The relationship between leaf nitrogen, nitrogen metabolites and herbivory in two species of Nyctaginaceae from the Brazilian Cerrado

Guapira graciliflora and Neea theifera are taxonomically related species of the tribe Pisoneae. Both species are found in the same environment, the Brazilian Cerrado, and therefore, are subjected to similar selective pressures. These species occur in oligotrophic environments, yet contain high concentrations of nitrogen in their leaves. The present study was carried out to investigate the ecological role of nitrogen in herbivory on these species. The differences in the N content, compositions of secondary N-metabolites, mechanical resistance, and water content between their leaves indicate that these species have different adaptations as defense mechanisms. In both species, their high nitrogen content seems to promote herbivory. The presence of secondary nitrogen metabolites does not prevent the species from suffering intense damage by herbivores on their early leaves. The herbivory rates observed were lower for mature leaves of both species than for young leaves. In G. graciliflora, nutritional content and leaf hardness are the most important variables correlated with reduction of herbivory rates, whereas in N. theifera, N compounds are also correlated with herbivory rates. Despite the differences in the strategies of these two species, they exhibit a similar efficiency of protection against natural enemies because their total herbivory rates are similar. The difference in their N defense allocation may imply benefits for survival under Cerrado conditions. We briefly discuss the oligotrophic habitat conditions of the studied plants and possible advantages of their strategies of N accumulation and metabolic uses. (C) 2011 Elsevier B.V. All rights reserved.

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

Abstract Background The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of nitrogen fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of nitrogen fixation genes. The current practice for computational prediction of nitrogen fixation is to use the presence of the nifH and/or nifD genes. Results Based on a careful comparison of the repertoire of nitrogen fixation genes in known diazotroph species we propose a new criterion for computational prediction of nitrogen fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix nitrogen. The taxonomic distribution of nitrogen fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that nitrogen fixation occurs in 13 different phyla. Of these, seven phyla had not hitherto been known to contain species capable of nitrogen fixation. Our analyses also identified protein sequences that are similar to nitrogenase in organisms that do not meet the minimum-gene-set criteria. The existence of nitrogenase-like proteins lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests their potential for performing other, as yet unidentified, metabolic functions. Conclusions Our predictions expand the known phylogenetic diversity of nitrogen fixation, and suggest that this trait may be much more common in nature than it is currently thought. The diverse phylogenetic distribution of nitrogenase-like proteins indicates potential new roles for anciently duplicated and divergent members of this group of enzymes.

Nitrogen fertilizer (15N) leaching in a central pivot fertigated coffee crop

Nitrogen has a complex dynamics in the soil-plant-atmosphere system. N fertilizers are subject to chemical and microbial transformations in soils that can result in significant losses. Considering the cost of fertilizers, the adoption of good management practices like fertigation could improve the N use efficiency by crops. Water balances (WB) were applied to evaluate fertilizer N leaching using 15N labeled urea in west Bahia, Brazil. Three scenarios (2008/2009) were established: i) rainfall + irrigation the full year, ii) rainfall only; and iii) rainfall + irrigation only in the dry season. The water excess was considered equal to the deep drainage for the very flat area (runoff = 0) with a water table located several meters below soil surface (capillary rise = 0). The control volume for water balance calculations was the 0 - 1 m soil layer, considering that it involves the active root system. The water drained below 1 m was used to estimate fertilizer N leaching losses. WB calculations used the mathematic model of Penman-Monteith for evapotranspiration, considering the crop coefficient equal to unity. The high N application rate associated to the high rainfall plus irrigation was found to be the main cause for leaching, which values were 14.7 and 104.5 kg ha-1 for the rates 400 and 800 kg ha-1 of N, corresponding to 3.7 and 13.1 % of the applied fertilizer, respectively.

The nitrogen sufficiency index underlying estimates of nitrogen fertilization requirements of common bean

