewardship, of course, begs an understanding of the bio/chemical transformations of N and of how plants acquire and use it. On a dry weight basis N is the most abundant plant macronutrient derived from the soil. It is also one of the three plant macronutrients (NPK) in common compound

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fertilizers. In relative abundance N is significantly higher than phosphorus (P) in plant dry weight1. To be utilized N and P must be presented to the plant in proper chemical form, meaning that abundance of these elements in the environment is not necessarily equivalent to their availability to plants. The atmosphere is about 80% N2 but, because of the stability of its triple bond, N2 is usually not available as a biological N source. Further, N is relatively rare in the earth’s crust so that natural and many agricultural systems are usually limited by N availability. This was especially true in the pre-industrial era before mass production of artificial fertilizers. The biological route of N2 to reactive N (Nr) is exclusively by reductive fixation to ammonia in some bacteria. (Nr is defined in Chapter 1 as all forms of inorganic N different from N2, essentially N with a non-zero valence.) Since plants are anchored in the soil, which is usually relatively N-poor, and since their aerial portions do not fix N2 (unlike their superb ability to fix the much less abundant CO2), plants have evolved strategies to acquire, conserve, and recycle Nr. These strategies form part of the N cycle, whereby bacteria convert N2 to NH3 which, in turn, is sequestered in carbon skeletons as organic molecules, or which is used by soil bacteria as an electron source, oxidizing NH3 to nitrite and nitrate, compounds for which plants have evolved efficient uptake and reduction mechanisms. Nitrate and nitrite, in turn, can be electron acceptors for denitrifying bacteria in anaerobic soils, leading to re-release of N2 (Chapters 1 and 17), and obligate co-release of the pollutant, N2O2. This very simplistic description does not do justice to the roles that plants play in the cycle, nor does it consider the massive 16

anthropogenic inputs of Nr into the cycle and the causes and ramifications of those inputs. One goal of this book is an attempt to address aspects of plant roles in the (new) global N cycle (Chapter 1). Nr encompasses both plant nutrients and pollutants. Negative players among the latter can be carcinogens, greenhouse gases, and ozone depleters. Within the “environmental” theme, our goal is the coverage of various operative environmental scales in plant N acquisition and assimilation. One ‘micro-scale’ deals with the many specialized interactions of plants with the bacterial world: associations of legumes with rhizobia (Chapters 2, 8, and 16) and of many trees with actinorhizal bacteria (Chapters 6 and 7), the latter of great importance in boreal forests. Even more primordial associations are those of plant roots with fungi: The mycorrhizae play a crucial role in N provisioning to plants, and N-providers are not limited to the ectomycorrhiza (ERM) (Chapter 4). The arbuscular mycorrhiza (ARM), well-recognized as aiding in P provision, also play a role in “virtual extension” of the plant root system, and N provision culminates from an interesting spatial and root-fungal delimitation of components of the arginine/urea cycle (Chapter 3). Indeed, plants do not excrete arginine-derived urea as do terrestrial mammals but employ it as a recyclable N intermediate. “Never say never” is a proper adage applied to interactions in nature. Two-component symbioses are often our first view of an association, later revealed to contain other players. A case in point is the potential role(s) of bacteria in the ARM association, considered in Chapter 3. Bacterial 17

endophytes may provide N directly to the plant, or improve the plant’s ability to “mine” N. These questions on endophytes are addressed in Chapter 11, which also considers potential agronomic applications of the endophytic bacteria. And, the extensive leaf surface area provided by plants is an environment not ignored by microbes; Chapter 10 discusses ramifications of phylloplane colonization on plant N acquisition. One is that there is much nutrient and “waste” exchange on the leaf surface, and much of it influenced by phylloplane microorganisms. Clearly, N is not only a nutrient, but also a component of simple, inorganic signaling compounds, such as nitric oxide (NO) and nitrate (NO3−). NO is but one of the possible forms between NH3 (N valence –3) and nitrate (N valence +5). Such inter-conversions catalyzed by soil and endophytic bacteria are considered in Chapter 17, especially in light of regulatory effects on the plant. NO and nitrate also have profound effects on legume nodulation and root development. In general the polluting effects of excessive Nr need also to take into account the altered environmental levels of regulatory Nr molecules. At higher trophic levels, plant interactions with insects and herbivores are worthy of increased study. Chapters 12 and 14 portray the evolutionary and environmental complexities of plant interactions with insects, from the “exotic” ant-plant associations to more general questions of N flux between plant and insect. Such a flux is highly regulated given the incredible panoply of plant proteins aimed at insect proteases, discussed in Chapter 13, a

