Nitrogen management and the future of food: Lessons from the management of energy and carbon

The food system dominates anthropogenic disruption of the nitrogen cycle by generating excess fixed nitrogen. Excess fixed nitrogen, in various guises, augments the greenhouse effect, diminishes stratospheric ozone, promotes smog, contaminates drinking water, acidifies rain, eutrophies bays and estuaries, and stresses ecosystems. Yet, to date, regulatory efforts to limit these disruptions largely ignore the food system. There are many parallels between food and energy. Food is to nitrogen as energy is to carbon. Nitrogen fertilizer is analogous to fossil fuel. Organic agriculture and agricultural biotechnology play roles analogous to renewable energy and nuclear power in political discourse. Nutrition research resembles energy end-use analysis. Meat is the electricity of food. As the agriculture and food system evolves to contain its impacts on the nitrogen cycle, several lessons can be extracted from energy and carbon: (i) set the goal of ecosystem stabilization; (ii) search the entire production and consumption system (grain, livestock, food distribution, and diet) for opportunities to improve efficiency; (iii) implement cap-and-trade systems for fixed nitrogen; (iv) expand research at the intersection of agriculture and ecology, and (v) focus on the food choices of the prosperous. There are important nitrogen-carbon links. The global increase in fixed nitrogen may be fertilizing the Earth, transferring significant amounts of carbon from the atmosphere to the biosphere, and mitigating global warming. A modern biofuels industry someday may produce biofuels from crop residues or dedicated energy crops, reducing the rate of fossil fuel use, while losses of nitrogen and other nutrients are minimized.

Nitrogen metabolism in haloarchaea

The nitrogen cycle (N-cycle), principally supported by prokaryotes, involves different redox reactions mainly focused on assimilatory purposes or respiratory processes for energy conservation. As the N-cycle has important environmental implications, this biogeochemical cycle has become a major research topic during the last few years. However, although N-cycle metabolic pathways have been studied extensively in Bacteria or Eukarya, relatively little is known in the Archaea. Halophilic Archaea are the predominant microorganisms in hot and hypersaline environments such as salted lakes, hot springs or salted ponds. Consequently, the denitrifying haloarchaea that sustain the nitrogen cycle under these conditions have emerged as an important target for research aimed at understanding microbial life in these extreme environments. The haloarchaeon Haloferax mediterranei was isolated 20 years ago from Santa Pola salted ponds (Alicante, Spain). It was described as a denitrifier and it is also able to grow using NO3-, NO2- or NH4+ as inorganic nitrogen sources. This review summarizes the advances that have been made in understanding the N-cycle in halophilic archaea using Hfx mediterranei as a haloarchaeal model. The results obtained show that this microorganism could be very attractive for bioremediation applications in those areas where high salt, nitrate and nitrite concentrations are found in ground waters and soils.

A contribution to the characterization of Illinois reference/background conditions for setting nitrogen criteria for surface waters in Illinois /

"Final report to Illinois Council on Food and Agricultural Research (C-FAR)."

d13C and d15N stable isotopes values, total nitrogen and C/N ratios of sediment core GeoB4801-1

Rising stable nitrogen isotope ratios (d15N) in dated sediment records of the German Bight/SE North Sea track river-induced coastal eutrophication over the last 2 centuries. Fully exploiting their potential for reconstructions of pristine conditions and quantitative analysis of historical changes in the nitrogen cycle from these sediment records requires knowledge on processes that alter the isotopic signal in non-living organic matter (OM) of sinking particles and sediments. In this study, we analyze the isotopic composition of particulate nitrogen (PN) in the water column during different seasons, in surface sediments, and in sediment cores to assess diagenetic influences on the isotopic composition of OM. Amino acid (AA) compositions of suspended matter, surface sediments, and dated cores at selected sites of the German Bight serve as indicators for quality and degradation state of PN. The d15N of PN in suspended matter had seasonal variances caused by two main nitrate sources (oceanic and river) and different stages of nitrate availability during phytoplankton assimilation. Elevated d15N values (> 20 per mil) in suspended matter near river mouths and the coast coincide with a coastal water mass receiving nitrate with elevated isotope signal (d15N > 10 per mil) derived from anthropogenic input. Particulate nitrogen at offshore sites fed by oceanic nitrate having a d15N between 5 and 6 per mil had low d15N values (< 2 per mil), indicative of an incipient phytoplankton bloom. Surface sediments along an offshore-onshore transect also reflect the gradient of low d15N of nitrate in offshore sites to high values near river mouths, but the range of values is smaller than between the end members listed above and integrates the annual d15N of detritus. Sediment cores from the coastal sector of the gradient show an increasing d15N trend (increase of 2.5 per mil) over the last 150 years. This is not related to any change in AA composition and thus reflects eutrophication. The d15N signals from before AD 1860 represent a good estimation of pre-industrial isotopic compositions with minimal diagenetic overprinting. Rising d13C in step with rising d15N in these cores is best explained by increasing productivity caused by eutrophication.