Chlorophyll determination with a portable chlorophyll meter can indicate the period of highest N demand of plants and whether sidedressing is required or not. In this sense, defining the optimal timing of N application to common bean is fundamental to increase N use efficiency, increase yields and reduce the cost of fertilization. The objectives of this study were to evaluate the efficiency of N sufficiency index (NSI) calculated based on the relative chlorophyll index (RCI) in leaves, measured with a portable chlorophyll meter, as an indicator of time of N sidedressing fertilization and to verify which NSI (90 and 95 %) value is the most appropriate to indicate the moment of N fertilization of common bean cultivar Perola. The experiment was carried out in the rainy and dry growing seasons of the agricultural year 2009/10 on a dystroferric Red Nitosol, in Botucatu, São Paulo State, Brazil. The experiment was arranged in a randomized complete block design with five treatments, consisting of N managements (M1: 200 kg ha-1 N (40 kg at sowing + 80 kg 15 days after emergence (DAE) + 80 kg 30 DAE); M2: 100 kg ha-1 N (20 kg at sowing + 40 kg 15 DAE + 40 kg 30 DAE); M3: 20 kg ha-1 N at sowing + 30 kg ha-1 when chlorophyll meter readings indicated NSI < 95 %; M4: 20 kg ha-1 N at sowing + 30 kg ha-1 N when chlorophyll meter readings indicated NSI < 90 % and, M5: control (without N application)) and four replications. The variables RCI, aboveground dry matter, total leaf N concentration, production components, grain yield, relative yield, and N use efficiency were evaluated. The RCI correlated with leaf N concentrations. By monitoring the RCI with the chlorophyll meter, the period of N sidedressing of common bean could be defined, improving N use efficiency and avoiding unnecessary N supply to common bean. The NSI 90 % of the reference area was more efficient to define the moment of N sidedressing of common bean, to increase N use efficiency.

Validation of models for predicting milk urea nitrogen concentrations, estimating dry matter intake by the NRC (2001)

The objective of this study was to validate three different models for predicting milk urea nitrogen using field conditions, attempting to evaluate the nutritional adequacy diets for dairy cows and prediction of nitrogen excreted to the environment. Observations (4,749) from 855 cows were used. Milk yield, body weight (BW), days in milk and parity were recorded on the milk sampling days. Milk was sampled monthly, for analysis of milk urea nitrogen (MUN), fat, protein, lactose and total solids concentration and somatic cells count. Individual dry matter intake was estimated using the NRC (2001). The three models studied were derived from a first one to predict urinary nitrogen (UN). Model 1 was MUN = UN/12.54, model 2 was MUN = UN/17.6 and model 3 was MUN = UN/(0.0259 × BW), adjusted by body weight effect. To evaluate models, they were tested for accuracy, precision and robustness. Despite being more accurate (mean bias = 0.94 mg/dL), model 2 was less precise (residual error = 4.50 mg/dL) than model 3 (mean bias = 1.41 and residual error = 4.11 mg/dL), while model 1 was the least accurate (mean bias = 6.94 mg/dL) and the least precise (residual error = 5.40 mg/dL). They were not robust, because they were influenced by almost all the variables studied. The three models for predicting milk urea nitrogen were different with respect to accuracy, precision and robustness.

Tiller population density and tillering dynamics in marandu palisade grass subjected to strategies of rotational stocking management and nitrogen fertilization

The objective of this experiment was to evaluate tiller population density and the dynamics of the tillering process in marandu palisade grass subjected to strategies of rotational stocking management and nitrogen fertilization. Treatments corresponded to combinations between two targets of pre-grazing conditions (sward surface height of 25 and 35 cm) and two rates of nitrogen application (50 and 200 kg ha-1 year-1), and were allocated to experimental units according to a 2 x 2 factorial arrangement in a randomised complete block design, with four replications. The following response variables were studied: initial (TPDi), intermediate (TPDm) and final (TPDf) tiller population density as well as the rates of tiller appearance (TAR) and death (TDR) and the tiller population stability index (SI). TPDi was similar to all treatments, with differences in tiller population density becoming more pronounced as the experiment progressed, resulting in larger TPDf on swards managed at 25 cm pre-grazing height. Tiller death was larger on swards managed at 35 cm, with differences in tiller appearance being recorded only from February 2010 onwards. Stability of tiller population was higher on swards managed at 25 cm pre-grazing height. Overall, there was no effect of nitrogen on the studied variables, and the most adequate grazing strategy corresponded to the pre-grazing height of 25 cm, regardless of the nitrogen application rate used.

Database of diazotrophs in global ocean: abundances, biomass and nitrogen fixation rates

[EN] Marine N2 fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N2) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems 5 and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR 10 assays targeting the nifH genes) and N2 fixation rates. Biomass conversion factors are estimated based on cell sizes to convert  abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. 15 Lower mean N2 fixation rate was found in the North Atlantic Ocean than the Pacific Ocean. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N2 fixation rate in the global ocean is estimated to be 62 (53–73) TgNyr−1 and the pelagic diazotrophic biomass in the global ocean is estimated to be 4.7 (2.3–9.6) TgC from cell counts and to 89 (40–20 200) TgC from nifH-based abundances. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about ±70 %. This evolving database can be used to study spatial and temporal distributions and variations of marine N2 fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models. The database is 25 stored in PANGAEA (http://doi.pangaea.de/10.1594/PANGAEA.774851).