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discussion also germane to “plant investment strategies” in N-containing insecticides. On a global scale, massive anthropogenic inputs of Nr from burning of fossil and biofuels, human waste treatment, the Haber-Bosch process and concomitant intensive agriculture open up issues of equitable distribution of nitrogenous fertilizer—its overuse in Europe, North America, and China compared to under-use in much of the developing world3. Excessive inputs lead to Nr being not only a soil pollutant, but also a greenhouse gas and an ozone-depleter, in the form of N2O4. Ice core analyses indicate rising atmospheric nitrate (derived from NO and N2O) with the advent of the industrial age5. So, a new mandate, in addition to more equitable distribution of fertilizer, is to reduce fertilizer use overall (thus avoiding such negative outcomes as eutrophication, health problems, dead zones, reduced species diversity, etc.) To lower Nr in soil, water, and air requires improved cultural practices, increased biological N-fixation, and efficient means of industrial denitrification (anammox avoids N2O evolution2). A more long-range strategy is to improve the N use efficiency of plants, topics broached in Chapter 1. Badly degraded and eroded soils, of course, suffer from N-depletion, and Chapter 9 shows how recruitment of proper leguminous trees and rhizobial and ARM isolates can lead to dramatic recovery of three types of degraded soils (erosion ditches, mine sites, “detopped” mountains) in Brazil’s Rio de Janeiro state. To be sure, soil is more than a semi-solid solution of nutrients; amendments of proteins, N-rich polypeptides secreted by plants and ARM, undoubtedly influence soil texture, tilth, humidity, and 19

other factors. Roles of plant-secreted proteins in influencing the microbial rhizosphere are considered in Chapter 5. And, it has been reported that plants can consume intact microbes as nutrient sources6. Hundreds of millions of years of N-acquisition have led to evolved associations of plants with bacteria (rhizobial and actinorhizal) and fungi (ARM and ERM). Intriguing evolutionary questions on the origins and relatedness of these associations are discussed in Chapters 2, 6, and 16. Chapter 15 discusses roles of flavones and isoflavones in the complex chemical signaling between plants and their potential symbionts, chemical signals operative not only in the rhizosphere but in the establishment and development of N2-fixing nodules. The need is clear for integrating the complexities inherent in plant performance, environmental interactions, and N inter-conversions. A greater appreciation of these interactions will lead to better understanding of our place, and that of plants, in our shared environment. We thank the authors for their excellent contributions to an appreciation of the complex N-Plant-Environmental interactions. We thank Justin Jeffryes for reinforcing the need for this volume. And our interactions with Justin’s Wiley-Blackwell colleagues, Shelby Allen and Susan Engelken, to name two, have been nothing short of pleasant, and productive, in bringing the volume to fruition. Literature Cited

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1

Güsewell, S. 2004. N: P ratios in terrestrial plants: variation and functional significance (Tansley review). New Phytologist 164: 243–266. 2

Canfield, D.E., Glazer, A.N., Falkowski, P.G. 2010. The evolution and future of Earth’s nitrogen cycle. Science 330: 1519–1520. 3

Vitousek, P.M., Naylor, R., Crews, T., David, M.B., Drinkwater, L.E., Holland, E., Johnes, P.J., Katzenberger, J., Martinelli, L.A., Matson, P.A., Nziguheba, G., Ojima, D., Palm, C.A., Robertson, G.P., Sanchez, P.A., Townsend, A.R., Zhang, F.S. 2009. Nutrient imbalances in agricultural development. (Policy Forum). Science 324: 1519–1520. 4

Ravishankara, A.R., Daniel, J.S., Portmann, R.W. 2009. Nitrous oxide (N2O): The dominant ozone-depleting substance emitted in the 21st century. Science 326: 123–125. 5

Hastings, M.G., Jarvis, J.C., Steig, E.J. 2009. Anthropogenic impacts on nitrogen isotopes of ice-core nitrate. Science 324: 1288. 6

Paungfoo-Lonhienne, C., Rentsch, D., Robatzek, S., Webb, R.I., Sagulenko, E., Nashölm, T., Schmidt, S., Lonhienne, T.G.A. 2010. Turning the Table: Plants Consume Microbes as a Source of nutrients. Plos One 5, issue 7 (July).

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Ecological Aspects of Nitrogen Metabolism in Plants

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Section 1 The Nitrogen Cycle

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Chapter 1 The New Global Nitrogen Cycle Jan Willem Erisman Introduction Almost 80% of the atmosphere is N2. And nitrogen, in reactive forms is essential for life on earth and is crucial for sustainable development.* Nitrogen in our environment has both benefits as well as negative consequences. The primary benefit of nitrogen is the stimulation of plant growth in agriculture for food, feed, and fuel, whereas the negative aspects include almost all environmental impacts. Compared to elements such as carbon, sulfur, or phosphorus, nitrogen contributes to a variety of negative impacts, most interrelated, such as climate change, eutrophication, soil acidification, degraded human health, loss of biodiversity, etc. In 2008 we celebrated the one-hundredth anniversary of the invention of the production of ammonia by Fritz Haber in 1908. Ammonia is the basis for fertilizer production, and Carl Bosch was able to turn that ammonia production into an industrial process (Smil, 2001; Erisman et al., 2008). Bosch and Haber were awarded the Nobel Prize for their achievements. Ammonia is not only the basis for fertilizer, but also for many industrial chemicals, including explosives. So, overall, the Haber-Bosch process was beyond doubt one of the most important inventions of the twentieth century (Erisman et al., 2008). Over the past decades the production of fertilizer has become very energy and economically efficient (Kongshaug, 1998) and