Effects of nitrogen limitation on Dunaliella sp.–Alteromonas sp. interactions: from mutualistic to competitive relationships.

Interactions between photosynthetic and non-photosynthetic microorganisms play an essential role in natural aquatic environments and the contribution of bacteria and microalgae to the nitrogen cycle can lead to both competitive and mutualistic relationships. Nitrogen is considered to be, with phosphorus and iron, one of the main limiting nutrients for primary production in the oceans and its availability experiences large temporal and geographical variations. For these reasons, it is important to understand how competitive and mutualistic interactions between photosynthetic and heterotrophic microorganisms are impacted by nitrogen limitation. In a previous study performed in batch cultures, the addition of a selected bacterial strain of Alteromonas sp. resulted in a final biomass increase in the green alga Dunaliella sp. as a result of higher nitrogen incorporation into the algal cells. The present work focuses on testing the potential of the same microalgae–bacteria association and nitrogen interactions in chemostats limited by nitrogen. Axenic and mixed cultures were compared at two dilution rates to evaluate the impact of nitrogen limitation on interactions. The addition of bacteria resulted in increased cell size in the microalgae, as well as decreased carbon incorporation, which was exacerbated by high nitrogen limitation. Biochemical analyses for the different components including microalgae, bacteria, non-living particulate matter, and dissolved organic matter, suggested that bacteria uptake carbon from carbon-rich particulate matter released by microalgae. Dissolved organic nitrogen released by microalgae was apparently not taken up by bacteria, which casts doubt on the remineralization of dissolved organic nitrogen by Alteromonas sp. in chemostats. Dunaliella sp. obtained ammonium-nitrogen more efficiently under lower nitrogen limitation. Overall, we revealed competition between microalgae and bacteria for ammonium when this was in continuous but limited supply. Competition for mineral nitrogen increased with nitrogen limitation. From our study we suggest that competitive or mutualistic relationships between microalgae and bacteria largely depend on the ecophysiological status of the two microorganisms. The outcome of microalgae–bacteria interactions in natural and artificial ecosystems largely depends on environmental factors. Our results indicate the need to improve understanding of the interaction/s between these microbial players

Nitrogen removal and sustainability of vertical flow constructed wetlands for small scale wastewater treatment

The challenge for wastewater professionals is to design and operate treatment processes that support human well being and are environmentally sensitive throughout the life-cycle. This research focuses on one technology for small-scale wastewater treatment: the vertical flow constructed wetland (VFCW), which is herein investigated for the capacity to remove ammonium and nitrate nitrogen from wastewater. Hydraulic regime and presence/absence of vegetation are the basis for a three-phase bench scale experiment to determine oxygen transfer and nitrogen fate in VFCWs. Results show that 90% NH4+-N removal is achieved in aerobic downflow columns, 60% NO3--N removal occurs in anaerobic upflow columns, and 60% removal of total nitrogen can be achieved in downflow-upflow in-series. The experimental results are studied further using a variably saturated flow and reactive transport model, which allows a mechanistic explanation of the fate and transport of oxygen and nitrogen. The model clarifies the mechanisms of oxygen transport and nitrogen consumption, and clarifies the need for readily biodegradable COD for denitrification. A VFCW is then compared to a horizontal flow constructed wetland (HFCW) for life cycle environmental impacts. High areal emissions of greenhouse gases from VFCWs compared to HFCWs are the driver for the study. The assessment shows that because a VFCW is only 25% of the volume of an HFCW designed for the same treatment quality, the VFCW has only 25-30% of HFCW impacts over 12 impact categories and 3 damage categories. Results show that impacts could be reduced by design improvements. Design recommendations are downflow wetlands for nitrification, upflow wetlands for denitrification, series wetlands for total nitrogen removal, hydraulic load of 142 L/m2d, 30 cm downflow wetland depth, 1.0 m upflow wetland depth, recycle, vegetation and medium-grained sand. These improvements will optimize nitrogen removal, minimize gaseous emissions, and reduce wetland material requirements, thus reducing environmental impact without sacrificing wastewater treatment quality.