Role of reactive oxygen and nitrogen species in the response of Prunus spp. to bicarbonate

In calcareous soils, which are a large share of agricultural soils worldwide, iron availability is limited. Consequently, the whole plant physiology is affected, because of the key role of iron in redox metabolism, resulting in reduced crop yield and quality. Peach cultivation is economically important in northern Italy, and is easily subjected to iron chlorosis. The management of iron nutrition in peach includes grafting on bicarbonate-tolerant rootstocks; other forms of management may be expensive and environmentally impacting. Four genotypes, used as rootstocks for peach and characterized by different degrees of tolerance to chlorosis, were tested in vitro on optimal and bicarbonate-enriched medium. Their redox status and antioxidant responses were assayed; the production and possible roles of nitric oxide (NO) and related compounds were also studied. The most sensitive genotypes show a stronger reduction of the antioxidant enzymatic activities and an increased oxidative stress. A high production of NO was found to be associated to resistant genotypes, whereas sensitive genotypes reacted to stress by downregulating nitrosoglutathione reductase activity. Therefore, NO is proposed to improve the internal iron availability, or to stimulate iron intake.

Modelling the effects of nitrogen deposition and carbon dioxide enrichment on forest carbon balance

Atmospheric CO2 concentration ([CO2]) has increased over the last 250 years, mainly due to human activities. Of total anthropogenic emissions, almost 31% has been sequestered by the terrestrial biosphere. A considerable contribution to this sink comes from temperate and boreal forest ecosystems of the northern hemisphere, which contain a large amount of carbon (C) stored as biomass and soil organic matter. Several potential drivers for this forest C sequestration have been proposed, including increasing atmospheric [CO2], temperature, nitrogen (N) deposition and changes in management practices. However, it is not known which of these drivers are most important. The overall aim of this thesis project was to develop a simple ecosystem model which explicitly incorporates our best understanding of the mechanisms by which these drivers affect forest C storage, and to use this model to investigate the sensitivity of the forest ecosystem to these drivers. I firstly developed a version of the Generic Decomposition and Yield (G’DAY) model to explicitly investigate the mechanisms leading to forest C sequestration following N deposition. Specifically, I modified the G’DAY model to include advances in understanding of C allocation, canopy N uptake, and leaf trait relationships. I also incorporated a simple forest management practice subroutine. Secondly, I investigated the effect of CO2 fertilization on forest productivity with relation to the soil N availability feedback. I modified the model to allow it to simulate short-term responses of deciduous forests to environmental drivers, and applied it to data from a large-scale forest Free-Air CO2 Enrichment (FACE) experiment. Finally, I used the model to investigate the combined effects of recent observed changes in atmospheric [CO2], N deposition, and climate on a European forest stand. The model developed in my thesis project was an effective tool for analysis of effects of environmental drivers on forest ecosystem C storage. Key results from model simulations include: (i) N availability has a major role in forest ecosystem C sequestration; (ii) atmospheric N deposition is an important driver of N availability on short and long time-scales; (iii) rising temperature increases C storage by enhancing soil N availability and (iv) increasing [CO2] significantly affects forest growth and C storage only when N availability is not limiting.

Organic fertilization of peach trees: implication on nitrogen availability, root growth and carbon distribution within plant

In the last years, sustainable horticulture has been increasing; however, to be successful this practice needs an efficient soil fertility management to maintain a high productivity and fruit quality standards. For this purpose composted organic materials from agri-food industry and municipal solid waste has been used as a source to replace chemical fertilizers and increase soil organic matter. To better understand the influence of compost application on soil fertility and plant growth, we carried out a study comparing organic and mineral nitrogen (N) fertilization in micro propagated plants, potted trees and commercial peach orchard with these aims: 1. evaluation of tree development, CO2 fixation and carbon partition to the different organs of two-years-old potted peach trees. 2. Determination of soil N concentration and nitrate-N effect on plant growth and root oxidative stress of micro propagated plant after increasing rates of N applications. 3. Assessment of soil chemical and biological fertility, tree growth and yield and fruit quality in a commercial orchard. The addition of compost at high rate was effective in increasing CO2 fixation, promoting root growth, shoot and fruit biomass. Furthermore, organic fertilizers influenced C partitioning, favoring C accumulation in roots, wood and fruits. The higher CO2 fixation was the result of a larger tree leaf area, rather than an increase in leaf photosynthetic efficiency, showing a stimulation of plant growth by application of compost. High concentrations of compost increased total soil N concentration, but were not effective in increasing nitrate-N soil concentration; in contrast mineral-N applications increased linearly soil nitrate-N, even at the lowest rate tested. Soil nitrate-N concentration influenced positively plant growth at low rate (60- 80 mg kg-1), whereas at high concentrations showed negative effects. In this trial, the decrease of root growth, as a response to excessive nitrate-N soil concentration, was not anticipated by root oxidative stress. Continuous annual applications of compost for 10 years enhanced soil organic matter content and total soil N concentration. Additionally, high rate of compost application (10 t ha-1 year-1) enhanced microbial biomass. On the other hand, different fertilizers management did not modify tree yield, but influenced fruit size and precocity index. The present data support the idea that organic fertilizers can be used successfully as a substitute of mineral fertilizers in fruit tree nutrient management, since they promote an increase of soil chemical and biological fertility, prevent excessive nitrate-N soil concentration, promote plant growth and potentially C sequestration into the soil.

