Carbon cycling in the northern Humboldt Current off Chile

The structure of the zooplankton foodweb and their dominant carbon fluxes were studied in the upwelling system off northern Chile (Mejillones Bay; 23°S) between October 2000 and December 2002. High primary production (PP) rates (18 gC/m**2 d) were mostly due to the net-phytoplankton size fraction (>23 µm). High PP has been traditionally associated with the wind-driven upwelling fertilizing effect of equatorial subsurface waters, which favour development of a short food chain dominated by a few small clupeiform fish species. The objective of the present work was to study the trophic carbon flow through the first step of this 'classical chain' (from phytoplankton to primary consumers such as copepods and euphausiids) and the carbon flow towards the gelatinous web composed of both filter-feeding and carnivorous zooplankton. To accomplish this objective, feeding experiments with copepods, appendicularians, ctenophores, and chaetognaths were conducted using naturally occurring plankton prey assemblages. Throughout the study, the total carbon ingestion rates showed that the dominant appendicularian species and small copepods consumed an average of 7 and 5 µgC/ind d, respectively. In addition, copepods ingested particles mainly in the size range of nano- and microplankton, whereas appendicularians ingested in the range of pico- and nanoplankton. Small copepods and appendicularians removed a small fraction of total daily PP (range 6-11%). However, when the pico- + nanoplankton fractions were the major contributors to total PP (oligotrophic conditions), grazing by small copepods increased markedly to 86% of total PP. Under these more oligotrophic conditions, the euphausiids grazing increased as well, but only reached values lower than 5% of total PP. During this study, chaetognaths and ctenophores ingested an average of 1 and 14 copepods/ind d, respectively. In terms of biomass consumed, the potential impact of carnivorous gelatinous zooplankton on the small-size copepod community (preferred prey) was important (2-12% of biomass removed daily). However, their impact produced more significant results on copepod abundance (up to 33%), which suggests that carnivorous gelatinous zooplankton may even modulate (control) the abundance of some species as well as the size structure of the copepod community.

Rates of nitrogen cycling and chemo-autotrophy in the cold-water coral Lophelia pertusa

Cold-water corals (CWC) are widely distributed around the world forming extensive reefs at par with tropical coral reefs. They are hotspots of biodiversity and organic matter processing in the world's deep oceans. Living in the dark they lack photosynthetic symbionts and are therefore considered to depend entirely on the limited flux of organic resources from the surface ocean. While symbiotic relations in tropical corals are known to be key to their survival in oligotrophic conditions, the full metabolic capacity of CWC has yet to be revealed. Here we report isotope tracer evidence for efficient nitrogen recycling, including nitrogen assimilation, regeneration, nitrification and denitrification. Moreover, we also discovered chemoautotrophy and nitrogen fixation in CWC and transfer of fixed nitrogen and inorganic carbon into bulk coral tissue and tissue compounds (fatty acids and amino acids). This unrecognized yet versatile metabolic machinery of CWC conserves precious limiting resources and provides access to new nitrogen and organic carbon resources that may be essential for CWC to survive in the resource-depleted dark ocean.

Phytoplankton responses and associated carbon cycling during shipboard carbonate chemistry manipulation experiments conducted around Northwest European shelf seas

The ongoing oceanic uptake of anthropogenic carbon dioxide (CO2) is significantly altering the carbonate chemistry of seawater, a phenomenon referred to as ocean acidification. Experimental manipulations have been increasingly used to gauge how continued ocean acidification will potentially impact marine ecosystems and their associated biogeochemical cycles in the future; however, results amongst studies, particularly when performed on natural communities, are highly variable, which may reflect community/environment-specific responses or inconsistencies in experimental approach. To investigate the potential for identification of more generic responses and greater experimentally reproducibility, we devised and implemented a series (n = 8) of short-term (2-4 days) multi-level (>=4 conditions) carbonate chemistry/nutrient manipulation experiments on a range of natural microbial communities sampled in Northwest European shelf seas. Carbonate chemistry manipulations and resulting biological responses were found to be highly reproducible within individual experiments and to a lesser extent between geographically separated experiments. Statistically robust reproducible physiological responses of phytoplankton to increasing pCO2, characterised by a suppression of net growth for small-sized cells (<10 µm), were observed in the majority of the experiments, irrespective of natural or manipulated nutrient status. Remaining between-experiment variability was potentially linked to initial community structure and/or other site-specific environmental factors. Analysis of carbon cycling within the experiments revealed the expected increased sensitivity of carbonate chemistry to biological processes at higher pCO2 and hence lower buffer capacity. The results thus emphasise how biogeochemical feedbacks may be altered in the future ocean.

