Nitrogen fixation (15N dilution) with soybeans under Thai field conditions

Controlled environment and field studies were conducted to determine relationships between various measurements of N₂ fixation using soybeans and to use these measures to evaluate a number ofBradyrhizobium japonicum strains for effectiveness in N₂ fixation in Thai soils.¹⁵N dilution measurements of N₂ fixation showed levels of fixation ranging from 32 to 161 kg N ha⁻¹ depending on bacterial strain, host cultivar and location. Midseason measures of N₂ fixation were correlated with each other, but not related measures taken at maturity. Ranking ofB. japonicum strains based on performance under controlled conditions in N-free media were highly correlated with rankings based on soybean seed yields and N₂ fixation under field conditions. This study showed that inoculation of soybeans with effectiveB. japonicum strains can result in significant increases in yield and uptake of N through fixation. The most effective strains tested for use in Thai conditions were those isolated from Thai soils; however, effective strains from other locations were also of benefit.     

Validity of N2 fixation rate measurements in marine Oscillatoria (Trichodesmium)

No measurable differences in Trichodesmium nitrogenase activitywere observed between colonies collected by diving and incubatedunder ultra-clean conditions compared with those collected andincubated using standard techniques. Measurements were madein the northeastern Caribbean Sea, near the Bahama Islands andin the Sargasso Sea. Surprisingly, mean rates of ethylene productionwere high relative to most previous in situ measurements onTrichodesmium. The calculated cellular N doubling times (viaN₂ fixation) ranged from 1.13 days in the northeastern CaribbeanSea, 1.48 days in the Sargasso Sea to 1.8 days near the BahamaIslands. A comparison of these doubling times with those inthe literature illustrates the high variability in rate of N₂fixation by Trichodesmium. From this study, we conclude thatthe often observed slow rates of N₂ fixation are valid. Populationsof Trichodesmium can probably remain within the water columnat low growth rates via gas vesicles, which keep the colonysuspended, and low grazing rates by herbivores.     

Effect of disabling bacteroid proline catabolism on the response of soybeans to repeated drought stress

The aim of this study is to evaluate the contribution of bacteroidproline catabolism as an adaptation to drought stress in soybeanplants. To accomplish this, soybeans (Glycine max L. Merr.)were inoculated with either a parental strain of Bradyrhizobiumjaponicum which was able to catabolize proline, or a mutantstrain unable to catabolize proline. A large strain-dependentdifference in nodule number and size was observed. In orderto separate inoculant-dependent effects on nodulation from effectson bacteroid proline catabolism, plants inoculated with eachstrain were only compared to other plants inoculated with thesame strain, thus removing the observed inoculant-dependentdifferences in nodulation as a bar to interpretation of theresults. This experimental design allowed a comparison of thedrought penalty on yield for plants with parental bacteroidsand for plants with mutant bacteroids. The two results werethen compared to each other in order to evaluate the impactof the ability of bacteroids to catabolize proline on the responseto drought stress. When water stress was mild, soybean plants inoculated with bacteriaunable to catabolize proline suffered twice the percentage decreasein seed yield as did plants inoculated with bacteria able tocatabolize proline. However, when stress was severe there wasno significant effect of the ability of bacteroids to catabolizeproline on drought imposed decrease in seed yield. These resultssuggest that increasing the oxidative flux of proline in bacteroidsmight provide an agronomically significant yield advantage whenstress is modest, but that severe drought stress would probablyoverwhelm this yield benefit. Key words: N₂-fixation, proline dehydrogenase, drought stress     

Structural biology of proline catabolism

The proline catabolic enzymes proline dehydrogenase and Δ¹-pyrroline-5-carboxylate dehydrogenase catalyze the 4-electron oxidation of proline to glutamate. These enzymes play important roles in cellular redox control, superoxide generation, apoptosis and cancer. In some bacteria, the two enzymes are fused into the bifunctional enzyme, proline utilization A. Here we review the three-dimensional structural information that is currently available for proline catabolic enzymes. Crystal structures have been determined for bacterial monofunctional proline dehydrogenase and Δ¹-pyrroline-5-carboxylate dehydrogenase, as well as the proline dehydrogenase and DNA-binding domains of proline utilization A. Some of the functional insights provided by analyses of these structures are discussed, including substrate recognition, catalytic mechanism, biochemical basis of inherited proline catabolic disorders and DNA recognition by proline utilization A.     

