Aboveground community and species-specific plant biomass from the Jena Experiment (Main Experiment, time series since 2002)

This data set comprises a time series of aboveground community plant biomass (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) and species-specific biomass from the sown species of the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Aboveground community biomass was harvested twice a year just prior to mowing (during peak standing biomass twice a year, generally in May and August; in 2002 only once in September) on all experimental plots of the main experiment. This was done by clipping the vegetation at 3 cm above ground in up to four rectangles of 0.2 x 0.5 m per large plot. The location of these rectangles was assigned by random selection of new coordinates every year within the core area of the plots (i.e. the central 10 x 15 m). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: individual species for the sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. Sown plant community biomass was calculated as the sum of the biomass of the individual sown species. The data for individual samples and the mean over samples for the biomass measures on the community level are given. Overall, analyses of the community biomass data have identified species richness as well as functional group composition as important drivers of a positive biodiversity-productivity relationship.

(Supplemental Table 2) Plant characteristics, GHG fluxes, and soil chemical and microbial properties in experimental treatments in Alexandra Fiord

We evaluated above- and belowground ecosystem changes in a 16 year, combined fertilization and warming experiment in a High Arctic tundra deciduous shrub heath (Alexandra Fiord, Ellesmere Island, NU, Canada). Soil emissions of the three key greenhouse gases (GHGs) (carbon dioxide, methane, and nitrous oxide) were measured in mid-July 2009 using soil respiration chambers attached to a FTIR system. Soil chemical and biochemical properties including Q10 values for CO2, CH4, and N2O, Bacteria and Archaea assemblage composition, and the diversity and prevalence of key nitrogen cycling genes including bacterial amoA, crenarchaeal amoA, and nosZ were measured. Warming and fertilization caused strong increases in plant community cover and height but had limited effects on GHG fluxes and no substantial effect on soil chemistry or biochemistry. Similarly, there was a surprising lack of directional shifts in the soil microbial community as a whole or any change at all in microbial functional groups associated with CH4 consumption or N2O cycling in any treatment. Thus, it appears that while warming and increased nutrient availability have strongly affected the plant community over the last 16 years, the belowground ecosystem has not yet responded. This resistance of the soil ecosystem has resulted in limited changes in GHG fluxes in response to the experimental treatments.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2003)

This data set contains measurements of plant height: vegetative height (length of the main axis) in 2003 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2003, plant height was recorded twice a year just before biomass harvest (during peak standing biomass in late May and in late August). For 30 target plant individuals harvested at 10 cm distances along a 5 m transect in a control area at the margin of each experimental plot, vegetative height (length of the main axis) was measured as the length of the main axis of the plant. Provided is the mean over the measured plants per plot.

Plant communities and soil chemistry of shrub-steppe and pine savannah grasslands in southern British Columbia, Canada

Habitat fragmentation alters the edges of remnant habitat patches. We examined changes in the plant community and soil in relation to distance from edge and edge type for shrub-steppe and pine savannah grasslands in southern British Columbia, Canada. Community composition showed significant nonlinear relationships with distance-to-edge more frequently at paved roads and fruit crops than at dirt roads or control sites (i.e., in the interior of grassland patches), with changes typically extending 25-30 m. More exotic species and fewer native species were found near edges, and edges showed decreased cryptogam cover and increased bare ground, especially near paved roads. The soil factors that best predicted compositional changes were soil pH and Cu/Mn at paved roads, soil pH and nitrogen at fruit crops, and soil resistance at dirt roads. Variation partitioning suggested that both direct (e.g., propagule pressure) and indirect (environmental change) factors mediated edge-related community changes, and provided evidence that nonlinear responses at developed edges were not due to natural gradients. Given the range of grassland patch sizes in this region (many patches 1-100 ha), the edge effects we observed represent a considerable loss of "core" habitat, which must be accounted for in conservation planning and site restoration.