Upwelling and isolation in oxygen-depleted anticyclonic modewater eddies and implications for nitrate cycling

The physical (temperature, salinity, velocity) and biogeochemical (oxygen, nitrate) structure of an oxygen depleted coherent, baroclinic, anticyclonic mode-water eddy (ACME) is investigated using high-resolution autonomous glider and ship data. A distinct core with a diameter of about 70 km is found in the eddy, extending from about 60 to 200 m depth and. The core is occupied by fresh and cold water with low oxygen and high nitrate concentrations, and bordered by local maxima in buoyancy frequency. Velocity and property gradient sections show vertical layering at the flanks and underneath the eddy characteristic for vertical propagation (to several hundred-meters depth) of near inertial internal waves (NIW) and confirmed by direct current measurements. A narrow region exists at the outer edge of the eddy where NIW can propagate downward. NIW phase speed and mean flow are of similar magnitude and critical layer formation is expected to occur. An asymmetry in the NIW pattern is seen that possible relates to the large-scale Ekman transport interacting with ACME dynamics. NIW/mean flow induced mixing occurs close to the euphotic zone/mixed layer and upward nutrient flux is expected and supported by the observations. Combing high resolution nitrate (NO3-) data with the apparent oxygen utilization (AOU) reveals AOU:NO3- ratios of 16 which are much higher than in the surrounding waters (8.1). A maximum NO3- deficit of 4 to 6 µmol kg-1 is estimated for the low oxygen core. Denitrification would be a possible explanation. This study provides evidence that the recycling of NO3-, extracted from the eddy core and replenished into the core via the particle export, may quantitatively be more important. In this case, the particulate phase is of keys importance in decoupling the nitrogen from the oxygen cycling.

Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone

Oxygen minimum zones are expanding globally, and at present account for around 20-40% of oceanic nitrogen loss. Heterotrophic denitrification and anammox-anaerobic ammonium oxidation with nitrite-are responsible for most nitrogen loss in these low-oxygen waters. Anammox is particularly significant in the eastern tropical South Pacific, one of the largest oxygen minimum zones globally. However, the factors that regulate anammox-driven nitrogen loss have remained unclear. Here, we present a comprehensive nitrogen budget for the eastern tropical South Pacific oxygen minimum zone, using measurements of nutrient concentrations, experimentally determined rates of nitrogen transformation and a numerical model of export production. Anammox was the dominant mode of nitrogen loss at the time of sampling. Rates of anammox, and related nitrogen transformations, were greatest in the productive shelf waters, and tailed off with distance from the coast. Within the shelf region, anammox activity peaked in both upper and bottom waters. Overall, rates of nitrogen transformation, including anammox, were strongly correlated with the export of organic matter. We suggest that the sinking of organic matter, and thus the release of ammonium into the water column, together with benthic ammonium release, fuel nitrogen loss from oxygen minimum zones.

Emissions and economic costs of cycling compact fluorescent lamps with integrated ballasts

This paper proposes a way to quantify the emissions of mercury (Hg) and CO2 associated with the manufacture and operation of compact fluorescent lamps with integrated ballasts (CFLis), as well as the economic cost of using them under different operating cycles. The main purpose of this paper is to find simple criteria for reducing the polluting emissions under consideration and the economic cost of CFLi to a minimum. A lifetime model is proposed that allows the emissions and costs to be described as a function of degradation from turning CFLi on and their continuous operation. An idealized model of a CFLi is defined that combines characteristics stated by different manufacturers. In addition, two CFLi models representing poor-quality products are analyzed. It was found that the emissions and costs per unit of time of operation of the CFLi depend linearly on the number of times per unit of time it is turned on and the time of continuous operation. The optimal conditions (lowest emissions and costs) depend on the place of manufacture, the place of operation and the quality of the components of the lamp/ballast. Finally, it was also found that for each lamp, there are intervals when it is turned off during which emissions of pollutants and costs are identical regardless of how often the lamp is turned on or the time it remains on. For CO2 emissions, the lamp must be off up to 5 minutes; for the cost, up to 7 minutes and for Hg emissions, up to 43 minutes. It is advisable not to turn on a CFLi sooner than 43 minutes from the last time it was turned off.

Nitrogen deposition alters nitrogen cycling and reduces soil carbon content in low-productivity semiarid Mediterranean ecosystems.