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on a large scale has increased agricultural productivity. Without fertilizer input, the biosphere would produce 48% less food (Erisman et al., 2008). Therefore, at present, we cannot live without fertilizer. At the same time, industrialization increased the use of fossil fuels. To use the energy from fossil fuels, they are burned, resulting in a large release of oxidized nitrogen (NOx) into the atmosphere. Vehicular traffic, energy use, and industry are the principal sources of oxidized forms of Nr. The dispersion of NOx has affected human health and increased nitrogen deposition in remote areas leading to eutrophication (Erisman and Fowler, 2003). This book is dedicated to plant “strategies” to acquire, assimilate, and conserve N. Much emphasis is given to plant interactions with microorganisms (Frankia, rhizobia, mycorrhizae). Biological N-fixation is prominently covered and is an important part of the nitrogen cycle. However, in order to establish the need for knowledge in the area of biological N fixation (and the N “conduits” that mycorrhizae provide for delivering soil N to plant), we have to address the “big picture” first, providing background on the major components of the nitrogen cycle on different scales, emphasizing the human contribution to the increased cycling of nitrogen in the biosphere and the resulting impacts on ecosystems and humans. This introductory chapter addresses these issues as a global overview of the human influence on the nitrogen cycle. The Preindustrial Nitrogen Cycle Nitrogen is an important element—the most abundant constituent of the atmosphere, hydrosphere, as well as the 25

biosphere. It is also one of the essential elements for the growth of plants and animals and has a crucial role in ecology and in the environment. It is useful to look at the reactions of elements in the form of a closed cycle. Such a cycle is often termed a biogeochemical cycle because chemistry, biology, and geology all provide important inputs. Cycling of elements is often governed by kinetics and may involve the input of energy, so that chemical equilibrium states are not attained. The ultimate source of energy for driving energetically uphill reactions is the sun. The earth’s surface receives an average radiation input of 100–300 W/m2 % day, depending on latitude. Some of this is captured by photosynthesis, and is used to produce high-energy content molecules, such as oxygen. Because of the inherently low efficiency of the photosynthetic process and the production of phytomass, energy supply from this source has low power densities and hence high land demands. Recent estimates of the global terrestrial net primary productivity (NPP) average approximately 120 gigaton (Gton) of dry biomass produced annually, and that contains some 1,800 × 1018 joules (1,800 exajoule [EJ]) of energy (Smil, 2004). In principle, there is globally enough possible annual crop growth to produce the food needed to feed the population currently and for the coming decades. Furthermore, there is enough annual production of new biomass to cover up to four times current human annual energy use. However, in order to grow, collect, and use biomass in a sustainable way to satisfy human food and energy needs, a well-regulated and optimized process is needed. The atmosphere contains mostly elemental di-nitrogen, along with other nitrogen containing trace gases 26

(ammonia, nitric oxide, nitrogen dioxide, and nitrous oxide). Aquatic systems primarily contain soluble forms of nitrogen, such as nitrate and ammonia/ammonium, as well as biological nitrogen found in proteins, DNA, RNA, and other compounds that make up living systems. Since lone pairs of electrons on nitrogen are usually basic, ammonia coexists in both the protonated and de-protonated forms near neutral pH. The most important aspect of the environmental nitrogen cycle is the dynamic exchange of chemical species that occurs between the atmosphere and the surface landmasses and oceans. Figure 1.1 illustrates the nitrogen cycle. Figure 1.1. Illustration of the nitrogen cycle.

From Figure 1.1, it is obvious that living systems are the main players in the interconversions of the reduced and 27

oxidized forms of nitrogen. They play an important role in providing reduced nitrogen compounds for the global cycle, by denitrification processes (the conversion of nitrate to N2 and N2O), biosynthesis (making amino acids, DNA, and RNA), and nitrogen fixation (reduction of N2 to NH2 by both free-living bacteria and bacteria associated with plants, usually in root nodules, the so-called biological nitrogen fixation [BNF]) (Marschner, 1997). Nearly all organisms can use ammonia for biosynthesis (ammonia assimilation). Ammonia is also a major metabolic end product, as in the bacterial decomposition of dead organisms (ammonification). Mammals eliminate ammonia; however, the liver transforms it into the less toxic compound urea before excreting it. Although reduced nitrogen is preferred for biosynthetic reactions, plants have also learned to capture needed nitrogen by assimilatory nitrate reduction (Marschner, 1997). This evolutionary consequence came about because nitrate is the dominant soluble form of nitrogen in aerated soils. Formation of reduced nitrogen compounds is energetically uphill. Besides plant use of nitrate, its reduction also occurs by bacterial action in oxygen-free soil and sediments. Reduced nitrogen can however be formed in a different way in the soil, where bacteria and plants work together. Symbiotic nitrogen-fixing bacteria in aerated soils provide an oxygen-free environment for their oxygen-sensitive nitrogenase within nodules induced on the roots of legumes, such as clover and alfalfa (Marschner, 1997). BNF symbioses also occur in many trees associated with gram-positive Frankia.

