(Advances in agronomy 96) donald l sparks (eds ) advances in agronomy academic press (2007)

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V O LU M E N I N E T Y ADVANCES IN S I X AGRONOMY ADVANCES IN AGRONOMY Advisory Board PAUL M BERTSCH RONALD L PHILLIPS University of Georgia 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 FREY 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 MICHEL D RANSOM KENNETH A BARBARICK CRAIG A ROBERTS HARI B KRISHNAN APRIL L ULERY SALLY D LOGSDON V O LU M E N I N E T Y ADVANCES S I X IN AGRONOMY EDITED BY DONALD L SPARKS Department of Plant and Soil Sciences University of Delaware Newark, Delaware AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 84 Theobald’s Road, London WC1X 8RR, UK Radarweg 29, PO Box 211, 1000 AE Amsterdam, The Netherlands Linacre House, Jordan Hill, Oxford OX2 8DP, UK 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 525 B Street, Suite 1900, San Diego, CA 92101-4495, USA First edition 2007 Copyright # 2007, 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 (ỵ44) (0) 1865 843830; fax (ỵ44) (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 permissions 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: 978-0-12-374206-3 ISSN: 0065-2113 (series) For information on all Academic Press publications visit our website at books.elsevier.com Printed and bound in USA 07 08 09 10 11 10 CONTENTS Contributors Preface Microbial Ecology of Methanogens and Methanotrophs ix xiii R Conrad Introduction Microbial Ecology of Methanogens Microbial Ecology of Methanotrophs Mitigation of Methane Emission from Rice Fields Conclusions and Outlook References Strategies of Plants to Adapt to Mineral Stresses in Problem Soils 31 42 43 45 65 S Hiradate, J F Ma, and H Matsumoto Introduction Fe-Deficiency Stress Al-Toxicity Stress P-Deficiency Stress Future Prospects References Water Flow in the Roots of Crop Species: The Influence of Root Structure, Aquaporin Activity, and Waterlogging 66 69 86 104 112 112 133 H Bramley, D W Turner, S D Tyerman, and N C Turner Introduction Water Movement Through the Plant Root Characteristics and Water Flow Changes in Lpr Plant Aquaporins (AQPs) The Role of AQPs in Root Water Transport Waterlogging Conclusion Acknowledgments References 134 135 140 146 147 167 171 180 181 182 v vi Contents Phytoremediation of Sodic and Saline-Sodic Soils 197 M Qadir, J D Oster, S Schubert, A D Noble, and K L Sahrawat Introduction Description of Sodic and Saline-Sodic Soils Degradation Processes in Sodic and Saline-Sodic Soils Phytoremediation of Sodic and Saline-Sodic Soils Perspectives Acknowledgments References 199 201 203 206 236 239 239 Ecology of Denitrifying Prokaryotes in Agricultural Soil 249 L Philippot, S Hallin, and M Schloter Introduction Agronomical and Environmental Importance of Denitrification Who are the Denitrifiers? Assessing Denitrifiers Density, Diversity, and Activity Natural Factors Causing Variations in Denitrification Denitrification in the Rhizosphere of Crops Impact of Fertilization on Denitrification Effect of Environmental Pollution on Denitrifiers Conclusions and Outlook References 250 253 255 258 262 266 273 279 285 287 Linking Soil Organisms Within Food Webs to Ecosystem Functioning and Environmental Change 307 J R Powell Introduction Overview of the Soil Food Web Impacts on Soil Food Web Dynamics Associated with Human Activities Alternative Approaches: Seeing the Forest for the Trees Missing and Ambiguous Components of Current Soil Food Web Knowledge Summary and Conclusions Acknowledgments References 308 309 313 322 335 340 341 341 Contents Comparative Typology in Six European Low-Intensity Systems of Grassland Management vii 351 R Caballero, J A˚ Riseth, N Labba, E Tyran, W Musial, E Molik, A Boltshauser, P Hofstetter, A Gueydon, N Roeder, H Hoffmann, M B Moreira, I S Coelho, O Brito, and A´ Gil Introduction Presentation of Study Areas Material and Methods Results Discussion References Index 353 355 361 370 408 414 421 This page intentionally left blank CONTRIBUTORS Numbers in parentheses indicate the pages on which the authors’ contributions begin Andrea Boltshauser ( 351) UNESCO Biosphere Reserve Entlebuch, CH-Schupfheim, Entlebuch, Switzerland H Bramley* (133) Wine and Horticulture, Faculty of Agriculture, Food and Wine, The University of Adelaide (Waite Campus), Plant Research Centre, PMB 1, Glen Osmond, South Australia 5064, Australia Olga Brito ( 351) Instituto Superior de Agronomia, Technical University of Lisbon, Baixo Alentejo, Portugal Rafael Caballero ( 351) Centro de Ciencias Medioambientales, CSIC, Madrid, Castile-La Mancha, Spain Inoceˆncio Seita Coelho ( 351) Instituto Nacional de Investigacáaăoo Agraria e Pescas, Ministerio da Agricultura, Desenvolvimento Rural e Pescas, Lisbon, Baixo Alentejo, Portugal Ralf Conrad (1) Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany A´ngel Gil ( 351) Centro de Ciencias Medioambientales, CSIC, Madrid, Castile-La Mancha, Spain Anne Gueydon ( 351) Lehrstuhl fuăr Wirtschaftslehre des Landbaues, Technische Universitaăt Muănchen, Bavaria, Germany Sara Hallin (249) Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden Syuntaro Hiradate (65) National Institute for Agro-Environmental Sciences (NIAES), Tsukuba, Ibaraki 305-8604, Japan * Present address: Department of Renewable Resources, 444 Earth Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E3, Canada ix 414 Rafael Caballero et al alpine ewes’ milk did not comply with EU sanitary rules In Entlebuch, only 7% of alpine units processed cows’ milk, and in Castile-La Mancha, although a regulatory council was functioning, attachment to production rules (indigenous breeds and linking to land-based resources) were not assured Of these two main pillars for indigenous products’ assurance, the latter is more at risk Our results showed a progressive detachment of production methods from land-based grazing resources, as consequence of harsh working conditions on grazing units and higher costs of changing to wage from family labor conditions The cost of bringing animals to grazing grounds, including waged labor and grazing fees should be lower than income, including value of production and subsidies An assessment tool that allow, on the basis of available geographic data (CORINE data, biotope mapping, digital terrain models), save upper and lower bounds for acceptable stocking levels for each MU This would allow to emphasizing the linkage between public payments and the provision of environmental services In many mountain areas the productivity of pastures varied significantly and to establish a minimum stocking (0.5 LU/ha) makes little sense Large-scale extensive systems in developed countries can be categorized as losers within a hyper-competitive economic environment In dealing with losers, we may assess whether these systems are ‘‘born losers’’ (structural or chronic) or there are some alternatives to improve their economic and social performance Our results supported the view that, although these systems are plagued with structural and physical constraints (harsh climatic conditions, poor soils, mobility, accessibility, steep slopes), much can be done to correct many other nonstructural constraints (insensible policy schemes is probably the most important) in support of alternative management plans Most pundits would agree on the requirement to overhaul and modernizing the extensive livestock systems in Europe to refrain the abandonment trend The question is what path should be chosen to that end If we remain strongly attached to traditional production rules, more farmers may detach But if loose rules are devised modernizing would mean increasing number of farmers at the expense of lack of fidelity to extensive principles At the end, 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M., Lasanta, T., and Romo, A (2004) Analysis of spatial and temporal evolution of vegetation cover in the Spanish central Pyrenees: Role of human management Environ Manage 34, 802–818 Vicente, N., Moreira, M., and Coelho, I (2005) Herdsmen, a changing profession Int J Agr Sci 135, 95–114 von Boberfeld, W O., Wohler, K., Erhardt, G., Gauly, M., Urban, C., Seufert, H., and Wagner, A (2002) Perspectives of grassland utilization in peripheral regions Ber Landwirtsch 80, 419–445 Waldhardt, R., Simmering, D., and Otte, A (2004) Estimation and prediction of plant species richness in a mosaic landscape Landscape Ecol 19, 211–226 Watkinson, A R., and Ormerod, S J (2001) Grassland, grazing and biodiversity: Editors’ introduction J Appl Ecol 38, 233–237 Wirz, Handbuch (2004) Landwirtschaftliche Beratungszentrale (Lindau) Planzen und Tiere Wirz Handbuch fuăr das landwirtschaftliche Unternehmen Wirz Verlag Basel Zebisch, M., Wechsung, F., and Kenneveg, H (2004) Landscape response functions for biodiversity—assessing the impact of land use changes at the county level Landscape Urban Plan 67, 157–172 Zervas, G (1998) Quantifying and optimizing grazing regimes in Greek mountain systems J Appl Ecol 35, 983–986 Index A Abscisic acid (ABA), 146–147, 157 Acacia nilotica (L.), 230–231, 236 Acetoclastic methanogens, 10–12 Acetotrophic methanogens, 9, 13 Acetylcoenzyme A (acetyl-CoA), 9, 11 Acetylene (C2H2), 258 Acetyl-P, Agroecosystems, 250, 279 Agropyron elongatum, 214 Agrosilvopastoral system, 360 Al-activated malate transporter gene, 100, 102 Alanine (CH3CH(NH2) COOH), 92 Albizia lebbeck (L.), 230–231 AlCl3-NaOH system, 88 Al-detoxifying agents in soils, plant-originated chemistry and behavior of, 89–94 phytotoxic Al in soils, 87–89 Alentejano pig, 360, 364 Alfalfa See Medicago sativa L Allmende, 360 Allmende (CLS) system, 380 ALMT1–1 cRNA, 100 ALMT1 gene See Al-activated malate transporter gene Al-(oxalate) complexes, 92 Alphaproteobacteria, 24 Alquevadam irrigation system, 374 AltBH gene See Al-toxicity tolerance gene Al toxicity mechanism symptoms calcium, 96 callose formation, 97 cell division, 94 cell wall, 95–96 hormone, 96–97 oxidative stress, 97–98 plasma membrane (PM), 94–95 tolerance ALMT1 gene, 100 exudation regulation of organic acids, from root apex, 98–100 genes in major crops, 102–103 gene transformation, 101–102 internal Al-detoxification mechanism, 101 malate exudation from root tips and, 99 Al-toxicity stress, 86 mechanism, 94–98 plant-originated Al-detoxifying agents in soils, Al chemistry and, 87–94 tolerance mechanisms, 98–103 Al-toxicity tolerance gene, 102–103 Ammonia-oxidizing strains, 255 Ammonia volatilization, 251 Ammonium monooxygenase (AMO), 39 amoA gene coding for, 31, 33 AMO Cluster I, 36 Anaerobic degradation, of organic matter to methane, methanogenic pathway of, 4, Anaeromyxobacter spp., 25 Anammox, 251 Andropogon bladhii, 316 Animals’ performance indicators, 364–365 ANME clusters, 33 Annual grazing cycle, 362 Anoxia, AQP activity and, 176–180 Anoxic–oxic interface, at soil surface, Anthropogenic greenhouse effect, 254 AQP gating, 163–168 Aquaporins (AQPs), 134–135 discovery of, 146 plant (See plant AQPs) Arabidopsis thaliana, 75–76, 85–86, 148, 157, 170, 176, 179 Arachis hypogaea, 107 Arbuscular mycorrhizal (AM) fungi, 312 Artemisia tridentata, 319 Asphyxiation, 254 AtALMT1 (At1g08430), 100 A thaliana FRO2 encoding protein (AtFRO2), 75 Atmospheric methane, oxidation of, 41–42 AtNRAMP1/3/4, 76 Atriplex species, 222, 235 Avena sativa L., 209 B baca flock, 358 Bahia grass See Paspalum notatum Baixo Alentejo, Portugal, 360–361, 374 Barley See Hordeum vulgare Bavaria, Germany, 359–360, 374 Begonia evansiana, 92 Biodiversity loss, ecosystem responses to, 313–315 linkages of communties effect on plants, 315 421 422 Index Biodiversity loss, ecosystem responses to (cont.) resource quality homogeneity, 314 Biological denitrification, 253 Biological nitrogen cycle, 250 Biotite (K(FeII,Mg)3Si3AlO10(OH)2), 70 Blue baby syndrome, 254 BnALMT1/2, ALMT1 homologues, 100 Boreal-alpine biogeographical region, Northern Sapmi, 354 Brachiaria mutica, 224 Brassica napus, 93, 100, 171, 220 Bromus tectorum, 316 Brown Swiss, 401 Brunoniella acaulis, 217 bundz and oscypek cheeses, 368 C Cajanus cajan, 107 Calcite (CaCO3), 207 Calliandra calothyrsus, 217 Camellia sinensis, 101 Campo Branco open fields, 354 Capsicum annuum, 168 Carbohydrates, methanogenic degradation of, 15 Carbon cycling and methane emission, methanogens and methanotrophs