Anthropogenic N deposition poses a threat to European Mediterranean ecosystems. We combined data from an extant N deposition gradient (4.3–7.3 kg N ha−1 yr−1) from semiarid areas of Spain and a field experiment in central Spain to evaluate N deposition effects on soil fertility, function and cyanobacteria community. Soil organic N did not increase along the extant gradient. Nitrogen fixation decreased along existing and experimental N deposition gradients, a result possibly related to compositional shifts in soil cyanobacteria community. Net ammonification and nitrification (which dominated N-mineralization) were reduced and increased, respectively, by N fertilization, suggesting alterations in the N cycle. Soil organic C content, C:N ratios and the activity of β-glucosidase decreased along the extant gradient in most locations. Our results suggest that semiarid soils in low-productivity sites are unable to store additional N inputs, and that are also unable to mitigate increasing C emissions when experiencing increased N deposition.

Cycling habits and other psychological variables affecting commuting by bicycle in Madrid, Spain

To develop effective cycling policies, decision makers and administrators should know the factors influencing the use of the bicycle for daily mobility. Traditional discrete choice models tend to be based on variables such as time and cost, which do not sufficiently explain the choice of the bicycle as a mode of transportation. Because psychological factors have been identified as particularly influential in the decision to commute by bicycle, this paper examines the perceptions of cycling factors and their influence on commuting by bicycle. Perceptions are measured by attitudes, other psychological variables, and habits. Statistical differences in the variables are established in relation to the choice of commuting mode and bicycle experience (commuter, sport-leisure, no use). Doing so enables the authors to identify the main barriers to commuting by bicycle and to make recommendations for cycling policies. Two underlying structures (factors) of the attitudinal variables are identified: direct benefits and long-term benefits. Three other factors are related to variables of difficulty: physical conditions, external facilities, and individual capacities. The effect of attitudes and other psychological variables on people's decision to cycle to work-place of study is tested by using a logit model. In the case study of Madrid, Spain, the decision to cycle to work-place of study is heavily influenced by cycling habits (for noncommuting trips). Because bicycle commuting is not common, attitudes and other psychological variables play a less important role in the use of bikes.

Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses.

DNA binding with One Finger (DOF) transcription factors are involved in multiple aspects of plant growth and development but their precise roles in abiotic stress tolerance are largely unknown. Here we report a group of five tomato DOF genes, homologous to Arabidopsis Cycling DOF Factors (CDFs), that function as transcriptional regulators involved in responses to drought and salt stress and flowering-time control in a gene-specific manner. SlCDF1?5 are nuclear proteins that display specific binding with different affinities to canonical DNA target sequences and present diverse transcriptional activation capacities in vivo. SlCDF1?5 genes exhibited distinct diurnal expression patterns and were differentially induced in response to osmotic, salt, heat, and low-temperature stresses. Arabidopsis plants overexpressing SlCDF1 or SlCDF3 showed increased drought and salt tolerance. In addition, the expression of various stress-responsive genes, such as COR15, RD29A, and RD10, were differentially activated in the overexpressing lines. Interestingly, overexpression in Arabidopsis of SlCDF3 but not SlCDF1 promotes late flowering through modulation of the expression of flowering control genes such as CO and FT. Overall, our data connect SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites

Cycling habits and other psychological variables affecting commuting by bicycle in city of Madrid

To develop effective cycling policies, decision makers and administrators should know the factors influencing the use of the bicycle for daily mobility. Traditional discrete choice models tend to be based on variables such as time and cost, which do not sufficiently explain the choice of the bicycle as a mode of transportation. Because psychological factors have been identified as particularly influential in the decision to commute by bicycle, this paper examines the perceptions of cycling factors and their influence on commuting by bicycle. Perceptions are measured by attitudes, other psychological variables, and habits. Statistical differences in the variables are established in relation to the choice of commuting mode and bicycle experience (commuter, sport–leisure, no use). Doing so enables the authors to identify the main barriers to commuting by bicycle and to make recommendations for cycling policies. Two underlying structures (factors) of the attitudinal variables are identified: direct benefits and long-term benefits. Three other factors are related to variables of difficulty: physical conditions, external facilities, and individual capacities. The effect of attitudes and other psychological variables on people’s decision to cycle to work–place of study is tested by using a logit model. In the case study of Madrid, Spain, the decision to cycle to work– place of study is heavily influenced by cycling habits (for noncommuting trips). Because bicycle commuting is not common, attitudes and other psychological variables play a less important role in the use of bikes.

