ALBERT

Description: Methane plays an important role in the Earth’s atmospheric chemistry and radiative balance being the second most important greenhouse gas after carbon dioxide. Methane is released to the atmosphere by a wide number of sources, both natural and anthropogenic, with the latter being twice as large as the former (IPCC, 2007). It has recently been established that significant amounts of geological methane, produced within the Earth’s crust, are currently released naturally into the atmosphere (Etiope, 2004). Active or recent volcanic/geothermal areas represent one of these sources of geological methane. But due to the fact that methane flux measurements are laboratory intensive, very few data have been collected until now and the contribution of this source has been generally indirectly estimated (Etiope et al., 2007). The Greek territory is geodynamically very active and has many volcanic and geothermal areas. Here we report on methane flux measurements made at two volcanic/geothermal systems along the South Aegean volcanic arc: Sousaki and Nisyros. The former is an extinct volcanic area of Plio-Pleistocene age hosting nowadays a low enthalpy geothermal field. The latter is a currently quiescent active volcanic system with strong fumarolic activity due to the presence of a high enthalpy geothermal system. Both systems have gas manifestations that emit significant amounts of hydrothermal methane and display important diffuse carbon dioxide emissions from the soils. New data on methane isotopic composition and higher hydrocarbon contents point to an abiogenic origin of the hydrothermal methane in the studied systems. Measured methane flux values range from –48 to 29,000 (38 sites) and from –20 to 1100 mg/mˆ2/d (35 sites) at Sousaki and Nisyros respectively. At Sousaki measurement sites covered almost all the degassing area and the diffuse methane output can be estimated in about 20 t/a from a surface of about 10,000 mˆ2. At Nisyros measurements covered the Stephanos and Kaminakia areas, which represent only a part of the entire degassing area. The two areas show very different methane degassing pattern with latter showing much higher flux values. Methane output can be estimated in about 0.25 t/a from an area of about 30,000 mˆ2 at Stephanos and about 1 t/a from an area of about 20,000 mˆ2 at Kaminakia. The total output from the entire geothermal system of Nisyros probably should not exceed 2 t/a.

Description: Published

Description: Vienna, Austria

Description: 4.5. Studi sul degassamento naturale e sui gas petroliferi

Description: open

Description: A biomonitoring survey, above tree line level, using two endemic species (Senecio aethnensis and Rumex aethnensis) was performed on Mt. Etna, in order to evaluate the dispersion and the impact of volcanic atmospheric emissions. Samples of leaves were collected in summer 2008 from 30 sites in the upper part of the volcano (1500- 3000 m a.s.l). Acid digestion of samples was carried out with a microwave oven, and 44 elements were analyzed by using plasma spectrometry (ICP-MS and ICP-OES). The highest concentrations of all investigated elements were found in the samples collected closest to the degassing craters, and in the downwind sector, confirming that the eastern flank of Mt. Etna is the most impacted by volcanic emissions. Leaves collected along two radial transects from the active vents on the eastern flank, highlight that the levels of metals decrease one or two orders of magnitude with increasing distance from the source. This variability is higher for volatile elements (As, Bi, Cd, Cs, Pb, Sb, Tl) than for more refractory elements (Al, Ba, Sc, Si, Sr, Th, U). The two different species of plants do not show significant differences in the bioaccumulation of most of the analyzed elements, except for lanthanides, which are systematically enriched in Rumex leaves. The high concentrations of many toxic elements in the leaves allow us to consider these plants as highly tolerant species to the volcanic emissions, and suitable for biomonitoring researches in the Mt. Etna area.