Aboveground community and species-specific plant biomass from the Jena Experiment (Main Experiment, year 2008)

This data set contains aboveground community biomass (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) and species-specific biomass from the sown species of the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Aboveground community biomass was harvested twice in 2008 just prior to mowing (during peak standing biomass in early June and in late August) on all experimental plots of the main experiment. This was done by clipping the vegetation at 3 cm above ground in three rectangles of 0.2 x 0.5 m per large plot. The location of these rectangles was assigned prior to each harvest by random selection of coordinates within the core area of the plots (i.e. the central 10 x 15 m). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: individual species for the sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. Sown plant community biomass was calculated as the sum of the biomass of the individual sown species. The data for individual samples and the mean over samples for the biomass measures on the community level are given. Overall, analyses of the community biomass data have identified species richness as well as functional group composition as important drivers of a positive biodiversity-productivity relationship.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2007)

This data set contains measurements of plant height: vegetative height (heighest leaf) and regenerative height (heighest flower) in 2007 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2007, plant height was recorded twice a year just before biomass harvest (during peak standing biomass in late May and in late August). For target plant individuals at 10 points separated by 1 m each along a transect in the central area in the plots, vegetative height (heighest leaf) and regenerative height (heighest flower) were measured as standing height (without stretching the plant). In 2007, also the plots of the management experiment, that altered mowing frequency and fertilized subplots (see further details below) were sampled by measuring vegatation height five times, every 0.5m on a 3m transekt along the side of the management plots. Provided are the individual measurements and the mean over the measured plants.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2008)

This data set contains measurements of plant height: vegetative height (heighest leaf) and regenerative height (heighest flower) in 2008 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2008, plant height was recorded twice a year just before biomass harvest (during peak standing biomass in late May and in late August). For target plant individuals at 10 points separated by 1 m each along a transect in the central area in the plots, vegetative height (heighest leaf) and regenerative height (heighest flower) were measured as standing height (without stretching the plant). In 2008, also the plots of the management experiment, that altered mowing frequency and fertilized subplots (see further details below) were sampled by measuring vegatation height five times, every 1m on a 5m transekt along the side of the management plots. Provided are the individual measurements and the mean over the measured plants.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2005)

This data set contains measurements of plant height: vegetative height (heighest leaf) and regenerative height (heighest flower) in 2005 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2005, plant height was recorded twice a year just before biomass harvest (during peak standing biomass in late May and in late August). For target plant individuals at 10 points separated by 1 m each along a transect in the central area in the plots, vegetative height (heighest leaf) and regenerative height (heighest flower) were measured as standing height (without stretching the plant). Provided are the individual measurements and the mean over the measured plants.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2006)

This data set contains measurements of plant height: vegetative height (heighest leaf) and regenerative height (heighest flower) in 2006 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2006, plant height was recorded twice a year just before biomass harvest (during peak standing biomass in late May and in late August). For target plant individuals at 10 points separated by 1 m each along a transect in the central area in the plots, vegetative height (heighest leaf) and regenerative height (heighest flower) were measured as standing height (without stretching the plant). In 2006, also the plots of the management experiment, that altered mowing frequency and fertilized subplots (see further details below) were sampled by measuring vegatation height five times, every 1m on a 5m transekt along the side of the management plots. Provided are the individual measurements and the mean over the measured plants.

The European Hare (Lepus europaeus): A Picky Herbivore Searching for Plant Parts Rich in Fat