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The preindustrial nitrogen cycle could be characterized as a careful preservation of the very low amount of Nr available in nature. Nr is created and distributed by natural processes such as forest fires, lightning, volcanic eruptions, and biological nitrogen fixation (Smil, 2001; Reid et. al., 2005). The natural production of Nr is estimated by many authors to be around 125 (Tg) N per year, with 5 Tg from lightning and 120 Tg from biological nitrogen fixation (Galloway et al., 2003, 2008; Schlesinger, 2009). Human-induced Changes of the Nitrogen Cycle In addition to the natural formation of Nr, there are also significant geophysical and anthropogenic sources. The Haber-Bosch process is the first high-pressure industrial process that fixes nitrogen to ammonia on a large scale and “helps” nature increase plant growth (Smil, 2001). The second largest bulk industrial nitrogen feedstock, nitric acid, lies at the other extreme of the redox series. Ammonia is oxidized to produce nitric acid in the Oswald process, named after its discoverer Wilhelm Oswald. It makes good chemical sense that the principal industrial nitrogen compounds lie at opposite ends of the redox series (valencies of −3 for ammonia to +5 for nitrate). With these two reagents, it is ultimately possible to synthesize any desired compound with an intermediate oxidation state for nitrogen. The major use for nitrogen compounds is as fertilizers. Industrial nitrogen fixation is estimated to be 125 Tg/yr, of which 82% is for fertilizer production, and the remaining is for industrial use and explosives (Galloway et al., 2008).Fertilizer application to cultivated plants is more than double the natural amount of BNF. 29

Cultivation of arable land has increased BNF by about 40 million metric tons per year (Tg/yr) (Galloway et al., 2008). Fossil fuel combustion adds another 25 Tg/yr of oxidized nitrogen, released to the atmosphere (Galloway et al., 2008; Schlesinger, 2009). For 2005 the total human-induced Nr added up to 170 (Schlesinger, 2009) to 187 Tg/yr (Galloway et al., 2008). Adding the naturally produced Nr results in about 300 Tg/yr generated globally. Figure 1.2 shows the increase in human-induced Nr production since the beginning of the last century. By 1980 human Nr production became larger than natural production and, until 1980, the production increase was higher than the population increase. This changed after the 1990s when the economic situation in Eastern Europe affected agricultural production in that area. Since then the increase in fertilizer use matches the population growth. One can conclude that there is room for improvement in the fertilizer use efficiency and at the same time, that as world population grows, fertilizer use will grow at least at the same rate if no measures are taken. Figure 1.2. Changes in global Nr production (modified from Reid et al., 2005; Erisman et al., 2008; Van Aardenne, 2001).

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Too Much or Too Little of a Good Thing There are two major problems with Nr: some regions of the world have too little and others too much. In the latter case burning of fossil fuel and inefficient incorporation of nitrogen into food has resulted in a large number of major human health and ecological problems. In the N-deficient areas, too little food, especially proteins, will cause more malnutrition eventually leading to increased mortality. The rate of change in N distribution is enormous and probably greater than that for other ecological problems. According to the Food and Agriculture Organization of the United Nations (FAO), currently more than 1 billion people, especially in the south of the world, suffer from malnutrition. In those regions of the world where there is not enough food, nitrogen availability through fertilizers might be the limiting factor, apart from availability of water and other nutrients. Obviously, fertilizer distribution depends on infrastructure and social and/or economic factors. 31

In Europe, the US, and more recently in China, food production is stimulated by government support (e.g., by subsidizing fertilizers). This has created a shift from good nutrient management to industrialized food production with appreciable waste of inexpensive nitrogen and its release to the environment. Global nitrogen fertilizer production occurs in a limited part of the globe, but nitrogen is transported to other regions in the form of food and feed and through the air (NOx). Human creation and use of Nr (see Figure 1.2) has created a new nitrogen cycle, especially because the efficiency of N use has decreased along with its increased, but less efficient, production. The energy efficiency of nitrogen in fossil fuel is, in essence, zero, because the NOx formed during combustion is an unwanted by-product and has no function in the production of energy. In agriculture Nr is added in the form of fertilizer to increase crop yield. However, only 5–10% of fertilizer N ends up in our food depending on the type of food (meat or vegetables), the agricultural system, and management (Smil, 2001; UNEP, 2007). Meat production is an additional inefficient step in the food N chain with further Nr losses to the environment (Steinfeld et al., 2006). Most of the nitrogen lost to the environment is through air emissions (ammonia, nitrogen oxides, nitrous oxide) and water (NO3 run-off and/or leaching), in addition to that returned to the atmosphere as N2 (Galloway et al., 2003). These losses cascade through the different environment compartments, exchanging forms and contributing to many different effects in time and space. This is called the “cascade effect of nitrogen” (Galloway et al., 2003).