Description: Published

Description: Vienna, Austria

Description: 4.4. Scenari e mitigazione del rischio ambientale

Description: open

Description: Etna volcano, Italy, hosts one of the major groundwater systems of the island of Sicily. Waters circulate within highly permeable fractured, mainly hawaiitic, volcanic rocks. Aquifers are limited downwards by the underlying impermeable sedimentary terrains. Thickness of the volcanic rocks generally does not exceed some 300 m, preventing the waters to reach great depths. This is faced by short travel times (years to tens of years) and low thermalisation of the Etnean groundwaters. Measured temperatures are, in fact, generally lower than 25 °C. But the huge annual meteoric recharge (about 0.97 kmˆ3) with a high actual infiltration coefficient (0.75) implies a great underground circulation. During their travel from the summit area to the periphery of the volcano, waters acquire magmatic heat together with volcanic gases and solutes through water-rock interaction processes. In the last 20 years the Etnean aquifers has been extensively studied. Their waters were analysed for dissolved major, minor and trace element, O, H, C, S, B, Sr and He isotopes, and dissolved gas composition. These data have been published in several articles. Here, after a summary of the obtained results, the estimation of the magmatic heat flux through the aquifer will be discussed. To calculate heat uptake during subsurface circulation, for each sampling point (spring, well or drainage gallery) the following data have been considered: flow rate, water temperature, and oxygen isotopic composition. The latter was used to calculate the mean recharge altitude through the measured local isotopic lapse rate. Mean recharge temperatures, weighted for rain amount throughout the year, were obtained from the local weather station network. Calculations were made for a representative number of sampling points (216) including all major issues and corresponding to a total water flow of about 0.315 kmˆ3/a, which is 40% of the effective meteoric recharge. Results gave a total energy output of about 140 MW/a the half of which is ascribable to only 13 sampling points. These correspond to the highest flow drainage galleries with fluxes ranging from 50 to 1000 l/s and wells with pumping rates from 70 to 250 l/s. Geographical distribution indicates that, like magmatic gas leakage, heat flow is influenced by structural features of the volcanic edifice. The major heat discharge through groundwater are all tightly connected either to the major regional tectonic systems or to the major volcanic rift zones along which the most important flank eruptions take place. But rift zones are much more important for heat upraise due to the frequent dikes injection than for gas escape because generally when dikes have been emplaced the structure is no more permeable to gases because it becomes sealed by the cooling magma.

Description: Published

Description: Vienna, Austria

Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive

Description: open

Description: During the 2007-2008 antarctic campaign, the Italian PNRA installed a Low Power Magnetometer within the framework of the AIMNet (Antarctic International Magnetometer Network) project, proposed and coordinated by BAS. The magnetometer is situated at Talos Dome, around 300 km geographically North-West from Mario Zucchelli Station (MZS), and approximately at the same geomagnetic latitude as MZS. In this work we present a preliminary analysis of the geomagnetic field 1-min data, and a comparison with simultaneous data from different Antarctic stations.

Description: Published

Description: Vienna, Austria

Description: 1.6. Osservazioni di geomagnetismo

Description: open

Description: In this study temporal variations of coccolithophore blooms are investigated using satellite data. Eight years, from 2003 to 2010, of data of SCIAMACHY, a hyper-spectral satellite sensor on-board ENVISAT, were processed by the PhytoDOAS method to 5 monitor the biomass of coccolithophores in three selected regions. These regions are characterized by frequent occurrence of large coccolithophore blooms. The retrieval results, shown as monthly mean time-series, were compared to related satellite products, including the total surface phytoplankton, i.e., total chlorophyll-a (from GlobColour merged data) and the particulate inorganic carbon (from MODIS-Aqua). The 10 inter-annual variations of the phytoplankton bloom cycles and their maximum monthly mean values have been compared in the three selected regions to the variations of the geophysical parameters: sea-surface temperature (SST), mixed-layer depth (MLD) and surface wind speed, which are known to affect phytoplankton dynamics. For each region the anomalies and linear trends of the monitored parameters over the period of this 15 study have been computed. The patterns of total phytoplankton biomass and specific dynamics of coccolithophores chlorophyll-a in the selected regions are discussed in relation to other studies. The PhytoDOAS results are consistent with the two other ocean color products and support the reported dependencies of coccolithophore biomass’ dynamics to the compared geophysical variables. This suggests, that PhytoDOAS 20 is a valid method for retrieving coccolithophore biomass and for monitoring its bloom developments in the global oceans. Future applications of time-series studies using the PhytoDOAS data set are proposed, also using the new upcoming generations of hyper-spectral satellite sensors with improved spatial resolution.

Description: The gradual cooling of the climate during the Cenozoic has generally been attributed to a decrease in CO2 concentration in the atmosphere. The lack of transient climate models and in particular the lack of high-resolution proxy records of CO2, beyond the ice-core record prohibit however a full understanding of for example the inception of the Northern Hemisphere glaciation and mid-Pleistocene transition. Here we elaborate on an inverse modelling technique to reconstruct a continuous CO2 series over the past 20 million year (Myr), by decomposing the global deep-sea benthic d18O record into a mutually consistent temperature and sea level record, using a set of 1-D models of the major Northern and Southern Hemisphere ice sheets. We subsequently compared the modelled temperature record with ice core and proxy-derived CO2 data to create a continuous CO2 reconstruction over the past 20 Myr. Results show a gradual decline from 450 ppmv around 15 Myr ago to 225 ppmv for mean conditions of the glacial-interglacial cycles of the last 1 Myr, coinciding with a gradual cooling of the global surface temperature of 10 K. Between 13 to 3 Myr ago there is no long-term sea level variation caused by ice-volume changes. We find no evidence for a change in the long-term relation between temperature change and CO2, other than the effect following from the saturation of the absorption bands for CO2. The reconstructed CO2 record shows that the Northern Hemisphere glaciation starts once the long-term average CO2 concentration drops below 265 ppmv after a period of strong decrease in CO2. Finally, only a small long-term decline of 23 ppmv is found during the mid-Pleistocene transition, constraining theories on this major transition in the climate system. The approach is not accurate enough to revise current ideas about climate sensitivity.

Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 5 (2010): e10741, doi:10.1371/journal.pone.0010741.

Description: Bisphenol A (BPA), used in the manufacture of plastics, is ubiquitously distributed in the aquatic environment. However, the effect of maternal transfer of these xenobiotics on embryonic development and growth is poorly understood in fish. We tested the hypothesis that BPA in eggs, mimicking maternal transfer, impact development, growth and stress performance in juveniles of rainbow trout (Oncorhynchus mykiss). Trout oocytes were exposed to 0, 30 and 100 µg.mL−1 BPA for 3 h in ovarian fluid, followed by fertilization. The embryos were maintained in clean water and sampled temporally over 156-days post-fertilization (dpf), and juveniles were sampled at 400-dpf. The egg BPA levels declined steadily after exposure and were undetectable after 21- dpf. Oocyte exposure to BPA led to a delay in hatching and yolk absorption and a consistently lower body mass over 152-dpf. The growth impairment, especially in the high BPA group, correlated with higher growth hormone (GH) content and lower GH receptors gene expression. Also, mRNA abundances of insulin-like growth factors (IGF-1 and IGF-2) and their receptors were suppressed in the BPA treated groups. The juvenile fish grown from the BPA-enriched eggs had lower body mass and showed perturbations in plasma cortisol and glucose response to an acute stressor. BPA accumulation in eggs, prior to fertilization, leads to hatching delays, growth suppression and altered stress response in juvenile trout. The somatotropic axis appears to be a key target for BPA impact during early embryogenesis, leading to long term growth and stress performance defects in fish.

Description: This work was supported by funds from the Natural Science and Engineering Research Council (NSERC) of Canada Discovery grant and the Ontario Ministry of Agriculture and Food.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e23259, doi:10.1371/journal.pone.0023259.

Description: The ChEss project of the Census of Marine Life (2002–2010) helped foster internationally-coordinated studies worldwide focusing on exploration for, and characterization of new deep-sea chemosynthetic ecosystem sites. This work has advanced our understanding of the nature and factors controlling the biogeography and biodiversity of these ecosystems in four geographic locations: the Atlantic Equatorial Belt (AEB), the New Zealand region, the Arctic and Antarctic and the SE Pacific off Chile. In the AEB, major discoveries include hydrothermal seeps on the Costa Rica margin, deepest vents found on the Mid-Cayman Rise and the hottest vents found on the Southern Mid-Atlantic Ridge. It was also shown that the major fracture zones on the MAR do not create barriers for the dispersal but may act as trans-Atlantic conduits for larvae. In New Zealand, investigations of a newly found large cold-seep area suggest that this region may be a new biogeographic province. In the Arctic, the newly discovered sites on the Mohns Ridge (71°N) showed extensive mats of sulfur-oxidisng bacteria, but only one gastropod potentially bears chemosynthetic symbionts, while cold seeps on the Haakon Mossby Mud Volcano (72°N) are dominated by siboglinid worms. In the Antarctic region, the first hydrothermal vents south of the Polar Front were located and biological results indicate that they may represent a new biogeographic province. The recent exploration of the South Pacific region has provided evidence for a sediment hosted hydrothermal source near a methane-rich cold-seep area. Based on our 8 years of investigations of deep-water chemosynthetic ecosystems worldwide, we suggest highest priorities for future research: (i) continued exploration of the deep-ocean ridge-crest; (ii) increased focus on anthropogenic impacts; (iii) concerted effort to coordinate a major investigation of the deep South Pacific Ocean – the largest contiguous habitat for life within Earth's biosphere, but also the world's least investigated deep-ocean basin.

Description: Alfred P. Sloan Foundation for the ChEss-Census of Marine Life programme (2002–2010) and the SYNDEEP synthesis project (2009–2010) (www.coml.org). Fondation Total for the ChEss synthesis phase and SYNDEEP synthesis project (2007–2010) (http://fondation.total.com/). Petersen Fellowship in IFM-GEOMAR to CRG.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22913, doi:10.1371/journal.pone.0022913.

Description: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species.

Description: This work was supported by grants (N-HKUST602/09 and AoE/P-04/04-II) from the Research Grants Council of the Hong Kong Special Administrative Region and an award (SA-C0040/UK-C0016) made by KAUST to P-Y Qian.

Description: © The Authors, 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e16018, doi:10.1371/journal.pone.0016018.

