NITROGEN IN THE ENVIRONMENT: NITROGEN BEHAVIOR IN FIELD SOIL

By ISABELLA LEWIS

2 PHASEOLUS SP AND VIGNA SP (BEANS) 3 ARACHIS HYPOGAEA (GROUNDNUT, PEANUT) 4 CICER ARIETINUM (CHICKPEA) 5 CAJANUS CAJAN (PIGEON PEA) 6 MUCUNA PRURIENS (VELVET BEAN) AND OTHER LEGUMES ACKNOWLEDGEMENTS REFERENCES CHAPTER 2 NITROGEN FIXATION BY SOYBEAN IN NORTH AMERICA 1 SOYBEAN: PATHWAYS TO NORTH AMERICA AND ESTABLISHMENT AS A CROP 2 SOYBEAN PRODUCTION IN NORTH AMERICA 3 MAJOR SOYBEAN CROPPING SYSTEMS 4 BIOLOGICAL NITROGEN FIXATION BY SOYBEAN IN NORTH AMERICA 5 PERSPECTIVES CHAPTER 3 THE IMPORTANCE OF NITROGEN FIXATION TO SOYBEAN CROPPING IN SOUTH AMERICA 1 INTRODUCTION 2 TAXONOMY, ORIGINS, AND IMPORTANCE OF SOYBEAN 3 BIOLOGICAL NITROGEN FIXATION 4 ECONOMIC IMPORTANCE OF BIOLOGICAL NITROGEN FIXATION (BNF) IN SOUTH AMERICA 5 CROP MANAGEMENT IN SOUTH AMERICA 6 FINAL CONSIDERATIONS ACKNOWLEDGEMENT CHAPTER 4 PRODUCTION, REGIONAL DISTRIBUTION OF CULTIVARS, AND AGRICULTURAL ASPECTS OF SOYBEAN IN INDIA 1 INTRODUCTION AND HISTORICAL BACKGROUND 2 ALL-INDIA AREA COVERAGE, PRODUCTIVITY, AND PRODUCTION OF SOYBEAN BETWEEN 1970-2003 3 ALL-INDIA STATE-WISE AREA COVERAGE, PRODUCTIVITY, AND PRODUCTION OF SOYBEAN 4 REGIONAL DISTRIBUTION OF SOYBEAN CULTIVARS 5 REGIONAL AGRICULTURAL ASPECTS OF SOYBEAN CULTIVATION CHAPTER 5 SOYBEAN CULTIVATION AND BNF IN CHINA 1 SUMMARY 2 SOYBEAN CULTIVATION IN CHINA: HISTORICAL ASPECTS AND CURRENT SITUATION 3 NITROGEN-FIXING BACTERIA THAT NODULATE SOYBEAN 4 THE SOYBEAN GERMPLASM COLLECTION IN CHINA 5 SOYBEAN IN CROP ROTATION AND IN CONTINUOUS CULTIVATION 6 CONCLUSIONS CHAPTER 6 SOIL STRESS FACTORS INFLUENCING SYMBIOTIC NITROGEN FIXATION 1 INTRODUCTION 2 IMPORTANCE OF SYMBIOTIC NITROGEN FIXATION 3 SYMBIOTIC INTERACTION OF LEGUMES WITH RHIZOBIA 4 NODULATION AND NITROGEN-FIXATION GENETICS IN THE RHIZOBIA AND BRADYRHIZOBIA 5 RHIZOBIA IN THE SOIL ENVIRONMENT 6 STRESS FACTORS IN THE SOIL ENVIRONMENT THAT INFLUENCE N2 FIXATION 7 CONCLUDING REMARKS CHAPTER 7 NODULATED LEGUME TREES 1 INTRODUCTION 2 LEGUMINOSAE 3 RHIZOBIA THAT NODULATE LEGUME TREES 4 TYPES OF NODULE FORMED ON TREES 5 MYCORRHIZAS AND OTHER NUTRIENT-ACQUISITION SYSTEMS 6 MEASUREMENT OF NITROGEN FIXATION BY TREES 7 ROLE OF LEGUME TREES IN NATURAL AND MANAGED SYSTEMS CHAPTER 8 NITROGEN FIXING TREES WITH ACTINORHIZA IN FORESTRY AND AGROFORESTRY 1 INTRODUCTION 2 GENERAL CHARACTERISTICS OF THE ACTINORHIZAL SYMBIOSIS 3 HOST BOTANICAL FAMILIES 4 NITROGEN FIXATION IN ACTINORHIZAL TREES 5 MYCORRHIZAL ASSOCIATIONS