Influence of nitrogen and soil physical characteristics on belowground carbon flux dynamics of woody plants

At ecosystem level soil respiration (Rs) represents the largest carbon (C) flux after gross primary productivity, being mainly generated by root respiration (autotrophic respiration, Ra) and soil microbial respiration (heterotrophic respiration, Rh). In the case of terrestrial ecosystems, soils contain the largest C-pool, storing twice the amount of C contained in plant biomass. Soil organic matter (SOM), representing the main C storage in soil, is decomposed by soil microbial community. This process produces CO2 which is mainly released as Rh. It is thus relevant to understand how microbial activity is influenced by environmental factors like soil temperature, soil moisture and nutrient availability, since part of the CO2 produced by Rh, directly increases atmospheric CO2 concentration and therefore affects the phenomenon of climate change. Among terrestrial ecosystems, agricultural fields have traditionally been considered as sources of atmospheric CO2. In agricultural ecosystems, in particular apple orchards, I identified the role of root density, soil temperature, soil moisture and nitrogen (N) availability on Rs and on its two components, Ra and Rh. To do so I applied different techniques to separate Rs in its two components, the ”regression technique” and the “trenching technique”. I also studied the response of Ra to different levels of N availability, distributed either in a uniform or localized way, in the case of Populus tremuloides trees. The results showed that Rs is mainly driven by soil temperature, to which it is positively correlated, that high levels of soil moisture have inhibiting effects, and that N has a negligible influence on total Rs, as well as on Ra. Further I found a negative response of Rh to high N availability, suggesting that microbial decomposition processes in the soil are inhibited by the presence of N. The contribution of Ra to Rs was of 37% on average.

Nitrogen-bridged polyphenylene-based materials for electronic applications

Conjugated polymers are macromolecules that possess alternating single and double bonds along the main chain. These polymers combine the optoelectronic properties of semiconductors with the mechanical properties and processing advantages of plastics. In this thesis we discuss the synthesis, characterization and application of polyphenylene-based materials in various electronic devices. Poly(2,7-carbazole)s have the potential to be useful as blue emitters, but also as donor materials in solar cells due to their better hole-accepting properties. However, it is associated with two major drawbacks (1) the emission maximum occurs at 421 nm where the human eye is not very sensitive and (2) the 3- and 6- positions of carbazole are susceptible to chemical or electrochemical degradation. To overcome these problems, the ladder-type nitrogen-bridged polymers are synthesized. The resulting series of polymers, nitrogen-bridged poly(ladder-type tetraphenylene), nitrogen-bridged poly(ladder-type pentaphenylene), nitrogen-bridged poly(ladder-type hexaphenylene) and its derivatives are discussed in the light of photophysical and electrochemical properties and tested in PLEDs, solar cell, and OFETs. A promising trend which has emerged in recent years is the use of well defined oligomers as model compounds for their corresponding polymers. However, the uses of these molecules are many times limited by their solubility and one has to use vapor deposition techniques which require high vacuum and temperature and cannot be used for large area applications. One solution to this problem is the synthesis of small molecules having enough alkyl chain on the backbone so that they can be solution or melt processed and has the ability to form thin films like polymers as well as retain the high ordered structure characteristics of small molecules. Therefore, in the present work soluble ladderized oligomers based on thiophene and carbazole with different end group were made and tested in OFET devices. Carbazole is an attractive raw material for the synthesis of dyes since it is cheap and readily available. Carbazoledioxazine, commercially known as violet 23 is a representative compound of dioxazine pigments. As part of our efforts into developing cheap alternatives to violet 23, the synthesis and characterization of a new series of dyes by Buchwald-type coupling of 3-aminocarbazole with various isomers of chloroanthraquinone are presented.