European hares of both sexes rely on fat reserves, particularly during the reproduc-tive season. Therefore, hares should select dietary plants rich in fat and energy. However, hares also require essential polyunsaturated fatty acids (PUFA) such as linoleic acid (LA) and alpha-linolenic acid (ALA) to reproduce and survive. Although hares are able to absorb PUFA selectively in their gastrointestinal tract, it is unknown whether this mechanism is sufficient to guarantee PUFA supply. Thus, diet selection may involve a trade-off between a preference for energy versus a preference for crucial nutrients, namely PUFA. We compared plant and nutrient availability and use by hares in an arable landscape in Austria over three years. We found that European hares selected their diet for high energy content (crude fat and crude protein), and avoided crude fibre. There was no evidence of a preference for plants rich in LA and ALA. We conclude that fat is the limiting resource for this herbivorous mammal, whereas levels of LA and ALA in forage are sufficiently high to meet daily requirements, especially since their uptake is enhanced by physiological mechanisms. Animals selected several plant taxa all year round, and preferences did not simply correlate with crude fat content. Hence, European hares might not only select for plant taxa rich in fat, but also for high-fat parts of preferred plant taxa. As hares preferred weeds/grasses and various crop types while avoiding cereals, we suggest that promoting heterogeneous habitats with high crop diversity and set-asides may help stop the decline of European hares throughout Europe.

Cysteine-proteases and cystatins from barley: molecular and functional characterization in housekeeping and defense processes

Plant cysteine-proteases (CysProt) represent a well-characterized type of proteolytic enzymes that fulfill tightly regulated physiological functions (senescence and seed germination among others) and defense roles. This article is focused on the group of papain-proteases C1A (family C1, clan CA) and their inhibitors, phytocystatins (PhyCys). In particular, the protease–inhibitor interaction and their mutual participation in specific pathways throughout the plant's life are reviewed. C1A CysProt and PhyCys have been molecularly characterized, and comparative sequence analyses have identified consensus functional motifs. A correlation can be established between the number of identified CysProt and PhyCys in angiosperms. Thus, evolutionary forces may have determined a control role of cystatins on both endogenous and pest-exogenous proteases in these species. Tagging the proteases and inhibitors with fluorescence proteins revealed common patterns of subcellular localization in the endoplasmic reticulum–Golgi network in transiently transformed onion epidermal cells. Further in vivo interactions were demonstrated by bimolecular fluorescent complementation, suggesting their participation in the same physiological processes.

Auxin - oxylipin crosstalk in stress responses of plant roots

Phytohormones regulate a wide array of developmental processes throughout the life cycle of plants. Over recent years, mounting evidence led to the widely accepted concept that plant hormone action is not the read-out of linear pathways, but determined by the extensive combinatorial activity of the signaling molecules and the integration of their signaling pathways, both in terms of regulating growth and development and in adapting to external stimuli. Recent work is beginning to shed light on the crosstalk of both nominally synergistically and antagonistically acting plant hormones such as, for example, auxins with oxylipins. Here, we report that oxylipins directly contribute to the regulation of the expression of two Arabidopsis YUCCA (YUC) genes, YUC8 and YUC9. Similar to previously characterized YUC family members, we identify both YUC8 and YUC9 as involved in local auxin biosynthesis, as demonstrated by the altered auxin contents and auxin-dependent phenotypes displayed by loss-of function mutants and transgenic overexpressing lines. Gene expression data obtained by qPCR analysis and microscopic examination of promoter-reporter lines reveal an oxylipin-mediated regulation of YUC9 expression that is dependent on the COI1 signal transduction pathway. The microscopic data indicate a functional overlap of the two analyzed auxin biosynthesis genes, but also point out specific functions for YUC8 and YUC9, which are in part related to different spatio-temporal expression pattern. In support of these findings, the analyzed yuc knockout mutants had lower free auxin contents and displayed a reduced response to oxylipins. This work provides evidence of a molecular mechanism that links oxylipin signaling with auxin homeostasis.

DAEDALUS at ImageCLEF 2011 Plant Identification Task: Using SIFT Keypoints for Object Detection

This paper describes the participation of DAEDALUS at ImageCLEF 2011 Plant Identification task. The task is evaluated as a supervised classification problem over 71 tree species from the French Mediterranean area used as class labels, based on visual content from scan, scan-like and natural photo images. Our approach to this task is to build a classifier based on the detection of keypoints from the images extracted using Lowe’s Scale Invariant Feature Transform (SIFT) algorithm. Although our overall classification score is very low as compared to other participant groups, the main conclusion that can be drawn is that SIFT keypoints seem to work significantly better for photos than for the other image types, so our approach may be a feasible strategy for the classification of this kind of visual content.