WITH ACTINORHIZAL TREES 6 ACTINORHIZAL TREES IN AGROFORESTRY 7 THE GENUS CASUARINA 8 THE EXPERIENCE OF THE CENTRAL AMERICA FUELWOOD PROJECT 9 THE CASE OF ALNUS ACUMINATA IN TROPICAL HIGHLANDS 10 OTHER USES OF ACTINORHIZAL TREES 11 CONCLUDING CONSIDERATIONS CHAPTER 9 MOLECULAR ECOLOGY OF N2-FIXING MICROBES ASSOCIATED WITH GRAMINEOUS PLANTS: HIDDEN ACTIVITIES OF UNKNOWN BACTERIA 1 INTRODUCTION 2 THE PROBLEM OF IDENTIFYING KEY DIAZOTROPHIC BACTERIA IN GRAMINEOUS PLANTS: THE CLASSICAL APPROACH 3 THE SIGNIFICANCE OF DIAZOTROPHIC GRASS ENDOPHYTES 4 THE SIGNIFICANCE OF CULTURE-INDEPENDENT METHODS 5 THE SIGNIFICANCE OF NIFH-TARGETED METHODS 6 LIMITATIONS OF NIFH-TARGETED METHODS 7 MANY DIAZOTROPHS DEFY CULTIVATION 8 DIAZOTROPHIC GRASS ENDOPHYTES AS KEY ORGANISMS FOR BNF IN GRAMINEOUS PLANTS 9 SUMMARY AND OUTLOOK CHAPTER 10 INTERACTIONS OF ARBUSCULAR MYCORRHIZA AND NITROGEN-FIXING SYMBIOSIS IN SUSTAINABLE AGRICULTURE 1 INTRODUCTION 2 PURPOSE OF REVIEW 3 NITROGEN-FIXING SYMBIOSES 4 ARBUSCULAR MYCORRHIZA 5 INTERACTIONS BETWEEN AM FUNGI AND RHIZOBIA TO IMPROVE LEGUME PRODUCTIVITY IN AGRICULTURE CHAPTER 11 INOCULANT PREPARATION, PRODUCTION AND APPLICATION 1 INTRODUCTION 2 STRAIN SELECTION 3 INOCULANT PRODUCTION 4 INOCULANT APPLICATION 5 FACTORS AFFECTING THE SUCCESS OF INOCULATION 6 MAIN CONCLUSIONS CHAPTER 12 NITRIFYING BACTERIA 1 NITRIFICATION AS PART OF THE NITROGEN CYCLE 3 ECOLOGY AND DETECTION OF NITRIFYING BACTERIA 4 METABOLISM OF NITRIFYING BACTERIA CHAPTER 13 THE NITROGEN CYCLE: DENITRIFICATION AND ITS RELATIONSHIP TO N2 FIXATION 1 INTRODUCTION 2 THE NITROGEN CYCLE 3 DENITRIFICATION 4 BACTERIAL RESPIRATORY NITRATE REDUCTASES 5 NITRITE REDUCTASES 6 NITRIC OXIDE REDUCTASES 7 NITROUS OXIDE REDUCTASE 8 LINKAGE OF THE DENITRIFICATION GENE CLUSTERS 9 BIOENERGETICS OF DENITRIFICATION 10 REGULATION OF TRANSCRIPTION OF DENITRIFICATION GENES 11 REGULATION OF DENITRIFICATION BY ENVIRONMENTAL FACTORS 12 DIVERSITY OF DENITRIFICATION 13 YEAST AND FUNGAL DENITRIFICATION 14 CONCLUDING REMARKS CHAPTER BOTH FOR THE DIETS OF THE POPULATION AND FOR THE PRODUCTION BY SMALL FARMERS IN TERMS OF SUSTAINABLE AGRICULTURE, BOTH FODDER LEGUMES AND LEGUMES USED AS GREEN 2 PHASEOLUS SP AND VIGNA SP (BEANS) MORE THAN 200 SPECIES OF THE GENUS PHASEOLUS HAVE BEEN DESCRIBED (SMARTT, 1988) THE MOST IMPORTANT SPECIES ECONOMICALLY ARE PHASEOLUS VULGARIS VAR NANUS, PHASEOLUS COCCINEUS, PHASEOLUS LUNATUS, PHASEOLUS ACUTIFOLIUS AND PHASEOLUS NITROGEN IN THE ENVIRONMENT, VOLUME 1: NITROGEN BEHAVIOR IN