Transition to a cyclable city: policies and variables affecting cycling commuting

The growing interest in achieving the objectives of cycling policies has increased the need to know the key variables that influence the use of the bicycle for daily mobility. This paper makes a contribution in this research line by examining a varying nature of variables – objective and psychological - and their influence on cycling commuting in the context of a “climber cycling city”: Vitoria-Gasteiz (Spain). Statistical differences of the variables were determined between cycling commuters and commuters by other modes. The objective variables analyzed allowed us to identify the cycling commuting profile in Vitoria-Gasteiz, but showed a small effect on cycling commuting. However, analyses on seven cycling psychological variables identified and defined, showed a higher influence, especially “Individual capacities” and “Non-commuting cycling habit”. Their results allowed recommending a wide et of policy initiatives. These policy recommendations were made considering that Vitoria-Gasteiz is a “city in transition” towards cycling: a high level of cycling share for the Spanish contex t and the safety issue not being the main barrier for cycling. However the psychological latent variable “Non-commuting cycling habit” indicates that normalization of the bicycle as a mode of transport needs more progress.

Cycling Dof Factors: Molecular and functional characterization of Arabidopsis thaliana AtCDF3 and tomato (Solanum lycopersicum L.) SlCDF3 in response to abiotic stress

El tomate (Solanum lycopersicum L.) es considerado uno de los cultivos hortícolas de mayor importancia económica en el territorio Español. Sin embargo, su producción está seriamente afectada por condiciones ambientales adversas como, salinidad, sequía y temperaturas extremas. Para resolver los problemas que se presentan en condiciones de estrés, se han empleado una serie de técnicas culturales que disminuyen sus efectos negativos, siendo de gran interés el desarrollo de variedades tolerantes. En este sentido la obtención y análisis de plantas transgénicas, ha supuesto un avance tecnológico, que ha facilitado el estudio y la evaluación de genes seleccionados en relación con la tolerancia al estrés. Estudios recientes han mostrado que el uso de genes reguladores como factores de transcripción (FTs) es una gran herramienta para obtener nuevas variedades de tomate con mayor tolerancia a estreses abióticos. Las proteínas DOF (DNA binding with One Finger) son una familia de FTs específica de plantas (Yangisawa, 2002), que están involucrados en procesos fisiológicos exclusivos de plantas como: asimilación del nitrógeno y fijación del carbono fotosintético, germinación de semilla, metabolismo secundario y respuesta al fotoperiodo pero su preciso rol en la tolerancia a estrés abiótico se desconoce en gran parte. El trabajo descrito en esta tesis tiene como objetivo estudiar genes reguladores tipo DOF para incrementar la tolerancia a estrés abiotico tanto en especies modelo como en tomate. En el primer capítulo de esta tesis se muestra la caracterización funcional del gen CDF3 de Arabidopsis, así como su papel en la respuesta a estrés abiótico y otros procesos del desarrollo. La expresión del gen AtCDF3 es altamente inducido por sequía, temperaturas extremas, salinidad y tratamientos con ácido abscísico (ABA). La línea de inserción T-DNA cdf3-1 es más sensible al estrés por sequía y bajas temperaturas, mientras que líneas transgénicas de Arabidopsis 35S::AtCDF3 aumentan la tolerancia al estrés por sequía, osmótico y bajas temperaturas en comparación con plantas wild-type (WT). Además, estas plantas presentan un incremento en la tasa fotosintética y apertura estomática. El gen AtCDF3 se localiza en el núcleo y que muestran una unión específica al ADN con diferente afinidad a secuencias diana y presentan diversas capacidades de activación transcripcional en ensayos de protoplastos de Arabidopsis. El dominio C-terminal de AtCDF3 es esencial para esta localización y su capacidad activación, la delección de este dominio reduce la tolerancia a sequía en plantas transgénicas 35S::AtCDF3. Análisis por microarray revelan que el AtCDF3 regula un set de genes involucrados en el metabolismo del carbono y nitrógeno. Nuestros resultados demuestran que el gen AtCDF3 juega un doble papel en la regulación de la respuesta a estrés por sequía y bajas temperaturas y en el control del tiempo de floración. En el segundo capítulo de este trabajo se lleva a cabo la identificación de 34 genes Dof en tomate que se pueden clasificar en base a homología de secuencia en cuatro grupos A-D, similares a los descritos en Arabidopsis. Dentro del grupo D se han identificado cinco genes DOF que presentan características similares a los Cycling Dof Factors (CDFs) de Arabidopsis. Estos genes son considerados ortólogos de Arabidopsis CDF1-5, y han sido nombrados como Solanum lycopersicum CDFs o SlCDFs. Los SlCDF1-5 son proteínas nucleares que muestran una unión específica al ADN con diferente