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Schlesinger (2009) estimated that the fates of natural Nr were mainly conversion to N2 via denitrification (92 of the 125 Tg/yr), the other major flux being river flow. Figure 1.3 shows the increase in the fates of Nr from the preindustrial era to the current situation. For anthropogenic nitrogen, the biospheric increment amounts to 9 Tg, river flow increment amounts to 35 Tg, groundwater leaching to 15 Tg, denitrification to 17 Tg, and atmospheric transport to the ocean to 48 Tg per year. The fate of anthropogenic nitrogen is therefore much less as N2 than the fate of natural nitrogen. These data are, however, highly uncertain as discussed in Galloway and others (2008). What is clear, though, is that the losses of Nr to the environment have increased substantially, especially in the areas of intensive fossil fuel use and agriculture. Figure 1.3. Increase in the fates of Nr currently (2005) compared to preindustrial (Tg/y).

Anthropogenic disruptions in the nitrogen cycle have led to an 1,100% increase in the flux of nonreactive atmospheric nitrogen (N2) to Nr compounds. Once converted to a reactive state, nitrogen persists in the environment, “cascading” through various compounds 33

(NH3, N2O, NOx, NO3), resulting in impacts such as the production of ground-level ozone, acidification, eutrophication, hypoxia, stratospheric ozone depletion, and climate change (Vitousek and Melillo 1997; Mansfield et al., 1998; Langan, 1999; Cowling et al., 2002; Galloway et al., 2003, 2008). N-limitation and Biodiversity In the natural environment nitrogen is a limiting factor for growth, leading to a rich biodiversity of strategies for N acquisition, N “management,” and N “preservation.” Trees, for example, retreat their leaf nitrogen before senescence. If Nr becomes increasingly available, the fast growing species, no longer growth limited (provided other nutrients and water are sufficiently available), will overgrow slow-growing species resulting in serious loss of biodiversity, algal blooms, hypoxic zones, etc. (e.g., Goulding et al., 1998; Bobbink, 2004; Stevens et al., 2004; Dise and Stevens, 2005; Phoenix et al., 2006; Klimek et al., 2007). The effects due to high N deposition extend to fauna, a notable example of which is the disappearance of the red-backed shrike (Lanius collurio) in coastal dunes of the Netherlands and in other parts of Western Europe. The red-backed shrike is a good indicator of fauna diversity, since its breeding success depends highly on the availability of large insects and small vertebrates (Beusink et al., 2003). Evidence for serious adverse effects on faunal species diversity and marine systems exists, but the level of scientific understanding is rather low. The negative impacts of Nr emissions include eutrophication of seminatural ecosystems and surface 34

waters, soil acidification, nitrate pollution of groundwater, particulate formation leading to impacts on human health, and alterations of the earth’s radiation balance, such as ozone formation leading to effects on humans and vegetation, and to climate change when N is transformed into nitrous oxide, one of the most important greenhouse gases (e.g., Galloway, 1998; Galloway and Cowling, 2002; Matson et al., 2002; Galloway et al., 2003). Although the effects of N inputs on the carbon cycle remain controversial (Houghton et al., 1998; Nadelhoffer et al., 1999; de Vries et al., 2008), there are indications of a strong relationship with stimulation of greenhouse gas emissions as well as with carbon sequestration and plant/ forest growth. Increased inputs of N to aquatic ecosystems from atmospheric deposition, sewage, and agricultural runoff can cause eutrophication, including damage to fisheries in coastal ecosystems (Rabalais, 2002). The formation of N2O during nitrification and denitrification in all systems results in tropospheric warming and stratospheric ozone depletion (Prather et al., 2001). These undesirable “cascading effects,” as Galloway and others (2003) call them, of Nr moving through aquatic and terrestrial ecosystems and the atmosphere do not stop until the Nr is fixed or eventually converted back to N2 through the process of denitrification. Therefore, one molecule of Nr can contribute to a cascade of effects, each changing natural biodiversity. Strategies to Limit N-effects The science of Nr in the environment has advanced beyond recognition of the seriousness of the problem. Evidence of Nr’s multiple effects has been presented not only at the 35