FIELD SOIL SEMIERECTUS COMMON NAMES FOR PHASEOLUS VULGARIS ARE DWAR BEANS, BUSH BEANS AND DRY BEANS (IN SPANISH “FRIELOS SECOS”) THE GENE CENTER FOR PHASEOLUS SPECIES IS IN CENTRAL AND SOUTH AMERICA AND FOR VIGNA IN ASIA THE ORIGINAL WILD FORM OF PHASEOLUS VULGARIS IS PHASEOLUS VULGARIS SSP ABORIGINEUS, WHICH IS FOUND IN MOIST VALLEYS IN MIDDLE AMERICA THE GENUS PHASEOLUS HAS A CHROMOSOME NUMBER OF 2N = 22 THE MAIN GENE BANKS ARE AT THE CIAT IN CALI (COLUMBIA), IN GATERSLEBEN (GERMANY), AND IN THE WAVILOV-INSTITUTE IN ST PETERSBURG (RUSSIA) A LARGE NUMBER OF GENETIC VARIATIONS ARE KNOWN THAT IMPACT YIELD, SEED COLOUR, AND EARLY RIPENING SPECIFIC MORPHOLOGICAL AND PHYSIOLOGICAL CHARACTERS ARE A SHALLOW ROOT SYSTEM, SELF POLLINATION, AND LIGHT- INDEPENDENT DEVELOPMENT SPECIES CAN DEVELOP NORMALLY UNDER SHADING CONDITIONS, MAKING THIS GENUS SUITABLE FOR AGROFORESTRY SYSTEMS THE DNA CONTENT OF PHASEOLUS, VIGNA, AND PSOPHOCARPUS SPECIES ARE SUMMARIZED IN TABLE 3 IT RANGES FROM 590 UNITS IN PHASEOLUS VULGARIS UP TO IN VIGNA ACONITIFOLIA DESIRED CHARACTERISTICS OF NEW BEAN CULTIVARS HAVE BEEN FORMULATED BY BROUGHTON ET AL (2003) AND THE TARGETS AND GENETICAL COMPONENTS ARE SUMMARIZED IN TABLE 4 THEY INCLUDE ?-AMYLASE-INHIBITORS, SPECIFIC SUGAR SYNTHESIS, AND RHIZOBIUM NODULATION CHARACTERISTICS TABLE 3 DNA CONTENT OF PHASEOLUS, VIGNA AND PSOPHOCARPUS SPECIES MODIFIED FROM BENNETT AND LEITCH (2001) AND SMARTT (1990) VERNACULAR NAME LATIN NAME (SUB-FAMILY - PAPILIONOIDEAE) IC DNA CONTENT COMMON BEANS PHASEOLUS VULGARIS L LIMA BEANS PHASEOLUS LUNATUS L SCARLET RUNNER BEANS PHASEOLUS COCCINEUS L TEPARY BEANS PHASEOLUS ACUTIFOLIUS A GRAY LONG BEANS/COWPEAS VIGNA UNGUICULATU (L ) WALP MUNG BEANS (GREEN GRAM) VIGNA RADIATA (L ) WILCZEK URD (BLACK GRAM) VIGNA MUNGO (L ) HEPPER ADZUKI BEANS VIGNA ANGULARIS (WILLD ) OHWI AND OHASHI RICE BEANS VIGNA UMBELLATA (JACQ ) OHWI AND OHASHI MOTH BEANS VIGNA ACONITIFOLIA (JACQ ) MARÉCHAL WINGED BEANS PSOPHOCARPUS TETRAGONOLOBUS (L ) DC SEVERAL OTHER TARGETS AND PLANT COMPONENTS HAVE BEEN PROPOSED BY THE PHASEOMICS CONSORTIUM, WHICH HAS 43 GROUPS WORLDWIDE (TABLE 5) THESE TARGETS INCLUDE CLASSICAL PHYSIOLOGICAL TRAITS, SUCH AS NUTRIENTS AND SOIL FACTORS, AND ALSO NEW MOLECULAR GENETICAL TECHNIQUES TO FACILITATE AND IMPROVE BREEDING PROGRAMMES AT THE END, AS IN CLASSICAL BREEDING, THE GOAL IS STABLE OR ADAPTED AND PRODUCTIVE NEW CULTIVARS IT IS INTERESTING TO COMPARE THESE NEW GOALS WITH THOSE OF AN FAO/IAEA COORDINATED RESEARCH PROGRAMME THAT RAN FROM 1986 TO 1991 (BLISS AND HARDARSON, F NITROGEN IN THE ENVIRONMENT, VOLUME 1: NITROGEN BEHAVIOR IN FIELD SOIL TABLE 4 TARGETS AND GENES FOR BEAN BREEDING MODIFIED FROM BROUGHTON ET AL (2003) PROBLEM TARGET GENETIC COMPONENT ANTI-NUTRITIONAL FACTORS ?