N2 fixation in Thai soybeans: Effect of tillage and inoculation on15N-determined N2 fixation in recommended cultivars and advanced breeding lines

The practice of seeding soybeans following paddy rice in Thailand has encountered difficulties in seedling germination, nodulation and crop establishment. This research project evaluated the choice of a non-fixing control to quantify N₂ fixation by¹⁵N isotope dilution, and the effect of tillage regime, soybean cultivar, strain ofBradyrhizobium japonicum and P fertilization on yield and N₂ fixation after paddy rice in northern and central Thailand.Japanese non-nodulating lines Tol-0 and A62-2 were the most appropriatecontrol plants for¹⁵N isotope dilution for Thai soybeans in these soils which contained indigenous rhizobia. Cereals such as maize, sorghum and barley were also appropriate controls at some sites. The choice of the appropriate non-fixing control plant for the¹⁵N isotope dilution technique remains a dilemma and no alternative exists other than to use several possible controls with each experiment. Acetylene reduction assay (ARA) proved of little value for screening varieties on their N₂ fixing capacity.The recommended Thai soybean cultivars (SJ1, 2, 4, 5) and an advanced line 16–4 differed little in their ability to support N₂ fixation or yield, possibly due to similar breeding ancestry. The ten AVRDC (ASET) lines showed considerable genotypic control in their ability to utilize their three available N sources (soil, fertilizer, atmosphere) and to translate them into yields. None of these lines were consistently superior to Thai cultivars SJ4 or SJ5 although ASET lines 129, 209 and 217 showed considerable promise.Neither recommended Thai or ASET cultivars were affected by tillage regime. Zero tillage resulted in superior N₂ fixation and yield at two sites but conventional tillage was superior at another site. Soybean cultivars grown in Thailand were well adapted to zero tillage. Levels of N₂ fixation were similar to world figures, averaging more than 100 kg N ha^–1 and supplying over 50% of the plant's N yield. However, seed yields seldom exceeded 2 t ha^–1, well below yields for temperately-grown soybeans. It is not clear why Thai soybeans support N₂ fixation, but do not translate this into higher seed yields.     

Estimates of n(2) fixation based on differences in the natural abundance of N in nodulating and nonnodulating isolines of soybeans

Estimates of the contribution of biologically fixed N to the total N of nodulating soybeans (Glycine max (L) Merrill, variety Harosoy) grown under a variety of conditions were made from: (a) differences in N yield between nodulating and nonnodulating isolines; and (b) differences in ¹⁵N abundance between the two isolines. For plants grown in a greenhouse in nutrient-poor soil, both estimates showed a high level of N₂ fixation; from 58 to 89% N fixed by differences in N yield and from 51 to 95% by differences in ¹⁵N abundance. Decreasing contributions of fixed N were estimated by both methods with increasing levels of added NO₃⁻. Results of field experiments carried out over two years on an unamended highly fertile midwestern soil showed a modest level of N₂ fixation by both methods (7.3 to 51% by differences in N yield, and 5.4 to 46% by differences in ¹⁵N abundance). When the soil was amended with ground corn cobs, both methods showed higher contributions of fixed N. The two methods of estimating N₂ fixation gave similar results. Both appear to be semiquantitative and the standard errors of the estimates were about the same (6% on the average).     

