Advances in agronomy volume 125

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ADVANCES IN AGRONOMY Advisory Board PAUL M BERTSCH RONALD L PHILLIPS University of Kentucky University of Minnesota KATE M SCOW LARRY P WILDING University of California, Davis Texas A&M University Emeritus Advisory Board Members JOHN S BOYER KENNETH J FREYw University of Delaware Iowa State University EUGENE J KAMPRATH MARTIN ALEXANDER North Carolina State University 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 CRAIG A ROBERTS WARREN A DICK MARY C SAVIN HARI B KRISHNAN APRIL L ULERY SALLY D LOGSDON w deceased Academic Press is an imprint of Elsevier 525 B Street, Suite 1800, 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, OX5 1GB, UK Radarweg 29, PO Box 211, 1000 AE Amsterdam, The Netherlands First edition 2014 Copyright © 2014 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 Department in Oxford, UK: phone: (+44) (0) 1865 843830; fax: (+44) (0) 1865 853333; 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: 978-0-12-800137-0 ISSN: 0065-2113 For information on all Academic Press publications visit our website at store.elsevier.com Printed and bound in USA 14 15 16 17 10 CONTRIBUTORS Dominique Arrouays INRA, InfoSol Unit, Orleans, France Ruth E Blake Department of Geology and Geophysics, Yale University, New Haven, Connecticut, USA Guanglong Feng State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China Bruno Gerard International Maize and Wheat Improvement Centre (CIMMYT), El Batan, Mexico Michael G Grundy CSIRO, EcoSciences Precinct, Dutton Park, Queensland, Australia Alfred E Hartemink University of Wisconsin-Madison, Department of Soil Science, Madison, USA Ji-Zheng He State Key Laboratory of Urban and Regional Ecology, Research Center for EcoEnvironmental Sciences, Chinese Academy of Sciences, Beijing, China, and Melbourne School of Land and Environment, The University of Melbourne, Parkville, Victoria, Australia Jonathan W Hempel United States Department of Agriculture, Natural Resources Conservation Service, Lincoln, Nebraska, USA Gerard B.M Heuvelink ISRIC—World Soil Information, Wageningen, Netherlands S.Young Hong National Academy of Agricultural Science, Rural Development Administration, Suwon, South Korea Hang-Wei Hu State Key Laboratory of Urban and Regional Ecology, Research Center for EcoEnvironmental Sciences, Chinese Academy of Sciences, Beijing, China, and Melbourne School of Land and Environment, The University of Melbourne, Parkville, Victoria, Australia Deb P Jaisi Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA Mangi L Jat International Maize and Wheat Improvement Centre (CIMMYT), NASC Complex, Pusa, New Delhi, India ix x Contributors Xiangbin Kong The College of Resources and Environmental Science, China Agricultural University, and Key Laboratory of Farmland Quality, Monitoring and Control, National Ministry of Land Resources, Beijing, China Dinesh Kumar Division of Agronomy, Indian Agricultural Research Institute, Pusa, New Delhi, India Philippe Lagacherie INRA, IRD, Lab Etud Interact Sols Agrosyst Hydrosyst, Montpellier, France Rattan Lal Carbon Management and Sequestration Center, The Ohio State University, Columbus, Ohio, USA Glenn Lelyk Agriculture and Agri-Food Canada, University of Manitoba, Winnipeg, Manitoba, Canada Baoguo Li The College of Resources and Environmental Science, China Agricultural University, and Key Laboratory of Farmland Quality, Monitoring and Control, National Ministry of Land Resources, Beijing, China Kejiang Li Institute of Dryland Farming, Key Field Scientific Observation Station of Hengshui Fluvoaquic Soil Ecology Environment, Ministry of Agriculture, Hengshui, China Hongbin Liu Ministry of Agriculture Key Laboratory of Crop Nutrition and Fertilization/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China Alexander B McBratney Faculty of Agriculture and Environment, The University of Sydney, Sydney, New South Wales, Australia Neil J McKenzie CSIRO Australia, Campus International de Baillarguet, Montpellier, Cedex, France Maria d.L Mendonca-Santos EMBRAPA-Brazilian Agricultural Research Corporation/The National Centre of Soil Research (Embrapa Solos), Rio de Janeiro, Brazil Budiman Minasny Faculty of Agriculture and Environment, The University of Sydney, Sydney, New South Wales, Australia Luca Montanarella European Commission—DG JRC, Ispra, Varese, Italy Inakwu O.A Odeh Faculty of Agriculture and Environment, The University of Sydney, Sydney, New South Wales, Australia Contributors xi Rajendra Prasad Indian National Science Academy, and Division of Agronomy, Indian Agricultural Research Institute, Pusa, New Delhi, India Pedro A Sanchez The Earth Institute at Columbia University, Palisades, New York, USA Yashbir S Shivay Division of Agronomy, Indian Agricultural Research Institute, Pusa, New Delhi, India Bijay Singh Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab, India James A Thompson West Virginia University, Morgantown, West Virginia, USA Zhi-Hong Xu Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia Bangbang Zhang The College of Resources and Environmental Science, China Agricultural University, Beijing, China Gan-Lin Zhang State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China Qingpu Zhang The College of Resources and Environmental Science, China Agricultural University, Beijing, China PREFACE Volume 125 of Advances in Agronomy contains six cutting-edge reviews by internationally recognized scientists Chapter is a state-of-the-art review on the use of novel oxygen isotope ratios of phosphate to assess phosphorus cycling in soil and water environments Chapter is a timely overview of agronomic biofortification of cereal grains with iron and zinc Chapter presents exciting advances on the Global Soil Map, a digital soil map that provides a fine-resolution global grid of soil functional properties Chapter covers the effect of fertilizer intensification and its impacts in China’s Huang Huai Hai plains Chapter discusses nutrient management and use efficiency in South Asian wheat systems Chapter is a state-of-theart review on ammonia-oxidizing archaea and their important role in soil acidification I am most grateful to the authors for their excellent contributions DONALD L SPARKS Newark, Delaware, USA xiii CHAPTER ONE Advances in Using Oxygen Isotope Ratios of Phosphate to Understand Phosphorus Cycling in the Environment Deb P Jaisi*,1, Ruth E Blake† *Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA † Department of Geology and Geophysics, Yale University, New Haven, Connecticut, USA Corresponding author: e-mail address: jaisi@udel.edu Contents Introduction 1.1 Origin of phosphorus 1.2 Overview of P chemistry and P cycling Stable Isotope Systematics: Oxygen Isotope Ratios of Phosphate 2.1 Oxygen isotope ratios of phosphate: Historical development 2.2 Apatite versus dissolved inorganic phosphate 2.3 Dissolved Pi–water oxygen isotopic fractionation and calibration 2.4 pH effect on Pi–water oxygen isotopic fractionation 2.5 Resistance to Pi–water O exchange and inorganic hydrolysis 2.6 Phosphate in the environment: recent developments Organic Phosphorus and Isotope Effects of Organic Phosphate Mineralization: Enzyme- and Substrate-Specific Isotope Effects Measuremnt of Oxygen Isotope Ratios of Phosphate in Sediments, Soils, and Natural Waters 4.1 Processing of dissolved phosphate in water for silver phosphate precipitation 4.2 Organic phosphorus and isotope effects of organic phosphate mineralization 4.3 Extraction of soil/sediment P and processing for silver phosphate precipitation 4.4 Methods of measuring oxygen isotope ratios in phosphate Isotope Effects of Abiotic and Biotic Processes Involving Phosphates 5.1 Fractionation during abiotic processes of sorption, desorption, and mineral transformation 5.2 Bioavailability and cycling of phosphate at the mineral-water interface 5.3 Fractionation during transport and mobilization of phosphate 5.4 Marine sediments with multiple pulses of authigenic phosphate precipitation 5.5 Detrital phosphate from different provenances Advances in Agronomy, Volume 125 ISSN 0065-2113 http://dx.doi.org/10.1016/B978-0-12-800137-0.00001-7 # 2014 Elsevier Inc All rights reserved 2 11 11 14 15 16 17 21 22 22 25 27 30 31 34 35 37 38 Deb P Jaisi and Ruth E Blake Application of Oxygen Isotope Ratios in Phosphate to Understand P Cycling in Soil Environments and Agricultre Concluding Remarks and Perspectives Acknowledgments References 39 42 43 43 Abstract Phosphorus (P) is universally recognized as an essential nutrient for all known forms of life and a key element in mediating between living and nonliving parts of the biosphere Here, we provide a comprehensive review of the development of oxygen isotope methods of phosphate and application to understand the biogeochemical cycling of P With the advent of robust analytical techniques able to accurately determine stable oxygen isotope ratios in phosphate (d18OP) and the increased understanding of isotope effects from controlled process- or reaction-based studies, d18OP values have been increasingly applied to identify sources and cycling of P in many natural environments Because different sources have distinct isotopic compositions and various processes impart specific isotopic fractionation or produce distinct pathways of isotopic evolution, application of d18OP values as a tracer for P in biogeochemical processes is expected to continue to expand as an exciting field of research in the future INTRODUCTION 1.1 Origin of phosphorus Phosphorus (P) in Greek mythology is “FosjόrοB” meaning “lightbearer.” The element P was first produced accidentally by a German physician, Hennig Brand (ca 1630–1692), after distillation of evaporated urine in the hope of changing metals in urine into gold It is presumably the reduction of phosphate by pyrolytic carbon (Goldwhite, 1981) that produced elemental phosphorus Early Christians noted the use of phosphorus as “perpetual lamps” that glowed in the dark The glow of phosphorus originates from chemiluminescence during aerial oxidation of elemental (white) phosphorus Similarly, ammonium sodium hydrogen phosphate tetrahydrate (NaNH4HPO4Á4H2O) was historically used by alchemists as “microcosmic salt.” Thus, the employment of P for useful purposes started long ago in human civilization P is the eleventh most abundant element in the Earth’s crust with a crustal abundance of 0.099% It is widely distributed as orthophosphate ðPO4 3À Þ in soils, rocks, oceans, all living beings, and in many man-made materials (e.g., pharmaceuticals, agrochemicals, food additives) However, the importance Oxygen Isotope Studies of Phosphorus Cycling in Soils of P as a nutrient was not realized until the mid-1800 s Since its discovery as a plant nutrient and its extraction from phosphorite rocks to produce fertilizers, other applications of P in military, medical, technological, and nutritional applications have greatly expanded in recent centuries 1.2 Overview of P chemistry and P cycling 1.2.1 P chemistry P has atomic number 15, atomic mass 30.97, and its electron configuration is 1s2 2s22p6 3s23p3 The promotional energy s ! 3d orbital in P is small enough to allow vacant d-orbitals to participate in bonding and forming hybridized orbitals This ready availability of d-orbitals permits a relatively large number of potential configurations of electrons around the nucleus and therefore accounts for the origin of diverse P compounds Similarly, the higher contribution of the d-orbital leads to an effectively large atom with low electronegativity and greater polarizability (Corbridge, 1985) These properties along with high first ionization energy (10.48 eV) result in overwhelmingly covalent character of P in chemical reactions Its coordination number varies from (P0, elemental P) to (PCl6 À , phosphorus hexachloride), and its oxidation state from (PH3, phosphine gas) to ỵ5 (PO4 , phosphate) (Fig 1.1) These properties are likely responsible for the ubiquity of P-containing compounds in Earth environments (Westheimer, 1987) O H Inorganic P H−P P O H –3 R R −P Organic P R Orthophosphate Elemental P Phosphine Oxidation states O−P−O –1 R R− P=O R Trialkyl phosphine Phosphine oxides +1 O R − P = OH R +3 O +5 O R − P = OH R −P−O −R OH O −R Phosphonic acid Phosphenic acid Phosphate ester OR RO − P OR Phosphite ester Figure 1.1 Oxidation states of P and examples of organic and inorganic compounds in different oxidation states In general, P compounds with low oxidation state are less common on Earth Deb P Jaisi and Ruth E Blake Inorganic orthophosphate (referred to as Pi hereafter), the most prevalent form of P in the lithosphere and biosphere, is a compound in which the P atom is surrounded tetrahedrally by four oxygen atoms (i.e., in ỵ5 oxidation state and coordination number) A variety of condensed phosphates including pyrophosphate and polyphosphate originates from sharing of oxygens in PO4 3À ions The next most common form of P, organophosphorus compounds, is substituted phosphate esters in which P and C are linked through O as a PdOdC bond Also common in biological system are phosphosulfur compounds such as APS (adenosine phosphosulfate) a key intermediate in bacterial respiration of sulfate ðSO4 2À Þ which is highly prominent in marine sediments Phosphonates, in which P(5ỵ) is bonded directly to C, in PdC linkage, were once thought to be relatively rare and insignificant forms of P in earth environments Recent