Identificación y caracterización de la ruta mediada por la proteína G heterotrimérica de Arabidopsis thaliana en la respuesta inmune

La resistencia de las plantas a los hongos necrótrofos como Plectosphaerella cucumerina es genéticamente compleja y depende de la activación coordinada de distintas rutas de señalización (Llorente et al, 2005; Sanchez-Vallet et al, 2010). Entre éstas se encuentran las mediadas por la proteína G heterotrimérica, un complejo formado por tres subunidades (Gα, Gβ y Gγ) que regula tanto la respuesta de inmunidad a diferentes patógenos como distintos procesos de desarrollo (Temple and Jones, 2007). En esta Tesis hemos demostrado que, en Arabidopsis, el monómero funcional formado por las subunidades Gβ y Gγ1/Gγ2 es el responsable de la regulación de la respuesta de defensa, ya que mutantes nulos en estas subunidades (agb1 y agg1 agg2) presentan una alta susceptibilidad al hongo P. cucumerina. Además, hemos identificado varios aminoácidos (Q102, T188 y R235) de la proteína AGB1 esenciales en la interacción con los efectores correspondientes para la regulación de la respuesta inmune (Jiang et al, enviado). Para determinar las bases moleculares de la resistencia mediada por la proteína G heterotrimérica, llevamos a cabo un análisis transcriptómico comparativo entre los genotipos agb1 y Col-0, el cual reveló que la resistencia mediada por AGB1 no depende de rutas defensivas implicadas en la resistencia a hongos necrotrofos, como las mediadas por el ácido salicílico (SA), etileno (ET), jasmónico (JA) o ácido abscísico (ABA), o la ruta de biosíntesis de metabolitos derivados del triptófano. Este estudio mostró que un número significativo de los genes desregulados en respuesta a P. cucumerina en el genotipo agb1 respecto a las plantas silvestres codificaban proteínas con funciones relacionadas con la pared celular. La evaluación de la composición y estructura de la pared de los mutantes de las subunidades de la proteína G heterotrimérica reveló que los genotipos agb1 y agg1 agg2 presentaban alteraciones similares diferentes de las observadas en plantas silvestres Col-0, como una reducción significativa en el contenido de xilosa en la pared. Estos datos sugieren que la proteína G heterotrimérica puede modular la composición/estructura de la pared celular y contribuir, de esta manera, en la regulación de la respuesta inmune (Delgado- Cerezo et al, 2011). La caracterización del interactoma de la proteína G heterotrimérica corroboró la relevancia funcional que presenta en la regulación de la pared celular, ya que un número significativo de las interacciones identificadas estaban comprendidas por proteínas relacionadas directa o indirectamente con la biogénesis y remodelación de la pared celular (Klopffleisch et al, 2011). El papel en inmunidad de algunos de estos potenciales efectores ha sido validado mediante el análisis de la resistencia a P. cucumerina de los mutantes de pérdida de función correspondientes. Con el objetivo de caracterizar las rutas de señalización mediadas por AGB1 e identificar efectores implicados en esta señalización, llevamos a cabo una búsqueda de mutantes supresores de la susceptibilidad de agb1 a P. cucumerina, identificándose varios mutantes sgb (supressor of Gbeta). En esta Tesis hemos caracterizado en detalle el mutante sgb10, que presenta una activación constitutiva de las rutas de señalización mediadas por SA y JA+ET y suprime el fenotipo de susceptibilidad de agb1. SGB10 y AGB1 forman parte de rutas independientes en la regulación de la respuesta inmune, mientras que interaccionan de forma compleja en el control de determinados procesos de desarrollo. La mutación sgb10 ha sido cartografiada entre los genes At3g55010 y At3g56408, que incluye una región con 160 genes. ABSTRACT Plant resistance to necrotrophic fungi Plectosphaerella cucumerina is genetically complex and depends on the interplay of different signalling pathways (Llorente et al, 2005; Sanchez-Vallet et al, 2010). Among others, the heterotrimeric G protein complex has a relevant role. The G protein that is formed by three subunits (Gα, Gβ and Gγ) is a pleiotropic regulator of immune responses to different types of pathogens and developmental issues (Temple and Jones, 2007). Throughout the Thesis, we have demonstrated that Arabidopsis’ functional monomer formed by the Gβ and Gγ1/Gγ2 subunits is a key regulator of defense response, as null mutants (agb1 and agg1 agg2) are equally hypersusceptible to P. cucumerina infection. In addition we have identified several AGB1 aminoacids (Q102, T188 y R235) essentials to interact with specific effectors during the regulation of immune response (Jiang et al, sent).To determine the molecular basis of heterotrimeric G protein mediated resistance we have performed a microarray analysis with agb1-1 and wild type Col-0 plants before and after P. cucumerina challenge. A deep and exhaustive comparative transcriptomical analysis of these plants revealed that AGB1 mediated resistance does not rely on salicilic acid (SA), ethylene (ET), jasmonates (JA), abscisic acid (ABA) or triptophan derived metabolites biosynthesis. However the analysis revealed that a significant number of cell wall related genes are misregulated in the agb1 mutant after pathogen challenge when compared to wild-type plants. The analysis of cell wall composition and structure showed similar cell wall alterations between agb1 and agg1 agg2 mutants that are different from those of wild-type plants, so far the mutants present a significant reduction in xylose levels. All these results suggest that heterotrimeric G protein may regulate immune response through modifications in the cell wall composition/structure (Delgado-Cerezo et al, 2011). The characterization of Heterotrimeric G protein interactome revealed highly connected interactions between the G-protein core and proteins involved in cell wall composition or structure (Klopffleisch et al, 2011). To test the role in immunity of several effectors identified above, we have performed resistance analysis of corresponding null mutants against P. cucumerina. In order to characterize AGB1 mediated signalling pathway and identify additional effectors involved in AGB1-mediated immune response against P. cucumerina, we have performed a screening to isolate mutants with suppression of agb1 phenotype. One of the mutants, named sgb10, has been characterized during the Thesis. The mutant shows constitutive expression of SA, JA+ET-mediated defense signaling pathways to suppres agb1 hypersusceptibility. SGB10 and AGB1 proteins seem to be part of independent pathways in immunity, however its function during development remains unclear. At present, we have mapped the sgb10 mutation between At3g55010 and At3g56408 genes. This region contains 160 genes.