A rust-inducible gene from flax (fis1) is involved in proline catabolism

A gene fis1 from flax (Linum usitatissimum), which is induced in mesophyll cells at the site of rust (Melampsora lini) infection, is also expressed in vascular tissue, particularly in floral structures of healthy plants. This paper reports that the promoter controlling this expression is contained within 282 bp 5′ to the coding region and that fis1 gene induction is specifically by the rust pathogen and not by other fungal pathogens or by wounding. The fis1 gene has 73% homology with an Arabidopsis gene which encodes delta-1-pyrroline-5-carboxylate dehydrogenase (P5CDH) which is a part of the proline degradation pathway. Transgenic flax plants that either over-express fis1 or show reduced fis1 expression due to RNA-mediated gene silencing have an unaltered morphology. However, plants with reduced fis1 expression have markedly increased sensitivity to exogenous proline and show alteration in epidermal cell morphology, callose deposition and the production of hydrogen peroxide during proline-induced death. These lines, which show a biologically significant level of fis1 suppression, have an unaltered reaction to either virulent or avirulent rust infections, as do fis1 over-expression lines. These data indicate that the fis1 gene plays a role in proline metabolism and most likely encodes for a P5CDH enzyme. However, the precise role of fis1 and P5C catabolism in the development of rust disease remains unclear.     

Products of Dark CO(2) Fixation in Pea Root Nodules Support Bacteroid Metabolism

Products of the nodule cytosol in vivo dark [¹⁴C]CO₂ fixation were detected in the plant cytosol as well as in the bacteroids of pea (Pisum sativum L. cv “Bodil”) nodules. The distribution of the metabolites of the dark CO₂ fixation products was compared in effective (fix⁺) nodules infected by a wild-type Rhizobium leguminosarum (MNF 300), and ineffective (fix⁻) nodules of the R. leguminosarum mutant MNF 3080. The latter has a defect in the dicarboxylic acid transport system of the bacterial membrane. The ¹⁴C incorporation from [¹⁴C]CO₂ was about threefold greater in the wild-type nodules than in the mutant nodules. Similarly, in wild-type nodules the in vitro phosphoenolpyruvate carboxylase activity was substantially greater than that of the mutant. Almost 90% of the ¹⁴C label in the cytosol was found in organic acids in both symbioses. Malate comprised about half of the total cytosol organic acid content on a molar basis, and more than 70% of the cytosol radioactivity in the organic acid fraction was detected in malate in both symbioses. Most of the remaining ¹⁴C was contained in the amino acid fraction of the cytosol in both symbioses. More than 70% of the ¹⁴C label found in the amino acids of the cytosol was incorporated in aspartate, which on a molar basis comprised only about 1% of the total amino acid pool in the cytosol. The extensive ¹⁴C labeling of malate and aspartate from nodule dark [¹⁴C]CO₂ fixation is consistent with the role of phosphoenolpyruvate carboxlase in nodule dark CO₂ fixation. Bacteroids from the effective wild-type symbiosis accumulated sevenfold more ¹⁴C than did the dicarboxylic acid transport defective bacteroids. The bacteroids of the effective MNF 300 symbiosis contained the largest proportion of the incorporated ¹⁴C in the organic acids, whereas ineffective MNF 3080 bacteroids mainly contained ¹⁴C in the amino acid fraction. In both symbioses a larger proportion of the bacteroid ¹⁴C label was detected in malate and aspartate than their corresponding proportions of the organic acids and amino acids on a molar basis. The proportion of ¹⁴C label in succinate, 2-oxogultarate, citrate, and fumarate in the bacteroids of the wild type greatly exceeded that of the dicarboxylate uptake mutant. The results indicate a central role for nodule cytosol dark CO₂ fixation in the supply of the bacteroids with dicarboxylic acids.     

Cloning of Azorhizobium caulinodans nicotinate catabolism genes and characterization of their importance in N2 fixation.