discoveries, however, have shown the widespread occurrence of phosphonates throughout the world’s oceans (Clark et al., 1999) and identified their role as P sources for primary oceanic productivity (Dyhrman et al., 2006), sources of atmospheric methane (Karl et al., 2008), and possible role in prebiotic earth chemistry (Glindemann et al., 1999; Pasek, 2008) These developments have drawn new attention to the reactions, origins, and biogeochemical cycling of phosphonates over the full span of earth’s history Unlike other essential elements in living beings, P was classically viewed as a redox-insensitive element, with phosphate (oxidation state 5ỵ) being the only redox state naturally present in the environment However, existence of other P phases (Fig 1.1) in the environment has been increasingly realized (see above) and the redox chemistry of P has been explored (e.g., Metcalf and Wolfe, 1998; Metcalf et al., 2012; Pasek and Block, 2009; Schink and Friedrich, 2000) The reduction of P (5ỵ) to ỵ, ỵ, or À redox states occurs under extremely reducing conditions Although oxidative degradation of these reduced compounds was known, reductive pathways to produce PO3, PO2, and PH3 in the environment remained elusive Most recently, organisms have been found to readily utilize reduced-P compounds (e.g., phosphite, hypophosphite) as a P source (Metcalf and Wolfe, 1998) and undergo dissimilatory oxidation of phosphite (PO3)3À in marine sediments (Schink and Friedrich, 2000; Schink et al., 2002) Sources of reduced-P in the environment include phosphite in corroding meteorites (Bryant et al., 2009; Pasek and Lauretta, 2005), phosphites and phosphides produced from lightning-reduced phosphate (Pasek and Block, 2009), phosphite in geothermal waters (Pech et al., 2009), and phosphine gas in soils and sediments (Glindemann et al., 2005) Similarly, phosphonate comprises about 5% of 296 Hang-Wei Hu et al De Boer, W., Kowalchuk, G.A., 2001 Nitrification in acid soils: micro-organisms and mechanisms Soil Biol Biochem 33, 853–866 De Boer, W., Laanbroek, H.J., 1989 Ureolytic nitrification at low pH by Nitrosospira spec Arch Microbiol 152, 178–181 De Boer, W., Duyts, H., Laanbroek, H.J., 1989 Urea stimulated autotrophic nitrification in suspensions of fertilized, acid heath soil Soil Biol Biochem 21, 349–354 De Boer, W., Gunnewiek, P.J.A.K., Veenhuis, M., Bock, E., Laanbroek, H.J., 1991 Nitrification at low pH by aggregated chemolithotrophic bacteria Appl Environ Microbiol 57, 3600–3604 de la Torre, J.R., Walker, C.B., Ingalls, A.E., Koănneke, M., Stahl, D.A., 2008 Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol Environ Microbiol 10, 810–818 Delgado-Baquerizo, M., Gallardo, A., Wallenstein, W.D., Maestre, F.T., 2013 Vascular plants mediate the effects of aridity and soil properties on ammonia-oxidizing bacteria and archaea FEMS Microbiol Ecol 85, 273–282 Di, H.J., Cameron, K.C., Shen, J.P., Winefield, C.S., O’Callaghan, M., Bowatte, S., He, J.Z., 2009 Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils Nat Geosci 2, 621–624 Erguder, T.H., Boon, N., Wittebolle, L., Marzorati, M., Verstraete, W., 2009 Environmental factors shaping the ecological niches of ammonia-oxidizing archaea FEMS Microbiol Rev 33, 855–869 Fan, F.L., Yang, Q.B., Li, Z.J., Wei, D., Cui, X.A., Liang, Y.C., 2011 Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are the bacterial ammonia oxidizer community Microb Ecol 62, 982–990 Fierer, N., Carney, K.M., Horner-Decine, M.C., Megonigal, J.P., 2009 The biogeography of ammonia-oxidizing bacterial communities in soil Microb Ecol 58, 435–445 Frank, D.A., Groffman, P.M., Evans, R.D., Tracy, B.F., 2000 Ungulate stimulation of nitrogen cycling and retention in Yellowstone Park grasslands Oecologia 123, 116–121 French, E., Kozlowski, J.A., Mukherjee, M., Bullerjahn, G., Bollmann, A., 2012 Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater Appl Environ Microbiol 78, 5773–5780 Frijlink, M.J., Abee, T., Laanbroek, H.J., Boer, W., Konings, W.N., 1992 Secondary transport of amino acids in Nitrosomonas europaea Arch Microbiol 157, 389–393 Goedert, W., Lobato, E., Louren, O.S., 1997 Nutrient use efficiency in Brazilian acid soils: nutrient management and plant efficiency In: Moniz, A.C., Furlani, A.M.C., Schaffert, R.E., Fageria, N.K., Rosolem, C.A., Cantarella, H (Eds.), Plant–Soil Interactions at Low pH Brazilian Soil Science Society, Campinas, SP, Brazil, pp 97–104 Groeneweg, J., Sellner, B., Tappe, W., 1994 Ammonia oxidation in nitrosomonas at NH3 concentration near Km: effects of pH and temperature Water Res 28, 2561–2566 Gubry-Rangin, C., Nicol, G.W., Prosser, J.I., 2010 Archaea rather than bacteria control nitrification in two agricultural acidic soils FEMS Microbiol Ecol 74, 566–574 Gubry-Rangin, C., Hai, B., Quince, C., Engel, M., Thomson, B.C., James, P., et al., 2011 Niche specialization of terrestrial archaeal ammonia oxidizers Proc Natl Acad Sci U.S.A 108, 21206–21211 Hai, B., Diallo, N.H., Sall, S., Haesler, F., Schauss, K., Bonzi, M., Assigbetse, K., Chotte, J.L., Munch, J.C., Schloter, M., 2009 Quantification of key genes steering the microbial nitrogen cycle in the rhizosphere of sorghum cultivars in tropical agroecosystems Appl Environ Microbiol 75, 4993–5000 Hall, A.D., Miller, N.H.J., Gimingham, C.T., 1908 Nitrification in acid soils Proc R Soc B 80, 196–212 Microbial Mechanisms of Nitrification in Acid Soils 297 Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M., et al., 2006 Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota PLoS Biol 4, 520–536 Hankinson, T.R., Schmidt, E.L., 1984 Examination of an acid forest soil for ammoniaoxidizing and nitrite-oxidizing autotrophic bacteria Can J Microbiol 30, 1125–1132 Hart, S.C., Binkley, D., Perry, D.A., 1997 Influence of red alder on soil nitrogen transformations in two conifer forests of contrasting productivity Soil Biol Biochem 29, 1111–1123 Hatzenpichler, R., 2012 Diversity, physiology, and niche differentiation of ammoniaoxidizing archaea Appl Environ Microbiol 78, 7501–7510 Hatzenpichler, R., Lebedeva, E.V., Spieck, E., Stoecker, K., Richter, A., Daims, H., Wagner, M., 2008 A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring Proc Natl Acad Sci U.S.A 105, 2134–2139 Haynes, R.J., 1996 Nitrification In: Haynes, R.J (Ed.), Mineral Nitrogen in the Plant–Soil System Academic Press, New York, USA, pp 127–165 He, J.Z., Shen, J.P., Zhang, L.M., Zhu, Y.G., Zheng, Y.M., Xu, M.G., et al., 2007 Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices Environ Microbiol 9, 2364–2374 He, J.Z., Hu, H.W., Zhang, L.M., 2012 Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils Soil Biol Biochem 55, 146–154 Hommes, N.G., Sayavedra-Soto, L.A., Arp, D.J., 2003 Chemolithoorganotrophic