role in, 3–8 Carica papaya, 101 Cassia tora, 98 Castile-La Mancha, Spain, 361 Castor See Ricinum communis Castro Verde zonal plan, cereal-fallow rotation and, 407 Catechol See 1,2-dihydroxybenzene Cation exchange capacity (CEC), 201 cDNA microarray analysis, 79 Centaurea jacea, 314 Cereal-sheep system in Spain, 354 CFB group See Cytophaga-FlavobacteriumBacteroides group CFR See Complementary forage resources Channel index (CI), 323–324 Chara corallina, 167 Chemolithoautotrophic acetogens See Homoacetogenic bacteria Citrate synthase, 101 Climatic changes, effects on soil biota concentrations of CO2 studies, 318–320 fungal-feeding taxa sensitivity, 319 soil conditions, 320 temperature changes, 317–318 Clostridium Cluster XIVa, 15 Clostridium spp., 24 CLS See Cooperative livestock system C/N ratios, 23, 275–276, 326, 332 Cohesion-tension (CT) theory, 136 Colocasia esculenta, 98 Common Agricultural Policy (CAP) of EU, 354 Complementary forage resources, 363 Connemara west of Ireland study area, 355 Cooperative livestock systems, 359 actors in, 377 actors involved, 377 Cotton See Gossypium hirsutum L Crenothrix polyspora, 33 Crop management, CH4 emission and, 43 Crotalaria juncea, 325 CS See Citrate synthase Cucumis melo, 168 Cultivators-pastoralists relationships, 407 Cynodon dactylon (L.), 209 Cytochrome, 252 Cytophaga-Flavobacterium-Bacteroides group, 15 CytoplasmicpH, 165 D Dalbergia sissoo, 222, 231, 235 Daucus carota, 110 DCCD See Dicyclohexylcarbodiimide Deferriferrioxamine B, 81 Dehydrogenase activity (DHA), in soils, 229 Denitrification, 250–251, 253 activity, 280–282 effect of crops on, 267 inhibition/stimulation of, 280 inorganic and organic fertilizer effects on, 273 negative effects of heavy metals on, 283 nitrogen application rates and poor soil drainage on, 273 for agriculture, 253 cascade/electron acceptor, 251, 255 impact, on environment and human health, 254 measurement acetylene inhibition method, 258–259 isotope N-labeled methods, 259 rates, 250 total annual for global agricultural area, 253 Denitrification, impact of fertilization on denitrifier communities and, 277–279 inorganic and organic fertilizer effects on, 274–276 nitrous oxide emissions and, 276–277 secondary effects and heavy metal content effect, 273 Denitrification, natural factors causing variations in dry–wet cycles, 265–266 freeze–thaw cycles, 263–265 temperature and water, 262–263 Denitrifier communities, 260, 277, 283, 286 freeze–thaw effects on, 264–265 Denitrifiers, 255 423 Index culture-independent molecular and fingerprinting techniques, 260 diversity of, 259 most probable number (MPN) and molecular method for quantification, 260–261 Denitrifiers, effect of environmental pollution on heavy metals, 283–285 influence of pesticides on, 280–283 organic pollutants, 279–280 Denitrifying microorganisms, 255–258 Denitrifying strains See Denitrifying microorganisms 20 Àdeoxymugineic acid, 77, 79, 81 Desulfotomaculum, 20 Detritivore food web, 310–311 Diazotrophs, 251, 255 Dicyclohexylcarbodiimide, 79 Diethylenetriaminepentaacetic acid, 81, 83 1,2-dihydroxybenzene, 67 Discolaimus arenicolus, 336 Dissimilatory NOÀ reduction to ammonium, 251 Dissimilatory NOÀ reduction to ammonium (DNRA), 251 DMA See 20 Àdeoxymugineic acid DTPA See Diethylenetriaminepentaacetic acid E Echinochloa colona (L.), 225 E crusgalli (L.), 235 Ectomycorrhizal fungi, 337 Effective cation exchange capacity (ECEC), 202 Eleusine coracana (L.), 225 Enrichment index (EI), 323–324 Entlebuch, sampled lowland farm, 372–373 Entomopathogenic nematodes, 337 Environment conservation, sodic and saline-sodic soils and, 230–233 Eriales, shrub-steppe vegetation, 371 Escherichia coli, 340 ESF See Exchangeable sodium fraction ESP See Exchangeable sodium percentage Ethylenediaminetetraacetic acid (EDTA), 81 EUagricultural subsidy programs, 397 Eucalyptus tereticornis Sm., 230 Euphorbia esula, 316 European grazing systems, organization forms and actions, 378 European livestock systems threats, 411 Euryarchaeota, Exchangeable sodium fraction, 201 Exchangeable sodium percentage, 201–202 ranges in soils, 235 