Twenty Azorhizobium caulinodans vector insertion (Vi) mutants unable to catabolize nicotinate (Nic- phenotype) were identified and directly cloned as pVi plasmids. These pVi plasmids were used as DNA hybridization probes to isolate homologous wild-type sequences. From subsequent physical mapping experiments, the nic::Vi mutants defined four distinct loci. Two, possibly three, of these loci are physically linked. A. caulinodans nic loci II and III encode the structural genes for nicotinate catabolism; nic loci I and IV encode nicotinate-driven respiratory chain components. Recombinant lambda bacteriophages corresponding to three of these loci were subcloned in pRK293; resulting plasmids were used for complementation tests with resolved nic::IS50 derivatives of the nic::Vi mutants. When wild-type A. caulinodans was cultured in defined liquid medium under 3% O2, nicotinate catabolism stimulated N2 fixation 10-fold. In these exponentially growing cultures, the entire (300 microM) nicotinate supplement was exhausted within 10 h. While nic::Vi mutants retained the ability to fix some N2, they did so at rates only 10% of that of the wild type: nitrogenase activity by nic::Vi mutants was not stimulated by 300 microM added nicotinate. Higher-level (5 mM) nicotinate supplementation inhibited N2 fixation. Because 5 mM nicotinate repressed nitrogenase induction in all nic::Vi mutants as well, this repression was independent of nicotinate catabolism. During catabolism, nicotinate is first oxidized to 6-OH-nicotinate by a membrane-bound nicotinate hydroxylase which drives a respiratory chain to O2. In A. caulinodans wild-type cultures, added 300 microM 6-OH-nicotinate stimulated N2 fixation twofold better than did added 300 microM nicotinate. Likewise, nic::Vi mutant 61302, defective in nicotinate hydroxylase, fixed N2 at wild-type levels when supplemented with 300 microM 6-OH-nicotinate. Therefore, nicotinate catabolism stimulates N2 fixation not by nicotinate hydroxylase-driven respiration but rather by some subsequent aspect(s) of nicotinate catabolism.     

N(2) fixation and h(2) evolution by six species of tropical leguminous trees

The C₂H₄/¹⁵N₂ and H₂/¹⁵N₂ ratios for six species of tropical leguminous trees are reported. C₂H₄/¹⁵N₂ ratios ranged from 2.4 to 4.7; values for the H₂/¹⁵N₂ ratios were between 0.6 and 1.4. Relative efficiency values, based on C₂H₂ reduction, ¹⁵N incorporation, and H₂ evolution during ¹⁵N incorporation varied between 0.68 and 0.84 for the six species. Overall, approximately 30% of the electron flow through nitrogenase was used for H₂ evolution.     

Regulation of proline catabolism in Pseudomonas aeruginosa PAO

Mutants of Pseudomonas aeruginosa deficient in the utilization of l-proline as the only carbon and nitrogen source have been found to be defective either in proline dehydrogenase activity or in both proline dehydrogenase and ¹-pyrroline-5-carboxylate dehydrogenase activities of the bifunctional proline degradative enzyme. The latter type of mutants was unable to utilize l-ornithine, indicating that a single ¹-pyrroline-5-carboxylate dehydrogenase activity is involved in the degradation of ornithine and proline. Proline dehydrogenase and ¹-pyrroline-5-carboxylate dehydrogenase activities were strongly and coordinately induced by proline. It was excluded that ¹-pyrroline-5-carboxylate acted as an inducer of the bifunctional enzyme and it was shown that the low level induction observed during growth on ornithine was due to the intracellular formation of proline. The formation of the proline degradative enzyme was shown to be subject to catabolite repression by citrate and nitrogen control.Abbreviations EMS Ethylmethane sulfonate - NG N-methyl-N-nitro-N-nitrosoguanidine - P Minimal medium P - Pro-DH Proline dehydro-genase - P5C ¹-Pyrroline-5-carboxylate - P5C-DH ¹-Pyrroline-5-carboxylate dehydrogenase     

Response to drought stress of nitrogen fixation (acetylene reduction) rates by field-grown soybeans