A simplified Probabilistic Safety Assesment of a Steam-Methane Reforming Hydrogen Production Plant coupled to a High-Temperature Gas Cooled Nuclear Reactor

A Probabilistic Safety Assessment (PSA) is being developed for a steam-methane reforming hydrogen production plant linked to a High-Temperature Gas Cooled Nuclear Reactor (HTGR). This work is based on the Japan Atomic Energy Research Institute’s (JAERI) High Temperature Test Reactor (HTTR) prototype in Japan. This study has two major objectives: calculate the risk to onsite and offsite individuals, and calculate the frequency of different types of damage to the complex. A simplified HAZOP study was performed to identify initiating events, based on existing studies. The initiating events presented here are methane pipe break, helium pipe break, and PPWC heat exchanger pipe break. Generic data was used for the fault tree analysis and the initiating event frequency. Saphire was used for the PSA analysis. The results show that the average frequency of an accident at this complex is 2.5E-06, which is divided into the various end states. The dominant sequences result in graphite oxidation which does not pose a health risk to the population. The dominant sequences that could affect the population are those that result in a methane explosion and occur 6.6E-8/year, while the other sequences are much less frequent. The health risk presents itself if there are people in the vicinity who could be affected by the explosion. This analysis also demonstrates that an accident in one of the plants has little effect on the other. This is true given the design base distance between the plants, the fact that the reactor is underground, as well as other safety characteristics of the HTGR. Sensitivity studies are being performed in order to determine where additional and improved data is needed.