Exotic soil organisms, 316 Extensification process, 354 F FD mass-balance model, 364 Fe-deficiency stress, 69 Fe acquisition, in plants, 73–85 Fe chemistry, in soils, 70–72 genetic improvement of Fe-acquisition, in plants, 85–86 Ferrihydrite (Fe2O3Á2FeOOHÁ2.6H2O), 25, 70–71, 80 Fertilization effects with Fe, S, and N, 25–28 Fertilizers, inorganic and organic, 273 Festuca arundinacea (L.), 221 Finland, regional data of reindeer husbandry family, 358 Finnmark Norway, Migratory reindeer herding, 382 Fluorescent pseudomonads, 255 Folsomia quadrioculata, 339 Food web dynamics modeling application of, 332–335 consumption coefficient, 330 death of consumers, and consumption of detritus study, 330 energy flux, 331 estimates of parameter values used, 333 functional and energy web using feeding rates, 329–330 modeling flux of energy, 329 species richness and linkages, 328 strength to speed of energy flow, interaction, 331 theory of, 328–332 two-channel food web, 331–332 Forage coverage model, 381 FRO2 genes, 75–76, 85 G gazdas, 358 Genetically modified (GM) crops, 313 Gene transformation, Al-toxicity tolerance and, 101–102 Geobacter spp., 25 Gibberelic acid (GA), 157 Gibbsite (g-Al(OH)3), 83 Global warming, 254 Globobulimina pseudospinescens, 258 Glycine max, 76, 151 Glycyrrhiza glabra L., 235 GM cropping systems Bt-corn variety, 321 endophytic and rhizosphere microbial communities, effect on, 320 glyphosate tolerant cropping, 321 herbicide-tolerant varieties, 322 insecticidal Cry protein, 321 transgenic proteinase inhibitor I, 320 424 Index Goethite (aÀFeOOH), 70–71, 79 Gossypium hirsutum L., 209 Grazing fee and grazing rights, 374 Grazing infrastructure, 385–388 Grazing management, 364 and biodiversity, 406–408 economic performance of, 395–401 infrastructure of, 385–388 labor in, 388–390 limiting factors of, 404–406 productivity estimation of, 390–394 trends in, 401–404 Grazing systems typology, 370 Great Bustard, 407 Greenhouse effect, Greenhouse gases, 250–251 Gypsum (CaSO4Á2H2O), 207–211, 216, 219, 225 H Hedychium gardnerianum, 316 Helianthus annuus, 146 Hematite (a-Fe2O3), 70–71, 80 Herbivore food web, 310–311 High nature value (HNV) farmland, 352 Holcus lanatus, 314 Homoacetogenic bacteria, Homoacetogenic microorganisms, 14 Hordeum distichon, 139 Hordeum marinum, 174, 176 Hordeum vulgare, 77, 157, 208, 267 Hornblende, Ca2(Mg,Fe,Al)5(Si,Al)8 O22(OH)2, 70 HS-HTP See N-7-mercaptoheptanoyl-Ophospho-L-threonine HvYS1 gene, 84 Hydrangea macrophylla, 101 Hydraulic conductance, water movement and, 137–138 Hydraulic conductivity of roots (Lpr) changes in, 146–147 water movement and, 138–140 Hydrogenotrophic methanogens, 9, 12–14 Gibbs free energy (DG) of, 19 Hydroxyaluminum (HyA), 105 20 -hydroxyavenic acid A, 77 3-hydroxy-20 -deoxymugineic acid, 77 I Ilmenite (FeTiO3), 70 Intergovernmental Panel on Climate Change (IPCC), 254 Iron-containing components, in soils, 70 Iron-reducing bacteria, 25 Iron-regulated transporter (IRT1), 75–76 K Karasjok area of eastern Finnmark, 364 Kochia scoparia L., 235 Kyoto protocol, 250 L LACOPE study areas, 355, 357 Land use coefficient of variation (CV), 372 Large-scale grazing systems, 352–353 Leaching, 213, 251, 258, 276 for calcareous sodic and saline-sodic soils, 216 of Naỵ, 210, 215, 219, 223 NO3- and, 258, 276 LeIRT1, 76 Lepidocrocite (g-FeOOH), 70–71, 80 Leptochloa fusca (L.), 210 Less favored areas, 353 Leucaena leucocephala, 236 Leucanthemum vulgare, 314 LFAs See Less favored areas LGC See Local Grazing Commissions Linum usitatissimum, 171 Local Grazing Commissions, 381 Lolium perenne, 77 Lotus japonicus, 146 LSGS See Large-scale grazing systems Lupinus albus, 100, 146 Lupinus angustifolius, 139 Lycopersicon esculentum, 76 M MA See Mugineic acid Maas–Hoffman equation, 233 Maghemite (gÀFe2O3), 70, 80 Magnetite (Fe3O4), 70, 80 Maireana, 235 Maize See Zea mays Malate dehydrogenase, 108 M albus, 208 Management unit (MU), 354 Maturity index (MI), 323 MBC See Microbial biomass carbon mcrA genes, 10, 33 MDH See Malate dehydrogenase Medicago sativa L., 209 Melilotus indicus L., 208 N-7-mercaptoheptanoyl-O-phospho-Lthreonine, Mercuric