A síntese da amônia: alguns aspectos históricos

The ammonia synthesis from its elements plays an important role in the survival of humankind. A short historical development of discoveries of the nitrogen cycle, the nitrogen sources for agriculture and the ammonia synthesis (in laboratory and industry) are presented. Some brief aspects of nitrogen chemistry are described. Short biographies of Fritz Haber and Carl Bosch, the main persons in this epopee, are also presented.

Characterization of Nitric Oxide Reductase (NOR) from pseudomonas nautica, a study on biologic nitric oxide reduction

Dissertation submitted to obtain the phD degree in Biochemistry, specialty in Physical- Biochemistry, by the Faculdade de Ciências e Tecnologia from the Universidade Nova de Lisboa

Impacts of climate change scenarios on terrestrial productivity and biomass for energy in the Iberian Peninsula: assessment through the JSBACH model

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente, Perfil de Gestão e Sistemas Ambientais

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares [sim]54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

Avaluació ambiental del cicle del nitrògen a Catalunya: evolució 1997-2003

Aquesta memòria és un estudi sobre l’avaluació ambiental del nitrogen a Catalunya, tot analitzant l’evolució que aquest element tant important ha tingut des del 1997 al 2003 en el nostre país

A síntese da amônia: alguns aspectos históricos

The ammonia synthesis from its elements plays an important role in the survival of humankind. A short historical development of discoveries of the nitrogen cycle, the nitrogen sources for agriculture and the ammonia synthesis (in laboratory and industry) are presented. Some brief aspects of nitrogen chemistry are described. Short biographies of Fritz Haber and Carl Bosch, the main persons in this epopee, are also presented.

Da escassez ao estresse do planeta: um século de mudanças no ciclo do nitrogênio

Heavy metals and pesticides are usually associated with the main problems humankind has created in the natural environment. However, compounds with characteristics of essential macronutrients are causing serious environmental changes that could intensify, compromising the diversity of life on the planet. This is the case of nitrogen compounds, produced by industrial processes for use in intensive agriculture in addition to those unwittingly produced from human activities, available in excess in the environment. These compounds warrant greater attention from researchers in various fields of knowledge and public agencies for environmental control, toward minimizing their availability in the environment, thereby returning conditions closer to the natural environmental balance of the planet.

The Role of Specific Amino Acids in the Formation of Ternary Complexes in Nitrogenase Regulation in the Photosynthetic Bacterium Rhodobacter capsulatus