afinidad a secuencias diana y presentan diversas capacidades de activación transcripcional in vivo. Análisis de expresión de los genes SlCDF1-5 muestran diferentes patrones de expresión durante el día y son inducidos de forma diferente en respuesta a estrés osmótico, salino, y de altas y bajas temperaturas. Plantas de Arabidopsis que sobre-expresan SlCDF1 y SlCDF3 muestran un incremento de la tolerancia a la sequía y salinidad. Además, de la expresión de varios genes de respuesta estrés como AtCOR15, AtRD29A y AtERD10, son expresados de forma diferente en estas líneas. La sobre-expresión de SlCDF3 en Arabidopsis promueve un retardo en el tiempo de floración a través de la modulación de la expresión de genes que controlan la floración como CONSTANS (CO) y FLOWERING LOCUS T (FT). En general, nuestros datos demuestran que los SlCDFs están asociados a funciones aun no descritas, relacionadas con la tolerancia a estrés abiótico y el control del tiempo de floración a través de la regulación de genes específicos y a un aumento de metabolitos particulares. ABSTRACT Tomato (Solanum lycopersicum L.) is one of the horticultural crops of major economic importance in the Spanish territory. However, its production is being affected by adverse environmental conditions such as salinity, drought and extreme temperatures. To resolve the problems triggered by stress conditions, a number of agricultural techniques that reduce the negative effects of stress are being frequently applied. However, the development of stress tolerant varieties is of a great interest. In this direction, the technological progress in obtaining and analysis of transgenic plants facilitated the study and evaluation of selected genes in relation to stress tolerance. Recent studies have shown that a use of regulatory genes such as transcription factors (TFs) is a great tool to obtain new tomato varieties with greater tolerance to abiotic stresses. The DOF (DNA binding with One Finger) proteins form a family of plant-specific TFs (Yangisawa, 2002) that are involved in the regulation of particular plant processes such as nitrogen assimilation, photosynthetic carbon fixation, seed germination, secondary metabolism and flowering time bur their precise roles in abiotic stress tolerance are largely unknown. The work described in this thesis aims at the study of the DOF type regulatory genes to increase tolerance to abiotic stress in both model species and the tomato. In the first chapter of this thesis, we present molecular characterization of the Arabidopsis CDF3 gene as well as its role in the response to abiotic stress and in other developmental processes. AtCDF3 is highly induced by drought, extreme temperatures, salt and abscisic acid (ABA) treatments. The cdf3-1 T-DNA insertion mutant was more sensitive to drought and low temperature stresses, whereas the AtCDF3 overexpression enhanced the tolerance of transgenic plants to drought, cold and osmotic stress comparing to the wild-type (WT) plants. In addition, these plants exhibit increased photosynthesis rates and stomatal aperture. AtCDF3 is localized in the nuclear region, displays specific binding to the canonical DNA target sequences and has a transcriptional activation activity in Arabidopsis protoplast assays. In addition, the C-terminal domain of AtCDF3 is essential for its localization and activation capabilities and the deletion of this domain significantly reduces the tolerance to drought in transgenic 35S::AtCDF3 overexpressing plants. Microarray analysis revealed that AtCDF3 regulated a set of genes involved in nitrogen and carbon metabolism. Our results demonstrate that AtCDF3 plays dual roles in regulating plant responses to drought and low temperature stress and in control of flowering time in vegetative tissues. In the second chapter this work, we carried out to identification of 34 tomato DOF genes that were classified by sequence similarity into four groups A-D, similar to the situation in Arabidopsis. In the D group we have identified five DOF genes that show similar characteristics to the Cycling Dof Factors (CDFs) of Arabidopsis. These genes were considered orthologous to the Arabidopsis CDF1 - 5 and were named Solanum lycopersicum CDFs or SlCDFs. SlCDF1-5 are nuclear proteins that display specific binding to canonical DNA target sequences and have transcriptional activation capacities in vivo. Expression analysis of SlCDF1-5 genes showed distinct diurnal expression patterns and were differentially induced in response to osmotic, salt and low and high temperature stresses. Arabidopsis plants overexpressing SlCDF1 and SlCDF3 showed increased drought and salt tolerance. In addition, various stress-responsive genes, such as AtCOR15, AtRD29A and AtERD10, were expressed differently in these lines. The overexpression of SlCDF3 in Arabidopsis also results in the late flowering phenotype through the modulation of the expression of flowering control genes such CONSTANS (CO) and FLOWERING LOCUS T (FT). Overall, our data connet SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites.