Carbon and nitrogen metabolism in legume root nodules

The literature concerning the metabolism of carbon compounds during the reduction, assimilation and translocation of nitrogen in root nodules of leguminous plants is reviewed. The reduction of dinitrogen requires an energy source (ATP) and a reluctant which are both supplied by respiratory catabolism of carbohydrates produced by the host plant. Photosynthates are also required to generate the carbon skeletons for amino acid or urcide synthesis during the assimilation of ammonia produced by the bacteria within the nodule tissue. Competition for photosynthates occurs between the bacteroids, nodule tissue and the various vegetative and reproductive sinks in the host plant. The nature of carbon compounds involved in these processes, their routes of metabolism, the mechanisms of control and the partitioning of metabolises between the various sites of utilization are only poorly understood. It is apparent that dinitrogen is reduced to ammonia in the bacteroids. Both fast- and slow-growing strains of Rhizobium possess the Entner-Doudoroff pathway of glucose catabolism, and some, if not all, enzymes of the Emden-Meyerhof pathway. Some bacterial cultures also metabolize carbon through the ketogluconate pathway but only the fast-growing strains of cultured rhizobia possess the key enzyme of the pentose phosphate pathway (6-phosphogluconate dehydrogenase). The host cells are thought to contain the complete Emden-Meyerhof pathway and tricarboxylic acid cycle, which provides the carbon skeletons for assimilation of the ammonia, formed by the bacteroids, into α-amino acids. A pathway of anapleurotic carbon conservation, operative in the host cells, synthesizes oxaloacetic acid through β-carboxylation of phosphoenol pyruvate. This process could be important in the recapture and assimilation of respired CO₂ in the rhizosphere. The main route of assimilation of ammonia produced by the bacteroids would appear to be via the glutamine synthetase-glutamate synthase pathway in the host cells. However, glutamate dehydrogenase may also be involved in ammonia assimilation. These enzymes also occur in in vitro cultures of Rhizobium and in bacteroids where they presumably participate in the synthesis of amino acids for growth of the bacteria or bacteroids. Nitrogen assimilated into glutamine or glutamate is exported from the nodules in a variety of forms, which include asparagine, glutamine, aspartate, homoserine and allantoates, in proportions which depend on the legume species. Studies on regulation of the overall process have focussed on expression of bacteroid genes and on the control of enzyme activity, at the level of nitrogenase and enzymes of nitrogen assimilation in particular. However, due to the wide range of experimental techniques, environmental conditions and plant species which have been used, no clear conclusions can yet be drawn. The pathways of carbon flow in nitrogen metabolism, particularly in relation to the synthesis of ureides and the regulation of carbon metabolism, remain key areas for future research in symbiotic nitrogen fixation.     

Carbon and nitrogen metabolism in ectomycorrhizal fungi and ectomycorrhizas

The literature concerning the metabolism of carbon and nitrogen compounds in ectomycorrhizal associations of trees is reviewed. The absorption and translocation of mineral ions by the mycelia require an energy source and a reductant which are both supplied by respiratory catabolism of carbohydrates produced by the host plant. Photosynthates are also required to generate the carbon skeletons for amino acid and carbohydrate syntheses during the growth of the mycelia. Competition for photosynthates occurs between the fungal cells and the various vegetative sinks in the host tree. The nature of carbon compounds involved in these processes, their routes of metabolism, the mechanisms of control and the partitioning of metabolites between the various sites of utilization are only poorly understood. Both ascomycetous and basidiomycetous ectomycorrhizal fungi synthesize and some, if not all, accumulate mannitol, trehalose and triglycerides. The fungal strains employ the Embden--Meyerhof pathway of glucose catabolism and the key enzymes of the pentose phosphate pathway (6-phosphogluconate dehydrogenase, glucose-6-phosphate dehydrogenase, transaldolase and transketolase). Anaplerotic CO2 fixation, via pyruvate carboxylase and/or phosphoenolpyruvate carboxykinase, provides high pools of amino acids. This process could be important in the recapture and assimilation of respired CO2 in the rhizosphere. The ectomycorrhizas are thought to contain the Embden--Meyerhof pathway, the pentose phosphate pathway and the tricarboxylic acid cycle, which provide the carbon skeletons for the assimilation of ammonia into amino acids. The main route of assimilation of ammonia appears to be through the glutamine synthetase-glutamate synthase cycle in the ectomycorrhizas. Glutamate dehydrogenase plays a minor role in this process. Glutamate dehydrogenase and glutamine synthetase are present in free-living ectomycorrhizal fungi and they participate in the assimilation of ammonia and the synthesis of amino acids through the glutamate dehydrogenase/glutamine synthetase sequence. In both in vitro cultures of fungi and ectomycorrhizas, the assimilated nitrogen accumulates in glutamine. Glutamine, but also ammonia, are thought to be exported from the fungal tissues to the host cells. Studies on the metabolism of ectomycorrhizas and ectomycorrhizal fungi have focused on the metabolic pathways and compounds which accumulate in the symbiotic tissues. Studies on regulation of the overall process, and the control of enzyme activity in particular, are still fragmentary.(ABSTRACT TRUNCATED AT 400 WORDS)     

Carbon and nitrogen metabolism regulated by the ubiquitin-proteasome system

The ubiquitin-proteasome system (UPS) is a unique protein degradation mechanism conserved in the eukaryotic cell. In addition to the control of protein quality, UPS regulates diverse cellular signal transduction via the fine-tuning of target protein degradation. Protein ubiquitylation and subsequent degradation by the 26S proteasome are involved in almost all aspects of plant growth and development and response to biotic and abiotic stresses. Recent studies reveal that the UPS plays an essential role in adaptation to carbon and nitrogen availability in plants. Here we highlight ubiquitin ligase ATL31 and the homologue ATL6 target 14-3-3 proteins for ubiquitylation to be degraded, which control signaling for carbon and nitrogen metabolisms and C/N balance response. We also give an overview of the UPS function involved in carbon and nitrogen metabolisms.     

Carbon and nitrogen metabolism in barley plants exposed to UV-B radiation

The effect of UV-B radiation on FW, leaf and stem length, photosynthetic O₂ evolution, levels of carbohydrates and nitrates, and extractable activities of some of the enzymes involved in C and N metabolism was evaluated in barley ( Hordeum vulgare L. cv. Express) seedlings during the 9 days following transfer to an UV-B enriched environment. The results show that under our experimental conditions UV-B radiation scarcely affects the photosynthetic competence of barley leaves, expressed as RuBP carboxylase (EC 4.1.1.39) activity, O₂ evolution rate and chlorophyll content. Nevertheless, this treatment induced significant alterations of the enzyme activity of nitrate reductase (EC 1.6.6.1) and glutamine synthetase (EC 6.3.1.2), although only after a few days of treatment. The effects were not confined to the exposed tissue, but were detectable also at the root level. In fact, nitrate reductase decreased in response to UV-B in both leaf and root tissue, whereas glutamine synthetase was affected only in the root. In contrast, nitrate content was not influenced by the treatment, neither in root nor in leaf tissue, whilst leaf sucrose diminished in exposed plants only on the last day of treatment.     

Carbon and nitrogen metabolism during Dendrobium huoshanense protocorm-like body development in suspension culture

Abstract

The aim of this work was to study carbon and nitrogen metabolism during suspension culture of protocorm-like bodies (PLBs) from Dendrobium huoshanense. No significant lag phase of PLB growth was found, and a maximum biomass of 288.6 g l^?1 was obtained at day 30 of culture. Sucrose concentration was halved as PLB growth proceeded, while no change in glucose and fructose levels in the medium was found in the first 3 days, followed by a gradual increase until day 9 of culture. Conversely, sucrose in PLBs accumulated dramatically in the first 6 days of culture, followed by a rapid decrease. At the same time, glucose and fructose content of PLBs increased, then declined after 9 days of culture. Soluble acidic invertase (soluble acidic IT) and alkaline invertase (alkaline IT) were activated after inoculation, and reached the highest value on day 6 and day 18, respectively whereas cell wall-bound invertase (cell wall-bound IT) seemed to be repressed throughout culture. The maximum value of sucrose synthase (SuSy) activity was observed on day 18, while sucrose phosphate synthase (SPS) stayed low and constant from inoculation to the end of culture. Ammonium concentration in the medium decreased rapidly, and was hardly detectable after 12 days, when the rapid utilization of nitrate began. Conversely, ammonium in PLBs showed a sharp increase in the first 3 days of culture, followed a rapid decrease until day 12, corresponding to nitrate depletion. Peaks in glutamine synthase (GS) and glutamate synthase (GOGAT) activity were observed on day 12 and 15, respectively. Nitrate reductase (NR) was repressed in the early culture stage, and activated from day 9 to 15 of culture. These results suggest that soluble acidic IT, alkaline IT, SuSy, GS, GOGAT and NR control carbon and nitrogen metabolism at different PLB growth stages.     

Carbon and nitrogen metabolism in mycorrhizal networks and mycoheterotrophic plants of tropical forests: a stable isotope analysis

Most achlorophyllous mycoheterotrophic (MH) plants obtain carbon (C) from mycorrhizal networks and indirectly exploit nearby autotrophic plants. We compared overlooked tropical rainforest MH plants associating with arbuscular mycorrhizal fungi (AMF) to well-reported temperate MH plants associating with ectomycorrhizal basidiomycetes. We investigated (13)C and (15)N abundances of MH plants, green plants, and AMF spores in Caribbean rainforests. Whereas temperate MH plants and fungi have higher δ(13)C than canopy trees, these organisms displayed similar δ(13)C values in rainforests, suggesting differences in C exchanges. Although temperate green and MH plants differ in δ(15)N, they display similar (15)N abundances, and likely nitrogen (N) sources, in rainforests. Contrasting with the high N concentrations shared by temperate MH plants and their fungi, rainforest MH plants had lower N concentrations than AMF, suggesting differences in C/N of exchanged nutrients. We provide a framework for isotopic studies on AMF networks and suggest that MH plants in tropical and temperate regions evolved different physiologies to adapt in diverging environments.     

Micronutrients and nitrogen metabolism

A sand-culture experiment was conducted to study the influence of a deficiency of and an excess of micronutrients on the uptake and assimilation of NH ₄ ⁺ and NO ₃ ⁻ ions by maize. By studying the fate of¹⁵N supplied as¹⁵NH₄NO₃ or NH₄ ¹⁵NO₃, it was demonstrated that in maize plants NH₄−N was absorbed in preference to NO ₃ ⁻ −N. The uptake and distribution of N originating from both NH ₄ ⁺ and NO ₃ ⁻ was considerably modified by deficiency of, or an excess of, micronutrients in the growth medium. The translocation of NH ₄ ⁺ −N from roots to shoots was relatively less than that of NO ₃ ⁻ −N. Deficiency as well as excessive amounts of micronutrients, in the growth medium, substantially reduced the translocation of absorbed N into protein. This effect was more pronounced in the case of N supplied as NO ₃ ⁻ . Amino-N was the predominant non-protein fraction in which N from both NH ₄ ⁺ and NO ₃ ⁻ tended to accumulate. The next important non-protein fractions were NO ₃ ⁻ −N when N was supplied as NO ₃ ⁻ and amide-N when NH ₄ ⁺ was the source. The relative accumulation of¹⁵N into different protein fractions was also a function of imposed micronutrient levels.     

