ALBERT

Description: The composition and abundance of algal pigments provide information on characteristics of a phytoplankton community in respect to its photoacclimation, overall biomass, and taxonomic composition. Particularly, these pigments play a major role in photoprotection and in the light-driven part of photosynthesis. Most phytoplankton pigments can be measured by High Performance Liquid Chromatography (HPLC) techniques to filtered water samples. This method, like others when water samples have to be analysed in the laboratory, is time consuming and therefore only a limited number of data points can be obtained. In order to receive information on phytoplankton pigment composition with a higher temporal and spatial resolution, we have developed a method to assess pigment concentrations from continuous optical measurements. The method applies an Empirical Orthogonal Function (EOF) analysis to remote sensing reflectance data derived from ship-based hyper-spectral underwater radiometric and from multispectral satellite data (using the MERIS Polymer product developed by Steinmetz et al., 2011) measured in the Eastern Tropical Atlantic. Subsequently we developed statistically linear models with measured (collocated) pigment concentrations as the response variable and EOF loadings as predictor variables. The model results, show that surface concentrations of a suite of pigments and pigment groups can be well predicted from the ship-based reflectance measurements, even when only a multi-spectral resolution is chosen (i.e. eight bands similar to those used by MERIS). Based on the MERIS reflectance data, concentrations of total and monovinyl chlorophyll a and the groups of photoprotective and photosynthetic carotenoids can be predicted with high quality. The fitted statistical model constructed on the satellite reflectance data as input was applied to one month of MERIS Polymer data to predict the concentration of those pigment groups for the whole Eastern Tropical Atlantic area. Bootstrapping explorations of cross-validation error indicate that the method can produce reliable predictions with relatively small data sets (e.g., 〈 50 collocated values of reflectance and pigment concentration). The method allows for the derivation of time series from continuous reflectance data of various pigment groups at various regions, which can be used to study variability and change of phytoplankton composition and photo-physiology.

Description: Background The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organism's ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems is accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation. Methodology/Principal findings We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to well-supported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious “guilty-by-association” approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs. Conclusion/Significance Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge.

Description: Background: Trace elements have been hypothesised to be involved in the pathogenesis of Multiple Sclerosis and volcanic degassing is the major natural sources of trace elements. Both incidence of Multiple Sclerosis in Catania and volcanic activity of Mount Etna have been significantly increased during the last 30 years. Due to prevailing trade winds direction, volcanic gases from Etna summit craters are mostly blown towards the eastern and southern sectors of the volcano. Objective: To evaluate the possible association between Multiple Sclerosis and exposure to volcanogenic trace elements. Methods: We evaluated prevalence and incidence of Multiple Sclerosis in four communities (47,234 inhabitants) located in the eastern flank and in two communities (52,210 inhabitants) located in the western flank of Mount Etna, respectively the most and least exposed area to crater gas emissions. Results: A higher prevalence was found in the population of the eastern flank compared to the population of the western one (137.6/100,000 versus 94.3/100,000; p-value 0.04). We found a borderline significantly higher incidence risk during the incidence study period (1980–2009) in the population of the eastern flank 4.6/100,000 (95% CI 3.1–5.9), compared with the western population 3.2/100,000 (95% CI 2.4–4.2) with a RR of 1.41 (95% CI 0.97–2.05; p-value 0.06). Incidence risks have increased over the time in both populations reaching a peak of 6.4/100,000 in the eastern flank and of 4.4/100.000 in the western flank during 2000–2009. Conclusion: We found a higher prevalence and incidence of Multiple Sclerosis among populations living in the eastern flank of Mount Etna. According to our data a possible role of TE cannot be ruled out as possible co-factor in the MS pathogenesis. However larger epidemiological study are needed to confirm this hypothesis.

Description: Published

Description: e74259

Description: 6A. Monitoraggio ambientale, sicurezza e territorio

Description: JCR Journal

Description: open

Description: Hule and Rı´o Cuarto are maar lakes located 11 and 18 km N of Poa´s volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Rı´o Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).

Description: Published

Description: e102456

Description: 4V. Vulcani e ambiente

Description: JCR Journal

Description: open

Description: In this paper we present one year of meteorological and flux measurements obtained near Ny-Ålesund, Spitsbergen. Fluxes are derived by the eddy covariance method and by a hydrodynamic model approach (HMA) as well. Both methods are compared and analyzed with respect to season and mean wind direction. Concerning the wind field we find a clear distinction between 3 prevailing regimes (which have influence on the flux behavior) mainly caused by the topography at the measurement site. Concerning the fluxes we find a good agreement between the HMA and the eddy covariance method in cases of turbulent mixing in summer but deviations at stable conditions, when the HMA almost always shows negative fluxes. Part of the deviation is based on a dependence of HMA fluxes on friction velocity and the influence of the molecular boundary layer. Moreover, the flagging system of the eddy covariance software package TK3 is briefly revised. A new quality criterion for the use of fluxes obtained by the eddy covariance method, which is based on integral turbulence characteristics, is proposed.

Description: The reconstruction of the stable carbon isotope evolution in atmospheric CO2 (δ13Catm), as archived in Antarctic ice cores, bears the potential to disentangle the contributions of the different carbon cycle fluxes causing past CO2 variations. Here we present a new record of δ13Catm before, during and after the Marine Isotope Stage 5.5 (155 000 to 105 000 yr BP). The dataset is archived on the data repository PANGEA® (www.pangea.de) under 10.1594/PANGAEA.817041. The record was derived with a well established sublimation method using ice from the EPICA Dome C (EDC) and the Talos Dome ice cores in East Antarctica. We find a 0.4‰ shift to heavier values between the mean δ13Catm level in the Penultimate (~ 140 000 yr BP) and Last Glacial Maximum (~ 22 000 yr BP), which can be explained by either (i) changes in the isotopic composition or (ii) intensity of the carbon input fluxes to the combined ocean/atmosphere carbon reservoir or (iii) by long-term peat buildup. Our isotopic data suggest that the carbon cycle evolution along Termination II and the subsequent interglacial was controlled by essentially the same processes as during the last 24 000 yr, but with different phasing and magnitudes. Furthermore, a 5000 yr lag in the CO2 decline relative to EDC temperatures is confirmed during the glacial inception at the end of MIS5.5 (120 000 yr BP). Based on our isotopic data this lag can be explained by terrestrial carbon release and carbonate compensation.

Description: Stable carbon isotope analysis of methane (δ13C of CH4) on atmospheric samples is one key method to constrain the current and past atmospheric CH4 budget. A frequently applied measurement technique is gas chromatography (GC) isotope ratio mass spectrometry (IRMS) coupled to a combustion-preconcentration unit. This report shows that the atmospheric trace gas krypton (Kr) can severely interfere during the mass spectrometric measurement, leading to significant biases in δ13C of CH4, if krypton is not sufficiently separated during the analysis. According to our experiments, the krypton interference is likely composed of two individual effects, with the lateral tailing of the doubly charged 86Kr peak affecting the neighbouring m/z 44 and partially the m/z 45 Faraday cups. Additionally, a broad signal affecting m/z 45 and especially m/z 46 is assumed to result from scattered ions of singly charged krypton. The introduced bias in the measured isotope ratios is dependent on the chromatographic separation, the krypton-to-CH4 mixing ratio in the sample, the focusing of the mass spectrometer as well as the detector configuration and can amount to up to several per mil in δ13C. Apart from technical solutions to avoid this interference, we present correction routines to a posteriori remove the bias.

Description: The Toba eruption that occurred some 74 ka ago in Sumatra, Indonesia, is among the largest volcanic events on Earth over the last 2 million years. Tephra from this eruption has been spread over vast areas in Asia, where it constitutes a major time marker close to the Marine Isotope Stage 4/5 boundary. As yet, no tephra associated with Toba has been identified in Greenland or Antarctic ice cores. Based on new accurate dating of Toba tephra and on accurately dated European stalagmites, the Toba event is known to occur between the onsets of Greenland interstadials (GI) 19 and 20. Furthermore, the existing linking of Greenland and Antarctic ice cores by gas records and by the bipolar seesaw hypothesis suggests that the Antarctic counterpart is situated between Antarctic Isotope Maxima (AIM) 19 and 20. In this work we suggest a direct synchronization of Greenland (NGRIP) and Antarctic (EDML) ice cores at the Toba eruption based on matching of a pattern of bipolar volcanic spikes. Annual layer counting between volcanic spikes in both cores allows for a unique match. We first demonstrate this bipolar matching technique at the already synchronized Laschamp geomagnetic excursion (41 ka BP) before we apply it to the suggested Toba interval. The Toba synchronization pattern covers some 2000 yr in GI-20 and AIM-19/20 and includes nine acidity peaks that are recognized in both ice cores. The suggested bipolar Toba synchronization has decadal precision. It thus allows a determination of the exact phasing of inter-hemispheric climate in a time interval of poorly constrained ice core records, and it allows for a discussion of the climatic impact of the Toba eruption in a global perspective. The bipolar linking gives no support for a long-term global cooling caused by the Toba eruption as Antarctica experiences a major warming shortly after the event. Furthermore, our bipolar match provides a way to place palaeo-environmental records other than ice cores into a precise climatic context.

Description: The Lena Delta in Northern Siberia is one of the largest river deltas in the world. During peak discharge, after the ice melt in spring, it delivers between 60–8000 m3 s−1 of water and sediment into the Arctic Ocean. The Lena Delta and the Laptev Sea coast also constitute a continuous permafrost region. Ongoing climate change, which is particularly pronounced in the Arctic, is leading to increased rates of permafrost thaw. This has already profoundly altered the discharge rates of the Lena River. But the chemistry of the river waters which are discharged into the coastal Laptev Sea have also been hypothesized to undergo considerable compositional changes, e.g. by increasing concentrations of inorganic nutrients such as dissolved organic carbon (DOC) and methane. These physical and chemical changes will also affect the composition of the phytoplankton communities. However, before potential consequences of climate change for coastal arctic phytoplankton communities can be judged, the inherent status of the diversity and food web interactions within the delta have to be established. In 2010, as part of the AWI Lena Delta programme, the phyto- and microzooplankton community in three river channels of the delta (Trofimov, Bykov and Olenek) as well as four coastal transects were investigated to capture the typical river phytoplankton communities and the transitional zone of brackish/marine conditions. Most CTD profiles from 23 coastal stations showed very strong stratification. The only exception to this was a small, shallow and mixed area running from the outflow of Bykov channel in a northerly direction parallel to the shore. Of the five stations in this area, three had a salinity of close to zero. Two further stations had salinities of around 2 and 5 throughout the water column. In the remaining transects, on the other hand, salinities varied between 5 and 30 with depth. Phytoplankton counts from the outflow from the Lena were dominated by diatoms (Aulacoseira species) cyanobacteria (Aphanizomenon, Pseudanabaena) and chlorophytes. In contrast, in the stratified stations the plankton was mostly dominated by dinoflagellates, ciliates and nanoflagellates, with only an insignificant diatom component from the genera Chaetoceros and Thalassiosira (brackish as opposed to freshwater species). Ciliate abundance was significantly coupled with the abundance of total flagellates. A pronounced partitioning in the phytoplankton community was also discernible with depth, with a different community composition and abundance above and below the thermocline in the stratified sites. This work is a first analysis of the phytoplankton community structure in the region where Lena River discharge enters the Laptev Sea.

Description: There are a number of clear examples in the instrumental period where positive El Niño events were coincident with a severely weakened summer monsoon over India (ISM). ENSO's influence on the Indian Monsoon has therefore remained the centerpiece of various predictive schemes of ISM rainfall for over a century. The teleconnection between the monsoon and ENSO has undergone a protracted weakening since the late 1980's suggesting the strength of ENSO's influence on the monsoon may vary considerably on multidecadal timescales. The recent weakening has specifically prompted questions as to whether this shift represents a natural mode of climate variability or a fundamental change in ENSO and/or ISM dynamics due to anthropogenic warming. The brevity of empirical observations and large systematic errors in the representation of these two systems in state-of-the-art general circulation models hamper efforts to reliably assess the low frequency nature of this dynamical coupling under varying climate forcings. Here we place the 20th century ENSO-Monsoon relationship in a millennial context by assessing the phase angle between the two systems across the time spectrum using a continuous tree-ring ENSO reconstruction from North America and a speleothem oxygen isotope (δ18O) based reconstruction of the ISM. The results suggest that in the high-frequency domain (≤ 15 yr), El Niño (La Niña) events persistently lead to a weakened (strengthened) monsoon consistent with the observed relationship between the two systems during the instrumental period. However, in the low frequency domain (≥ 60 yr), periods of strong monsoon are, in general, coincident with periods of enhanced ENSO variance. This relationship is opposite to which would be predicted dynamically and leads us to conclude that ENSO is not pacing the prominent multidecadal variability that has characterized the ISM over the last millennium.

Description: Sea ice thickness information is important for sea ice modelling and ship operations. Here a method to detect the thickness of sea ice up to 50 cm during the freeze-up season based on high incidence angle observations of the Soil Moisture and Ocean Salinity (SMOS) satellite working at 1.4 GHz is suggested. By comparison of thermodynamic ice growth data with SMOS brightness temperatures, a high correlation to intensity and an anticorrelation to the difference between vertically and horizontally polarised brightness temperatures at incidence angles between 40 and 50° are found and used to develop an empirical retrieval algorithm sensitive to thin sea ice up to 50 cm thickness. The algorithm shows high correlation with ice thickness data from airborne measurements and reasonable ice thickness patterns for the Arctic freeze-up period.

Description: Following the launch of ESA's Soil Moisture and Ocean Salinity (SMOS) mission, it has been shown that brightness temperatures at a low microwave frequency of 1.4 GHz (L-band) are sensitive to sea ice properties. In the first demonstration study, sea ice thickness up to 50 cm has been derived using a semi-empirical algorithm with constant tie-points. Here, we introduce a novel iterative retrieval algorithm that is based on a thermodynamic sea ice model and a three-layer radiative transfer model, which explicitly takes variations of ice temperature and ice salinity into account. In addition, ice thickness variations within the SMOS spatial resolution are considered through a statistical thickness distribution function derived from high-resolution ice thickness measurements from NASA's Operation IceBridge campaign. This new algorithm has been used for the continuous operational production of a SMOS-based sea ice thickness data set from 2010 on. The data set is compared to and validated with estimates from assimilation systems, remote sensing data, and airborne electromagnetic sounding data. The comparisons show that the new retrieval algorithm has a considerably better agreement with the validation data and delivers a more realistic Arctic-wide ice thickness distribution than the algorithm used in the previous study (Kaleschke et al., 2012).