growth of Nitrosomonas europaea on fructose J Bacteriol 185, 6809–6814 Houzeau, A., 1872 Faits pour servir a l’histoire de la nitrification, composition des terreaux de tantah (basse-e´gypte) Ann Chim Phys 25, 161–167 Hu, H.W., Zhang, L.M., Dai, Y., Di, H.J., He, J.Z., 2013a pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing J Soils Sediments 13, 1439–1449 Hu, H.W., Zhang, L.M., Yuan, C.L., He, J.Z., 2013b Contrasting Euryarchaeota communities between upland and paddy soils exhibited similar pH-impacted biogeographic patterns Soil Biol Biochem 64, 18–27 Huang, R., Wu, Y., Zhang, J., Zhong, W., Jia, Z., Cai, Z., 2012 Nitrification activity and putative ammonia-oxidizing archaea in acidic red soils J Soils Sediments 12, 420–428 Ingalls, A.E., Shah, S.R., Hansman, R.L., Aluwihare, L.I., Santos, G.M., Druffel, E.R.M., Pearson, A., 2006 Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon Proc Natl Acad Sci U.S.A 103, 6442–6447 Islam, A., Chen, D., White, R.E., 2007 Heterotrophic and autotrophic nitrification in two acid pasture soils Soil Biol Biochem 39, 972–975 Isobe, K., Koba, K., Suwa, Y., Ikutani, J., Fang, Y., Yoh, M., Mo, J., Otsuka, S., Senoo, K., 2012 High abundance of ammonia-oxidizing archaea in acidified subtropical forest soils in southern China after long-term N deposition FEMS Microbiol Ecol 80, 193–203 Jia, Z.J., Conrad, R., 2009 Bacteria rather than archaea dominate microbial ammonia oxidation in an agricultural soil Environ Microbiol 11, 1658–1671 Jiang, Q.Q., Bakken, L.R., 1999 Comparison of Nitrosospira strains isolated from terrestrial environments FEMS Microbiol Ecol 30, 171–186 Jordan, F.L., Cantera, J.J.L., Fenn, M.E., Stein, L.Y., 2005 Autotrophic ammonia-oxidizing bacteria contribute minimally to nitrification in a nitrogen-impacted forested ecosystem Appl Environ Microbiol 71, 197–206 Jung, M.Y., Park, S.J., Min, D., Kim, J.S., Rijpstra, W.I.C., Damste´, J.S.S., Kim, G.J., Madsen, E.L., Rhee, S.K., 2011 Enrichment and characterization of an autotrophic ammonia-oxidizing archaeaon of mesophilic crenarchaeal group I.1a from an agricultural soil Appl Environ Microbiol 77, 8635–8647 298 Hang-Wei Hu et al Kemnitz, D., Kolb, S., Conrad, R., 2007 High abundance of crenarchaeota in a temperate acidic forest soil FEMS Microbiol Ecol 60, 442–448 Killham, K., 1990 Nitrification in coniferous forest soils Plant Soil 128, 31–44 Kim, B.K., Jung, M.Y., Yu, D.S., Park, S.J., Oh, T.K., Rhee, S.K., Kim, J.F., 2011 Genome sequence of an ammonia-oxidizing soil archaeon, ‘Candidatus Nitrosoarchaeum koreensis’ MY1 J Bacteriol 193, 5539–5540 Klemedtsson, L., Jiang, Q.Q., Kasimir-Klemedtsson, A., Bakken, L.R., 1999 Autotrophic ammonium-oxidizing bacteria in Swedish mor humus Soil Biol Biochem 31, 839847 Koănneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., Stahl, D.A., 2005 Isolation of an autotrophic ammonia-oxidizing marine archaeon Nature 437, 543–546 Kool, D.M., Dolfing, J., Wrage, N., Van Groenigen, J.W., 2011 Nitrifier denitrification as a distinct and significant source of nitrous oxide from soil Soil Biol Biochem 43, 174–178 Koops, H.P., Pommerening-Roser, A., 2001 Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species FEMS Microbiol Ecol 37, 1–9 Koper, T.E., Ei-Sheikh, A.F., Norton, J.M., Klotz, M.G., 2004 Urease-encoding genes in ammonia-oxidizing bacteria Appl Environ Microbiol 70, 2342–2348 Kowalchuk, G.A., Stephen, J.E., 2001 Ammonia-oxidizing bacteria: a model for molecular microbial ecology Annu Rev Microbiol 55, 485–529 Kreitinger, J.P., Klein, T.M., Novick, N.J., Alexander, M., 1985 Nitrification and characteristics of nitrifying microorganisms in an acid forest soil Soil Sci Soc Am J 49, 1407–1410 Laverman, A.M., Speksnijder, A.G.C.L., Braster, M., Kowalchuk, G.A., Verhoef, H.A., van Verseveld, H.W., 2001 Spatiotemporal stability of an ammonia-oxidizing community in a nitrogen-saturated forest soil Microb Ecol 42, 35–45 Lehtovirta-Morley, L.E., Prosser, J.I., Nicol, G.W., 2009 Soil pH regulates the abundance and diversity of group 1.1c crenarchaeota FEMS Microbiol Ecol 70, 367–376 Lehtovirta-Morley, L.E., Stoecker, K., Vilcinskas, A., Prosser, J.I., Nicol, G.W., 2011 Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil Proc Natl Acad Sci U.S.A 108, 15892–15897 Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., Prosser, J.I., Schuster, S.C., Scleper, C., 2006 Archaea predominate among ammonia-oxidizing prokaryotes in soils Nature 442, 806809 Levicnik-Hoăfferle, S., Nicol, G.W., Pal, L., Hacin, J., Prosser, J.I., Mandic-Mulec, I., 2010 Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile FEMS Microbiol Ecol 74, 302315 Levicnik-Hoăfferle, S., Nicol, G.W., Ausec, L., Mulec, I., Prosser, J.I., 2012 Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not inorganic nitrogen FEMS Microbiol Ecol 80, 114–123 Liu, Y.R., Zheng, Y.M., Shen, J.P., Zhang, L.M., He, J.Z., 2010 Effects of mercury on the activity and community composition of soil ammonia oxidizers Environ Sci Pollut Res Int 17, 1237–1244 Lu, L., Jia, Z.J., 2013 Urease gene-containing archaea dominate autotrophic ammonia oxidation in two acid soils Environ Microbiol 15, 1795–1809 Lu, L., Han, W.Y., Zhang, J.B., Wu, Y.C., Wang, B.Z., Lin, X.G., Zhu, J.G., Cai, Z.C., Jia, Z.J., 2012 Nitrification of archaeal ammonia oxidation in acid soils is supported by hydrolysis of urea ISME J 6, 1978–1984 Mackelprang, R., Waldrop, M.P., DeAngelis, K.M., David, M.M., Chavarria, K.L., Blazewicz, S.J., Rubin, E.M., Jansson, J.K., 2011 Metagenomic analysis of a permafrost microbial community reveal a rapid response to thaw Nature 480, 368–371 Microbial Mechanisms of Nitrification in Acid Soils 299 Martens-Habbena, W., Stahl, D.A., 2011 Nitrogen metabolism and kinetics of ammoniaoxidizing archaea Methods Enzymol 496, 465–487 Martens-Habbena, W., Berube, P.M., Urakawa, H., de la Torre, J.R., Stahl, D.A., 2009 Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria Nature 461, 976–979 Mertens, J., Broos, K., Wakelin, S.A., Kowalchuk, G.A., Springael, D., Smolders, E., 2009 Bacteria, not archaea, restore nitrification in a zinc-contaminated soil ISME J 3, 916–923 Mintie, A.T., Heichen, R.S., Cromack, K., Myrold, D.D., Bottomley, P.J., 2003 Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon cascade mountains Appl Environ Microbiol 69, 3129–3136 Mosier, A.C., Allen, E.E., Kim, M., Ferriera, S., Francis, C.A., 2012 Genome sequence of ‘Candidatus Nitrosopumilus salaria’ BD1, an ammonia-oxidizing archaeon form the San Francisco Bay estuary J Bacteriol 194, 2121–2122 Mußmann, M., Brito, I., Pitcher, A., Damste, J.S.S., Hatzenpichler, R., Richter, A., Nielsen, J.L., Nielsen, P.H., Muller, A., Daims, H., Wagner, M., Head, I.M., 2011 Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers Proc Natl Acad Sci U.S.A 108, 16771–16776 Nicol, G.W., Tscherko, D., Embley, T.M., Prosser, J.I., 2005 Primary succession of soil Crenarchaeota across a receding glacier foreland Environ Microbiol 7, 337–347 Nicol, G.W., Leininger, S., Schleper, C., Prosser, J.I., 2008 The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria Environ Microbiol 10, 2966–2978 Noyes, H.A., Conner, S.D., 1919 Nitrates, nitrification, and bacterial contents of five typical acid soils as affected by lime, fertilizer, crops, and moisture J Agric Res 16, 27–42 Nugroho, R.A., Roling, W.F.M., Laverman, A.M., Zoomer, H.R., Verhoef, H.A., 2005 Presence of Nitrosospira cluster bacteria corresponds to N transformation rates in nine acid Scots pine forest soils FEMS Microbiol Ecol 53, 473–481 Offre, P., Prosser, J.I., Nicol, G.W., 2009 Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene FEMS Microbiol Ecol 70, 99–108 Ouverney, C.C., Fuhrman, J.A., 2000 Marine planktonic archaea take up amino acids Appl Environ Microbiol 66, 4829–4833 Papen, H., Von Berg, R., 1998 A most probable number (MPN) for estimation of cell numbers of heterotrophic nitrifying bacteria in soil Plant Soil 199, 123–130 Park, B.J., Park, S.J., Yoon, D.N., Schouten, S., Damste´, J.S.S., Rhee, S.K., 2010 Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria Appl Environ Microbiol 76, 7575–7587 Pedersen, H., Dunkin, K.A., Firestone, M.K., 1999 The relative importance of autotrophic and heterotrophic nitrification in a conifer forest soil as measured by 15N tracer and pool dilution techniques Biogeochemistry 44, 135–150 Pester, M., Schleper, C., Wagner, M., 2011 The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology Curr Opin Microbiol 14, 300–306 Pester, M., Rattei, T., Flechl, S., Groăngroăft, A., Richter, A., Overmann, J., et al., 2012 amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions Environ Microbiol 14, 525–539 Prosser, J.I., 1989 Autotrophic nitrification in bacteria Adv Microb Physiol 30, 125–181 Prosser, J.I., Nicol, G.M., 2008 Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment Environ Mcirobiol 10, 2931–2941 Prosser, J.I., Nicol, G.M., 2012 Archaeal and bacterial ammonia-oxidizers in soil: the quest for niche specialization and differentiation Trends Microbiol 20, 523–531 300 Hang-Wei Hu et al Purkhold, U., Pommerening-Roser, A., Juretschko, S., et al., 2000 Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys Appl Environ Microbiol 66, 5368–5382 Rosso, L., Lobry, J.R., Bajard, S., Flandrois, J.P., 1995 Convenient model to describe the combined effects of temperature and pH on microbial growth Appl Environ Microbiol 61, 610–616 Rousk, J., Ba˚a˚th, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R., Fierer, N., 2010 Soil bacterial and fungal communities across a pH gradient in an arable soil ISME J 4, 1340–1351 Santoro, A.E., Buchwald, C., McIlvin, M.R., Casciotti, K.L., 2011 Isotopic signature of N2O produced by marine ammonia-oxidizing archaea Science 333, 1282–1285 Sato, C., Schnoor, J.L., Mcdonald, D.B., Huey, J., 1985 Test medium for the growth of Nitrosomonas europaea Appl Environ Microbiol 49, 1101–1107 Schauss, K., Focks, A., Leininger, S., Kotzerke, A., Heuer, H., Thiele-Bruhn, S., Sharama, S., Wilke, B.M., Matthies, M., Smalla, K., Munch, J.C., Amelung, W., Kaupenjohann, M., Schloter, M., Schleper, C., 2009 Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils Environ Microbiol 11, 446–456 Schleper, C., 2010 Ammonia oxidation: different niches for bacteria and archaea? ISME J 4, 1092–1094 Schleper, C., Nicol, G.W., 2010 Ammonia-oxidizing archaea—physiology, ecology and evolution Adv Microb Physiol 57, 1–41 Schleper, C., Jurgens, G., Jonuscheit, M., 2005 Genomic studies of uncultivated archaea Nat Rev Microbiol 3, 479–488 Schmidt, I., 2009 Chemoorganoheterotrophic growth of Nitrosomonas europaea and Nitrosomonas eutropha Curr Microbiol 59, 130–138 Schmidt, C.S., Hultman, K.A., Robinson, D., Killham, K., Prosser, J.I., 2007 PCR profiling of ammonia-oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition FEMS Microbiol Ecol 61, 305–316 Schramm, A., de Boer, D., Wagner, M., Amann, R., 1998 Identification and activities in situ of nitrosospira and nitrospira spp as dominant populations in a nitrifying fluidized bed reactor Appl Environ Microbiol 64, 3480–3485 Shen, J.P., Zhang, L.M., Zhu, Y.G., Zhang, J.B., He, J.Z., 2008 Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam Environ Microbiol 10, 1601–1611 Shen, X.Y., Zhang, L.M., Shen, J.P., Li, L.H., Yuan, C.L., He, J.Z., 2011 Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland J Soils Sediments 11, 1234–1252 Shen, J.P., Zhang, L.M., Di, H.J., He, J.Z., 2012 A review of ammonia-oxidizing bacteria and archaea in Chinese soils Front Microbiol 3, 296 Sinninghe Damste, J.S., Rijpstra, W.I., Hopmans, E.C., et al., 2012 Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids of group I.1a and I.1b Thaumarchaeota in soil Appl Environ Microbiol 78, 6866–6874 Smits, N.A.C., Hefting, M.M., Kamst-van Agterveld, M.P., Laanbroek, H.J., Paalman, A.J., Robbink, R., 2010 Nitrification along a grassland gradient: inhibition found in matgrass swards Soil Biol Biochem 42, 635–641 Spang, A., Harzenpichler, R., Brochier-Armanet, C., Rattei, T., Tischler, P., Spieck, E., Streit, W., Stahl, D.A., Wagner, M., Schleper, C., 2010 Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota Trends Microbiol 18, 331–340 Microbial Mechanisms of Nitrification in Acid Soils 301 Spang, A., Poehlein, A., Offre, P., Zumbragel, S., Haider, S., Rychlik, N., Nowka, B., Schmeisser, C., Lebedeva, E.V., Rattei, T., Bohm, C., Schmid, M., Galushko, A., Hatzenpichler, R., Weinmaier, T., Daniel, R., Schleper, C., Spieck, E., Streit, W., Wagner, M., 2012 The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations Environ Microbiol 14, 3122–3145 Stahl, D.A., de la Torre, J.R., 2012 Physiology and diversity of ammonia-oxidizing archaea Annu Rev Microbiol 66, 83–101 Stark, J.M., Hart, S.C., 1997 High rates of nitrification and nitrate turnover in undisturbed coniferous forests Nature 385, 61–74 Stehr, G., Bottcher, B., Dittberner, P., Rath, G., Koops, H.P., 1995 The ammonia-oxidizing nitrifying population of the river Elbe estuary FEMS Microbiol Ecol 17, 177–186 Ste-Marie, C., Pare, D., 1999 Soil pH and N availability effects on net nitrification in the forest floors of a range of boreal forest stands Soil Biol Biochem 31, 1579–1589 Stopnisˇek, N., Gubry-Rangin, C., Levicnik-Hoăfferle, S., Nicol, G.W., Mandic-Mulec, I., Prosser, J.I., 2010 Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment Appl Environ Microbiol 76, 7626–7634 Suwa, Y., Imamura, Y., Suzuki, T., Tashiro, T., Urushigawa, Y., 1994 Ammonia-oxidizing bacteria with different sensitivities to (NH4)2SO4 in activated sludges Water Res 28, 1523–1532 Suzuki, I., Dular, U., Kwok, S.C., 1974 Ammonia or ammonium ion as substrate for oxidation by Nitrosomonas europaea cells and extracts J Bacteriol 120, 556–558 Tourna, M., Stieglmeier, M., Spang, A., Koănneke, M., Schintlmeister, A., Urich, T., et al., 2011 Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil Proc Natl Acad Sci U.S.A 108, 8420–8425 Treusch, A.H., Leininger, S., Kletzin, A., Schuster, S.C., Klenk, H.P., Schleper, C., 2005 Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling Environ Microbiol 7, 1985–1995 Tully, B.J., Nelson, W.C., Heidelberg, J.F., 2012 Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine Environ Microbiol 14, 254–267 Vajrala, N., Martens-Habbena, W., Sayavedra-Soto, L.A., Schauer, A., Bottomley, P.J., Stahl, D.A., Arp, D.J., 2013 Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea Proc Natl Acad Sci U.S.A 110, 1006–1011 Valentine, D.L., 2007 Adaptations to energy stress dictate the ecology and evolution of the archaea Nat Rev Microbiol 5, 316–323 Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al., 2004 Environmental genome shotgun sequencing of the Sargasso Sea Science 304, 66–74 Verhamme, D.T., Prosser, J.I., Nicol, G.W., 2011 Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms ISME J 5, 1067–1071 Vitousek, P.M., Aber, J.D., Howarth, R.W., Likens, G.E., Matson, P.A., Schindler, D.W., Schlesinger, W.H., Tilman, D.G., 1997 Human alteration of the global nitrogen cycle: sources and consequences Ecol Appl 7, 737–750 Vonuexkull, H.R., Mutert, E., 1995 Global extent, development and economic-impact of acid soils Plant Soil 171, 1–15 Walker, C.B., de la Torre, J.R., Klotz, M.G., Urakawa, H., Pinel, N., Arp, D.J., et al., 2010 Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea Proc Natl Acad Sci U.S.A 107, 8818–8823 302 Hang-Wei Hu et al Xia, W.W., Zhang, C.X., Zeng, X.W., Feng, Y.Z., Weng, J.H., Lin, X.G., Zhu, J.G., Xiong, Z.Q., Xu, J., Cai, Z.C., Jia, Z.J., 2011 Autotrophic growth of nitrifying community in an agricultural soil ISME J 5, 1226–1236 Xu, Y.B., Cai, Z.C., Xu, Z.H., 2012 Production and consumption of N2O during denitrification in subtropical soils of China J Soils Sediments 12, 1339–1349 Xu, Y.B., Xu, Z.H., Cai, Z.C., Reverchon, F., 2013 Review of denitrification in tropical and subtropical soils of terrestrial ecosystems J Soils Sediments 13, 699–710 Yakimov, M.M., Cono, V.L., Smedile, F., DeLuca, T.H., Juarez, S., Ciordia, S., et al., 2011 Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep water (Central Mediterranean Sea) ISME J 5, 945–961 Yao, H.Y., Gao, Y.M., Nicol, G.W., Campbell, C.D., Prosser, J.I., Zhang, L.M., Han, W.Y., Singh, B.K., 2011 Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils Appl Environ Microbiol 77, 4618–4625 Yao, H.Y., Campbell, C.D., Chapman, S.J., Freitag, T.E., Nicol, G.W., Singh, B.K., 2013 Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey Environ Microbiol 15, 2545–2556 Ying, J.Y., Zhang, L.M., He, J.Z., 2010 Putative ammonia-oxidizing bacteria and archaea in an acidic red soil with different land utilization patterns Environ Microbiol Rep 2, 304–312 Zhalnina, K., de Quadros, P.D., Camargo, F.A.O., Triplett, E.W., 2012 Drivers of archaeal ammonia-oxidizing communities in soil Front Microbiol 3, 210 Zhang, L.M., Offre, P.R., He, J.Z., Verhamme, D.T., Nicol, G.W., Prosser, J.I., 2010 Autotrophic ammonia oxidation by soil thaumarchaea Proc Natl Acad Sci U.S.A 107, 17240–17245 Zhang, L.M., Hu, H.W., Shen, J.P., He, J.Z., 2012 Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils ISME J 6, 1032–1045 Zhu, X., Burger, M., Doane, T.A., Horwath, W.R., 2013 Ammonia oxidation pathways and nitrifier denitrification are significant source of N2O and NO under low oxygen availability Proc Natl Acad Sci U.S.A 110, 6328–6333 INDEX Note: Page numbers followed by “f ” indicate figures and “t ” indicate tables A Acetylene inhibition technique, 193 Acid soils See also AOA in acid soil nitrification AOA in, 265–268, 284–286 definition, 263–264 nitrification, 264–265, 272–274 Adenosine phosphosulfate (APS), Agriculture climate-resilient, 163 conservation, 200–203, 202t intensification, 136–137 P cycling in, 39–41 South Asian, 174, 241–242 Agronomic production chemical fertilizer, 148–159 fertilizer, crop yields, and production, 145–148 fertilizer intensification, 148–150, 159–162 SOM concentration, 154, 155–159 temporal changes in crop yields, 151–154 Alkaline phosphatase (APase), 18–19 Ammonia and AOA, 277–284, 282t exponential changes, 278f from organic matter mineralization, 285 oxidation in acid soils, 284–286 Ammonia monooxygenase (AMO) gene, 262–263 Ammonia-oxidizing archaea (AOA), 262–263 in acid soil nitrification, 265–268 active ammonia oxidation, 285 ammonia and, 277–284, 282t ammonia oxidation activity, 290 ammonia-oxidizing ecotypes, 270–271 amoA gene, 266–267, 268–270, 269f, 273f, 275–277, 276f denaturing gradient gel electrophoresis analysis, 275–277, 277f heterotrophic growth, 293–294 heterotrophic/mixotrophic lifestyles for, 288–290 pH-dependent distribution, 272 soil pH on, 268–275 and urea substrates, 286–288 ureolytic pathway, 287f Ammonia-oxidizing bacteria (AOB), 262–263 acid soil nitrification, 265–266 ammonia-oxidizing ecotypes, 270–271 amoA gene, 266–267, 268–270, 269f, 273f, 275–277, 276f AOA and, 282t denaturing gradient gel electrophoresis analysis, 275–277, 277f soil pH on, 268–275 AMO gene See Ammonia monooxygenase (AMO) gene Anemia, Fe deficiency, 56–57, 61 AOA in acid soil nitrification, 265–268 ammonia oxidation, 284–286 biochemical and genetic features, 290–292 mechanisms, 277–292 microbial mechanisms, 292–294 predominant role, 266–268 stable isotope probing methods and, 275–277 AOB See Ammonia-oxidizing bacteria (AOB) APase See Alkaline phosphatase (APase) APS See Adenosine phosphosulfate (APS) Arbuscular mycorrhizal fungi (AMF), 72 B Balanced fertilizer use, 217–225 Basmati rice, Zn application, 63t 303 304 Biofortification cereals, 58–59 in oats, 69 rice (see Rice) wheat, 67–69 Biogeochemical cycling inorganic orthophosphate, 34f of nutrients and trace metals, Bismuth phosphate (BiPO4), 22, 28 Brown rice, 65–66, 65t C Carbonic anhydrase (CA), 78 Cenarchaeum C maritimus, 286–287 C symbiosum, 286–287 Cereals, 56–58 biofortification, 58–59 corn, 69 to dietary energy, 57f fertilizer affecting Fe/Zn concentration in, 69–73 oats, 69 rice (see Rice) wheat (see Wheat) Chemical fertilizers application of, 136–137, 144t, 145–148, 147f corn, 143–144 wheat, 143–144 China’s HHH plains analysis and synthesis, 145 characteristics, 138–145 fertilizer intensification (see Huang Huai Hai (HHH) region, fertilizer intensification) geographical area, 138–140 research-based recommended practices, 141–144 soil types and distribution, 140–141 Climate change, 97 adverse effects, 163 soil quality and, 163 Climate-resilient agriculture, 163 Conservation agriculture, 200–203, 202t Corn, 69 Cotton–wheat cropping system, 175, 180–182 Index Cropping systems, 205 cotton–wheat, 175 maize–wheat, 175–176 millet–wheat, 176 rice–wheat, 182t, 188, 189–190, 195 soybean–wheat, 176 sugarcane–wheat, 175–176 wheat-based, 209, 210t, 241 Crop residues, 206–208 Crop yields in HHH region, 145–148, 146f soil types and, 148–150, 148f, 150f, 151f SOM concentration and, 156–159, 158f, 164 temporal changes, 151–154, 152f, 153t Cubist data mining tool, 121 D Desorption, abiotic processes, 31–33 Detrital phosphate, from provenances, 38–39 Diarrhea, 61 Digital soil mapping, 101–102, 114f Disability-adjusted life years, 56–57 Dwarfism, 61 E Electrical conductivity of soil, 109–110 Electrospray ionization mass spectrometry (ESI-MS), 17–18 Enzyme-specific isotope effects, 17–21 F Farmyard manure (FYM), 182–183, 197, 203–204 Ferrihydrite dissolution process, 32–33 mineral transformation of, 31–33 with sorbed phosphate, 31 Fertilizer affecting Fe/Zn concentration, 69–73 balanced application of N, P, and K, 222–225, 224t, 225t chemical (see Chemical fertilizers) nitrogen in wheat, 217, 218t, 226–229 305 Index phosphorus in wheat, 217–220, 227, 228, 229 potassium in wheat, 220–222, 221t, 227, 228, 229 recommendations for wheat, 176–177, 177t, 179–183 rice–wheat cropping system, 182t Fertilizer intensification chemical, 136–137 crop yield and stability, 148–150 dilemma in China, 164–166 by farm household, 164 impacts in HHH plains (see Huang Huai Hai (HHH) region, fertilizer intensification) soil quality, 159–162 SOM concentration, 154 Fertilizer management crop yield, 151–154 SOM concentration, 155–157, 157t in supplemental irrigation, 161 treatments, 143, 144t Fractionation abiotic, 32f during abiotic processes, 31–33 isotopic, 11–15 Pi–water, 10f during transport and mobilization of phosphate, 35–37 Fuzzy k-means clustering, 117 G Global Earth Observing System of Systems (GEOSS), 97–98, 120 GlobalSoilMap applications, 120–121 benefit, 128 examples, 121–126 geographic reference, 107–108 governance, 127–128 information architecture, 120–121 information system, 127–129 minimum data set, 109–113, 111t origins of, 101–102 Prediction Interval (PI), 117 quadratic-smoothing splines, 103–104, 105f research to operational implementation, 128–129 soil property estimation, 110–113 Technical Specifications (see Technical Specifications of GlobalSoilMap) time estimation, 113 uncertainty, 117–119 web services, 120–121 Glycine max, 176 GM rice, 58–59 Golden rice, 58–59 Green manure, 197, 205–206 Green Revolution, 173–174, 240 H HAO See Hydroxylamine oxidoreductase (HAO) Happy Seeder, 201–203 Harmonized World Soil Database (HWSD), 98–99 Homosoil, 115–116 Huang Huai Hai (HHH) region, fertilizer intensification, 136–137 characteristics of, 138–145 chemical fertilizers (see Chemical fertilizers) climate-resilient agriculture, 163 crop yields (see Crop yields) dilemma of, 164–166 farm household, 163, 164 fertilizer, 145–148 long-term experiment sites, 139f production, 145–148 research-based recommended practices, 141–144 roots and stubbles, 143–144, 145f soils, 140–141, 159–162 SOM concentration, 154, 154f, 155t synthesis of past achievements, 162–166 typical landscape, 140f Human nutrition, micronutrients in, 60 HWSD See Harmonized World Soil Database (HWSD) Hydrolysis, inorganic, 15–16 Hydroxylamine oxidoreductase (HAO), 290–292 Hypercube evaluation sampling method, 116 306 I Inorganic hydrolysis, Pi–water O exchange and, 15–16 Inorganic orthophosphate (Pi), 4, biogeochemical cycling, 34f cycling of, 13 soil development, Integrated nutrient management (INM), 154 International Plant Nutrition Institute (IPNI), 230–232 Ion exchange, 31, 32–33, 34–35 Iron concentration, fertilizer affecting, 69–73 functions/deficiency in human, 56–57, 60–61 nonheme proteins, 61 in soil, 73 Iron oxide, 31 Isotope exchange, 34–35 Pi–water oxygen, 12–13, 15–16, 16f Isotopic fractionation, Pi-water oxygen, 11–15 L Latin hypercube sampling method, 117 Long-term fertilization management, 155–157 M Maize–wheat cropping system, 175–176, 206 Marine sediments, 4, authigenic phosphate precipitation, 37–38 Micronutrients, in human nutrition, 60 Millet–wheat cropping system, 176 Mineralization of organic phosphate, 17–21, 22–25 Mineral transformation abiotic processes, 31–33 of ferrihydrite with sorbed phosphate, 31–33 Mycorrhiza, 72–73 N Neem-coated urea (NCU), 237–239 Nitrification, 262–263 Index acid soil (see Acid soil nitrification) inhibitors, 237–239 transformation rates, 264–265 and urease inhibitors, 237–239, 238t Nitrogen cycling, 262–264, 284 fertilizer in wheat, 217, 218t, 226–229 and irrigation interaction in wheat, 193–195 mineralization rates, 284 transformations/losses, in wheat, 191–193, 192t Nitrosoarchaeum limnia, 286–287 Nitrosopumilus N devanaterra, 281–284 N maritimus, 281–284, 288 Nitrososphaera N gargensis, 286–287 N viennensis, 286–287, 288 Nitrosotalea devanaterra, 267–268 Nitroxyl oxidoreductase (NxOR), 290–292 Nutrient interaction with, 71–72 management (see Nutrient management) micronutrients in human, 60 plant, 60 wheat and, 176–178, 187t, 189t Nutrient Expert—Wheat (NE-W), 235–237 Nutrient management, in wheat, 216–217 alkali soils, 196–197 conservation agriculture, 200–203 efficiency, 183–190, 184t, 187t, 189t long-term experiments, 209–215, 210t, 215t recommendations in, 176–178, 177t, 178t saline soils, 197–200 sustainability of, 209–215 Nutrient use efficiency, in wheat, 174 balanced application of N, P, and K, 222–225 method of application, 227–228 nitrogen, 217, 218t, 219t, 226–229 phosphorus, 217–220, 227, 228, 229 potassium, 220–222, 221t, 222t, 227, 229 source of, 228–229 strategies, 216–217 time of application, 226–227 trends in, 183–190 307 Index O Oats, 69 Organic carbon content and standard deviation, 125f, 126f standard deviation, 125f Organic phosphate mineralization ammonia released from, 284–286 isotope effects, 17–21, 22–25 Organic phosphorus (Po), 17–21, 22–25 mineralizing without hydrolysis, 24–25 removal of, 23–24 Organophosphorus compounds, Oxygen isotope ratio of phosphate, 7–8, 15–16 development, 8–10 evolution of methods, 27–29 oxygen yield issue, 29–30 in sediments, soils, and natural waters, 21–30 in soil environments and agriculture, 39–41 P Phosphate abiotic and biotic processes, 30–39 authigenic precipitation, 37–38 bioavailability and cycling, 34–35 detrital, 38–39 dissolving for silver phosphate precipitation, 22 in environment, 16–17 ferrihydrite with sorbed, 31 fractionation during transport and