chloride, 164–165, 167–167 Mesembranthemum crystallinum, 163 Methane emission, from rice fields carbon cycling, methanogens and methanotrophs role in, 3–8 mitigation of, 42–43 and production, microbiological explanations 425 Index fertilization with Fe, S, and N, effects of, 25–28 methanogenesis, sequential reduction and initiation of, 16–22 organic amendment effect, 23–25 plants effect, 29–30 short-term drainage effect, 22–23 temperature effect, 28–29 from rice fields, global methane budget and processes controlling, 2–3, Methane monooxygenase, 31, 33, 38–39 Methanobacteriales, 13 Methanobacterium, 12 Methanobrevibacter spp., 12 Methanofuran, 10 Methanogenesis, sequential reduction and initiation of, 16–22 Methanogenic substrates, microorganisms and, 14–16 Methanogens, microbial ecology diversity, habitats, and ecological niches, 10–16 methane production and emission, 16–30 physiology and phylogeny of, 8–10 Methanomicrobiales, 12–14, 24 Methanosaetaceae, Methanosaeta spp., 9–12, 22–23 Methanosarcinaceae, 9, 12–14, 20, 24 Methanosarcina spp., 9–12, 20, 22, 30 Methanospirillum spp., 12 Methanothermobacter spp., 24 Methanotrophic microorganisms, Methanotrophs microbial ecology atmospheric methane oxidation, 41–42 bulk rice field soil, 35–36 niche differentiation, 34–35 nitrogen fertilization effect, 38–41 physiology and phylogeny, 31–34 rice roots, 36–38 soil surface, 36 Methemoglobinemia, 254 l-Methionine, 77, 79 Methyl-CoM reductase, 8–9, 33 Methylobacter, 31, 35 Methylocaldum, 31, 35 Methylocapsa, 31 Methylocella, 31, 34 Methylococcus, 31, 35 Methylocystis, 31, 35 Methylohalobius, 31, 34 Methylomicrobium, 31, 35 Methylomonas, 31, 35 Methylosarcina, 31 Methylosinus, 31, 35 Methylosphaera, 31 Methylothermus, 31, 34 MFR See Methanofuran Microbial biomass carbon, 229–230 Microbial respiratory process, 250 Milk- and meat-oriented sheep flock, 388 Mimosa pudica, 165 1-M KCl, 87 MMO See Methane monooxygenase Molybdoenzymes, 251 Mononchus aquaticus, 336 Montado of Baixo Alentejo, 361 Montado system, 354, 360 Mucuna pruriens, 93 Mugineic acid, 81–83 chemical structures, 78 interactions to Fe minerals, 80–81 Multicopper homodimeric N2O reductase, 252 Multiindicator concept and landscapes situations, 362 Mycorrhizal fungi, 311, 337 N NAAR See Net acid addition rate naat genes, 86 National Oceanic and Atmospheric Administration, Neanurum muscorum, 339 Nematode faunal analysis, 323 functional groups of soil nematodes, 325 improvement in utility and sensitivity of, 327–328 indices, interpret nematode community shifts, 323–325 soil biodiversity and, 326–327 soil nutrient status and food web condition for, 326 theory of, 323–325 Net acid addition rate, 217 Neutral lipid fatty acid, 339 Niche differentiation, of aerobic methanotrophs, 34–35 Nicotiana tabacum, 85, 151 NIPs See Nodulin-like intrinsic proteins Nitrate-reducing bacteria, 26 Nitrification, 251 Nitrifiers, 255 Nitrogen fertilization, rice fields treatment and, 38–41 Nitrogen fertilizers, 273 Nitrogen, oxidation forms, 250 Nitrosomonas spp., 27, 36, 255 Nitrosospira spp., 27, 255 Nitrospira spp., 36 Nitrous oxide (N2O), 250–252 emissions, 254, 258, 262, 273 fertilization effects on, 276–277 freeze–thaw effects on, 263–265 NLFA See Neutral lipid fatty acid NLFA:PLFA ratios, 339 N-(1-napthyl)phtalamic acid (PA), 107 N2/N2O ratio, 262 426 Index NOAA See National Oceanic and Atmospheric Administration Nodulin-like intrinsic proteins, 148, 150 À NO3 reducers, 255 Northern Sapmi, Fennoscandia, 355–358 Norway, coastal adaptation reindeer management, 381 Norwegian LACOPE area, 364 NtAQP1, 170 O Oat See Avena sativa L O2-detoxifying enzymes, 17, 30 Olivine ((Mg,FeII)2SiO4), 70 Opuntia acanthocarpa, 168 Organic acids exudation, 98–99 regulation, from root apex, 99–100 Organic carbon effects, on CH4 production and emission, 23–25 Oryza sativa, 76 OsPTF1, 110 Oxide-reductive reactions, 69 P P acquisition in plants, mechanism of organic acids secretion, 108–109 phosphatase secretion, 109 P transporters, enhanced expression of, 109–110 root architecture alteration, 106–108 Pan-European coordinate