Description: The ice shelf caverns around Antarctica are sources of cold and fresh water which contributes to the formation of Antarctic bottom water and thus to the ventilation of the deep basins of the World Ocean. While a realistic simulation of the cavern circulation requires high resolution, because of the complicated bottom topography and ice shelf morphology, the physics of melting and freezing at the ice shelf base is relatively simple. We have developed an analytically solvable box model of the cavern thermohaline state, using the formulation of melting and freezing as in Olbers and Hellmer (2010). There is high resolution along the cavern's path of the overturning circulation whereas the cross-path resolution is fairly coarse. The circulation in the cavern is prescribed and used as a tuning parameter to constrain the solution by attempting to match observed ranges for outflow temperature and salinity at the ice shelf front as well as of the mean basal melt rate. The method, tested for six Antarctic ice shelves, can be used for a quick estimate of melt/freeze rates and the overturning rate in particular caverns, given the temperature and salinity of the inflow and the above mentioned constrains for outflow and melting. In turn, the model can also be used for testing the compatibility of remotely sensed basal mass loss with observed cavern inflow characteristics.

Description: Bio-optical measurements and sampling were carried out in the delta of the Lena River (northern Siberia, Russia) between 26 June and 4 July 2011. The aim of this study was to determine the inherent optical properties of the Lena water, i.e., absorption, attenuation, and scattering coefficients, during the period of maximum runoff. This aimed to contribute to the development of a bio-optical model for use as the basis for optical remote sensing of coastal water of the Arctic. In this context the absorption by CDOM (colored dissolved organic matter) and particles, and the concentrations of total suspended matter, phytoplankton-pigments, and carbon were measured. CDOM was found to be the most dominant parameter affecting the optical properties of the river, with an absorption coefficient of 4.5–5 m−1 at 442 nm, which was almost four times higher than total particle absorption values at visible wavelength range. The wavelenght-dependence of absorption of the different water constituents was chracterized by determining the semi logarithmic spectral slope. Mean CDOM, and detritus slopes were 0.0149 nm−1(standard deviation (stdev) = 0.0003, n = 18), and 0.0057 nm−1 (stdev = 0.0017, n = 19), respectively, values which are typical for water bodies with high concentrations of dissolved and particulate carbon. Mean chlorophyll a and total suspended matter were 1.8 mg m−3 (stdev = 0.734 n = 18) and 31.9 g m−3 (stdev = 19.94, n = 27), respectively. DOC (dissolved organic carbon) was in the range 8–10 g m−3 and the total particulate carbon (PC) in the range 0.25–1.5 g m−3. The light penetration depth (Secchi disc depth) was in the range 30–90 cm and was highly correlated with the suspended matter concentration. The period of maximum river runoff in June was chosen to obtain bio-optical data when maximum water constituents are transported into the Laptev Sea. However, we are aware that more data from other seasons and other years need to be collected to establish a general bio-optical model of the Lena water and conclusively characterize the light climate with respect to primary production.

Description: The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO2 values) and extended data coverage (from 1968–2007 to 1968–2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models.

Description: In a feasibility study, the potential of proxy data for the temperature and salinity during the Last Glacial Maximum (LGM, about 19 000 to 23 000 years before present) in constraining the strength of the Atlantic meridional overturning circulation (AMOC) with a general ocean circulation model was explored. The proxy data were simulated by drawing data from four different model simulations at the ocean sediment core locations of the Multiproxy Approach for the Reconstruction of the Glacial Ocean surface (MARGO) project, and perturbing these data with realistic noise estimates. The results suggest that our method has the potential to provide estimates of the past strength of the AMOC even from sparse data, but in general, paleo-sea-surface temperature data without additional prior knowledge about the ocean state during the LGM is not adequate to constrain the model. On the one hand, additional data in the deep-ocean and salinity data are shown to be highly important in estimating the LGM circulation. On the other hand, increasing the amount of surface data alone does not appear to be enough for better estimates. Finally, better initial guesses to start the state estimation procedure would greatly improve the performance of the method. Indeed, with a sufficiently good first guess, just the sea-surface temperature data from the MARGO project promise to be sufficient for reliable estimates of the strength of the AMOC.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56393, doi:10.1371/journal.pone.0056393.

Description: Evolutionary constraints which limit the forces produced during bell contractions of medusae affect the overall medusan morphospace such that jet propulsion is limited to only small medusae. Cubomedusae, which often possess large prolate bells and are thought to swim via jet propulsion, appear to violate the theoretical constraints which determine the medusan morphospace. To examine propulsion by cubomedusae, we quantified size related changes in wake dynamics, bell shape, swimming and turning kinematics of two species of cubomedusae, Chironex fleckeri and Chiropsella bronzie. During growth, these cubomedusae transitioned from using jet propulsion at smaller sizes to a rowing-jetting hybrid mode of propulsion at larger sizes. Simple modifications in the flexibility and kinematics of their velarium appeared to be sufficient to alter their propulsive mode. Turning occurs during both bell contraction and expansion and is achieved by generating asymmetric vortex structures during both stages of the swimming cycle. Swimming characteristics were considered in conjunction with the unique foraging strategy used by cubomedusae.

Description: This work was supported by an ONR MURI award (N000140810654) and National Science Foundation grant OCE 0623508 to JHC, SPC, JOD. And the work was supported by the Roger Williams University Foundation to Promote Scholarship.

Description: This article is distributed under the terms of the Creative Commons Public Domain. The definitive version was published in PLoS ONE 8 (2013): e55273, doi:10.1371/journal.pone.0055273.

Description: Georges Bank is a large, shallow feature separating the Gulf of Maine from the Atlantic Ocean. Previous studies demonstrated a strong tidal-mixing front during the warm season on the northern bank margin between thermally stratified water in the Gulf of Maine and mixed water on the bank. Tides transport warm water off the bank during flood tide and cool gulf water onto the bank during ebb tide. During 10 days in August 2009, we mapped frontal temperatures in five study areas along ~100 km of the bank margin. The seabed “frontal zone”, where temperature changed with frontal movment, experienced semidiurnal temperature maxima and minima. The tidal excursion of the frontal boundary between stratified and mixed water ranged 6 to 10 km. This “frontal boundary zone” was narrower than the frontal zone. Along transects perpendicular to the bank margin, seabed temperature change at individual sites ranged from 7.0°C in the frontal zone to 0.0°C in mixed bank water. At time series in frontal zone stations, changes during tidal cycles ranged from 1.2 to 6.1°C. The greatest rate of change (−2.48°C hr−1) occurred at mid-ebb. Geographic plots of seabed temperature change allowed the mapping of up to 8 subareas in each study area. The magnitude of temperature change in a subarea depended on its location in the frontal zone. Frontal movement had the greatest effect on seabed temperature in the 40 to 80 m depth interval. Subareas experiencing maximum temperature change in the frontal zone were not in the frontal boundary zone, but rather several km gulfward (off-bank) of the frontal boundary zone. These results provide a new ecological framework for examining the effect of tidally-driven temperature variability on the distribution, food resources, and reproductive success of benthic invertebrate and demersal fish species living in tidal front habitats.

Description: This study was supported by salary funds from the regular annual salary budget from Northeast Fisheries Science Center (NEFSC) and United States Geological Survey Woods Hole Coastal and Marine Science Center (USGS WH C&MSC), respectively; ship time funds from the NEFSC annual budget for days-at-sea ship operations; equipment from the NEFSC and USGS WH C&MSC annual equipment budgets.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e54443, doi:10.1371/journal.pone.0054443.

Description: Species-range expansions are a predicted and realized consequence of global climate change. Climate warming and the poleward widening of the tropical belt have induced range shifts in a variety of marine and terrestrial species. Range expansions may have broad implications on native biota and ecosystem functioning as shifting species may perturb recipient communities. Larger symbiont-bearing foraminifera constitute ubiquitous and prominent components of shallow water ecosystems, and range shifts of these important protists are likely to trigger changes in ecosystem functioning. We have used historical and newly acquired occurrence records to compute current range shifts of Amphistegina spp., a larger symbiont-bearing foraminifera, along the eastern coastline of Africa and compare them to analogous range shifts currently observed in the Mediterranean Sea. The study provides new evidence that amphisteginid foraminifera are rapidly progressing southwestward, closely approaching Port Edward (South Africa) at 31°S. To project future species distributions, we applied a species distribution model (SDM) based on ecological niche constraints of current distribution ranges. Our model indicates that further warming is likely to cause a continued range extension, and predicts dispersal along nearly the entire southeastern coast of Africa. The average rates of amphisteginid range shift were computed between 8 and 2.7 km year−1, and are projected to lead to a total southward range expansion of 267 km, or 2.4° latitude, in the year 2100. Our results corroborate findings from the fossil record that some larger symbiont-bearing foraminifera cope well with rising water temperatures and are beneficiaries of global climate change.

Description: This work was supported by grants from the German Science Foundation (DFG; www.dfg.de) to ML and SL (LA 884/10-1, LA 884/5-1).

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56993, doi:10.1371/journal.pone.0056993.

Description: The mxaF gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mxaF and 16S rRNA gene phylogenies were constructed based on over 100 database sequences of known proteobacterial methanotrophs and other methylotrophs to assess their evolutionary histories. Topology tests revealed that mxaF and 16S rDNA genes of methanotrophs do not show congruent evolutionary histories, with incongruencies in methanotrophic taxa in the Methylococcaceae, Methylocystaceae, and Beijerinckiacea. However, known methanotrophs generally formed coherent clades based on mxaF gene sequences, allowing for phylogenetic discrimination of major taxa. This feature highlights the mxaF gene’s usefulness as a biomarker in studying the molecular diversity of proteobacterial methanotrophs in nature. To verify this, PCR-directed assays targeting this gene were used to detect novel methanotrophs from diverse environments including soil, peatland, hydrothermal vent mussel tissues, and methanotroph isolates. The placement of the majority of environmental mxaF gene sequences in distinct methanotroph-specific clades (Methylocystaceae and Methylococcaceae) detected in this study supports the use of mxaF as a biomarker for methanotrophic proteobacteria.

Description: This work was supported in part by grants from the U.S. National Science Foundation Ecosystems Studies program (awards # DEB9708092 and DEB0089738).

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e61065, doi:10.1371/journal.pone.0061065.

Description: Ocean acidification, characterized by elevated pCO2 and the associated decreases in seawater pH and calcium carbonate saturation state (Ω), has a variable impact on the growth and survival of marine invertebrates. Larval stages are thought to be particularly vulnerable to environmental stressors, and negative impacts of ocean acidification have been seen on fertilization as well as on embryonic, larval, and juvenile development and growth of bivalve molluscs. We investigated the effects of high CO2 exposure (resulting in pH = 7.39, Ωar = 0.74) on the larvae of the bay scallop Argopecten irradians from 12 h to 7 d old, including a switch from high CO2 to ambient CO2 conditions (pH = 7.93, Ωar = 2.26) after 3 d, to assess the possibility of persistent effects of early exposure. The survival of larvae in the high CO2 treatment was consistently lower than the survival of larvae in ambient conditions, and was already significantly lower at 1 d. Likewise, the shell length of larvae in the high CO2 treatment was significantly smaller than larvae in the ambient conditions throughout the experiment and by 7 d, was reduced by 11.5%. This study also demonstrates that the size effects of short-term exposure to high CO2 are still detectable after 7 d of larval development; the shells of larvae exposed to high CO2 for the first 3 d of development and subsequently exposed to ambient CO2 were not significantly different in size at 3 and 7 d than the shells of larvae exposed to high CO2 throughout the experiment.

Description: This work was funded by a Woods Hole Oceanographic Institution Interdisciplinary Award to Mullineaux & McCorkle; and awards to Mullineaux & White, to McCorkle, and to Cohen & McCorkle through NOAA (National Oceanic and Admosphereic Administration) Sea Grant #NA10OAR4170083. White was funded through a National Defense Science and Engineering Graduate Fellowship through the American Society for Engineering Education.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e76096, doi:10.1371/journal.pone.0076096.

Description: DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8–11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types.

Description: LAZ and VS were funded by a Brown University Office of the Vice President of Research SEED grant (LAZ) entitled “Tracking disease spread through the wildlife trade: New techniques to identify infectious microbes in aquarium fishes.” SOO and MQ were funded by Wellcome Trust Sanger Institute grant numbers 098051 and 079355/Z/06/Z.

Description: This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 8 (2013): e83994, doi:10.1371/journal.pone.0083994.

Description: Gas bubbles in marine mammals entangled and drowned in gillnets have been previously described by computed tomography, gross examination and histopathology. The absence of bacteria or autolytic changes in the tissues of those animals suggested that the gas was produced peri- or post-mortem by a fast decompression, probably by quickly hauling animals entangled in the net at depth to the surface. Gas composition analysis and gas scoring are two new diagnostic tools available to distinguish gas embolisms from putrefaction gases. With this goal, these methods have been successfully applied to pathological studies of marine mammals. In this study, we characterized the flux and composition of the gas bubbles from bycaught marine mammals in anchored sink gillnets and bottom otter trawls. We compared these data with marine mammals stranded on Cape Cod, MA, USA. Fresh animals or with moderate decomposition (decomposition scores of 2 and 3) were prioritized. Results showed that bycaught animals presented with significantly higher gas scores than stranded animals. Gas composition analyses indicate that gas was formed by decompression, confirming the decompression hypothesis.

Description: This study was funded by the Woods Hole Oceanographic Institution Marine Mammal Center, and Wick and Sloan Simmons.

Description: This article is distributed under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e87720, doi:10.1371/journal.pone.0087720.