The effects of drought stress on soybean nodule conductance and the maximum rate of acetylene reduction were studied with in situ experiments performed during two seasons and under differing field conditions. In both years drought resulted in decreased nodule conductances which could be detected as early as three days after water was withheld. The maximum rate of acetylene reduction was also decreased by drought and was highly correlated with nodule conductance (r = 0.95). Since nodule conductance is equal to the nodule surface area times the permeability, the relationship of these variables to both whole-plant and unit-nodule nitrogenase activity was explored. Drought stress resulted in a decrease in nodule gas permeability followed by decreases in nodule surface area when drought was prolonged. Under all conditions studied acetylene reduction on a unit-nodule surface area basis was highly correlated with nodule gas permeability (r = 0.92). A short-term oxygen enrichment study demonstrated nodule gas permeability may limit oxygen flux into both drought-stressed and well-watered nodules of these field-grown soybeans.     

Regulation of arginine and proline catabolism in Bacillus licheniformis

The enzymes in the arginine breakdown pathway (arginase, ornithine-delta-transaminase, and Delta'-pyrroline-5-carboxylate dehydrogenase) were found to be present in Bacillus licheniformis cells during exponential growth on glutamate. These enzymes could be coincidentally induced by arginine or ornithine to a very high level and their synthesis could be repressed by the addition of glucose, clearly demonstrating catabolite repression control of the arginine degradative pathway. The strongest catabolite repression control of arginase occurred when cells were grown on glucose and this control decreased when cells were grown on glycerol, acetate, pyruvate, or glutamate. The proline catabolite pathway was present in B. licheniformis during exponential growth on glutamate. The proline oxidation and the Delta'-pyrroline-5-carboxylate dehydrogenase in this breakdown pathway were induced by l-proline to a high level. The Delta'-pyrroline-5-carboxylate dehydrogenase was found to be under catabolite repression control. Arginase could be induced by proline and arginine addition induced proline oxidation, suggesting a common in vivo inducer for these convergent pathways.     

N2-Succinylornithine in ornithine catabolism of Pseudomonas aeruginosa

Most Pseudomonas aeruginosa PAO mutants which were unable to utilize l-arginine as the sole carbon and nitrogen source (aru mutants) under aerobic conditions were also affected in l-ornithine utilization. These aru mutants were impaired in one or several enzymes involved in the conversion of N²-succinylornithine to glutamate and succinate, indicating that the latter steps of the arginine succinyltransferase pathway can be used for ornithine catabolism. Addition of aminooxyacetate, an inhibitor of the N²-succinylornithine 5-aminotransferase, to resting cells of P. aeruginosa in ornithine medium led to the accumulation of N²-succinylornithine. In crude extracts of P. aeruginosa an ornithine succinyltransferase (l-ornithine:succinyl-CoA N²-succinyltransferase) activity could be detected. An aru mutant having reduced arginine succinyltransferase activity also had correspondingly low levels of ornithine succinyltransferase. Thus, in P. aeruginosa, these two activities might be due to the same enzyme, which initiates aerobic arginine and ornithine catabolism.Abbreviations OAT ornithine 5-aminotransferase - SOAT N²-succinylornithine 5-aminotransferase - Oru ornithine utilization - Aru arginine utilization     

Glyphosate affects micro-organisms in rhizospheres of glyphosate-resistant soybeans

