Microbial community composition and bacterioplankton at time series station Helgoland Roads, North Sea

A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. This study explores such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. The surface water samples were taken at Helgoland Island about 40 km offshore in the southeastern North Sea in the German Bight at the station 'Kabeltonne' (54° 11.3' N, 7° 54.0' E) between the main island and the minor island, Düne (German for 'dune') using small research vessels (http://www.awi.de/en/expedition/ships/more-ships.html). Water depths at this site fluctuate from 6 to 10 m over the tidal cycle. Samples were processed as described previously (Teeling et al., 2012; doi:10.7554/eLife.11888.001) in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Assessment of absolute cell numbers and bacterioplankton community composition was carried out as described previously (Thiele et al., 2011; doi:10.1016/B978-0-444-53199-5.00056-7). To obtain total cell numbers, DNA of formaldehyde fixed cells filtered on 0.2 mm pore sized filters was stained with 4',6-diamidino-2-phenylindole (DAPI). Fluorescently labeled cells were subsequently counted on filter sections using an epifluores-cence microscope. Likewise, bacterioplankton community composition was assessed by catalyzedreporter deposition fluorescence in situ hybridization (CARD-FISH) of formaldehyde fixed cells on 0.2 mm pore sized filters.

Table 2: Water stable isotope results and sampling site information of samples taken between 2003 and 2009 on the island of Corsica (western Mediterranean)

The Mediterranean is regarded as a region of intense climate change. To better understand future climate change, this area has been the target of several palaeoclimate studies which also studied stable isotope proxies that are directly linked to the stable isotope composition of water, such as tree rings, tooth enamel or speleothems. For such work, it is also essential to establish an isotope hydrology framework of the region of interest. Surface waters from streams and lakes as well as groundwater from springs on the island of Corsica were sampled between 2003 and 2009 for their oxygen and hydrogen isotope compositions. Isotope values from lake waters were enriched in heavier isotopes and define a local evaporation line (LEL). On the other hand, stream and spring waters reflect the isotope composition of local precipitation in the catchment. The intersection of the LEL and the linear fit of the spring and stream waters reflect the mean isotope composition of the annual precipitation (dP) with values of -8.6(±0.2) per mil for d18O and -58(±2) per mil for d2H. This value is also a good indicator of the average isotope composition of the local groundwater in the island. Surface water samples reflect the altitude isotope effect with a value of -0.17(±0.02) per mil per 100 m elevation for oxygen isotopes. At Vizzavona Pass in central Corsica, water samples from two catchments within a lateral distance of only a few hundred metres showed unexpected but systematic differences in their stable isotope composition. At this specific location, the direction of exposure seems to be an important factor. The differences were likely caused by isotopic enrichment during recharge in warm weather conditions in south-exposed valley flanks compared to the opposite, north-exposed valley flanks.

Collection of aboveground community and species-specific plant biomass from the Jena Experiment (time series since 2002).

This data set comprises 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 several experiments at the field site of a large grassland biodiversity experiment (the Jena Experiment; see further details below). Aboveground community biomass was normally 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 in the Jena 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. 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. The following series of datasets are contained in this collection: 1. Plant biomass form the Main Experiment: 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). 2. Plant biomass from the Dominance Experiment: In the Dominance Experiment, 206 grassland plots of 3.5 x 3.5 m were established from a pool of 9 species that can be dominant in semi-natural grassland communities of the study region. 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, 3, 4, 6, and 9 species). 3. Plant biomass from the monoculture plots: In the monoculture plots the sown plant community contains only a single species per plot and this species is a different one for each plot. Which species has been sown in which plot is stated in the plot information table for monocultures (see further details below). The monoculture plots of 3.5 x 3.5 m were established for all of the 60 plant species of the Jena Experiment species pool with two replicates per species like the other experiments in May 2002. All plots were maintained by bi-annual weeding and mowing.

Collection of data on aboveground invertebrates in the Jena Experiment (time series since 2002)

This collection contains measurements of abundance and diversity of different groups of aboveground invertebrates sampled on the plots of the different sub-experiments at the field site 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. The following series of datasets are contained in this collection: 1. Measurements of ant abundance (number of individuals attracted to baits) and ant occurrence (binary data) in the Main Experiment in 2006 and 2013. Ants where sampled using two types of baited traps receiving ~10g of Tuna or ~10g of honey/Sucrose. After 30min the occurrence (presence = 1 / absence = 0) and abundance (number) of ants at the two types of baits was recorded and pooled per plot.

Collection of vegetation and soil surface cover in the Jena Experiment (time series since 2002)

This collection contains measurements of vegetation and soil surface cover measured on the plots of the different sub-experiments at the field site 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. The following series of datasets are contained in this collection: 1. Measurements of vegetation cover, i.e. the proportion of soil surface area that is covered by different categories of plants per estimated plot area. Data was collected on the plant community level (sown plant community, weed plant community, dead plant material, and bare ground) and on the level of individual plant species in case of the species that have been sown into the plots to create the gradient of plant diversity.