Pelagic carbon metabolism in a eutrophic lake during a clear-water phase

Dissolved and paniculate organic carbon (DOC and POC, respectively),primary production, bacterial production, bacterial carbon demandand community grazing were measured for 9 weeks in eutrophicFrederiksborg Slotssø. The period covered the declineof the spring bloom, a clear-water phase and a summer phasewith increasing phytoplankton biomass. The process rates andchanges in pools of organic carbon were combined in a carbonbudget for the epilimnion. The POC budget showed a close balancefor both the post-spring bloom and the clear-water phase, whilea surplus was found in the summer phase. Production of POC wasdominated by phytoplankton (2/3) compared to bacteria (1/3)during all phases, and there was a significant correlation betweenphytoplankton and bacterial production rates (r² = 0.48, P <0.039). Bacterial demand for DOC was balanced by productionand changes in the pool of DOC during the decline of the springbloom, but the calculated demand exceeded the supply by 81 and167%, respectively, during the other two periods. The discrepancywas most probably due to an underestimation of bacterial growthefficiency and an overestimation of in situ bacterial productionin carbon units. Production of bacterial substrate by zooplanktonactivity was estimated to be higher than the direct excretionof organic carbon from phytoplankton. The biological successionwas regulated by the balance between area primary productionand community grazing. The clear-water phase was initiated bya combination of low primary production due to low surface irradianceand high community grazing (100 mmol C m^–2 day^–1),which caused a decrease in phytoplankton biomass. However, dueto the high initial phytoplankton biomass, community grazingwas not high enough to cause a significant decrease in areaprimary production. The summer phase was initiated by a decreasein community grazing followed by an increase in phytoplanktonbiomass. Based on these observations and calculations of areaprimary production as a function of chlorophyll concentrations,we suggest that the possibility for zooplankton to regulatephytoplankton biomass in temperate lakes decreases with increasingnutrient level.     

Pelagic community respiration on the continental shelf off Georgia, USA

The South Atlantic Bight (SAB) has been a focus for the study of continental shelf ecosystem respiration during the past two decades. However, two questions concerning respiration in this area have yet to be answered. First, why do previous estimates of respiration in the SAB exceed measured carbon fixation rates by almost an order of magnitude? Second, considering that bacteria are responsible for most of the pelagic community respiration in the SAB, why is respiration almost uniform from the coastline to the shelf break, while bacterial production estimates decrease offshore? This study addresses these critical questions by presenting new pelagic community respiration data that were collected across the entire width of the continental shelf off Georgia, USA from June 2003 to May 2006. The respiration was calculated as in vitro changes of dissolved oxygen and dissolved inorganic carbon concentrations during deck incubations. The measured respiration rates ranged from 0.3(±0.1) to 21.2(±1.4) mmol m^?3 day^?1. They followed a clear seasonal pattern, being lowest over the entire shelf in winter and reaching maxima in summer. Summertime respiration rates were highest on the inner shelf and decreased with distance offshore. Consistent with this trend, bacterial abundance measurements taken during the sampling month of July 2005 followed a pattern of seaward decline. The SAB organic carbon fluxes calculated from the respiration data are close to the estimates for primary production, which resolves a long-standing mystery regarding perceived carbon imbalance in the SAB.     

Methanogenic toluene metabolism: community structure and intermediates

Toluene is a model compound used to study the anaerobic biotransformation of aromatic hydrocarbons. Reports indicate that toluene is transformed via fumarate addition to form benzylsuccinate or by unknown mechanisms to form hydroxylated intermediates under methanogenic conditions. We investigated the mechanism(s) of syntrophic toluene metabolism by a newly described methanogenic enrichment from a gas condensate-contaminated aquifer. Pyrosequencing of 16S rDNA revealed that the culture was comprised mainly of Clostridiales. The predominant methanogens affiliated with the Methanomicrobiales. Methane production from toluene ranged from 72% to 79% of that stoichiometrically predicted. Isotope studies using (13)C(7) toluene showed that benzylsuccinate and benzoate transiently accumulated revealing that members of this consortium can catalyse fumarate addition and subsequent reactions. Detection of a BssA gene fragment in this culture further supported fumarate addition as a mechanism of toluene activation. Transient formation of cresols, benzylalcohol, hydroquinone and methylhydroquinone suggested alternative mechanism(s) for toluene metabolism. However, incubations of the consortium with (18)O-H(2)O showed that the hydroxyl group in these metabolites did not originate from water and abiotic control experiments revealed abiotic formation of hydroxylated species due to reactions of toluene with sulfide and oxygen. Our results suggest that toluene is activated by fumarate addition, presumably by the dominant Clostridiales.     