-AMYLASE INHIBITORS, ARCELINS, LECTINS, PHENOLICS, TANNINS, PHYTATES, TRYPSIN INHIBITORS OFTEN SINGLE GENES FLATULENCE RAFFINOSE, STACHYOSE, VERBASCOSE GENOTYPIC VARIATION HARD-TO-COOK COTYLEDONARY MIDDLE LAMELLA GENOTYPIC VARIATION LOW %NDFA SINGLE, COMPLEX LOCI LOW PROTEIN SEED LEVELS PHASEOLIN AND APA GENE FAMILIES FIN LOCUS PLANT TYPE DETERMINANCY GENES ST LOCUS POD SHATTER POD STRING MANY POOR NODULATION LEGUME–RHIZOBIUM INTERACTIONS COK-4 (PROTEIN KINASE), B4 CLUSTER, AND OTHERS SENSITIVITY TO COLLETOTRICHUM SEVERAL MAJOR LOCI AND QTLS FOR RESISTANCE SINGLE, COMPLEX LOCUS SEEDS LOW IN S-AMINO ACIDS PHASEOLIN GENOTYPIC VARIATION SUSCEPTIBILITY TO SEED-BORING INSECTS ARCELIN-PHYTOHEM- AGGLUTININ-?, AMYLASE INHIBITOR (APA) SINGLE, COMPLEX LOCUS 1993) THE MAIN TOPICS THEN WERE METHODOLOGY TO STUDY NITROGEN FIXATION IN THE FIELD, THE USE OF GENOTYPIC VARIATION IN DIFFERENT BEAN BREEDING LINES AND CULTIVARS, AND THE CLASSICAL ECO-PHYSIOLOGY OF NITROGEN FIXATION WITH NINE DIFFERENT BEAN LINES, THE AMOUNT OF N2 FIXED VARIED BETWEEN 18 AND 36 KG HA–1 (KILOGRAMS PER HECTARE) AFTER 56 DAYS (KIPE-NOLT AND GILLER, 1993) IN ANOTHER EXPERIMENTAL SERIES, THE AMOUNT OF N2 FIXED WITHIN 60 DAYS VARIED BETWEEN 18 AND 50 KG HA–1 (KIPE-NOLT ET AL , 1993) BEANS ARE NODULATED BY SEVERAL SPECIES AND GENERA OF RHIZOBIA, AS SUMMARIZED IN TABLE 6 BEAN SPECIES ORIGINATING IN LATIN AMERICA HARBOUR MAINLY RHIZOBIUM ETLI STRAINS IN THEIR NODULES, WHEREAS IN EUROPE AND IN AFRICA, OTHER RHIZOBIUM SPECIES ARE PRESENT (GILLER, 2001) THE PROTEIN, LIPID, AND CARBOHYDRATE CONTENTS OF SEVEN VIGNA SPECIES ARE SUMMARIZED IN TABLE 2 THEY HAVE AN IMPORTANT ROLE IN AGRICULTURE IN MANY ASIAN AND AFRICAN COUNTRIES THE LIPID CONTENT IS RATHER LOW (1-2%) WITH THE EXCEPTION OF VIGNA SUBTERRANEAN, WHICH HAS A LIPID CONCENTRATION OF 7% IN DRY SEEDS VIGNA MUNGO (BLACK GRAM), VIGNA RADIATA (GREEN GRAM), AND VIGNA UNGUICULATA (COWPEA) ARE USED AS EITHER SEEDS OR AS VEGETABLES AS GREEN BEANS THE RESULTS OF THE PHASEOMICS CONSORTIUM, TOGETHER WITH THE METHODOLOGIES USED AND DEVELOPED, CAN BE TRANSFERRED IN THE FUTURE TO SEVERAL VIGNA SPECIES WITH AGRICULTURAL RELEVANCE NITROGEN IN THE ENVIRONMENT, VOLUME 1: NITROGEN BEHAVIOR IN FIELD SOIL