Collection of measurements on physical soil properties in plots of the Jena Experiment (time series since 2002)

This collection contains measurements on physical soil properties of the plots of the different sub-experiments at the field site 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

Sampling information, length measurements, DNA alignments, models and phylogenetics trees for Oithona similis s.l.

Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24 %, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level. Molecular clock application revealed that the evolutionary history of O. similis s.l. is possibly closely associated with the reorganization of the ocean circulation in the mid Miocene and may be an example of allopatric speciation in the pelagic zone.

Collection of measurements on environmental conditions in plots of the Jena Experiment (time series since 2002)

This collection contains measurements of environmental conditions measured on the plots of the different sub-experiments at the field site 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. The following series of datasets are contained in this collection: 1.Soil temperature measurements on plots of the Main Experiment; 2. Quantification of the duration that individual plots of the Main Experiment were submerged during a flooding event occurring in June 2013

On the feasibility of time-lapse superconducting gravimetry for reservoir monitoring

The feasibility of monitoring fluid flow subsurface processes that result in density changes, using the iGrav superconducting gravimeter, is investigated. Practical targets include steam-assisted gravity drainage (SAGD) bitumen depletion and water pumping from aquifers, for which there is currently a void in low-impact, inexpensive monitoring techniques. This study demonstrates that the iGrav has the potential to be applied to multi-scale and diverse reservoirs. Gravity and gravity gradient signals are forward modeled for a real SAGD reservoir at two time steps, and for surface-fed and groundwater-fed aquifer pumping models, to estimate signal strength and directional dependency of water flow. Time-lapse gravimetry on small-scale reservoirs exhibits two obstacles, namely, a µgal sensitivity requirement and high noise levels in the vicinity of the reservoir. In this study, both limitations are overcome by proposing (i) a portable superconducting gravimeter, and (ii) a pair of instruments under various baseline geometries. This results in improved spatial resolution for locating depletion zones, as well as the cancellation of noise common in both instruments. Results indicate that a pair of iGrav superconducting gravimeters meet the sensitivity requirements and the spatial focusing desired to monitor SAGD bitumen migration at the reservoir scales. For SAGD reservoirs, the well pair separation, reservoir depth, and survey sampling determine the resolvability of individual well pair depletion patterns during the steam chamber rising phase, and general reservoir depletion patterns during the steam chamber spreading phase. Results show that monitoring water table elevation changes due to pumping and tracking whether groundwater or surface water is being extracted are feasible.

On the multi-dimensionality and sampling of air transport networks

Complex network theory is a framework increasingly used in the study of air transport networks, thanks to its ability to describe the structures created by networks of flights, and their influence in dynamical processes such as delay propagation. While many works consider only a fraction of the network, created by major airports or airlines, for example, it is not clear if and how such sampling process bias the observed structures and processes. In this contribution, we tackle this problem by studying how some observed topological metrics depend on the way the network is reconstructed, i.e. on the rules used to sample nodes and connections. Both structural and simple dynamical properties are considered, for eight major air networks and different source datasets. Results indicate that using a subset of airports strongly distorts our perception of the network, even when just small ones are discarded; at the same time, considering a subset of airlines yields a better and more stable representation. This allows us to provide some general guidelines on the way airports and connections should be sampled.

Modeling, Analysis and Performance Comparison of Two Direct Sampling DCSK Receivers under Frequency Nonselective Fading Channels

Two direct sampling correlator-type receivers for differential chaos shift keying (DCSK) communication systems under frequency non-selective fading channels are proposed. These receivers operate based on the same hardware platform with different architectures. In the first scheme, namely sum-delay-sum (SDS) receiver, the sum of all samples in a chip period is correlated with its delayed version. The correlation value obtained in each bit period is then compared with a fixed threshold to decide the binary value of recovered bit at the output. On the other hand, the second scheme, namely delay-sum-sum (DSS) receiver, calculates the correlation value of all samples with its delayed version in a chip period. The sum of correlation values in each bit period is then compared with the threshold to recover the data. The conventional DCSK transmitter, frequency non-selective Rayleigh fading channel, and two proposed receivers are mathematically modelled in discrete-time domain. The authors evaluated the bit error rate performance of the receivers by means of both theoretical analysis and numerical simulation. The performance comparison shows that the two proposed receivers can perform well under the studied channel, where the performances get better when the number of paths increases and the DSS receiver outperforms the SDS one.

Sampling strategies for characterization of neuropeptides using mass spectrometry and functional implications into cell-cell signaling

In this dissertation, there are developed different analytical strategies to discover and characterize mammalian brain peptides using small amount of tissues. The magnocellular neurons of rat supraoptic nucleus in tissue and cell culture served as the main model to study neuropeptides, in addition to hippocampal neurons and mouse embryonic pituitaries. The neuropeptidomcis studies described here use different extraction methods on tissue or cell culture combined with mass spectrometry (MS) techniques, matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). These strategies lead to the identification of multiple peptides from the rat/mouse brain in tissue and cell cultures, including novel compounds One of the goals in this dissertation was to optimize sample preparations on samples isolated from well-defined brain regions for mass spectrometric analysis. Here, the neuropeptidomics study of the SON resulted in the identification of 85 peptides, including 20 unique peptides from known prohormones. This study includes mass spectrometric analysis even from individually isolated magnocellular neuroendocrine cells, where vasopressin and several other peptides are detected. At the same time, it was shown that the same approach could be applied to analyze peptides isolated from a similar hypothalamic region, the suprachiasmatic nucleus (SCN). Although there were some overlaps regarding the detection of the peptides in the two brain nuclei, different peptides were detected specific to each nucleus. Among other peptides, provasopressin fragments were specifically detected in the SON while angiotensin I, somatostatin-14, neurokinin B, galanin, and vasoactive-intestinal peptide (VIP) were detected in the SCN only. Lists of peptides were generated from both brain regions for comparison of the peptidome of SON and SCN nuclei. Moving from analysis of magnocellular neurons in tissue to cell culture, the direct peptidomics of the magnocellular and hippocampal neurons led to the detection of 10 peaks that were assigned to previously characterized peptides and 17 peaks that remain unassigned. Peptides from the vasopressin prohormone and secretogranin-2 are attributed to magnocellular neurons, whereas neurokinin A, peptide J, and neurokinin B are attributed to cultured hippocampal neurons. This approach enabled the elucidation of cell-specific prohormone processing and the discovery of cell-cell signaling peptides. The peptides with roles in the development of the pituitary were analyzed using transgenic mice. Hes1 KO is a genetically modified mouse that lives only e18.5 (embryonic days). Anterior pituitaries of Hes1 null mice exhibit hypoplasia due to increased cell death and reduced proliferation and in the intermediate lobe, the cells differentiate abnormally into somatotropes instead of melanotropes. These previous findings demonstrate that Hes1 has multiple roles in pituitary development, cell differentiation, and cell fate. AVP was detected in all samples. Interestingly, somatostatin [92-100] and provasopressin [151-168] were detected in the mutant but not in the wild type or heterozygous pituitaries while somatostatin-14 was detected only in the heterozygous pituitary. In addition, the putative peptide corresponding to m/z 1330.2 and POMC [205-222] are detected in the mutant and heterozygous pituitaries, but not in the wild type. These results indicate that Hes1 influences the processing of different prohormones having possible roles during development and opens new directions for further developmental studies. This research demonstrates the robust capabilities of MS, which ensures the unbiased direct analysis of peptides extracted from complex biological systems and allows addressing important questions to understand cell-cell signaling in the brain.

Evaluating Risks of Dam-Reservoir Systems Using Efficient Importance Sampling

The occurrence frequency of failure events serve as critical indexes representing the safety status of dam-reservoir systems. Although overtopping is the most common failure mode with significant consequences, this type of event, in most cases, has a small probability. Estimation of such rare event risks for dam-reservoir systems with crude Monte Carlo (CMC) simulation techniques requires a prohibitively large number of trials, where significant computational resources are required to reach the satisfied estimation results. Otherwise, estimation of the disturbances would not be accurate enough. In order to reduce the computation expenses and improve the risk estimation efficiency, an importance sampling (IS) based simulation approach is proposed in this dissertation to address the overtopping risks of dam-reservoir systems. Deliverables of this study mainly include the following five aspects: 1) the reservoir inflow hydrograph model; 2) the dam-reservoir system operation model; 3) the CMC simulation framework; 4) the IS-based Monte Carlo (ISMC) simulation framework; and 5) the overtopping risk estimation comparison of both CMC and ISMC simulation. In a broader sense, this study meets the following three expectations: 1) to address the natural stochastic characteristics of the dam-reservoir system, such as the reservoir inflow rate; 2) to build up the fundamental CMC and ISMC simulation frameworks of the dam-reservoir system in order to estimate the overtopping risks; and 3) to compare the simulation results and the computational performance in order to demonstrate the ISMC simulation advantages. The estimation results of overtopping probability could be used to guide the future dam safety investigations and studies, and to supplement the conventional analyses in decision making on the dam-reservoir system improvements. At the same time, the proposed methodology of ISMC simulation is reasonably robust and proved to improve the overtopping risk estimation. The more accurate estimation, the smaller variance, and the reduced CPU time, expand the application of Monte Carlo (MC) technique on evaluating rare event risks for infrastructures.