four international conferences on the subject but also in many papers published in refereed academic journals (see www.initrogen.org for the third [Nanjing, 2004] and fourth [Brazil, 2007] international nitrogen conferences and Erisman et al., 1998; Cowling et al., 2002). The next phase is to assess the issues in such a way that international cooperation to solve the problems becomes more likely. In 2004 The Nanjing declaration on nitrogen management was signed at the third international nitrogen conference (Erisman, 2004). The declaration affirms the need for an international protocol to reduce Nr to sustainable levels in agricultural systems, estuaries, and ecosystems. This might be achieved by improving utilization of nitrogen in food production, by limiting energy consumption, or by spurring changes in the fuels used as energy carriers. Since the Nanjing declaration, many scientific efforts have focused on management of nitrogen. In the Netherlands the introduction of regional nitrogen ceilings based on effect limits was proposed (Erisman et al., 2005). Current policies in the Netherlands that have succeeded in decreasing Nr focused on setting and meeting the targets through some freedom of choice for the stakeholders and not, as has been done mostly up till now, by prescribing what the stakeholder should do. Targets should be based on all effects (no trade-offs), on sound science, and on a clear long-term vision that takes into account the position of agriculture in relation to other sectors and human needs. We should aim to close the nutrient cycles and minimize resource use. Therefore, the scientific community should come up with simple, easy to determine indicators that can be used to implement, monitor, evaluate, and maintain policies, such as nitrogen use efficiency (NUE).

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Some of the options should be agreed upon within the framework of the European Union, or even on a larger scale, because it affects countries’ competitiveness. Such measures include taxes or financial grants, and setting targets for N losses. Furthermore, the closing of cycles should be done concurrently and at different scales. We are accustomed to seeking our improvements in technological options. There are potential technologies that might lead to substantial emission reduction (catalytic converters, hydrogen economy, nitrification inhibitors, fermentation of manure, etc.). Furthermore, important technology developments needed include traditional plant breeding that employs powerful new tools, such as marker-assisted selection, to identify genes associated with increased NUE, and genetic manipulation based on better understanding of the transition between nitrogen assimilation and nitrogen cycling (Good et al., 2004). These are important, but the reduction in environmental load they cause should not lead to other environmental risks or increased import of raw materials, leading to changes in cycles at supranational scales. Furthermore, other components (such as carbon) and such issues as access to freshwater should be taken into account to prevent trade-offs. If financial incentives are given, it is important to secure the period that these incentives will last, in order to guarantee a return on investment. Galloway and others (2008) recently quantified potential Nr reductions by implementation of four interventions to limit Nr production: • The first intervention point involves fossil fuel combustion. Using best available technologies, Nr creation during fossil

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fuel combustion can be decreased by about one-third from its current level. The barriers to such a decrease are primarily financial, as the scientific, engineering, and the policy instruments are all well developed. Utilizing this available technology, Nr creation by fossil fuel combustion would decrease from ~24 Tg N yr−1 to ~16 Tg N yr−1. • The second intervention point is to increase the NUE of crop production. Cassman and colleagues estimate that there will be a 38% increase in global cereal demand by 2025. They project that this demand can be met with a 25% decrease in N fertilizer application to cereals if the current decline in cereal harvest area is halted (−0.33% yr−1 over 20 years) and the crop yield response to applied N is increased by 20% (NUE increase). This ‘intervention’ would reduce the global Nr creation rate by ~15 Tg N yr−1. • The third intervention is improved animal feeding strategies and manure management. It is estimated that 13% of the N lost from animal waste in the EU-27 countries could be either eliminated or captured by a combination of low-protein animal feeding, barn adaptations, covered manure storage, air purification, and efficient manure applications (to crop land and grassland). Extending this to the animal populations of the world would result in a decrease of ~17 Tg N lost to the environment. In considering this intervention, it is equally important to address the fraction of meat and dairy products in human diets. In many developed countries, diets contain more animal protein than needed. Livestock are particularly effective at releasing Nr to the environment, so that eating less meat would both substantially decrease Nr losses while having potential health benefits. • The fourth intervention point is improved sewage treatment. Each year, the global population produces ~20 Tg N in human waste of which 75% colonization rates. Acacia mangium showed the greatest response to mycorrhizal inoculation, followed by A. holosericea and A. auriculiformis. The results suggest that the specificity may be host plant-associated, since all three Acacia species increased yield very significantly when Glomus clarum and Gigaspora margarita were substituted by Scutellospora calospora, S. gilmorei, S. heterogama, or Acaulospora morrowiae. Figure 9.3. Growth response of three Acacia species to inoculation with 10 different species of arbuscular mycorrhizal fungi. Plants were grown in 700 ml of autoclaved soil (pH 5.2) and inoculated with the strains of rhizobium recommended by Embrapa Agrobiologia. Symbiotic efficiency was measured as a percentage of growth of the non-inoculated control plants.