Carbon and nitrogen metabolism in the seagrass, Zostera marina L.: Environmental control of enzymes involved in carbon allocation and nitrogen assimilation

This study experimentally examined influences of environmental variables on the activities of key enzymes involved in carbon and nitrogen metabolism of the submersed marine angiosperm, Zostera marina L. Nitrate reductase activity in leaf tissue was correlated with both water-column nitrate concentrations and leaf sucrose levels. Under elevated nitrate, shoot nitrate reductase activity increased in both light and dark periods if carbohydrate reserves were available. When water-column nitrate was low, glutamine synthetase activity in leaf tissue increased with environmental ammonium. In contrast, glutamine synthetase activity in belowground tissues was statistically related to both nitrate and temperature. At the optimal growth temperature for this species (ca. 25 °C), increased water-column nitrate promoted an increase in glutamine synthetase activity of belowground tissues. As temperatures diverged from the optimum, this nitrate effect on glutamine synthetase was no longer evident. Activities of both sucrose synthase and sucrose-P synthase were directly correlated with temperature. Sucrose-P synthase activity also was correlated with salinity, and sucrose synthase activity was statistically related to tissue ammonium. Overall, the enzymatic responses that were observed indicate a tight coupling between carbon and nitrogen metabolism that is strongly influenced by prevailing environmental conditions, especially temperature, salinity, and environmental nutrient levels.     

Carbon and nitrogen stoichiometry and nitrogen cycling rates in streams

Stoichiometric analyses can be used to investigate the linkages between N and C cycles and how these linkages influence biogeochemistry at many scales, from components of individual ecosystems up to the biosphere. N-specific NH₄⁺ uptake rates were measured in eight streams using short-term ¹⁵N tracer additions, and C to N ratios (C:N) were determined from living and non-living organic matter collected from ten streams. These data were also compared to previously published data compiled from studies of lakes, ponds, wetlands, forests, and tundra. There was a significant negative relationship between C:N and N-specific uptake rate; C:N could account for 41% of the variance in N-specific uptake rate across all streams, and the relationship held in five of eight streams. Most of the variation in N-specific uptake rate was contributed by detrital and primary producer compartments with large values of C:N and small values for N-specific uptake rate. In streams, particulate materials are not as likely to move downstream as dissolved N, so if N is cycling in a particulate compartment, N retention is likely to be greater. Together, these data suggest that N retention may depend in part on C:N of living and non-living organic matter in streams. Factors that alter C:N of stream ecosystem compartments, such as removal of riparian vegetation or N fertilization, may influence the amount of retention attributed to these ecosystem compartments by causing shifts in stoichiometry. Our analysis suggests that C:N of ecosystem compartments can be used to link N-cycling models across streams.     

Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism

Beneath Australia''s large, dry Nullarbor Plain lies an extensive underwater cave system, where dense microbial communities known as ‘slime curtains'' are found. These communities exist in isolation from photosynthetically derived carbon and are presumed to be chemoautotrophic. Earlier work found high levels of nitrite and nitrate in the cave waters and a high relative abundance of Nitrospirae in bacterial 16S rRNA clone libraries. This suggested that these communities may be supported by nitrite oxidation, however, details of the inorganic nitrogen cycling in these communities remained unclear. Here we report analysis of 16S rRNA amplicon and metagenomic sequence data from the Weebubbie cave slime curtain community. The microbial community is comprised of a diverse assortment of bacterial and archaeal genera, including an abundant population of Thaumarchaeota. Sufficient thaumarchaeotal sequence was recovered to enable a partial genome sequence to be assembled, which showed considerable synteny with the corresponding regions in the genome of the autotrophic ammonia oxidiser Nitrosopumilus maritimus SCM1. This partial genome sequence, contained regions with high sequence identity to the ammonia mono-oxygenase operon and carbon fixing 3-hydroxypropionate/4-hydroxybutyrate cycle genes of N. maritimus SCM1. Additionally, the community, as a whole, included genes encoding key enzymes for inorganic nitrogen transformations, including nitrification and denitrification. We propose that the Weebubbie slime curtain community represents a distinctive microbial ecosystem, in which primary productivity is due to the combined activity of archaeal ammonia-oxidisers and bacterial nitrite oxidisers.     