Aims: Glyphosate‐resistant (GR) soybean production increases each year because of the efficacy of glyphosate for weed management. A new or ‘second’ generation of GR soybean (GR2) is now commercially available for farmers that is being promoted as higher yielding relative to the previous, ‘first generation’ (GR1) cultivars. Recent reports show that glyphosate affects the biology and ecology of rhizosphere micro‐organisms in GR soybean that affect yield. The objective of this research was to evaluate the microbiological interactions in the rhizospheres of GR2 and GR1 soybean and the performance of the cultivars with different rates of glyphosate applied at different growth stages. Methods and Results: A greenhouse study was conducted using GR1 and GR2 soybean cultivars grown in a silt loam soil. Glyphosate was applied at V2, V4 and V6 growth stages at three rates. Plants harvested at R1 growth stage had high root colonization by Fusarium spp.; reduced rhizosphere fluorescent pseudomonads, Mn‐reducing bacteria, and indoleacetic acid–producing rhizobacteria; and reduced shoot and root biomass. Conclusions: Glyphosate applied to GR soybean, regardless of cultivar, negatively impacts the complex interactions of microbial groups, biochemical activity and root growth that can have subsequent detrimental effects on plant growth and productivity. Significance and Impact of the Study: The information presented here will be crucial in developing strategies to overcome the potential detrimental effects of glyphosate in GR cropping systems.     

N(2) fixation by bacteria associated with maize roots at a low partial o(2) pressure

Nitrogen fixation by bacteria associated with roots of intact maize plants was measured by exposing the roots to N(2) at a partial O(2) pressure (pO(2)) of 2 or 10 kPa. The plants were grown in a mixture of Weswood soil and sand and then transferred to plastic cylinders containing an N-free plant nutrient solution. The solution was sparged continuously with a mixture of air and N(2) at a pO(2) of 2 or 10 kPa. Acetylene reduction was measured after the roots were exposed to the low pO(2) overnight. The air-N(2) atmosphere in the cylinders was then replaced with an O(2)-He atmosphere at the same pO(2), and the roots were exposed to 20 kPa of N(2) for 20 to 22 h. Incorporation of N into the roots was 200 times greater at 2 kPa of O(2) than at 10 kPa of O(2). Adding l-malate (1 g of C liter) to the nutrient solution increased root-associated nitrogenase activity, producing a strong N label which could be traced into the shoots. Fixed N was detected in the shoots within 5 days after the plants were returned to unfertilized soil. In a similar experiment with undisturbed plants grown in fritted clay, movement of fixed N into the shoots was evident within 4 days after the roots were exposed to N(2) at 2 kPa of O(2). Inoculation with Azospirillum lipoferum yielded no significant differences in shoot dry weight, total nitrogen content, percent nitrogen, or N enrichment of plant tissues. Inoculated plants did exhibit greater root dry weight than uninoculated plants, however.     

Nitrogen fixation by soybeans (Glycine max L.) in Zambia

Soybeans (Glycine max L.) are being introduced as a cash crop to small scale farmers in Zambia for rotation in their farming systems. The objectives of this study were to compare and select the most approriate non-fixing reference crop for estimating N₂ fixation by soybeans and assess yields and N₂ fixation of soybeans in Zambia. Nitrogen isotope dilution techniques using¹⁵N-labelled organic or inorganic materials were utilized. Two nonnodulating soybean cultivars, Clark RJ1 and N77 or in their absence Pearl millet (Panicum glaucum L.) were judged to be appropriate reference crops. A local soybean fixing cultivar (Glycine max L. cv. Magoye) rated highest among three cultivars tested for its ability to support symbiotic N₂ fixation byB. japonicum under the experimental conditions. Values of percent N derived from atomosphere for this cultivar were in the order of 65 to 70%.deceased.Contribution no R531 of the Saskatchewan Institute of Pedology. Present address (REK): Esso Chemical Canada, P.O. Box 3010, Lethbridge, Alberta Canada T1J 4A9.     

Dinitrogen (15N2) fixation and acetylene reduction in free-living strains ofRhizobium

Dinitrogen (¹⁵N₂) fixation of four free-livingRhizobium strains ranged from 0.8 to 2.3 μmol/mg biomass N. Parallel-grown cultures liberated 4–8 μmol hydrogen and reduced 12–23 μmol acetylene, giving a mean ratio of reduced acetylene-to-fixed¹⁵N₂ of 12. This ratio contrasts with lower values others have observed for asymbiotic diazotrophs.