mobilization, 35–37 inorganic, apatite vs dissolved, 11 oxygen isotopes ratios of (see Oxygen isotopes ratios of phosphate) Phosphate oxygen isotopes, 15–16 Phosphine gas, 4–5 Phosphite, 4–5 Phosphonate, Phosphorus chemistry, 3–5 cosmogenic radionuclides, cycling, 5–6, 39–41 environmental problems, 6–7 fertilizer in wheat, 217–220, 227, 228, 229 nutrient–sediment interactions, 6–7 origin of, 2–3 oxidation states, 3f pools in soil, 7f redox-insensitive element, 4–5 stable isotope systematics, 7–17 Phytosiderophores (PS), 76–77 Pi–water oxygen isotopic fractionation and calibration, dissolving, 11–14 inorganic exchange of oxygen, 15–16 pH effect on, 14–15 Plant growth promoting rhizobacteria (PGPR), 72–73 Plants exploitable depth, 106 factors affecting uptake of Fe/Zn, 76–79 Fe/Zn in soil, 73 mechanisms of Zn other than pH, 73 nutrition, 60 soil solution pH, 73–75, 74t translocation in, 78 Polyphosphate, Potassium, 177–178 fertilizer in wheat, 220–222, 221t, 227, 228, 229 Poultry manure, 205 Pressmud cake, 208 Pyrophosphate, Q Quantitative Evaluation of the Fertility of Tropical Soils (QUEFTS) model, 235 R Rice, 56–57 conventional lowland cultivation, 70 iron deficiency in, 70 method of application, 62–66 parboiled, 66 sources of zinc, 66–67 zinc concentration in, 65–66 zinc deficiency in, 70 Rice straw effect of, 202t management, 207–208 308 Rice–wheat cropping system, 188 fertilizer, 182t long-term experiment on, 213–214, 213f, 214t, 216t in northern Bangladesh, 189–190 phosphorus fertilizer, 217–219 subsoil compaction under, 195 Root characteristics, uptake of Fe/Zn, 76 S Salinization process, 140–141 Salt concentration soil, 159–160, 160f Scorpan approach, 115, 121 Sealed-tube method, 28–29 SEDEX sequential extraction method, 26, 27 Sediments oxygen isotope ratios of phosphate in, 21–30 provenance analysis, 38 Shuttle Radar Topographic Mission (SRTM), 107–108 Silver phosphate (Ag3PO4), 28 dissolving phosphate in water, 22 oxygen yield, 29–30 processing for, 25–27 soil/sediment phosphorus, 25–27 Site-specific nutrient management (SSNM), 174, 230, 231t need-based, 234 plant-based, 232–237, 236f, 238t soil-based, 230–232, 232t Sodic soil nitrogen losses in, 196 saline series, 197t South Asia, 196–197 wheat, 194 Soil assessment global imperative for, 96–98 information, 95–101 map coverage, 98–99 mapping, modeling, and monitoring, 96 simulation modeling, 96 Soil maps cross-validation, 118–119 detailed, 117 with point soil observations, 116 validation, 118–119 Index SoilML, 120 Soil organic carbon (SOC), 137–138 Soil organic matter (SOM) concentration, 136–138 crop yields and, 156–159, 158f, 164 fertilizer intensification in HHH region, 154, 154f, 155t to long-term fertilization management, 155–157, 157t residue retention, 201–202 Soil point data, 115, 116 detailed soil maps with, 114–115 Soil property data acquisition, 116–117 estimation using legacy data, 114–116 sampling, 116–117 statistical modeling, 118 values, 110f Soils degradation, 97 factors affecting Fe/Zn to plants, 73–75 function, 94–95, 101, 102, 124 individual, 103–107 Indo-Gangetic plain, 175 information, web-based delivery, 120 microcosm, 278–279, 280t, 285 oxygen isotope ratios of phosphate in, 21–30 P cycling, 39–41 quality improvement, 159–162 salt concentration, 159–160, 160f types in HHH region, 140–143, 142t, 143f Soil/sediment phosphorus sequential extraction, 25–27 silver phosphate precipitation, 27 Soil survey and classification, 99–100 depth function, 103–104 grids vs polygons, 100–101 measurement technologies, 117 polygon maps, 99–100 pragmatic treatment, 105–107 root depth, 106–107 SOM See Soil organic matter (SOM) concentration Sorption, abiotic processes, 31–33 309 Index South Asia sodic soil, 196–197 wheat production in (see Wheat production, in South Asia) South Asian Association for Regional Cooperation (SAARC), 172–173 Soybean, 176 SRTM See Shuttle Radar Topographic Mission (SRTM) State Soil Geographic (STATSGO2) database, 123 Substrate-specific isotope effects, 17–21 Sugarcane–wheat cropping systems, 175–176 T TC/EA See Thermochemolysis elemental analyzer (TC/EA) Technical Specifications of GlobalSoilMap, 102 depth function, 103–104 grid, 107–109 points and blocks estimation, 109 pragmatic treatment, 105–107 resolution of 100 m, 108–109 soil individual, 103–107 Thaumarchaeota acid soils, 272–274 operational taxonomic unit (OTU), 272, 274f relative abundance, 272, 273f Thermochemolysis elemental analyzer (TC/EA), 29, 30 Tillage, 69–70 Total profile depth, 106 U Ultraviolet (UV) oxidation, 24–25 Unhusked rice, Zn concentration in, 65–67, 65t Urea, 191–193, 228–229, 286–288 Urease inhibitors, 237–239 W Waters management techniques, 70–71 oxygen isotope ratios of phosphate in, 21–30 scarcity, 97 Wheat, 57–58, 65t, 67–69 zinc concentration in, 68t Wheat production, in South Asia, 175–176, 242t agronomic efficiency of, 184–185, 186t, 187t alkali soils, 196–197 composts and pressmud cake, 208 conservation agriculture and, 200–203, 202t cropping system, 172–174, 173t, 175–176 crop residues, 206–208 farmyard manure, 203–204 fertilizer use, 179–183, 181t, 183t green manure, 205–206 linear regression analyses, 213–214 nitrification inhibitors, 237–239 nitrogen/irrigation interaction in, 193–195 nutrient management (see Nutrient management) nutrient use efficiency (see Nutrient use efficiency) organic vs inorganic nutrient sources, 203–208 partial factor productivity of, 184–185, 186t, 187t phase, 174 phosphorus and, 190t poultry manure, 205 saline soils, 197–200, 198t, 199t salt-affected soils, 195–200 site-specific nutrient management (see Site-specific nutrient management) transformations/losses of nitrogen, 191–193, 192t urease inhibitors, 237–239 White rice, 65–66 Z Zinc accumulation in grain, 79 enzymes, 61 functions in human, 61 mechanisms other than pH, 75 phytosiderophores, 77 in soil, 73 utilization efficiency, 78 310 Zinc concentration fertilizer affecting, in cereal, 69–73 in rice, 65–66 in wheat, 68t, 71 Zinc deficiency in human, 56–57, 61 Index in rice, 70 root exudation of organic acids, 77–78 soils in world, 74f Zinc sulfate heptahydrate (ZSHH), 66–67 Zn prosthetic groups, 61 ... Qingpu Zhang The College of Resources and Environmental Science, China Agricultural University, Beijing, China PREFACE Volume 125 of Advances in Agronomy contains six cutting-edge reviews by internationally... Monitoring and Control, National Ministry of Land Resources, Beijing, China Dinesh Kumar Division of Agronomy, Indian Agricultural Research Institute, Pusa, New Delhi, India Philippe Lagacherie INRA,... China Agricultural University, Beijing, China Gan-Lin Zhang State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, PR China
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