Carbon and nitrogen metabolism in barley (Hordeum vulgare L.) mutants lacking ferredoxin-dependent glutamate synthase

Five mutant lines of barley (Hordeum vulgare L.), which are only able to grow at elevated levels of CO₂, contain less than 5% of the wild-type activity of ferredoxin-dependent glutamate synthase (EC 1.4.7.1). Two of these lines (RPr 82/1 and RPr 82/9) have been studied in detail. Leaves and roots of both lines contain normal activities of NADH-dependent glutamate synthase (EC 1.4.1.14) and the other enzymes of ammonia assimilation. Under conditions that minimise photorespiration, both mutants fix CO₂ at normal rates; on transfer to air, the rates drop rapidly to 15% of the wild-type. Incorporation of ¹⁴CO₂ into sugar phosphates and glycollate is increased under such conditions, whilst incorporation of radioactivity into serine, glycine, glycerate and sucrose is decreased; continuous exposure to air leads to an accumulation of ¹⁴C in malate. The concentrations of malate, glutamine, asparagine and ammonia are all high in air, whilst aspartate, alanine, glutamate, glycine and serine are low, by comparison with the wild-type parent line (cv. Maris Mink), under the same conditions. The metabolism of [¹⁴C]glutamate and [¹⁴C]glutamine by leaves of the mutants indicates a very much reduced ability to convert glutamine to glutamate. Genetic analysis has shown that the mutation in RPr 82/9 segregates as a single recessive nuclear gene.Abbreviations GDH glutamate dehydrogenase (EC 1.4.1.2) - GS glutamine synthetase (EC 6.3.1.2) - RuBP ribulose 1,5-bisphosphate     

Pelagic coelenterates and eutrophication: a review

Although eutrophication is a widespread problem in marine waters, its effects are often difficult to separate from normal fluctuations of pelagic coelenterate populations and from other anthropogenic changes due to industrial pollution, construction, introductions, global warming and overfishing. The least complex situations are in small coastal water bodies such as the Caribbean lagoons and Scandinavian fjords. Typically, the diversity of pelagic coelenterates decreases, but the biomass of a small number of species (such as the hydromedusae Aglantha digitale and Rathkea octopunctata and the scyphomedusae Aurelia aurita and Cassiopea spp.) may increase. Adaptations that may allow these species to survive under eutrophic conditions are discussed.     

The role of glutamine synthetase in regulation of nitrogen metabolism within the soil microbial community

Recent advances in our understanding of the enzymology and regulatory systems involved in microbial metabolism of N hold promise to elucidate some of the underlying factors controlling metabolism of N in soil ecosystems. A review of recent work is used to construct a paradigm for N metabolism regulation in soil based on the central role of glutamine synthetase (GS) in such regulation within the soil microbial community. The studies involved use of GS inhibitors to elucidate the role of GS activity in regulation of soil N metabolism. Such studies have shown that the glutamine formed by microbial assimilation of NH₄ ⁺ via GS activity influences the regulatory mechanisms controlling both the production and activity of enzymes involved in N metabolism. For example, these studies showed that the inhibition of GS activity within the soil microbial community relieved the repression of urease production caused by microbial assimilation of inorganic N and blocked the short-term regulation of assimilatory nitrate reductase (ANR) by NH₄ ⁺ assimilation. Other studies have indicated that common environmental factors in soil may influence GS activity in microorganisms and thereby may influence metabolism of N within the soil microbial community. The paradigm for N metabolism regulation in soil that has emerged from such studies should lead to a better understanding of the mechanisms controlling fate of N in soil ecosystems.