socioeconomic research, 353 Para grass See Brachiaria mutica Parkinsonia aculeata L., 236 Partial pressure of CO2, in root zone, 212–216 Paspalum notatum, 221 P cineraria (L.), 236 P-deficiency stress, 103 P acquisition in plants, mechanism of, 106–110 plant-originated P-dissolving agents in soils, chemistry of P and, 104–106 tolerance, genetic improvement in plants AND, 110–111 Peanut See Arachis hypogaea Pectin, photochemical decomposition of, 29 Pelotomaculum, 16 PEPC See Phosphoenolpyruvate carboxylase Pesticides denitrification activity and, 280–282 on size and structure of denitrifier community, 282–283 Phaseolus coccineus, 139 Phaseolus vulgaris, 93, 98, 146 Phosphoenolpyruvate carboxylase, 108 Phosphogypsum, 25–26 Phospholipid fatty acids, 14–15, 24, 35, 339 Phytoremediation, of sodic and saline-sodic soils, 206–208 comparative efficiency of, 223 environment conservation, 230–233 soil amelioration, zone of, 228–230 soil sodicity amelioration, 224–228 historical perspective, 208–211 mechanism and processes partial pressure of CO2, in root zone, 212–216 proton, release by plant roots, 216–218 roots, physical effects of, 218222 salt and Naỵ uptake, by shoots, 222223 plant species for, 233236 Phytosiderophore-Fe3ỵ complex uptake, by roots, 8385 Phytosiderophores in graminaceous plants, biosynthesis of, 77–79 low-solubility Fe, solubilization of, 79–83 secretion to rhizosphere, 79 Pigeon pea See Cajanus cajan PIPs See Plasma membrane intrinsic proteins Plantago lanceolata, 314 Plant AQPs, 147 control of water permeability and, 152–168 role, in root water transport expression and transformation studies, 170–171 inhibition studies, 168–170 radial water flow and, 171–172 selectivity, 150–151 structure of, 148–150 Plant roots, proton release by, 216–218 Plants, Fe acquisition in genetic improvement of, 85–86 mechanism of strategy I, 73–76 strategy II, 77–85 Plasma membrane intrinsic proteins, 148–150, 156–157, 164, 170, 176, 179 Plasma membrane (PM) P-type ATPase, 75 Pleiotropic effects, 320 PLFA See Phospholipid fatty acids PM28A, 163–164 pmoA gene coding, for pMMO, 31, 33, 35 Poa pratensis, 77 Poiseuille-Hagen equation, 142 Polysaccharides degradation, 21 Populus tremuloides, 147, 165, 169 Portulaca oleracea L., 235 Potential Denitrification Activity (PDA), 281 Predatory nematodes, 312 Prosopis juliflora, 222, 231, 235 Prosthetic metals, 252 Proteobacteria, 30 Pseudoazurin, 252 Pseudomonas aeruginosa, 101 Pseudomonas fluorescens, 259 427 Index Pulse labeling, of plants, Purple lupin (Lupinus pilosus), 100 Pyrite (FeS2), 70 Pyroxene [augite (Ca,Mg,FeII,Al,Ti)2 (Si,Al)2O6], 70 Q Q rotundifolia Lamk, 360 Quantitative trait locus (QTL) analysis, 103 Quercus suber L., 360 Quinol pool, 252 R Radial water flow, parallel pathways for, 144–146 Raphanus sativus (Radish), 141 RDP See Rural Development Policy Reindeer grazing system, 354 Reindeer management culture, by Sa´mi herders, 355 Rhizobial bacteria, 311 Rhizosphere effect, 266, 271 Rhizosphere of crops, denitrification in barley crop and maize plants, 267–268 crop species/cultivars impact on microorganisms, 270–271 effects, 271–272 factors regulating, 266–267 plant effect on denitrifier community, 268–270 selective advantage for denitrifiers in, 270 transgenic crop’s impact on, 272–273 Rice See Oryza sativa Rice Cluster I (RC-I), 12–14, 17, 20, 24 thermophilic methanogens, 29 Rice field ecosystems, 10–11 carbon cycling in, 23 iron cycling and methane suppression in, 25 methanotrophic biomass in, 35 Rice field soil, aerobic methanotrophs and, 35–36 Rice plants, CH4 emission and, 29–30 Rice roots, aerobic methanotrophs habitat and, 36–38 Rice straw, microbial colonization of, 23–24 Ricinum communis, 107, 146 Root anatomy, 141 axial pathway, 142 radial pathway, 142–146 Root-feeding arthropods, 337 Root water transport, plant AQPs role in expression and transformation studies, 170–171 inhibition studies, 168–170 radial water flow and, 171–172 16S rRNA genes, 8, 10–12, 14, 22, 33, 35 molecular analyses of, 15 rice straw and, 23 Rural Development Policy, 352 guidelines, 411 S Saccharomyces cerevisiae, 75 Saccharum spontaneum L., 210 Salicornia bigelovii, 235 Salt and Naỵ uptake, by shoots, 222223 SAR See Sodium adsorption ratio Scandinavian peninsula Northern Fennoscandia, 355 Scapteriscus spp., 317 Sesbania bispinosa, 210 Sesbania sesban (L.), 236 Shallow oxic soil surface layer, Short-term drainage, of flooded rice fields, 22–23 Sinorhizobium meliloti, 320 SIPs See Small basic intrinsic proteins Sisymbrium officinale, 93 Small basic intrinsic proteins, 148 Smithella, 16 Snapbean See Phaseolus vulgaris SNGS See Structural nongrazing season Sodic and saline-sodic soils, 201–203 degradation processes in, 203–206 phytoremediation of, 206–208 comparative efficiency of, 223–233 historical perspective, 208–211 mechanism and processes, 212–223 plant species for, 233–236 Sodium adsorption ratio, 201–202 Soil amelioration nutrient dynamics during, 228–230 zone of, 228 Soil biodiversity, 308 Soil biota, 312–313 Soil ecosystems, 254 Soil food web, 309–313 approaches, organism status, 323–335 components of detritivore and herbivore food webs integration, 336–338 resolution, 335–336 role of technology, 338–340 dynamics, human activities and, 313 biodiversity loss, 313–315 climate change, 317–320 GM cropping systems, 320–322 invasive species, 315–317 Soil-plant-atmosphere continuum, 136–137 Soil redox potential (Eh), 16–17, 21 Soils, Fe chemistry in iron-containing components, 70 secondary Fe minerals, 70–72 Soil slurries, 259 Soil sodicity amelioration, 224–228 Soils, phytotoxic Al in, 87–89 Soils, plant-originated P-dissolving agents, chemistry of P and, 104–106 428 Index Soil surface, aerobic methanotrophs habitat and, 36 Soil texture, 312 Soluble nitrogen oxides, 250 Sorghum bicolor, 93, 107 Soybean See Glycine max SPAC See Soil-plant-atmosphere continuum Spinacia oleracea (Spinach), 163–164 Structural nongrazing season, 363 Structure index (SI), nematode community shifts and, 323–324 Stylosanthes seabrana, 217 Sulfate reducers, methanogenic activity and, 26 Sunflower See Helianthus annuus Sweden, regional data of reindeer husbandry family, 358 Sweet clover See Melilotus indicus L Swiss Entlebuch UNESCO Biosphere reserve, 407 Symbiotic microorganisms, 310 Symbiotic organisms, 337 Syntrophic microorganisms, Syntrophobacter, 16 T Tajo and Guadiana rivers, 361 Tamarix dioica, 236 Taro See Colocasia esculenta Tatra mountains, Poland, 358–359 Temperature, effect on CH4 emission, 28–29 Terminalia arjuna, 230–231, 236 Tetrahydromethanopterin (H4MPT), 10 T3238fer, FER function, 76 Themeda triandra, 217 Thermodynamic analysis, hydrogenotrophic methanogenesis and, 17 Thermophilic methanogens proliferation, 28 Titanomagnetite (Fe3-xTixO4), 70 Tobacco See Nicotiana tabacum Tomato See Lycopersicon esculentum Tonoplast intrinsic proteins (TIPs), 148–149 Total agricultural land (TAL), 361 Tradescantia fluminensis, 316 2,3,5-triiodobenzoic acid (TIBA), 107 Triticum aestivum, 139, 141, 219 Typha latifolia, 25 U Ulex europaeus, 316 UNESCO Biosphere Entlebuch, Switzerland, 359 UN report GLOBIO, 379 Urea, CH4 emission by, 27 V Velvetbean See Mucuna pruriens Verrucomicrobia, 15 W Water flow, root characteristics and root anatomy, 142–146 root growth and water uptake, influencing factors, 140–141 Waterlogging anoxia, AQP activity and, 176–180 O2 effect, in rhizosphere, 172–173 root growth, effect on, 173–175 water use, effect on, 175–176 Water management, CH4 emission and, 42 Water movement, through plant driving forces, 135–137 hydraulic conductance, 137–138 hydraulic conductivity of roots (Lpr), 138–140 Water permeability control, AQPs and AQP abundance, changes in, 156–162 patterns of expression in roots, AQP abundance and, 152–156 posttranslational regulation, 162–168 Water potential (c), 135–137 Wheat See Triticum aestivum White lupin See Lupinus albus White sweet clover See M albus World Heath Organization, 254 X Xenopus laevis oocytes, 84, 100, 150, 156, 164 Z Zea mays, 79, 93, 139 ZmPIP2;5, 152 ZmYS1 gene, 84 ... on substrate availability Since H2 partial pressures in rice field soil are generally low (
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