Description: The abundance of the subarctic copepod, Calanus finmarchicus, and temperate, shelf copepod, Centropages typicus, was estimated from samples collected bi-monthly over the Northeast U.S. continental shelf (NEUS) from 1977–2010. Latitudinal variation in long term trends and seasonal patterns for the two copepod species were examined for four sub-regions: the Gulf of Maine (GOM), Georges Bank (GB), Southern New England (SNE), and Mid-Atlantic Bight (MAB). Results suggested that there was significant difference in long term variation between northern region (GOM and GB), and the MAB for both species. C. finmarchicus generally peaked in May – June throughout the entire study region and Cen. typicus had a more complex seasonal pattern. Time series analysis revealed that the peak time for Cen. typicus switched from November – December to January - March after 1985 in the MAB. The long term abundance of C. finmarchicus showed more fluctuation in the MAB than the GOM and GB, whereas the long term abundance of Cen. typicus was more variable in the GB than other sub-regions. Alongshore transport was significantly correlated with the abundance of C. finmarchicus, i.e., more water from north, higher abundance for C. finmarchicus. The abundance of Cen. typicus showed positive relationship with the Gulf Stream north wall index (GSNWI) in the GOM and GB, but the GSNWI only explained 12–15% of variation in Cen. typicus abundance. In general, the alongshore current was negatively correlated with the GSNWI, suggesting that Cen. typicus is more abundant when advection from the north is less. However, the relationship between Cen. typicus and alongshore transport was not significant. The present study highlights the importance of spatial scales in the study of marine populations: observed long term changes in the northern region were different from the south for both species.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50215, doi:10.1371/journal.pone.0050215.

Description: The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the “robust” clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.

Description: This study was funded by CTM2009-00496 and CGL2011-23306 projects of the “Ministerio de Ciencia e Innovación” (Spain). Research at sea was partly supported by the European Commission F. P.VI Project HERMES Contract No. GOCE-CT-2005-511234-1) and the EU F.P. VII Project HERMIONE(contract number no. 226354).

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e53889, doi:10.1371/journal.pone.0053889.

Description: Thecosome pteropods (Mollusca, Gastropoda) are an ecologically important, diverse, and ubiquitous group of holoplanktonic animals that are the focus of intense research interest due to their external aragonite shell and vulnerability to ocean acidification. Characterizing the response of these animals to low pH and other environmental stressors has been hampered by continued uncertainty in their taxonomic identification. An example of this confusion in species assignment is found in the genus Diacavolinia. All members of this genus were originally indentified as a single species, Cavolinia longirostris, but over the past fifty years the taxonomy has been revisited multiple times; currently the genus comprises 22 different species. This study examines five species of Diacavolinia, including four sampled in the Northeast Atlantic (78 individuals) and one from the Eastern tropical North Pacific (15 individuals). Diacavolina were identified to species based on morphological characteristics according to the current taxonomy, photographed, and then used to determine the sequence of the “DNA barcoding” region of the cytochrome c oxidase subunit I (COI). Specimens from the Atlantic, despite distinct differences in shell morphology, showed polyphyly and a genetic divergence of 〈3% (K2P distance) whereas the Pacific and Atlantic samples were more distant (~19%). Comparisons of Diacavolinia spp. with other Cavolinia spp. reveal larger distances (~24%). These results indicate that specimens from the Atlantic comprise a single monophyletic species and suggest possible species-level divergence between Atlantic and Pacific populations. The findings support the maintenance of Diacavolinia as a separate genus, yet emphasize the inadequacy of our current taxonomic understanding of pteropods. They highlight the need for accurate species identifications to support estimates of biodiversity, range extent and natural exposure of these planktonic calcifiers to environmental variability; furthermore, the apparent variation of the pteropods shell may have implications for our understanding of the species’ sensitivity to ocean acidification.

Description: This material is based upon work supported by the National Science Foundation under Grant Number OCE-0928801. AEM was funded through the WHOI Postdoctoral Scholarship. Support to LBB was provided by the College of Liberal Arts & Sciences, University of Connecticut; and by the Census of Marine Life/Alfred P. Sloan Foundation.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in International Journal of Distributed Sensor Networks 2012 (2012): 191235, doi:10.1155/2012/191235.

Description: In recent years, there has been significant concern about the impacts of offshore oil spill plumes and harmful algal blooms on the coastal ocean environment and biology, as well as on the human populations adjacent to these coastal regions. Thus, it has become increasingly important to determine the 3D extent of these ocean features (“plumes”) and how they evolve over time. The ocean environment is largely inaccessible to sensing directly by humans, motivating the need for robots to intelligently sense the ocean for us. In this paper, we propose the use of an autonomous underwater vehicle (AUV) network to track and predict plume shape and motion, discussing solutions to the challenges of spatiotemporal data aliasing (coverage versus resolution), underwater communication, AUV autonomy, data fusion, and coordination of multiple AUVs. A plume simulation is also developed here as the first step toward implementing behaviors for autonomous, adaptive plume tracking with AUVs, modeling a plume as a sum of Fourier orders and examining the resulting errors. This is then extended to include plume forecasting based on time variations, and future improvements and implementation are discussed.

Description: This research was made with Government support under and awarded by DoD, Air Force Office of Scientific Research, National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e63714, doi:10.1371/journal.pone.0063714.

Description: Anthropogenic carbon dioxide (CO2) is being absorbed into the ocean, altering seawater chemistry, with potentially negative impacts on a wide range of marine organisms. The early life stages of invertebrates with internal and external aragonite structures may be particularly vulnerable to this ocean acidification. Impacts to cephalopods, which form aragonite cuttlebones and statoliths, are of concern because of the central role they play in many ocean ecosystems and because of their importance to global fisheries. Atlantic longfin squid (Doryteuthis pealeii), an ecologically and economically valuable taxon, were reared from eggs to hatchlings (paralarvae) under ambient and elevated CO2 concentrations in replicated experimental trials. Animals raised under elevated pCO2 demonstrated significant developmental changes including increased time to hatching and shorter mantle lengths, although differences were small. Aragonite statoliths, critical for balance and detecting movement, had significantly reduced surface area and were abnormally shaped with increased porosity and altered crystal structure in elevated pCO2-reared paralarvae. These developmental and physiological effects could alter squid paralarvae behavior and survival in the wild, directly and indirectly impacting marine food webs and commercial fisheries.

Description: This study was supported by a WHOI Student Summer Fellowship and WHOI-MIT Joint Program, the Penzance Endowed Fund, the John E. and Anne W. Sawyer Endowed Fund and NSF Research Grant No. EF-1220034. Additional support came from NSF OCE 1041106 to ALC and DCM, and NOAA Sea Grant award #NA10OAR4170083 to ALC and DCM.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e79574, doi:10.1371/journal.pone.0079574.

Description: Transcription factors in the CNC-bZIP family (NFE2, NRF1, NRF2 and NRF3) regulate genes with a wide range of functions in response to both physiological and exogenous signals, including those indicating changes in cellular redox status. Given their role in helping to maintain cellular homeostasis, it is imperative to understand the expression, regulation, and function of CNC-bZIP genes during embryonic development. We explored the expression and function of six nrf genes (nfe2, nrf1a, nrf1b, nrf2a, nrf2b, and nrf3) using zebrafish embryos as a model system. Analysis by microarray and quantitative RT-PCR showed that genes in the nrf family were expressed throughout development from oocytes to larvae. The spatial expression of nrf3 suggested a role in regulating the development of the brain, brachia and pectoral fins. Knock-down by morpholino anti-sense oligonucleotides suggested that none of the genes were necessary for embryonic viability, but nfe2 was required for proper cellular organization in the pneumatic duct and subsequent swim bladder function, as well as for proper formation of the otic vesicles. nrf genes were induced by the oxidant tert-butylhydroperoxide, and some of this response was regulated through family members Nrf2a and Nrf2b. Our results provide a foundation for understanding the role of nrf genes in normal development and in regulating the response to oxidative stress in vertebrate embryos.

Description: This work was supported, in whole or in part, by National Institutes of Health grants F32ES019832 (to L.M.W.), F32ES017585 (to A.R.T.-L.), R01ES015912 (to J.J.S.), and R01ES016366 (to M.E.H.). This work was also supported by Walter A. and Hope Noyes Smith and the J. Seward Johnson Fund.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e81150, doi:10.1371/journal.pone.0081150.

Description: Parasitic dinoflagellates of the genus Amoebophrya infect free-living dinoflagellates, some of which can cause harmful algal blooms (HABs). High prevalence of Amoebophrya spp. has been linked to the decline of some HABs in marine systems. The objective of this study was to evaluate the impact of Amoebophrya spp. on the dynamics of dinoflagellate blooms in Salt Pond (MA, USA), particularly the harmful species Alexandrium fundyense. The abundance of Amoebophrya life stages was estimated 3–7 days per week through the full duration of an annual A. fundyense bloom using fluorescence in situ hybridization coupled with tyramide signal amplification (FISH- TSA). More than 20 potential hosts were recorded including Dinophysis spp., Protoperidinium spp. and Gonyaulax spp., but the only dinoflagellate cells infected by Amoebophrya spp. during the sampling period were A. fundyense. Maximum A. fundyense concentration co-occurred with an increase of infected hosts, followed by a massive release of Amoebophrya dinospores in the water column. On average, Amoebophrya spp. infected and killed ~30% of the A. fundyense population per day in the end phase of the bloom. The decline of the host A. fundyense population coincided with a dramatic life-cycle transition from vegetative division to sexual fusion. This transition occurred after maximum infected host concentrations and before peak infection percentages were observed, suggesting that most A. fundyense escaped parasite infection through sexual fusion. The results of this work highlight the importance of high frequency sampling of both parasite and host populations to accurately assess the impact of parasites on natural plankton assemblages.

Description: L. Velo-Sua´rez was supported by a Marie Curie International Outgoing Fellowship (IOF; grant agreement: MOHAB PIOF-GA-252260). This work was supported in part by NSF grants OCE-0430724 and OCE-0911031 and National Institute of Environmental Health Sciences grants 1P50-ES01274201 and 1P01ES021923-01 to D.M. Anderson and D.J. McGillicuddy through the Woods Hole Center for Oceans and Human Health, National Park Service Cooperative Agreement H238015504 to D.M. Anderson.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88170, doi:10.1371/journal.pone.0088170.

Description: Recent successful efforts to increase protection for manta rays has highlighted the lack of basic ecological information, including vertical and horizontal movement patterns, available for these species. We deployed pop-up satellite archival transmitting tags on nine reef manta rays, Manta alfredi, to determine diving behaviors and vertical habitat use. Transmitted and archived data were obtained from seven tagged mantas over deployment periods of 102–188 days, including three recovered tags containing 2.6 million depth, temperature, and light level data points collected every 10 or 15 seconds. Mantas frequented the upper 10 m during daylight hours and tended to occupy deeper water throughout the night. Six of the seven individuals performed a cumulative 76 deep dives (〉150 m) with one individual reaching 432 m, extending the known depth range of this coastal, reef-oriented species and confirming its role as an ecological link between epipelagic and mesopelagic habitats. Mean vertical velocities calculated from high-resolution dive data (62 dives 〉150 m) from three individuals suggested that mantas may use gliding behavior during travel and that this behavior may prove more efficient than continuous horizontal swimming. The behaviors in this study indicate manta rays provide a previously unknown link between the epi- and mesopelagic layers of an extremely oligotrophic marine environment and provide evidence of a third marine species that utilizes gliding to maximize movement efficiency.

Description: inancial support was provided in part by KAUST baseline research funds (to MLB), KAUST award numbers USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e87877, doi:10.1371/journal.pone.0087877.

Description: The aryl hydrocarbon receptor (AHR) binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17) and IL-22 versus regulatory T cells (Treg) involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1) tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2) many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA), is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.

Description: This work was supported in part by National Institutes of Health (NIH) grants OD000329 and R01AI40312 (to JMM), R01ES006272 (to MEH), P42ES007381 (Superfund Research Program at Boston University to JS, DHS and MEH), R21CA134882 (to JS), NIH Training Grant T32 GM007175 (MML), and the Harvey V. Berneking Living Trust. BK is supported by Career Development Awards from the NIH/National Institute of Diabetes and Digestive and Kidney Diseases (DK083334) and the NASPGHAN Foundation. JEM is a recipient of the Human Frontiers Science Program Long-Term Fellowship (LT000231/2011-L). JMM is a recipient of the NIH Director's Pioneer Award Program, part of the NIH Roadmap for Medical Research, through grant DPI OD00329.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e49474, doi:10.1371/journal.pone.0049474.

Description: Patterns of genetic connectivity are increasingly considered in the design of marine protected areas (MPAs) in both shallow and deep water. In the New Zealand Exclusive Economic Zone (EEZ), deep-sea communities at upper bathyal depths (〈2000 m) are vulnerable to anthropogenic disturbance from fishing and potential mining operations. Currently, patterns of genetic connectivity among deep-sea populations throughout New Zealand’s EEZ are not well understood. Using the mitochondrial Cytochrome Oxidase I and 16S rRNA genes as genetic markers, this study aimed to elucidate patterns of genetic connectivity among populations of two common benthic invertebrates with contrasting life history strategies. Populations of the squat lobster Munida gracilis and the polychaete Hyalinoecia longibranchiata were sampled from continental slope, seamount, and offshore rise habitats on the Chatham Rise, Hikurangi Margin, and Challenger Plateau. For the polychaete, significant population structure was detected among distinct populations on the Chatham Rise, the Hikurangi Margin, and the Challenger Plateau. Significant genetic differences existed between slope and seamount populations on the Hikurangi Margin, as did evidence of population differentiation between the northeast and southwest parts of the Chatham Rise. In contrast, no significant population structure was detected across the study area for the squat lobster. Patterns of genetic connectivity in Hyalinoecia longibranchiata are likely influenced by a number of factors including current regimes that operate on varying spatial and temporal scales to produce potential barriers to dispersal. The striking difference in population structure between species can be attributed to differences in life history strategies. The results of this study are discussed in the context of existing conservation areas that are intended to manage anthropogenic threats to deep-sea benthic communities in the New Zealand region.

Description: This work was funded in part by a Fulbright Fellowship administered by Fulbright New Zealand and the U.S. Department of State, awarded in 2011 to EKB. Funding and support for research expedition was provided by Land Information New Zealand, New Zealand Ministry of Fisheries, NIWA, Census of Marine Life on Seamounts (CenSeam), and the Foundation for Research, Science and Technology. Other research funding was provided by the New Zealand Ministry of Science and Innovation project “Impacts of resource use on vulnerable deep-sea communities” (FRST contract CO1X0906), the National Science Foundation (OCE-0647612), and the Deep Ocean Exploration Institute (Fellowship support to TMS).

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Public Library of Science, doi:10.1371/journal.pone.0052072.

Description: The low-frequency, powerful vocalizations of blue and fin whales may potentially be detected by conspecifics across entire ocean basins. In contrast, humpback and bowhead whales produce equally powerful, but more complex broadband vocalizations composed of higher frequencies that suffer from higher attenuation. Here we evaluate the active space of high frequency song notes of bowhead whales (Balaena mysticetus) in Western Greenland using measurements of song source levels and ambient noise. Four independent, GPS-synchronized hydrophones were deployed through holes in the ice to localize vocalizing bowhead whales, estimate source levels and measure ambient noise. The song had a mean apparent source level of 185±2 dB rms re 1 µPa @ 1 m and a high mean centroid frequency of 444±48 Hz. Using measured ambient noise levels in the area and Arctic sound spreading models, the estimated active space of these song notes is between 40 and 130 km, an order of magnitude smaller than the estimated active space of low frequency blue and fin whale songs produced at similar source levels and for similar noise conditions. We propose that bowhead whales spatially compensate for their smaller communication range through mating aggregations that co-evolved with broadband song to form a complex and dynamic acoustically mediated sexual display.

Description: This work was funded by the Oticon Foundation (grant # 08-3469 to Arctic Station, OT). OT and MC were additionally funded by AP Møller og Hustru Chastine Mc-Kinney Møllers Fond til almene Formaal, MS by a PhD scholarship from the Oticon Foundation, FHJ by a Danish Council for Independent Research, Natural Sciences post-doctoral grant, SEP by a grant from the U.S. Office of Naval Research, and PTM by frame grants from the Danish Natural Science Research Council.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e54069, doi:10.1371/journal.pone.0054069.

Description: Structural change in both the habitat and reef-associated fish assemblages within spatially managed coral reefs can provide key insights into the benefits and limitations of Marine Protected Areas (MPAs). While MPA zoning effects on particular target species are well reported, we are yet to fully resolve the various affects of spatial management on the structure of coral reef communities over decadal time scales. Here, we document mixed affects of MPA zoning on fish density, biomass and species richness over the 21 years since establishment of the Saba Marine Park (SMP). Although we found significantly greater biomass and species richness of reef-associated fishes within shallow habitats (5 meters depth) closed to fishing, this did not hold for deeper (15 m) habitats, and there was a widespread decline (38% decrease) in live hard coral cover and a 68% loss of carnivorous reef fishes across all zones of the SMP from the 1990s to 2008. Given the importance of live coral for the maintenance and replenishment of reef fishes, and the likely role of chronic disturbance in driving coral decline across the region, we explore how local spatial management can help protect coral reef ecosystems within the context of large-scale environmental pressures and disturbances outside the purview of local MPA management.

Description: Funding was provided by the Saba Conservation Foundation ((SCF), King Abdullah University of Science and Technology, The Australian National University and Australian Research Council.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e70966, doi:10.1371/journal.pone.0070966.

Description: Rising sea temperatures are causing significant destruction to coral reef ecosystems due to coral mortality from thermally-induced bleaching (loss of symbiotic algae and/or their photosynthetic pigments). Although bleaching has been intensively studied in corals, little is known about the causes and consequences of bleaching in other tropical symbiotic organisms. This study used underwater visual surveys to investigate bleaching in the 10 species of anemones that host anemonefishes. Bleaching was confirmed in seven anemone species (with anecdotal reports of bleaching in the other three species) at 10 of 19 survey locations spanning the Indo-Pacific and Red Sea, indicating that anemone bleaching is taxonomically and geographically widespread. In total, bleaching was observed in 490 of the 13,896 surveyed anemones (3.5%); however, this percentage was much higher (19–100%) during five major bleaching events that were associated with periods of elevated water temperatures and coral bleaching. There was considerable spatial variation in anemone bleaching during most of these events, suggesting that certain sites and deeper waters might act as refuges. Susceptibility to bleaching varied between species, and in some species, bleaching caused reductions in size and abundance. Anemones are long-lived with low natural mortality, which makes them particularly vulnerable to predicted increases in severity and frequency of bleaching events. Population viability will be severely compromised if anemones and their symbionts cannot acclimate or adapt to rising sea temperatures. Anemone bleaching also has negative effects to other species, particularly those that have an obligate relationship with anemones. These effects include reductions in abundance and reproductive output of anemonefishes. Therefore, the future of these iconic and commercially valuable coral reef fishes is inextricably linked to the ability of host anemones to cope with rising sea temperatures associated with climate change.

Description: This work was supported by funding from the Red Sea Research Center at the King Abdullah University of Science and Technology (KAUST), The ARC Centre of Excellence for Coral Reef Studies, the National Science Foundation (OCE 0424688), the Coral Reef Initiatives for the Pacific (CRISP), the TOTAL Foundation, Populations Fractionees et Insulares (PPF EPHE), the Connectivity Working Group of the Global University of Queensland – World Bank – Global Environmental Facility Project, Coral Reef Target Research and Capacity Building for Management, Great Barrier Reef Marine Park Authority, and the Australian Government Department of Sustainability, Environment, Water, Population and Communities. J-P Hobbs is supported by a UWA-AIMS-CSIRO fellowship.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e74265, doi:10.1371/journal.pone.0074265.

Description: Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand population structures. Among sequences classified to genus, Alcanivorax, Alteromonas, Marinobacter, Winogradskyella, and Zeaxanthinibacter exhibited the largest relative abundance increases in oiled sands.

Description: Financial support for this work was provided by the University of Wisconsin-Milwaukee National Institute of Environmental Health Sciences program, grant ES-004184 to SLM and the Alfred P. Sloan Foundation's grant for the Rare Biosphere in the Built Environment MLS.

Description: This article is distributed free of all copyright. The definitive version was published in PLoS One 9 (2014): e84006, doi:10.1371/journal.pone.0084006.

Description: Conservation and management efforts for white sharks (Carcharodon carcharias) remain hampered by a lack of basic demographic information including age and growth rates. Sharks are typically aged by counting growth bands sequentially deposited in their vertebrae, but the assumption of annual deposition of these band pairs requires testing. We compared radiocarbon (Δ14C) values in vertebrae from four female and four male white sharks from the northwestern Atlantic Ocean (NWA) with reference chronologies documenting the marine uptake of 14C produced by atmospheric testing of thermonuclear devices to generate the first radiocarbon age estimates for adult white sharks. Age estimates were up to 40 years old for the largest female (fork length [FL]: 526 cm) and 73 years old for the largest male (FL: 493 cm). Our results dramatically extend the maximum age and longevity of white sharks compared to earlier studies, hint at possible sexual dimorphism in growth rates, and raise concerns that white shark populations are considerably more sensitive to human-induced mortality than previously thought.

Description: This study was funded by the National Science Foundation (OCE 0825148 was awarded to SRT) and LLH was supported by the National Science Foundation Graduate Research Fellowship Program.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e85872, doi:10.1371/journal.pone.0085872.

Description: Assemblages of megabenthos are structured in seven depth-related zones between ~700 and 4000 m on the rocky and topographically complex continental margin south of Tasmania, southeastern Australia. These patterns emerge from analysis of imagery and specimen collections taken from a suite of surveys using photographic and in situ sampling by epibenthic sleds, towed video cameras, an autonomous underwater vehicle and a remotely operated vehicle (ROV). Seamount peaks in shallow zones had relatively low biomass and low diversity assemblages, which may be in part natural and in part due to effects of bottom trawl fishing. Species richness was highest at intermediate depths (1000–1300 m) as a result of an extensive coral reef community based on the bioherm-forming scleractinian Solenosmilia variabilis. However, megabenthos abundance peaked in a deeper, low diversity assemblage at 2000–2500 m. The S. variabilis reef and the deep biomass zone were separated by an extensive dead, sub-fossil S. variabilis reef and a relatively low biomass stratum on volcanic rock roughly coincident with the oxygen minimum layer. Below 2400 m, megabenthos was increasingly sparse, though punctuated by occasional small pockets of relatively high diversity and biomass. Nonetheless, megabenthic organisms were observed in the vast majority of photographs on all seabed habitats and to the maximum depths observed - a sandy plain below 3950 m. Taxonomic studies in progress suggest that the observed depth zonation is based in part on changing species mixes with depth, but also an underlying commonality to much of the seamount and rocky substrate biota across all depths. Although the mechanisms supporting the extraordinarily high biomass in 2000–2500 m depths remains obscure, plausible explanations include equatorwards lateral transport of polar production and/or a response to depth-stratified oxygen availability.

Description: Components of this work were supported by the National Science Foundation, the Australian Department of Environment, Water, Heritage, and the Arts, the Australian Commonwealth Environmental Research Fund, a grant of ship time by the Australian National Research Facility, and the CSIRO Wealth from Oceans and Climate Adaptation Flagships.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e88618, doi:10.1371/journal.pone.0088618.

Description: The taxon Syndermata comprises the biologically interesting wheel animals (“Rotifera”: Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.

Description: The work was funded by the Deutsche Forschungsgemeinschaft (DFG grant Ha2103/4-3, Priority Project "Deep Metazoan Phylogeny", SPP1174; www. dfg.de). Additional financial support came from the Center for Computational Sciences (SRFN) of Johannes Gutenberg University Mainz (http://www.csm.unimainz. de).

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e97338, doi:10.1371/journal.pone.0097338.

Description: Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e78275, doi:10.1371/journal.pone.0078275.

Description: Anaerobic ammonia oxidation (anammox) as an important nitrogen loss pathway has been reported in marine oxygen minimum zones (OMZs), but the community composition and spatial distribution of anammox bacteria in the eastern tropical North Pacific (ETNP) OMZ are poorly determined. In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2. The anammox communities revealed by hzo genes and proteins in CRD-OMZ showed a low diversity. Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration. Nitrite and oxygen concentrations may therefore colimit the distribution of anammox bacteria in this area. Furthermore, transcriptional activity of anammox bacteria was confirmed by obtaining abundant hzo mRNA transcripts through qRT-PCR. A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment. Our study demonstrated that both cluster 1 and 2 anammox bacteria play an active role in the CRD-OMZ, and the cluster 1 abundance and transcriptional activity were higher than cluster 2 in both free-living and particle-attached fractions at both gene and transcriptional levels.

Description: National Science Foundation (OCE #0961098) Hong Kong Research Grants Council (661911 and 661912) Chinese Academy of Science (SIDSSE-BR-201301).

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e77671, doi:10.1371/journal.pone.0077671.

Description: Bottlenose dolphins (Tursiops truncatus) produce many vocalisations, including whistles that are unique to the individual producing them. Such “signature whistles” play a role in individual recognition and maintaining group integrity. Previous work has shown that humans can successfully group the spectrographic representations of signature whistles according to the individual dolphins that produced them. However, attempts at using mathematical algorithms to perform a similar task have been less successful. A greater understanding of the encoding of identity information in signature whistles is important for assessing similarity of whistles and thus social influences on the development of these learned calls. We re-examined 400 signature whistles from 20 individual dolphins used in a previous study, and tested the performance of new mathematical algorithms. We compared the measure used in the original study (correlation matrix of evenly sampled frequency measurements) to one used in several previous studies (similarity matrix of time-warped whistles), and to a new algorithm based on the Parsons code, used in music retrieval databases. The Parsons code records the direction of frequency change at each time step, and is effective at capturing human perception of music. We analysed similarity matrices from each of these three techniques, as well as a random control, by unsupervised clustering using three separate techniques: k-means clustering, hierarchical clustering, and an adaptive resonance theory neural network. For each of the three clustering techniques, a seven-level Parsons algorithm provided better clustering than the correlation and dynamic time warping algorithms, and was closer to the near-perfect visual categorisations of human judges. Thus, the Parsons code captures much of the individual identity information present in signature whistles, and may prove useful in studies requiring quantification of whistle similarity.

Description: Arik Kershenbaum is a Postdoctoral Fellow at the National Institute for Mathematical and Biological Synthesis, an Institute sponsored by the National Science Foundation, the U.S. Department of Homeland Security, and the U.S. Department of Agriculture through NSF Award #EF-0832858, with additional support from The University of Tennessee, Knoxville. Part of this work was conducted while Arik Kershenbaum was provided with a doctoral scholarship by the University of Haifa. Funding for access to the dolphins for recordings was provided by Dolphin Quest and the Chicago Zoological Society.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e80192, doi:10.1371/journal.pone.0080192.

Description: In vertebrates and arthropods, blood clotting involves the establishment of a plug of aggregated thrombocytes (the cellular clot) and an extracellular fibrillar clot formed by the polymerization of the structural protein of the clot, which is fibrin in mammals, plasma lipoprotein in crustaceans, and coagulin in the horseshoe crab, Limulus polyphemus. Both elements of the clot function to staunch bleeding. Additionally, the extracellular clot functions as an agent of the innate immune system by providing a passive anti-microbial barrier and microbial entrapment device, which functions directly at the site of wounds to the integument. Here we show that, in addition to these passive functions in immunity, the plasma lipoprotein clot of lobster, the coagulin clot of Limulus, and both the platelet thrombus and the fibrin clot of mammals (human, mouse) operate to capture lipopolysaccharide (LPS, endotoxin). The lipid A core of LPS is the principal agent of gram-negative septicemia, which is responsible for more than 100,000 human deaths annually in the United States and is similarly toxic to arthropods. Quantification using the Limulus Amebocyte Lysate (LAL) test shows that clots capture significant quantities of LPS and fluorescent-labeled LPS can be seen by microscopy to decorate the clot fibrils. Thrombi generated in the living mouse accumulate LPS in vivo. It is suggested that capture of LPS released from gram-negative bacteria entrapped by the blood clot operates to protect against the disease that might be caused by its systemic dispersal.

Description: Grant # 0344360 from the National Science Foundation (PBA).

Description: We present first results from a coupled model setup, consisting of the state-of-the-art ice sheet model RIMBAY (Revised Ice Model Based on frAnk pattYn), and the community earth system model COSMOS. We show that special care has to be provided in order to ensure physical distributions of the forcings as well as numeric stability of the involved models. We demonstrate that a suitable statistical downscaling is crucial for ice sheet stability, especially for southern Greenland where surface temperatures are close to the melting point. The downscaling of net snow accumulation is based on an empirical relationship between surface slope and rainfall. The simulated ice sheet does not show dramatic loss of ice volume for pre-industrial conditions and is comparable with present-day ice orography. A sensitivity study with high CO2 level is used to demonstrate the effects of dynamic ice sheets onto climate compared to the standard setup with prescribed ice sheets.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50221, doi:10.1371/journal.pone.0050221.

Description: Lymphocytes are a key component of the immune system and their differentiation and function are directly influenced by cancer. We examined peripheral blood lymphocyte (PBL) gene expression as a biomarker of illness and treatment effect using the Affymetrix Human Gene ST1 platform in patients with metastatic renal cell carcinoma (mRCC) who received combined treatment with IL-2, interferon-?-2a and dendritic cell vaccine. We examined gene expression, cytokine levels in patient serum and lymphocyte subsets as determined by flow cytometry (FCM). Pre-treatment PBLs from patients with mRCC exhibit a gene expression profile and serum cytokine profile consistent with inflammation and proliferation not found in healthy donors (HD). PBL gene expression from patients with mRCC showed increased mRNA of genes involved with T-cell and TREG-cell activation pathways, which was also reflected in lymphocyte subset distribution. Overall, PBL gene expression post-treatment (POST) was not significantly different than pre-treatment (PRE). Nevertheless, treatment related changes in gene expression (post-treatment minus pre-treatment) revealed an increased expression of T-cell and B-cell receptor signaling pathways in responding (R) patients compared to non-responding (NR) patients. In addition, we observed down-regulation of TREG-cell pathways post-treatment in R vs. NR patients. While exploratory in nature, this study supports the hypothesis that enhanced inflammatory cytotoxic pathways coupled with blunting of the regulatory pathways is necessary for effective anti-cancer activity associated with immune therapy. This type of analysis can potentially identify additional immune therapeutic targets in patients with mRCC.

Description: This work was supported by grants from the National Institutes of Health (RO1 CA5648, R21CA112761, P20RR016437, and P30CA023108).

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.

Description: Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.

Description: This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e103536, doi:10.1371/journal.pone.0103536.

Description: Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009–2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5–7 m total length with a sex ratio of approximately 1:1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.

Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the United States National Science Foundation (OCE 0825148 to SRT and GBS).

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e112379, doi:10.1575/1912/6845.

Description: Increasing Transparent Exopolymer Particle (TEP) formation during diatom blooms as a result of elevated temperature and pCO2 have been suggested to result in enhanced aggregation and carbon flux, therewith potentially increasing the sequestration of carbon by the ocean. We present experimental results on TEP and aggregate formation by Thalassiosira weissflogii (diatom) in the presence or absence of bacteria under two temperature and three pCO2 scenarios. During the aggregation phase of the experiment TEP formation was elevated at the higher temperature (20°C vs. 15°C), as predicted. However, in contrast to expectations based on the established relationship between TEP and aggregation, aggregation rates and sinking velocity of aggregates were depressed in warmer treatments, especially under ocean acidification conditions. If our experimental findings can be extrapolated to natural conditions, they would imply a reduction in carbon flux and potentially reduced carbon sequestration after diatom blooms in the future ocean.

Description: This work was supported by National Science Foundation grants OCE-0926711 & OCE-1041038 to UP and Helmholtz Graduate School for Polar and Marine Research and Jacobs University Bremen to SS.

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e59284, doi:10.1371/journal.pone.0059284.

Description: Toothed whales (Cetacea, odontoceti) use biosonar to navigate their environment and to find and catch prey. All studied toothed whale species have evolved highly directional, high-amplitude ultrasonic clicks suited for long-range echolocation of prey in open water. Little is known about the biosonar signals of toothed whale species inhabiting freshwater habitats such as endangered river dolphins. To address the evolutionary pressures shaping the echolocation signal parameters of non-marine toothed whales, we investigated the biosonar source parameters of Ganges river dolphins (Platanista gangetica gangetica) and Irrawaddy dolphins (Orcaella brevirostris) within the river systems of the Sundarban mangrove forest. Both Ganges and Irrawaddy dolphins produced echolocation clicks with a high repetition rate and low source level compared to marine species. Irrawaddy dolphins, inhabiting coastal and riverine habitats, produced a mean source level of 195 dB (max 203 dB) re 1 µPapp whereas Ganges river dolphins, living exclusively upriver, produced a mean source level of 184 dB (max 191) re 1 µPapp. These source levels are 1–2 orders of magnitude lower than those of similar sized marine delphinids and may reflect an adaptation to a shallow, acoustically complex freshwater habitat with high reverberation and acoustic clutter. The centroid frequency of Ganges river dolphin clicks are an octave lower than predicted from scaling, but with an estimated beamwidth comparable to that of porpoises. The unique bony maxillary crests found in the Platanista forehead may help achieve a higher directionality than expected using clicks nearly an octave lower than similar sized odontocetes.

Description: This study was made possible through the logistical and field support of the Bangladesh Cetacean Diversity Project of the Wildlife Conservation Society, and funded by frame grants from the Danish Natural Science Foundation to PTM. FHJ was supported by the PhD School of Aquatic Sciences, Denmark, and is currently funded by a postdoctoral fellowship from the Danish Council for Independent Research | Natural Sciences. VMJ was supported by a fellowship of the Wissenschaftskolleg Berlin. PTM was supported by frame grants from the Danish Natural Science Foundation.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e92277, doi:10.1371/journal.pone.0092277.

Description: Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to “true” GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were 〈5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6±5.6 km) was nearly half that of LS estimates (11.6±8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales’ behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.

Description: This research was primarily funded by Fundação para a Ciência e a Tecnologia (FCT), Fundo Regional da Ciência, Tecnologia (FRCT), through research projects TRACE-PTDC/MAR/74071/2006 and MAPCET-M2.1.2/F/012/2011 [FEDER], the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, and Proconvergencia Açores/EU Program]. We acknowledge funds provided by FCT to LARSyS Associated Laboratory and IMAR-University of the Azores/the Thematic Area D & E of the Strategic Project PEst-OE/EEI/LA0009/2011–1012 and 2013–2014 (OE & Compete) and by the FRCT - Government of the Azores pluriannual funding. MAS was supported by an FCT postdoctoral grant (SFRH/BPD/29841/2006) and is currently supported by POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education through an FCT Investigator grant. RP was supported by an FCT doctoral grant (SFRH/BD/41192/2007) and by the research grant from the Azores Regional Fund for Science and Technology (M3.1.5/F/115/2012). IJ was supported by the Natural Sciences and Engineering Research Council (NSERC) and the Canada Foundation for Innovation (CFI) through their support of the Ocean Tracking Network. DJFR is funded by the United Kingdom Department of Energy and Climate Change as part of their Offshore Energy Strategic Environmental Assessment program. DT is funded by Natural Environment Research Council and Marine Scotland.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e94249, doi:10.1371/journal.pone.0094249.

Description: The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina and 454 pyrosequencing provide similar beta diversity measures, it remains to be demonstrated that pre-existing 454 pyrosequencing workflows can transfer directly from 454 to Illumina MiSeq sequencing by simply changing the sequencing adapters of the primers. In this study, we modified 454 pyrosequencing primers targeting the V4-V5 hyper-variable regions of the 16S rRNA gene to be compatible with Illumina sequencers. Microbial communities from cows, humans, leeches, mice, sewage, and termites and a mock community were analyzed by 454 and MiSeq sequencing of the V4-V5 region and MiSeq sequencing of the V4 region. Our analysis revealed that reference-based OTU clustering alone introduced biases compared to de novo clustering, preventing certain taxa from being observed in some samples. Based on this we devised and recommend an analysis pipeline that includes read merging, contaminant filtering, and reference-based clustering followed by de novo OTU clustering, which produces diversity measures consistent with de novo OTU clustering analysis. Low levels of dataset contamination with Illumina sequencing were discovered that could affect analyses that require highly sensitive approaches. While moving to Illumina-based sequencing platforms promises to provide deeper insights into the breadth and function of microbial diversity, our results show that care must be taken to ensure that sequencing and processing artifacts do not obscure true microbial diversity.

Description: This work was partially funded by an Emerging Frontiers in Research and Innovation – Multicellular and Inter-kingdom Signaling (EFRI-MIKS) grant awarded by the US National Science Foundation to Joerg Graf and NIH RO1 GM095390 to JG and HGM.

Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e101658, doi:10.1371/journal.pone.0101658.

Description: Profiling floats equipped with bio-optical sensors well complement ship-based and satellite ocean color measurements by providing highly-resolved time-series data on the vertical structure of biogeochemical processes in oceanic waters. This is the first study to employ an autonomous profiling (APEX) float in the Gulf of Mexico for measuring spatiotemporal variability in bio-optics and hydrography. During the 17-month deployment (July 2011 to December 2012), the float mission collected profiles of temperature, salinity, chlorophyll fluorescence, particulate backscattering (bbp), and colored dissolved organic matter (CDOM) fluorescence from the ocean surface to a depth of 1,500 m. Biogeochemical variability was characterized by distinct depth trends and local “hot spots”, including impacts from mesoscale processes associated with each of the water masses sampled, from ambient deep waters over the Florida Plain, into the Loop Current, up the Florida Canyon, and eventually into the Florida Straits. A deep chlorophyll maximum (DCM) occurred between 30 and 120 m, with the DCM depth significantly related to the unique density layer ρ = 1023.6 (R2 = 0.62). Particulate backscattering, bbp, demonstrated multiple peaks throughout the water column, including from phytoplankton, deep scattering layers, and resuspension. The bio-optical relationship developed between bbp and chlorophyll (R2 = 0.49) was compared to a global relationship and could significantly improve regional ocean-color algorithms. Photooxidation and autochthonous production contributed to CDOM distributions in the upper water column, whereas in deep water, CDOM behaved as a semi-conservative tracer of water masses, demonstrating a tight relationship with density (R2 = 0.87). In the wake of the Deepwater Horizon oil spill, this research lends support to the use of autonomous drifting profilers as a powerful tool for consideration in the design of an expanded and integrated observing network for the Gulf of Mexico.

Description: This project was funded by Bureau of Ocean Energy Management (BOEM) Contract M10PC00112 to Leidos, Inc. with subcontract to ASB (www.boem.gov).

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56335, doi:10.1371/journal.pone.0056335.

Description: The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.

Description: This work was performed with funding from the Center for Dark Energy Biosphere Investigations (C-DEBI) to William Orsi (OCE-0939564) and The Ocean Life Institute (WHOI) to Virginia Edgcomb (OLI-27071359).

Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 8 (2013): e82764, doi:10.1371/journal.pone.0082764.

Description: Many marine invertebrates have planktonic larvae with cilia used for both propulsion and capturing of food particles. Hence, changes in ciliary activity have implications for larval nutrition and ability to navigate the water column, which in turn affect survival and dispersal. Using high-speed high-resolution microvideography, we examined the relationship between swimming speed, velar arrangements, and ciliary beat frequency of freely swimming veliger larvae of the gastropod Crepidula fornicata over the course of larval development. Average swimming speed was greatest 6 days post hatching, suggesting a reduction in swimming speed towards settlement. At a given age, veliger larvae have highly variable speeds (0.8–4 body lengths s−1) that are independent of shell size. Contrary to the hypothesis that an increase in ciliary beat frequency increases work done, and therefore speed, there was no significant correlation between swimming speed and ciliary beat frequency. Instead, there are significant correlations between swimming speed and visible area of the velar lobe, and distance between centroids of velum and larval shell. These observations suggest an alternative hypothesis that, instead of modifying ciliary beat frequency, larval C. fornicata modify swimming through adjustment of velum extension or orientation. The ability to adjust velum position could influence particle capture efficiency and fluid disturbance and help promote survival in the plankton.

Description: K.Y.K. Chan was supported by the Postdoctoral Scholar 1 Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation, and the Royal Swedish Academy of Sciences. H. Jiang was supported by National Science Foundation grant NSF OCE-1129496 and an award from WHOI's Ocean Life Institute, and D.K. Padilla was supported by NSF IOS-0920032.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e93296, doi:10.1371/journal.pone.0093296.

Description: Direct and indirect human impacts on coastal ecosystems have increased over the last several centuries, leading to unprecedented degradation of coastal habitats and loss of ecological services. Here we document a two-century temporal disparity between salt marsh accretion and subsequent loss to indirect human impacts. Field surveys, manipulative experiments and GIS analyses reveal that crab burrowing weakens the marsh peat base and facilitates further burrowing, leading to bank calving, disruption of marsh accretion, and a loss of over two centuries of sequestered carbon from the marsh edge in only three decades. Analogous temporal disparities exist in other systems and are a largely unrecognized obstacle in attaining sustainable ecosystem services in an increasingly human impacted world. In light of the growing threat of indirect impacts worldwide and despite uncertainties in the fate of lost carbon, we suggest that estimates of carbon emissions based only on direct human impacts may significantly underestimate total anthropogenic carbon emissions.

Description: This research was made possible by a grant from the National Science Foundation Biological Oceanography Program and the Brown University Undergraduate Teaching and Research Award Program.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90785, doi:10.1371/journal.pone.0090785.

Description: Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals.

Description: A.A. was funded by a WHOI Ocean Life Institute post-doctoral scholar award, and this research was supported by a grant to A.A. and T.J.M. from Woods Hole Oceanographic Institution's (WHOI) Marine Mammal Center.

Description: The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 9 (2014): e95380, doi:10.1371/journal.pone.0095380.

Description: Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.

Description: This work was supported by NSF grants EF-826924 (R.S.), OCE-821374 (R.S.) and OCE-1232982 (R.S. and B.K.S.); the DOE JGI 2010 Microbes Program grant CSP77 (R.S. and M.E.S.); National Institutes of Health grant 1UH2DK083993 (H.G.M.). Work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The contributions of S.K. were funded under Agreement No. HSHQDC-07-C-00020 awarded by the Department of Homeland Security (DHS) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center.

Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50015, doi:10.1371/journal.pone.0050015.

Description: Deep-sea hydrothermal vents are subject to major disturbances that alter the physical and chemical environment and eradicate the resident faunal communities. Vent fields are isolated by uninhabitable deep seafloor, so recolonization via dispersal of planktonic larvae is critical for persistence of populations. We monitored colonization near 9°50′N on the East Pacific Rise following a catastrophic eruption in order to address questions of the relative contributions of pioneer colonists and environmental change to variation in species composition, and the role of pioneers at the disturbed site in altering community structure elsewhere in the region. Pioneer colonists included two gastropod species: Ctenopelta porifera, which was new to the vent field, and Lepetodrilus tevnianus, which had been rare before the eruption but persisted in high abundance afterward, delaying and possibly out-competing the ubiquitous pre-eruption congener L. elevatus. A decrease in abundance of C. porifera over time, and the arrival of later species, corresponded to a decrease in vent fluid flow and in the sulfide to temperature ratio. For some species these successional changes were likely due to habitat requirements, but other species persisted (L. tevnianus) or arrived (L. elevatus) in patterns unrelated to their habitat preferences. After two years, disturbed communities had started to resemble pre-eruption ones, but were lower in diversity. When compared to a prior (1991) eruption, the succession of foundation species (tubeworms and mussels) appeared to be delayed, even though habitat chemistry became similar to the pre-eruption state more quickly. Surprisingly, a nearby community that had not been disturbed by the eruption was invaded by the pioneers, possibly after they became established in the disturbed vents. These results indicate that the post-eruption arrival of species from remote locales had a strong and persistent effect on communities at both disturbed and undisturbed vents.

Description: The authors received funding from National Science Foundation grant OCE-0424953, WHOI Deep Ocean Exploration Institute, WHOI Summer Student Fellow program, Woods Hole Partnership in Education Program, IFREMER and CNRS, Fondation TOTAL Chair Extreme Marine Environment, Biodiversity and Global change.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.

Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.

Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).

Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 9 (2014): e98995, doi:10.1371/journal.pone.0098995.

Description: Management of marine ecosystems increasingly demands comprehensive and quantitative assessments of ocean health, but lacks a tool to do so. We applied the recently developed Ocean Health Index to assess ocean health in the relatively data-rich US west coast region. The overall region scored 71 out of 100, with sub-regions scoring from 65 (Washington) to 74 (Oregon). Highest scoring goals included tourism and recreation (99) and clean waters (87), while the lowest scoring goals were sense of place (48) and artisanal fishing opportunities (57). Surprisingly, even in this well-studied area data limitations precluded robust assessments of past trends in overall ocean health. Nonetheless, retrospective calculation of current status showed that many goals have declined, by up to 20%. In contrast, near-term future scores were on average 6% greater than current status across all goals and sub-regions. Application of hypothetical but realistic management scenarios illustrate how the Index can be used to predict and understand the tradeoffs among goals and consequences for overall ocean health. We illustrate and discuss how this index can be used to vet underlying assumptions and decisions with local stakeholders and decision-makers so that scores reflect regional knowledge, priorities and values. We also highlight the importance of ongoing and future monitoring that will provide robust data relevant to ocean health assessment.

Description: Beau and Heather Wrigley generously provided the founding grant. Additional financial and in-kind support was provided by the Pacific Life Foundation, Thomas W. Haas Fund of the New Hampshire Charitable Foundation, the Oak Foundation, Akiko Shiraki Dynner Fund for Ocean Exploration and Conservation, Darden Restaurants Inc. Foundation, Conservation International, New England Aquarium, National Geographic, and the University of California Santa Barbara's National Center for Ecological Analysis and Synthesis, which supported the Ecosystem Health Working Group as part of the Science of Ecosystem-Based Management project funded by the David and Lucile Packard Foundation. Individual authors also acknowledge support from the U.S. National Science Foundation.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109696, doi:10.1371/journal.pone.0109696.

Description: The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.

Description: Funding for sequencing of the viral metagenome was provided by the Gordon and Betty Moore Foundation. All other funding was provided by a NASA Astrobiology Institute grant through Cooperative Agreement NNA04CC09A to the Geophysical Laboratory at the Carnegie Institution for Science. R.A. was funded by a NSF Graduate Research Fellowship through NSF grant number DGE-0718124, an NSF IGERT grant to the University of Washington Astrobiology Program, and the ARCS Foundation.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e113158, doi:10.1371/journal.pone.0113158.

Description: Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect susceptibility to oxidants, but the embryonic response to oxidants is not well understood. To assess the response to chemically mediated oxidative stress and how it may vary during development, zebrafish embryos, eleutheroembryos, or larvae at 1, 2, 3, 4, 5, and 6 days post fertilization (dpf) were exposed to DMSO (0.1%), tert-butylhydroquinone (tBHQ; 10 µM) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 2 nM) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray. qRT-PCR showed strong (4- to 5-fold) induction of gstp1 by tBHQ as early as 1 dpf. tBHQ also induced gclc (2 dpf), but not sod1, nqo1, or cyp1a. TCDD induced cyp1a but none of the other genes. Microarray analysis showed that 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated eleutheroembryos at 4 dpf. There was substantial overlap between genes induced in developing zebrafish and a set of marker genes induced by oxidative stress in mammals. Genes induced by tBHQ in 4-dpf zebrafish included those involved in glutathione synthesis and utilization, signal transduction, and DNA damage/stress response. The strong induction of hsp70 determined by microarray was confirmed by qRT-PCR and by use of transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under control of the hsp70 promoter. Genes strongly down-regulated by tBHQ included mitfa, providing a molecular explanation for the loss of pigmentation in tBHQ-exposed embryos. These data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.

Description: This research was supported in part by National Institutes of Health grants R01ES016366 (MEH), R01ES006272 (MEH), R01ES015912 (JJS), and F32ES017585 (ART-L), the Andrew W. Mellon Foundation Endowed Fund for Innovative Research, a WHOI (Woods Hole Oceanographic Institution) Postdoctoral Scholar award, and the Walter A. and Hope Noyes Smith endowed chair (MEH). AGM and MJC were supported in part by the Marine Biological Laboratory's Program in Global Infectious Disease, funded by the Ellison Medical Foundation.

Description: 〈jats:p〉Abstract. The spatial and temporal variability of a low-centred polygon on the eastern floodplain area of the lower Anabar River (72.070° N, 113.921° E, northern Yakutia, Siberia) has been investigated using a multi-method approach. The present-day vegetation in each square metre was analysed revealing a community of Larix shrubby Betula and Salix on the polygon rim, a dominance of Carex and Andromeda polifolia in the rim-to-pond transition zone, and a predominantly monospecific Scorpidium scorpioides coverage within the pond. The TOC content, TOC/TN ratio, grain-size, vascular plant macrofossils, moss remains, diatoms, and pollen were analysed for two vertical sections and a sediment core from a transect across the polygon. Radiocarbon dating indicates that the formation of the polygon started at least 1500 yr ago; the general positions of the pond and rim have not changed since that time. Two types of pond vegetation were identified, indicating two contrasting development stages of the polygon. The first was a well-established moss association dominated by submerged or floating Scorpidium scorpioides and/or Drepanocladus spp. and overgrown by epiphytic diatoms such as Tabellaria flocculosa and Eunotia taxa. This stage coincides temporally with a period in which the polygon was only drained by lateral subsurface water flow, as indicated by mixed grain sizes. A different moss association occurred during times of repeated river flooding (indicated by homogeneous medium-grained sand that probably accumulated during the annual spring snow melt), characterized by an abundance of Meesia triquetra and a dominance of benthic diatoms (e.g. Navicula vulpina), indicative of a relatively high pH and a high tolerance of disturbance. A comparison of the local polygon vegetation (inferred from moss and macrofossil spectra) with the regional vegetation (inferred from pollen spectra) indicated that the moss association with Scorpidium scorpioides became established during relatively favourable climatic conditions while the association dominated by Meesia triquetra occurred during periods of harsh climatic conditions. Our study revealed a strong riverine influence (in addition to climatic influences) on polygon development and the type of peat accumulated. 〈/jats:p〉

Description: Sea urchins as broadcasting spawners, release their gametes into open water for fertilization, thus being particularly vulnerable to ocean acidification. In this study, we assessed the effects of different pH scenarios on fertilization success of Strongylocen- 5 trotus droebachiensis, collected at Spitsbergen, Arctic. We achieved acidification by bubbling CO2 into filtered seawater using partial pressures (pCO2) of 180, 380, 980, 1400 and 3000 μatm. Untreated filtered seawater was used as control. We recorded fertilization rates and diagnosed morphological aberrations after post-fertilization periods of 1 h and 3 h under different exposure conditions in experiments with and without 10 pre-incubation of the eggs prior to fertilization. In parallel, we conducted measurements of intracellular pH changes using BCECF/AM in unfertilized eggs exposed to a range of acidified seawater. We observed increasing rates of polyspermy in relation to higher seawater pCO2, which might be due to failures in the formation of the fertilization envelope. In addition, our experiments showed anomalies in fertilized eggs: incomplete 15 lifting-off of the fertilization envelope and blebs of the hyaline layer. Other drastic malformations consisted of constriction, extrusion, vacuolization or degeneration (observed as a gradient from the cortex to the central region of the cell) of the egg cytoplasm, and irregular cell divisions until 2- to 4-cell stages. The intracellular pH (pHi) decreased significantly from 1400 μatm on. All results indicate a decreasing fertilization success 20 at CO2 concentrations from 1400 μatm upwards. Exposure time to low pH might be a threatening factor for the cellular buffer capacity, viability, and development after fertilization.

Description: Regional and local patterns in depth to water table, hydrochemistry and peat properties of bogs and their laggs in coastal British Columbia Hydrology and Earth System Sciences, 17, 3421-3435, 2013 Author(s): S. A. Howie and H. J. van Meerveld In restoration planning for damaged raised bogs, the lagg at the bog margin is often not given considerable weight and is sometimes disregarded entirely. However, the lagg is critical for the proper functioning of the bog, as it supports the water mound in the bog. In order to include the lagg in a restoration plan for a raised bog, it is necessary to understand the hydrological characteristics and functions of this rarely studied transition zone. We studied 13 coastal British Columbia (BC) bogs and identified two different gradients in depth to water table, hydrochemistry and peat properties: (1) a local bog expanse–bog margin gradient, and (2) a regional gradient related to climate and proximity to the ocean. Depth to water table generally increased across the transition from bog expanse to bog margin. In the bog expanse, pH was above 4.2 in the Pacific Oceanic wetland region (cooler and wetter climate) and below 4.3 in the Pacific Temperate wetland region (warmer and drier climate). Both pH and pH-corrected electrical conductivity increased significantly across the transition from bog expanse to bog margin, though not in all cases. Na + and Mg 2+ concentrations were generally highest in exposed, oceanic bogs and lower in inland bogs. Ash content in peat samples increased across the bog expanse–bog margin transition, and appears to be a useful abiotic indicator of the location of the bog margin. The observed variation in the hydrological and hydrochemical gradients across the bog expanse–bog margin transition highlights both local and regional diversity of bogs and their associated laggs.

Description: Imperfect scaling in distributions of radar-derived rainfall fields Hydrology and Earth System Sciences Discussions, 10, 11385-11422, 2013 Author(s): M. J. van den Berg, L. Delobbe, and N. E. C. Verhoest Fine scale rainfall observations for modeling exercises are often not available, but rather coarser data derived from a variety of sources are used. Effectively using these data sources in models often requires the probability distribution of the data at the applicable scale. Although numerous models for scaling distributions exist, these are often based on theoretical developments, rather than on data. In this study, we develop a model based on the α-stable distribution of rainfall fields, and tested on 5 min radar data from a Belgian weather radar. We use these data to estimate functions that describe parameters of the distribution over various scales. Moreover, we study how the mean of the distribution and the intermittency change with scale, and validate and design functions to describe the shape parameter of the distribution. This information was combined into an effective model of the distribution. Finally, the model was fitted to data from numerous storms, and the resulting parameters were compared to investigate the change in scaling behavior through time.

Description: Spatially resolved information on karst conduit flow from in-cave dye-tracing Hydrology and Earth System Sciences Discussions, 10, 11311-11335, 2013 Author(s): U. Lauber, W. Ufrecht, and N. Goldscheider Artificial tracers are powerful tools to investigate karst systems. Tracers are commonly injected into sinking streams or dolines, while springs serve as monitoring sites. The obtained flow and transport parameters represent mixed information from the vadose, epiphreatic and phreatic zones, i.e., the aquifer remains a black box. Accessible active caves constitute valuable but underexploited natural laboratories to gain detailed insights into the hydrologic functioning of the aquifer. Two multi-tracer tests in the catchment of a major karst spring (Blautopf, Germany) with injections and monitoring in two associated water caves aimed at obtaining spatially and temporally resolved information on groundwater flow in different compartments of the system. Two tracers were injected in the caves to characterize the hydraulic connections between them and with the spring. Two injections at the land surface, far from the spring, aimed at resolving the aquifer's internal drainage structure. Tracer breakthrough curves were monitored by field fluorimeters in caves and at the spring. Results demonstrate the dendritic drainage structure of the aquifer. It was possible to obtain relevant flow and transport parameters for different sections of this system. The highest mean flow velocities (275 m h −1 ) were observed in the near-spring epiphreatic section (open-channel flow), while velocities in the phreatic zone (pressurized flow) were one order of magnitude lower. Determined conduit water volumes confirm results of water balances and hydrograph analyses. In conclusion, experiments and monitoring in caves can deliver spatially resolved information on karst aquifer heterogeneity and dynamics that cannot be obtained by traditional investigative methods.

Description: On the lack of robustness of hydrologic models regarding water balance simulation – a diagnostic approach on 20 mountainous catchments using three models of increasing complexity Hydrology and Earth System Sciences Discussions, 10, 11337-11383, 2013 Author(s): L. Coron, V. Andréassian, C. Perrin, M. Bourqui, and F. Hendrickx This paper investigates the robustness of rainfall–runoff models when their parameters are transferred in time. More specifically, we studied their ability to simulate water balance on periods with different hydroclimatic characteristics. The testing procedure consisted in a series of parameter transfers between 10-yr periods and the systematic analysis of mean-volume errors. This procedure was applied to three conceptual models of different structural complexity over 20 mountainous catchments in southern France. The results showed that robustness problems are common. Errors on 10-yr-mean flows were significant for all three models and calibration periods, even when the entire record was used for calibration. Various graphical and numerical tools were used to show strong similarities between the shapes of mean flow biases calculated on a 10-yr-long sliding window when various parameter sets are used. Unexpected behavioural similarities were observed between the three models tested, considering their large differences in structural complexity. While the actual causes for robustness problems in these models remain unclear, this work stresses the limited transferability in time of the water balance adjustments made through parameter optimization. Although absolute differences between simulations obtained with different calibrated parameter sets were sometimes substantial, relative differences in simulated mean flows between time periods remained similar regardless of the calibrated parameter sets.

Description: Bayesian networks modelling in support to cross-cutting analysis of water supply and sanitation in developing countries Hydrology and Earth System Sciences, 17, 3397-3419, 2013 Author(s): C. Dondeynaz, J. López Puga, and C. Carmona Moreno Despite the efforts made towards the Millennium Development Goals targets during the last decade, improved access to water supply or basic sanitation still remains unavailable for millions of people across the world. This paper proposes a set of models that use 25 key variables and country profiles from the WatSan4Dev data set involving water supply and sanitation (Dondeynaz et al., 2012). This paper suggests the use of Bayesian network modelling methods because they are more easily adapted to deal with non-normal distributions, and integrate a qualitative approach for data analysis. They also offer the advantage of integrating preliminary knowledge into the probabilistic models. The statistical performance of the proposed models ranges between 20 and 5% error rates, which are very satisfactory taking into account the strong heterogeneity of variables. Probabilistic scenarios run from the models allow an assessment of the relationships between human development, external support, governance aspects, economic activities and water supply and sanitation (WSS) access. According to models proposed in this paper, gaining a strong poverty reduction will require the WSS access to reach 75–76% through: (1) the management of ongoing urbanisation processes to avoid slums development; and (2) the improvement of health care, for instance for children. Improving governance, such as institutional efficiency, capacities to make and apply rules, or control of corruption is positively associated with WSS sustainable development. The first condition for an increment of the HDP (human development and poverty) remains of course an improvement of the economic conditions with higher household incomes. Moreover, a significant country commitment to the environment, associated with civil society freedom of expression constitutes a favourable setting for sustainable WSS services delivery. Intensive agriculture using irrigation practises also appears as a mean for sustainable WSS thanks to multi-uses and complementarities. With a WSS sector organised at national level, irrigation practices can support the structuring and efficiency of the agriculture sector. It may then induce rural development in areas where WSS access often is set back compared to urban areas 1 . External financial support, called Official Development Assistance (ODA CI), plays a role in WSS improvement but comes last in the sensitivity analyses of models. An overall 47% of the Official Development Assistance goes first to poor countries, and is associated to governance aspects: (1) political stability and (2) country commitment to the environment and civil society degree of freedom. These governance aspects constitute a good framework for aid implementation in recipient countries. Modelling is run with the five groups of countries as defined in Dondeynaz et al. (2012). Models for profile 4 (essential external support) and profile 5 (primary material consumption) are specifically detailed and analysed in this paper. For countries in profile 4, fighting against water scarcity and progressing desertification should be the priority. However, for countries in profile 5, efforts should first concentrate on consolidation of political stability while supporting diversification of the economic activities. Nevertheless, for both profiles, reduction of poverty should remain the first priority as previously indicated. 1 JMP statistics, 2004 http://www.wssinfo.org/data-estimates/table/ , last access: 22 July 2013.

Description: Technical Note: A comparison of model and empirical measures of catchment-scale effective energy and mass transfer Hydrology and Earth System Sciences, 17, 3389-3395, 2013 Author(s): C. Rasmussen and E. L. Gallo Recent work suggests that a coupled effective energy and mass transfer (EEMT) term, which includes the energy associated with effective precipitation and primary production, may serve as a robust prediction parameter of critical zone structure and function. However, the models used to estimate EEMT have been solely based on long-term climatological data with little validation using direct empirical measures of energy, water, and carbon balances. Here we compare catchment-scale EEMT estimates generated using two distinct approaches: (1) EEMT modeled using the established methodology based on estimates of monthly effective precipitation and net primary production derived from climatological data, and (2) empirical catchment-scale EEMT estimated using data from 86 catchments of the Model Parameter Estimation Experiment (MOPEX) and MOD17A3 annual net primary production (NPP) product derived from Moderate Resolution Imaging Spectroradiometer (MODIS). Results indicated positive and significant linear correspondence ( R 2 = 0.75; P 〈 0.001) between model and empirical measures with an average root mean square error (RMSE) of 4.86 MJ m −2 yr −1 . Modeled EEMT values were consistently greater than empirical measures of EEMT. Empirical catchment estimates of the energy associated with effective precipitation ( E PPT ) were calculated using a mass balance approach that accounts for water losses to quick surface runoff not accounted for in the climatologically modeled E PPT . Similarly, local controls on primary production such as solar radiation and nutrient limitation were not explicitly included in the climatologically based estimates of energy associated with primary production ( E BIO ), whereas these were captured in the remotely sensed MODIS NPP data. These differences likely explain the greater estimate of modeled EEMT relative to the empirical measures. There was significant positive correlation between catchment aridity and the fraction of EEMT partitioned into E BIO ( F BIO ), with an increase in F BIO as a fraction of the total as aridity increases and percentage of catchment woody plant cover decreases. In summary, the data indicated strong correspondence between model and empirical measures of EEMT with limited bias that agree well with other empirical measures of catchment energy and water partitioning and plant cover.

Description: A proper orthogonal decomposition (POD) method is used to interpolate the flow around an airfoil for various Mach numbers and angles of attack in the transonic regime. POD uses a few numerical simulations, called snapshots, to create eigenfunctions. These eigenfunctions are combined using weighting coefficients to create a new solution for different values of the input parameters. Since POD methods are linear, their interpolation capabilities are quite limited when dealing with flow presenting nonlinearities, such as shocks. In order to improve their performance for cases involving shocks, a new method is proposed using variable fidelity. The main idea is to use POD to interpolate the difference between the CFD solution obtained on two different grids, a coarse one and a fine one. Then, for any new input parameter value, a coarse grid solution is computed using CFD and the POD interpolated difference is added to predict the fine grid solution. This allows some nonlinearities associated with the flow to be introduced. Results for various Mach numbers and angles of attack are compared to full CFD results. The variable fidelity-based POD method shows good improvement over the classical approach.

Description: The preparation of carbon nanotube/metallic particle hybrids using pressed porous stainless steel pellets as a substrate is described. The catalytic growth of carbon nanotubes was carried out by CVD on a nickel catalyst obtained by impregnation of pellets with a highly dispersive colloidal solution of nickel acetate tetrahydrate in ethanol. Granular polyethylene was used as the carbon source. Metallic particles were deposited by thermal evaporation of Pt and Ag using pellets with grown carbon nanotubes as a base. The use of such composites as fuel cell electrodes is discussed.

Description: Analysis of projected changes in the occurrence of heat waves in Hungary Advances in Geosciences, 35, 115-122, 2013 Author(s): R. Pongrácz, J. Bartholy, and E. B. Bartha Heat wave events are important temperature-related hazards due to their impacts on human health. In 2004, a Heat Health Warning System including three levels of heat wave warning was developed on the basis of a retrospective analysis of mortality and meteorological data in Hungary to anticipate heat waves that may result in a large excess of mortality. Projected changes in the frequency of different heat wave warning levels are analysed for the 21st century. For this purpose, outputs of regional climate model PRECIS (Providing REgional Climates for Impacts Studies) are used taking into account three different global emissions scenarios (A2, A1B, B2). The results clearly show an increase in occurrence and length of heat waves with respect to the underlying emissions scenarios and regional climate model used. Moreover, the potential season of heat wave occurrences is projected to be lengthened by two months in 2071–2100 compared to 1961–1990.

Description: Review Article: On the relation between the seismic activity and the Hurst exponent of the geomagnetic field at the time of the 2000 Izu swarm Natural Hazards and Earth System Science, 13, 2189-2194, 2013 Author(s): F. Masci and J. N. Thomas Many papers document the observation of earthquake-related precursory signatures in geomagnetic field data. However, the significance of these findings is ambiguous because the authors did not adequately take into account that these signals could have been generated by other sources, and the seismogenic origin of these signals have not been validated by comparison with independent datasets. Thus, they are not reliable examples of magnetic disturbances induced by the seismic activity. Hayakawa et al. (2004) claim that at the time of the 2000 Izu swarm the Hurst exponent of the Ultra-Low-Frequency (ULF: 0.001–10 Hz) band of the geomagnetic field varied in accord with the energy released by the seismicity. The present paper demonstrates that the behaviour of the Hurst exponent was insufficiently investigated and also misinterpreted by the authors. We clearly show that during the Izu swarm the changes of the Hurst exponent were strongly related to the level of global geomagnetic activity and not to the increase of the local seismic activity.

Description: Forest fire danger rating in complex topography – results from a case study in the Bavarian Alps in autumn 2011 Natural Hazards and Earth System Science, 13, 2157-2167, 2013 Author(s): C. Schunk, C. Wastl, M. Leuchner, C. Schuster, and A. Menzel Forest fire danger rating based on sparse meteorological stations is known to be potentially misleading when assigned to larger areas of complex topography. This case study examines several fire danger indices based on data from two meteorological stations at different elevations during a major drought period. This drought was caused by a persistent high pressure system, inducing a pronounced temperature inversion and its associated thermal belt with much warmer, dryer conditions in intermediate elevations. Thus, a massive drying of fuels, leading to higher fire danger levels, and multiple fire occurrences at mid-slope positions were contrasted by moderate fire danger especially in the valleys. The ability of fire danger indices to resolve this situation was studied based on a comparison with the actual fire danger as determined from expert observations, fire occurrences and fuel moisture measurements. The results revealed that, during temperature inversion, differences in daily cycles of meteorological parameters influence fire danger and that these are not resolved by standard meteorological stations and fire danger indices (calculated on a once-a-day basis). Additional stations in higher locations or high-resolution meteorological models combined with fire danger indices accepting at least hourly input data may allow reasonable fire danger calculations under these circumstances.

Description: The Mediterranean Sea system: a review and an introduction to the special issue Ocean Science, 9, 789-803, 2013 Author(s): T. Tanhua, D. Hainbucher, K. Schroeder, V. Cardin, M. Álvarez, and G. Civitarese The Mediterranean Sea is a semi-enclosed sea characterized by high salinities, temperatures and densities. The net evaporation exceeds the precipitation, driving an anti-estuarine circulation through the Strait of Gibraltar, contributing to very low nutrient concentrations. The Mediterranean Sea has an active overturning circulation, one shallow cell that communicates directly with the Atlantic Ocean, and two deep overturning cells, one in each of the two main basins. It is surrounded by populated areas and is thus sensitive to anthropogenic forcing. Several dramatic changes in the oceanographic and biogeochemical conditions have been observed during the past several decades, emphasizing the need to better monitor and understand the changing conditions and their drivers. During 2011 three oceanographic cruises were conducted in a coordinated fashion in order to produce baseline data of important physical and biogeochemical parameters that can be compared to historic data and be used as reference for future observational campaigns. In this article we provide information on the Mediterranean Sea oceanographic situation, and present a short review that will serve as background information for the special issue in Ocean Science on "Physical, chemical and biological oceanography of the Mediterranean Sea". An important contribution of this article is the set of figures showing the large-scale distributions of physical and chemical properties along the full length of the Mediterranean Sea.

Description: Corrigendum to "NEMO on the shelf: assessment of the Iberia–Biscay–Ireland configuration" published in Ocean Sci., 9, 745–771, 2013 Ocean Science, 9, 787-787, 2013 Author(s): C. Maraldi, J. Chanut, B. Levier, N. Ayoub, P. De Mey, G. Reffray, F. Lyard, S. Cailleau, M. Drévillon, E. A. Fanjul, M. G. Sotillo, P. Marsaleix, and the Mercator Research and Development Team No abstract available.

Description: Preface "Landslide hazard and risk assessment at different scales" Natural Hazards and Earth System Science, 13, 2169-2171, 2013 Author(s): P. Reichenbach, A. Günther, and T. Glade

Description: The Chemistry CATT-BRAMS model (CCATT-BRAMS 4.5): a regional atmospheric model system for integrated air quality and weather forecasting and research Geoscientific Model Development, 6, 1389-1405, 2013 Author(s): K. M. Longo, S. R. Freitas, M. Pirre, V. Marécal, L. F. Rodrigues, J. Panetta, M. F. Alonso, N. E. Rosário, D. S. Moreira, M. S. Gácita, J. Arteta, R. Fonseca, R. Stockler, D. M. Katsurayama, A. Fazenda, and M. Bela Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT-BRAMS, version 4.5) is an on-line regional chemical transport model designed for local and regional studies of atmospheric chemistry from the surface to the lower stratosphere suitable both for operational and research purposes. It includes gaseous/aqueous chemistry, photochemistry, scavenging and dry deposition. The CCATT-BRAMS model takes advantage of BRAMS-specific development for the tropics/subtropics as well as the recent availability of preprocessing tools for chemical mechanisms and fast codes for photolysis rates. BRAMS includes state-of-the-art physical parameterizations and dynamic formulations to simulate atmospheric circulations down to the meter. This on-line coupling of meteorology and chemistry allows the system to be used for simultaneous weather and chemical composition forecasts as well as potential feedback between the two. The entire system is made of three preprocessing software tools for user-defined chemical mechanisms, aerosol and trace gas emissions fields and the interpolation of initial and boundary conditions for meteorology and chemistry. In this paper, the model description is provided along with the evaluations performed by using observational data obtained from ground-based stations, instruments aboard aircrafts and retrieval from space remote sensing. The evaluation accounts for model applications at different scales from megacities and the Amazon Basin up to the intercontinental region of the Southern Hemisphere.

Description: Influence of microphysical schemes on atmospheric water in the Weather Research and Forecasting model Geoscientific Model Development Discussions, 6, 4563-4601, 2013 Author(s): F. Cossu and K. Hocke This study examines how different microphysical parameterization schemes influence orographically-induced precipitation and the distributions of hydrometeors and water vapour for mid-latitude summer conditions in the Weather Research and Forecasting (WRF) model. A high-resolution two-dimensional idealized simulation is used to assess the differences between the schemes in which a moist air flow is interacting with a bell-shaped 2 km high mountain. Periodic lateral boundary conditions are chosen to recirculate atmospheric water in the domain. It is found that the 13 selected microphysical schemes conserve the water in the model domain. The gain or loss of water is less than 0.81% over a simulation time interval of 61 days. The differences of the microphysical schemes in terms of the distributions of water vapour, hydrometeors and accumulated precipitation are presented and discussed. The Kessler scheme, the only scheme without ice-phase processes, shows final values of cloud liquid water 14 times greater than the other schemes. The differences among the other schemes are not as extreme, but still they differ up to 79% in water vapour, up to 10 times in hydrometeors and up to 64% in accumulated precipitation at the end of the simulation. The microphysical schemes also differ in the surface evaporation rate. The WRF single-moment 3-class scheme has the highest surface evaporation rate compensated by the highest precipitation rate. The different distributions of hydrometeors and water vapour of the microphysical schemes induce differences up to 49 W m −2 in the downwelling shortwave radiation and up to 33 W m −2 in the downwelling longwave radiation.

Description: This work provides a distributed fault-tolerant event region detection algorithm for wireless sensor networks. The proposed algorithm can identify faulty and fault-free sensors and ignore the abnormal readings to avoid false alarm. Moreover, every event region can also be detected and identified. Simulation results show that fault detection accuracy (FDA) is greater than 92%, false alarm rate (FAR) is near 0%, and event detection accuracy (EDA) is greater than 99% under uniform distribution. FDA is greater than 92%, FAR is less than 1.2%, and EDA is greater than 88% under random distribution when sensor fault probability is less than 0.3.

Description: Pupylation, one of the most important posttranslational modifications of proteins, typically takes place when prokaryotic ubiquitin-like protein (Pup) is attached to specific lysine residues on a target protein. Identification of pupylation substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of pupylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of pupylation sites is much desirable for their convenience and fast speed. In this study, a new bioinformatics tool named EnsemblePup was developed that used an ensemble of support vector machine classifiers to predict pupylation sites. The highlight of EnsemblePup was to utilize the Bi-profile Bayes feature extraction as the encoding scheme. The performance of EnsemblePup was measured with a sensitivity of 79.49%, a specificity of 82.35%, an accuracy of 85.43%, and a Matthews correlation coefficient of 0.617 using the 5-fold cross validation on the training dataset. When compared with other existing methods on a benchmark dataset, the EnsemblePup provided better predictive performance, with a sensitivity of 80.00%, a specificity of 83.33%, an accuracy of 82.00%, and a Matthews correlation coefficient of 0.629. The experimental results suggested that EnsemblePup presented here might be useful to identify and annotate potential pupylation sites in proteins of interest. A web server for predicting pupylation sites was developed.

Description: The sensitivity of global climate to the episodicity of fire aerosol emissions Atmospheric Chemistry and Physics Discussions, 13, 23691-23717, 2013 Author(s): S. K. Clark, D. S. Ward, and N. M. Mahowald One of the major ways in which forest and grass fires have an impact on global climate is through the release of aerosols. Most studies focusing on calculating the radiative forcing and other climate impacts of fire aerosols use monthly mean emissions derived from the Global Fire Emissions Database that captures only the seasonal cycle of fire aerosol emissions. Here we present the results of a sensitivity study that investigates the climate response to the episodicity of the fires, based on the standard approach which releases emissions every day, and contrasts that to the response when fires are represented as intense pulses of emissions that occur only over 1–2 days on a monthly, yearly, or five-yearly basis. Overall we find that in the modified cases with increased levels of episodicity, the all sky direct effect radiative forcing increases, the clear sky direct effect radiative forcing remains relatively constant, and the magnitude of the indirect effect radiative forcing decreases by about 1 W m −2 (from −1.6 to −0.6 W m −2 ). In the long term, we find that an increase in aerosol emission episodicity leads to an asymmetric change in indirect radiative forcing in the Northern Hemisphere compared to the Southern Hemisphere contributes to a slight shift in the annual average position of the intertropical convergence zone (ITCZ). This shift is found to have a mixed effect on the overall performance of the model at predicting precipitation rates in the tropics. Given these results we conclude that future studies that look to assess the present day global climate impacts of fire aerosols should consider the need to accurately represent fire episodicity.

Description: Not all calcite ballast is created equal: differing effects of foraminiferan and coccolith calcite on the formation and sinking of aggregates Biogeosciences Discussions, 10, 14861-14885, 2013 Author(s): K. Schmidt, C. L. De La Rocha, M. Gallinari, and G. Cortese Correlation between particulate organic carbon (POC) and calcium carbonate sinking through the deep ocean has led to the idea that ballast provided by calcium carbonate is important for the export of POC from the surface ocean. While this idea is certainly to some extent true, it is worth considering in more nuance, for example, examining the different effects on the aggregation and sinking of POC of small, non-sinking calcite particles like coccoliths and large, rapidly sinking calcite like planktonic foraminiferan tests. We have done that here in a simple experiment carried out in roller tanks that allow particles to sink continuously without being impeded by container walls. Coccoliths were efficiently incorporated into aggregates that formed during the experiment, increasing their sinking speed compared to similarly sized aggregates lacking added calcite ballast. The foraminiferan tests, which sank as fast as 700 m d −1 , became associated with only very minor amounts of POC. In addition, when they collided with other, larger, foraminferan-less aggregates, they fragmented them into two smaller, more slowly sinking aggregates. While these effects were certainly exaggerated within the confines of the roller tanks, they clearly demonstrate that calcium carbonate ballast is not just calcium carbonate ballast- different forms of calcium carbonate ballast have notably different effects on POC aggregation, sinking, and export.

Description: Laboratory studies of immersion and deposition mode ice nucleation of ozone aged mineral dust particles Atmospheric Chemistry and Physics, 13, 9097-9118, 2013 Author(s): Z. A. Kanji, A. Welti, C. Chou, O. Stetzer, and U. Lohmann Ice nucleation in the atmosphere is central to the understanding the microphysical properties of mixed-phase and cirrus clouds. Ambient conditions such as temperature ( T ) and relative humidity (RH), as well as aerosol properties such as chemical composition and mixing state play an important role in predicting ice formation in the troposphere. Previous field studies have reported the absence of sulfate and organic compounds on mineral dust ice crystal residuals sampled at mountain top stations or aircraft based measurements despite the long-range transport mineral dust is subjected to. We present laboratory studies of ice nucleation for immersion and deposition mode on ozone aged mineral dust particles for 233 〈 T 〈 263 K. Heterogeneous ice nucleation of untreated kaolinite (Ka) and Arizona Test Dust (ATD) particles is compared to corresponding aged particles that are subjected to ozone concentrations of 0.4–4.3 ppmv in a stainless steel aerosol tank. The portable ice nucleation counter (PINC) and immersion chamber combined with the Zurich ice nucleation chamber (IMCA-ZINC) are used to conduct deposition and immersion mode measurements, respectively. Ice active fractions as well as ice active surface site densities ( n s ) are reported and observed to increase as a function of decreasing temperature. We present first results that demonstrate enhancement of the ice nucleation ability of aged mineral dust particles in both the deposition and immersion mode due to ageing. We also present the first results to show a suppression of heterogeneous ice nucleation activity without the condensation of a coating of (in)organic material. In immersion mode, low ozone exposed Ka particles showed enhanced ice activity requiring a median freezing temperature of 1.5 K warmer than that of untreated Ka, whereas high ozone exposed ATD particles showed suppressed ice nucleation requiring a median freezing temperature of 3 K colder than that of untreated ATD. In deposition mode, low exposure Ka had ice active fractions of an order of magnitude higher than untreated Ka, whereas high ozone exposed ATD had ice active fractions up to a factor of 4 lower than untreated ATD. From our results, we derive and present parameterizations in terms of n s ( T ) that can be used in models to predict ice nuclei concentrations based on available aerosol surface area.

Description: Antecedent flow conditions and nitrate concentrations in the Mississippi River Basin Hydrology and Earth System Sciences Discussions, 10, 11451-11484, 2013 Author(s): J. C. Murphy, R. M. Hirsch, and L. A. Sprague The influence of antecedent flow conditions on nitrate concentrations was explored at eight sites in the Mississippi River Basin, USA. Antecedent moisture conditions have been shown to influence nutrient export from small, relatively homogenous basins, but this influence has not been observed at a regional or continental scale. Antecedent flow conditions were quantified as the ratio between the mean daily flow of the previous year and the mean daily flow from the period of record ( Q ratio), and the Q ratio was statistically related to nitrate anomalies (the unexplained variability in nitrate concentration after filtering out season, long-term trend, and contemporaneous flow effects) at each site. Nitrate anomaly and Q ratio were negatively related at three of the four major tributary sites and upstream in the Mississippi River, indicating that when the previous year was drier than average, at these sites, nitrate concentrations were higher than expected. The strength of these relationships increased when data were subdivided by contemporaneous flow conditions. Five of the eight sites had significant negative relationships ( p ≤ 0.05) at high or moderately high contemporaneous flows, suggesting nitrate that accumulates in these basins during a drought is flushed during subsequent storm events. At half of the sites, when flow during the previous year was 50% drier than average, nitrate concentration can be from 9 and 27% higher than nitrate concentrations that follow a year with average daily flow. Conversely, nitrate concentration can be from 8 and 21% lower than expected when the previous year was 50% wetter than average. These relationships between nitrate concentration and Q ratio serve as the basis for future studies that can better define specific hydrologic processes occurring during and after a drought, which influence nitrate concentration, such as the duration or magnitude of low flows, and the timing of low and high flows.

Description: We used a one-dimensional simulation program Solar Cell Capacitance Simulator in 1 Dimension (SCAPS-1D) to investigate Copper-Indium-Gallium-Diselenide- (CIGS-) based solar cells properties. Starting with a conventional ZnO-B/i-ZnO/CdS/CIGS structure, we simulated the parameters of current-voltage characteristics and showed how the absorber layer thickness, hole density, and band gap influence the short-circuit current density (), open-circuit voltage (), fill factor (FF), and efficiency of solar cell. Our simulation results showed that all electrical parameters are greatly affected by the absorber thickness (w) below 1000 nm, due to the increase of back-contact recombination and very poor absorption. Increasing hole density (p) or absorber band gap () improves and leads to high efficiency, which equals value of 16.1% when p = 1016 cm−3 and  eV. In order to reduce back-contact recombination, the effect of a very thin layer with high band gap inserted near the back contact and acting as electrons reflector, the so-called back-electron reflector (EBR), has been investigated. The performances of the solar cells are significantly improved, when ultrathin absorbers (w 〈 500 nm) are used; the corresponding gain of due to the EBR is 3 mA/cm2. Our results are in good agreement with those reported in the literature from experiments.

Description: The work presents comparisons of the flame stabilization characteristics of axisymmetric disk and 2D slender bluff-body burner configurations, operating with inlet mixture stratification, under ultralean conditions. A double cavity propane air premixer formed along three concentric disks, supplied with a radial equivalence ratio gradient the afterbody disk recirculation, where the first flame configuration is stabilized. Planar fuel injection along the center plane of the leading face of a slender square cylinder against the approach cross-flow results in a stratified flame configuration stabilized alongside the wake formation region in the second setup. Measurements of velocities, temperatures, and chemiluminescence, local extinction criteria, and large-eddy simulations are employed to examine a range of ultralean and close to extinction flame conditions. The variations of the reacting front disposition within these diverse reacting wake topologies, the effect of the successive suppression of heat release on the near flame region characteristics, and the reemergence of large-scale vortical activity on approach to lean blowoff (LBO) are investigated. The cross-correlation of the performance of these two popular flame holders that are at the opposite ends of current applications might offer helpful insights into more effective control measures for expanding the operational margin of a wider range of stabilization configurations.

Description: This review covers methods for modifying the structures of polysaccharides. The introduction of hydrophobic, acidic, basic, or other functionality into polysaccharide structures can alter the properties of materials based on these substances. The development of chemical methods to achieve this aim is an ongoing area of research that is expected to become more important as the emphasis on using renewable starting materials and sustainable processes increases in the future. The methods covered in this review include ester and ether formation using saccharide oxygen nucleophiles, including enzymatic reactions and aspects of regioselectivity; the introduction of heteroatomic nucleophiles into polysaccharide chains; the oxidation of polysaccharides, including oxidative glycol cleavage, chemical oxidation of primary alcohols to carboxylic acids, and enzymatic oxidation of primary alcohols to aldehydes; reactions of uronic-acid-based polysaccharides; nucleophilic reactions of the amines of chitosan; and the formation of unsaturated polysaccharide derivatives.

Description: The electroreduction behaviour and determination of cefoperazone using a hanging mercury drop electrode were investigated. Cyclic voltammograms of cefoperazone recorded in universal Britton-Robinson buffers pH 3–6 exhibited a single irreversible cathodic peak. The process was adsorption-controlled. Britton-Robinson buffer 0.04 M pH 4.0 was selected as a supporting electrolyte for quantitative purposes by differential pulse and square wave adsorptive cathodic stripping voltammetry. The experimental voltammetric conditions were optimized using Central Composite Face design. A reduction wave was seen in the range from −0.7 to −0.8 V. These voltammetric techniques were successfully validated as per ICH guidelines and applied for the determination of cefoperazone in its single and sulbactam containing powders for injection and statistically comparable to USP-HPLC. They were further extended to determine cefoperazone in spiked human urine with no matrix effect.

Description: Tidally induced velocity variations of the Beardmore Glacier, Antarctica, and their representation in satellite measurements of ice velocity The Cryosphere, 7, 1375-1384, 2013 Author(s): O. J. Marsh, W. Rack, D. Floricioiu, N. R. Golledge, and W. Lawson Ocean tides close to the grounding line of outlet glaciers around Antarctica have been shown to directly influence ice velocity, both linearly and non-linearly. These fluctuations can be significant and have the potential to affect satellite measurements of ice discharge, which assume displacement between satellite passes to be consistent and representative of annual means. Satellite observations of horizontal velocity variation in the grounding zone are also contaminated by vertical tidal effects, the importance of which is highlighted here in speckle tracking measurements. Eight TerraSAR-X scenes from the grounding zone of the Beardmore Glacier are analysed in conjunction with GPS measurements to determine short-term and decadal trends in ice velocity. Diurnal tides produce horizontal velocity fluctuations of 〉50% on the ice shelf, recorded in the GPS data 4 km downstream of the grounding line. This variability decreases rapidly to 〈5% only 15 km upstream of the grounding line. Daily fluctuations are smoothed to 〈1% in the 11-day repeat pass TerraSAR-X imagery, but fortnightly variations over this period are still visible and show that satellite-velocity measurements can be affected by tides over longer periods. The measured tidal displacement observed in radar look direction over floating ice also allows the grounding line to be identified, using differential speckle tracking where phase information cannot be easily unwrapped.

Description: The problem of exponential stability for the uncertain neutral Markovian jump systems with interval time-varying delays and nonlinear perturbations is investigated in this paper. This study starts from the corresponding nominal systems with known and partially unknown transition rates, respectively. By constructing a novel augmented Lyapunov functional which contains triple-integral terms and fully utilizes the bound of the delay, the delay-range-dependent and rate-dependent exponential stability criteria are developed by the Lyapunov theory, reciprocally convex lemma, and free weighting matrices. Then, the results about nominal systems are extended to the uncertain case. Finally, numerical examples are given to demonstrate the effectiveness of the proposed methods.

Description: The local fractional Schrödinger equations in the one-dimensional Cantorian system are investigated. The approximations solutions are obtained by using the local fractional series expansion method. The obtained solutions show that the present method is an efficient and simple tool for solving the linear partial differentiable equations within the local fractional derivative.