L'azote est l'un des éléments les plus essentiels dans le monde pour les êtres vivants, car il est essentiel pour la production des éléments de base de la cellule, les acides aminés, les acides nucléiques et les autres constituants cellulaires. L’atmosphère est composé de 78% d'azote gazeux, une source d'azote inutilisable par la plupart des organismes à l'exception de ceux qui possèdent l’enzyme nitrogénase, tels que les bactéries diazotrophique. Ces micro-organismes sont capables de convertir l'azote atmosphérique en ammoniac (NH3), qui est l'une des sources d'azote les plus préférables. Cette réaction exigeant l’ATP, appelée fixation de l'azote, est catalysée par une enzyme, nitrogénase, qui est l'enzyme la plus importante dans le cycle de l'azote. Certaines protéines sont des régulateurs potentiels de la synthèse de la nitrogénase et de son activité; AmtB, DraT, DraG, les protéines PII, etc.. Dans cette thèse, j'ai effectué diverses expériences afin de mieux comprendre leurs rôles détailés dans Rhodobacter capsulatus. La protéine membranaire AmtB, très répandue chez les archaea, les bactéries et les eucaryotes, est un membre de la famille MEP / Amt / Rh. Les protéines AmtB sont des transporteurs d'ammonium, importateurs d'ammonium externe, et ont également été suggéré d’agir comme des senseurs d'ammonium. Il a été montré que l’AmtB de Rhodobacter capsulatus fonctionne comme un capteur pour détecter la présence d'ammonium externe pour réguler la nitrogénase. La nitrogénase est constituée de deux métalloprotéines nommées MoFe-protéine et Fe-protéine. L'addition d'ammoniaque à une culture R. capsulatus conduit à une série de réactions qui mènent à la désactivation de la nitrogénase, appelé "nitrogénase switch-off". Une réaction critique dans ce processus est l’ajout d’un groupe ADP-ribose à la Fe-protéine par DraT. L'entrée de l'ammoniac dans la cellule à travers le pore AmtB est contrôlée par la séquestration de GlnK. GlnK est une protéine PII et les protéines PII sont des protéines centrales dans la régulation du métabolisme de l'azote. Non seulement la séquestration de GlnK par AmtB est importante dans la régulation nitrogénase, mais la liaison de l'ammonium par AmtB ou de son transport partiel est également nécessaire. Les complexes AmtB-GlnK sont supposés de lier DraG, l’enzyme responsable pour enlever l'ADP-ribose ajouté à la nitrogénase par DraT, ainsi formant un complexe ternaire. Dans cette thèse certains détails du mécanisme de transduction du signal et de transport d'ammonium ont été examinés par la génération et la caractérisation d’un mutant dirigé, RCZC, (D335A). La capacité de ce mutant, ainsi que des mutants construits précédemment, RCIA1 (D338A), RCIA2 (G344C), RCIA3 (H193E) et RCIA4 (W237A), d’effectuer le « switch-off » de la nitrogénase a été mesurée par chromatographie en phase gazeuse. Les résultats ont révélé que tous les résidus d'acides aminés ci-dessus ont un rôle essentiel dans la régulation de la nitrogénase. L’immunobuvardage a également été effectués afin de vérifier la présence de la Fe-protéine l'ADP-ribosylée. D335, D388 et W237 semblent être cruciales pour l’ADP-ribosylation, puisque les mutants RCZC, RCIA1 et RCIA4 n'a pas montré de l’ADP-ribosylation de la Fe-protéine. En outre, même si une légère ADP-ribosylation a été observée pour RCIA2 (G344C), nous le considérons comme un résidu d'acide aminé important dans la régulation de la nitrogénase. D’un autre coté, le mutant RCIA3 (H193E) a montré une ADP-ribosylation de la Fe-protéine après un choc d'ammonium, par conséquent, il ne semble pas jouer un rôle important dans l’ADP-ribosylation. Par ailleurs R. capsulatus possède une deuxième Amt appelé AmtY, qui, contrairement à AmtB, ne semble pas avoir des rôles spécifiques. Afin de découvrir ses fonctionnalités, AmtY a été surexprimée dans une souche d’E. coli manquant l’AmtB (GT1001 pRSG1) (réalisée précédemment par d'autres membres du laboratoire) et la formation des complexes AmtY-GlnK en réponse à l'addition d’ammoniac a été examinée. Il a été montré que même si AmtY est en mesure de transporter l'ammoniac lorsqu'il est exprimé dans E. coli, elle ne peut pass’ associer à GlnK en réponse à NH4 +.

La dynamique spatio-temporelle des flux d’oxyde nitreux (N2O) des lacs, rivières, et étangs boréaux

L’oxyde nitreux (N2O), un puissant gaz à effet de serre (GES) ayant plus de 300 fois le potentiel de réchauffement du dioxyde de carbone (CO2), est produit par des processus microbiens du cycle de l’azote (N). Bien que les eaux de surface continentales soient reconnues comme des sites actifs de transformations de l’azote, leur intégration dans les budgets globaux de N2O comporte de nombreuses incertitudes, dont l’absence des lacs dans ces modèles. Le biome boréal est caractérisé par une des plus grandes densités d’eaux douces au monde, pourtant aucune évaluation exhaustive des émissions aquatiques de N2O n’a à date été conduite dans cette région. Dans la présente étude, nous avons mesuré les concentrations de N2O à travers une large gamme de lacs, rivières, et étangs, dans quatre régions boréales du Québec (Canada), et nous avons calculé les flux eau-air résultants. Les flux nets fluctuent entre -23.1 et 177.9 μmol m-2 J-1, avec une grande variabilité inter-système, inter-régionale, et saisonnière. Étonnamment, 40% des systèmes échantillonnés agissaient en tant que puits de N2O durant l’été, et le réseau d’eaux de surfaces d’une des régions était un net consommateur de N2O. Les concentrations maximales de N2O ont été mesurées en hiver dû à l’accumulation de ce gaz sous la glace. Nous avons estimé que l’émission qui en résulte lors de la fonte des glaces représente 20% des émissions annuelles des eaux douces. Parmi les types d’eaux douces échantillonnées, les lacs sont les principaux responsables du flux aquatique net (jusqu’à 90%), et doivent donc être intégrés dans les budgets globaux de N2O. En se basant sur les données empiriques de la littérature, nous avons éstimé l’émission globale de N2O des eaux douces à 0.78 Tg N (N2O) an-1. Ce chiffre est influencé par les émissions des régions de hautes latitudes (tel que le biome boréal) dont les flux nets varient de positif à négatif constituant -9 à 27 % du total.