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Preparation of Tree Seedlings for the Recovery of Degraded Areas The success of the Embrapa Agrobiologia RDA program is mainly due to the selection of fast-growing legume trees and their specific mycorrhizal and rhizobial symbiotic partners. A great deal of experience has been obtained with many legume trees suitable for different climates and soils that vary in salinity, acidity, etc. These species, classified by climatic region and soil restriction, can be found in the Technical Bulletin of Faria and others, 2010. (http://www.cnpab.embrapa.br/publicacoes/download/ cot127.pdf) For most trees employed in RDA, it is necessary to scarify the seeds to break dormancy and induce germination. This is normally performed with either hot water or concentrated sulfuric acid, and the time of immersion differs among species. The seedlings are produced in a mixture of sandy and clay soils and organic compost in the ratio of 1:1:1 (v/v) contained in polystyrene planting boxes (e.g., Plantagil®, Plantagil Comercial Agrícola, São Paulo, 474

SP) with typically 72 pockets (seedlings) per box, or in plastic tubes or plastic bags. The mycorrhizal fungal inoculant is prepared as follows: the mycorrhizal fungi (currently Glomus clarum and Gigaspora margarita) are multiplied in pots (20 L) using Brachiaria decumbens as a trap plant. The mycorrhizal inoculant is a mixture of soil, Brachiaria roots, and fungal mycelia/spores. The inoculant (approximately 1 g) is inserted in the hole made for the seed immediately prior to planting. At planting the seeds are treated with standard rhizobium inoculant using sterile peat as a base (Somasegaran and Hoben, 1994). Seeds are wetted and mixed with the peat-based inoculant to coat them—the objective is to make the seedling roots pass through both inoculants, thus making direct contact with them. The seedlings are left to grow in a nursery for 3 to 4 months, depending on the species and the season. Once ready, seedlings are transported to the field. Correction of soil pH is not usually necessary because these tree species withstand very acid soil and/or substrates. However, soil fertility analyses are always made. Holes spaced at about 30 cm × 30 cm × 30 cm are made in the area. For planting, 250 g of rock phosphate and 10 g of fritted trace elements, and usually 1 or 2 L of green manure or chicken dung (when available) are added because most of the subsoils and other substrates are almost completely devoid of phosphorus and micronutrients. Planting is carried out at the start of the rainy season where possible, although in dry areas it may be possible to plant if irrigation is available.

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Case Studies Recuperation of Erosion Gulleys at a Rural Site When Brazil was first “discovered” by the Portuguese in 1500 AD, the Atlantic coastal region was covered by a dense tropical forest that stretched from latitude 5° to 30° south and occupied approximately 100 Mha. Today it is estimated that less than 8% of this forest remains. The deforestation started with the extraction of the red dye from the “pau brasil” tree after which the country is named, and continued through the cycle of sugarcane, coffee, and timber extraction and, eventually, in the last century, large areas were felled for charcoal production for iron founding. This sad history has been related in detail by Dean (1995). A large proportion of this deforested land, especially in the states of Rio de Janeiro, Minas Gerais, and Espirito Santo is in mountainous areas. After deforestation and/or coffee cropping, the hillsides became colonized principally by grasses such as green panic (Panicum maximum) or molasses grass (Melinis minutiflora). Owing to the almost continuous presence of grazing animals and regular burning (usually intentional, to provoke new growth for forage), woody species have never returned to these hills. As mentioned in the Introduction, the heavy summer rainfall often opens up erosion gulleys that gradually expand. No complete survey of the area covered by such erosion gulleys appears to have been made but, to give an example, along a 70-km stretch of the valley of the river Paraíba do Sul (the source of much of Rio’s drinking

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water) in the interior of the State of Rio de Janeiro, 160 erosion gulleys have been counted (Machado et al., 2006). In this case study, we report the results of the use of the fast-growing legume tree (FGLT) technology on the environmental recovery of one such erosion gulley with a mean depth of 10 m and a volume of approximately 10,000 m3. The gulley before intervention is pictured in Figure 9.4. It is estimated that during the “growth” (erosion) of the gulley, the equivalent of 2,000 truckloads of sediment were washed out and deposited in the areas below and in the stream and rivers of the watershed. The intervention started in 2000. Initially, narrow terraces were formed at the upper and lower ends of the gulley, and walls of bamboo and rubber tires were formed in the central streambed within the gulley in order to trap sediments (Figure 9.5.) Following this engineering, the legume tree seedlings, all inoculated with strains of rhizobium and AMF selected at Embrapa Agrobiologia, were planted with a spacing of 2 × 2 m along the gulley and into holes cut into the walls. The success of the technology was evaluated by measurements on tree growth and the output of sediments collected in sediment tanks. The best results were obtained with the species Acacia mangium, Mimosa artemisiana, M. caesalpiniifolia, and Pseudosamanea guachapele. After 170 days the mean heights (cm) for these species were A. mangium 53, Mimosa artemisiana 38, M. caesalpiniifolia 67, and Pseudosamanea guachapele 67. The species Acacia auriculiformes, A. angustissima, Albizia lebbek, Enterolobium contortisiliquum, and Samanea saman 477

showed low indices of survival, sometimes because of their lower resistance to drought, or their position in the gulley where water was not retained, or because they suffered from attack by leaf-cutting ants. Figure 9.4. The erosion gulley at the start of the recovery program in 2000. Note the rubber tires and bamboo barriers installed to slow down stream flow. The white plastic netting hanging from the sides of the gulley have pockets to hold seedlings. .

Figure 9.5. Sediment trap at the bottom of the erosion gulley where no recuperation had been attempted. The image shows the scene shortly after a 30-mm rainfall in 30 minutes. The sediment traps had to be redesigned and rebuilt! Photo by Eduardo F.C. Campello.

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Sediment tanks were installed in three adjacent gulleys of similar size, one which was left without a recovery operation, one where the recovery operation started 2 years before, and the third 6 years before. From the no-intervention gulley 52.5, 20.5, and 29.0 Mg of sediment at the outlet was collected in three evaluations during the rainy season from November 2005 to February 2006: the first over a period of 17 days (134 mm rainfall), the second over the next 24 days (134 mm rainfall), and the final evaluation over a period of 8 days (123 mm rainfall). The gulley where the recuperation had started 2 years before produced quantities of sediment of 1.0, 1.7, and 1.8 Mg over the three measurement periods. The sediment output from the gulley where the recuperation had started 7 years before was too low to be measured, although it is possible

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that very fine particles did not have time to settle in the sediment tanks before washout. With respect to cost of this operation, a total of R$10,904 (one $US = ~R$1.70) was spent to recover one of the gullies. The largest proportion of the cost (64%) was for labor followed by the cost of the 4,000 seedlings (20%, or R$0.55 per seedling) and transport, and the other costs were for materials such as fencing posts and wire, rock phosphate and fritted trace elements (FTE), manure, and insecticide. Rehabilitation of a Decapitated Hillside in the Atlantic Forest Region The objective of this study was to examine the effect of soil rehabilitation using leguminous nitrogen-fixing trees on the recovery of nutrient cycling processes and soil C and N stocks 13 years after planting. The area was located in the town of Angra dos Reis, along the western coast of the State of Rio de Janeiro, 23° 02′ 30″ S and 44° 11′ 30″ W, 100–200 m above sea level, within the limits of the Atlantic Forest biome. According to Köppen’s method, the climate of Angra dos Reis is classified as Af, moist tropical forest. Average annual precipitation and temperature are 2,300 mm and 22.5°C, respectively, without a distinct dry season (Chada et al., 2004). The area is steeply sloping and the soil is classified as a Ferralsol under the FAO soil classification system (Oxisol, United States Department of Agriculture [USDA] Soil Taxonomy).

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In 1991, when the area was dominated by grass vegetation, the topsoil was removed from the site and used for the foundations of a shopping mall. Exposure of the subsoil to rainfall led to severe erosion, which, after a short period of time, resulted in the formation of erosion gullies. The area was restored by planting seedlings of Acacia mangium, A. auriculiformis, Enterolobium contortisiliquum, Gliricidia sepium, Leucaena leucocephala, Mimosa caesalpiniifolia, and Paraserianthes falcataria, all of which were inoculated with selected rhizobia and arbuscular mycorrhizal fungi as described in the Preparation of Tree Seedlings for the Recovery of Degraded Areas section. The recovered area was approximately 1 hectare (ha) in size. To avoid further erosion, when the seedlings were planted, bamboo stems were anchored crosswise in the erosion channels or gullies to slow down the rainwater running down the slope. In September 2004 soil samples were collected from the two reference areas and the area rehabilitated with legume trees. One of these reference areas was a fragment of native forest (Atlantic Forest), with few signs of human presence or disturbance, while the other consisted of 2 ha of deforested land. These three areas are located close to each other on the same hillside. The deforested area (where no intervention was performed) was spontaneously overgrown with green panic (Panicum maximum). In contrast to the rehabilitated area, the topsoil of this control area was not completely removed. Soil samples were collected from the following depth intervals: 0–5, 5–10, 10–20, 20–30, 30–40, and 40–60 cm. The samples were collected from three replicate trenches excavated to a total depth of 70 cm and spaced 4 m apart. Soil bulk density 481

was estimated from samples collected using volumetric rings at each depth interval. Four soil bulk density samples were used. Additional samples were taken from each depth interval for chemical analyses, which were performed on triplicate subsamples. To obtain bulk density, samples were dried at 105°C for >72h and weighed. Samples for analysis of texture, nutrient, and N and C concentration were air-dried and sieved to 2 mm. Soil samples were analyzed for the fertility parameters: pH, exchangeable Al, Ca, and Mg, available P and K (Mehlich-1 extractant) using standard methods (Embrapa, 1997). Total N was determined using semi-micro Kjeldahl digestion (Urquiaga et al., 1992). Total C content of finely ground (