Description: The shrimp Rimicaris exoculata dominates the faunal biomass at many deep-sea hydrothermal vent sites at the Mid-Atlantic Ridge. In its enlarged gill chamber it harbors a specialized epibiotic bacterial community for which a nutritional role has been proposed. We analyzed specimens from the Snake Pit hydrothermal vent field on the Mid-Atlantic Ridge by complementing a 16S rRNA gene survey with the analysis of genes involved in carbon, sulfur and hydrogen metabolism. In addition to Epsilon- and Gammaproteobacteria, the epibiotic community unexpectedly also consists of Deltaproteobacteria of a single phylotype, closely related to the genus Desulfocapsa. The association of these phylogenetic groups with the shrimp was confirmed by fluorescence in situ hybridization. Based on functional gene analyses, we hypothesize that the Gamma- and Epsilonproteobacteria are capable of autotrophic growth by oxidizing reduced sulfur compounds, and that the Deltaproteobacteria are also involved in sulfur metabolism. In addition, the detection of proteobacterial hydrogenases indicates the potential for hydrogen oxidation in these communities. Interestingly, the frequency of these phylotypes in 16S rRNA gene clone libraries from the mouthparts differ from that of the inner lining of the gill chamber, indicating potential functional compartmentalization. Our data show the specific association of autotrophic bacteria with Rimicaris exoculata from the Snake Pit hydrothermal vent field, and suggest that autotrophic carbon fixation is contributing to the productivity of the epibiotic community with the reductive tricarboxylic acid cycle as one important carbon fixation pathway. This has not been considered in previous studies of carbon fixation and stable carbon isotope composition of the shrimp and its epibionts. Furthermore, the co-occurrence of sulfur-oxidizing and sulfur-reducing epibionts raises the possibility that both may be involved in the syntrophic exchange of sulfur compounds, which could increase the overall efficiency of this epibiotic community.

Description: Funding was provided through NSF grant OCE-0452333 and the Alfried Krupp Wissenschaftskolleg Greifswald, Germany (SMS), the Max Planck Society, the German Research Foundation (DFG) Cluster of Excellence at Marum, and MOMARnet (ND, JMP), and IFM-GEOMAR (MH, JFI).

Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e16994, doi:10.1371/journal.pone.0016994.

Description: Chemical communication plays a critical role in sexual selection and speciation in fishes; however, it is generally assumed that most fish pheromones are passively released since most fishes lack specialized scent glands or scent-marking behavior. Swordtails (genus Xiphophorus) are widely used in studies of female mate choice, and female response to male chemical cues is important to sexual selection, reproductive isolation, and hybridization. However, it is unclear whether females are attending to passively produced cues, or to pheromones produced in the context of communication. We used fluorescein dye injections to visualize pulsed urine release in male sheepshead swordtails, Xiphophorus birchmanni. Simultaneous-choice assays of mating preference showed that females attend to species- and sex-specific chemical cues emitted in male urine. Males urinated more frequently in the presence and proximity of an audience (conspecific females). In the wild, males preferentially courted upstream of females, facilitating transmission of pheromone cues. Males in a teleost fish have evolved sophisticated temporal and spatial control of pheromone release, comparable to that found in terrestrial animals. Pheromones are released specifically in a communicative context, and the timing and positioning of release favors efficient signal transmission.

Description: This work was funded by the National Science Foundation (www.nsf.gov), IOB-0447665.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e20809, doi:10.1371/journal.pone.0020809.

Description: The net reproductive rate measures the expected lifetime reproductive output of an individual, and plays an important role in demography, ecology, evolution, and epidemiology. Well-established methods exist to calculate it from age- or stage-classified demographic data. As an expectation, provides no information on variability; empirical measurements of lifetime reproduction universally show high levels of variability, and often positive skewness among individuals. This is often interpreted as evidence of heterogeneity, and thus of an opportunity for natural selection. However, variability provides evidence of heterogeneity only if it exceeds the level of variability to be expected in a cohort of identical individuals all experiencing the same vital rates. Such comparisons require a way to calculate the statistics of lifetime reproduction from demographic data. Here, a new approach is presented, using the theory of Markov chains with rewards, obtaining all the moments of the distribution of lifetime reproduction. The approach applies to age- or stage-classified models, to constant, periodic, or stochastic environments, and to any kind of reproductive schedule. As examples, I analyze data from six empirical studies, of a variety of animal and plant taxa (nematodes, polychaetes, humans, and several species of perennial plants).

Description: Supported by National Science Foundation Grant DEB-0816514 and by a Research Award from the Alexander von Humboldt Foundation.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e25386, doi:10.1371/journal.pone.0025386.

Description: Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO2, carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.

Description: Funding has been provided by the NSF Microbial Observatories Program (KJE, DE), NSF’s Science and Technology Program, by the Gordon and Betty Moore Foundation (KJE), the College of Letters, Arts, and Sciences at the University of Southern California (KJE), and by the NASA Astrobiology Institute (KJE, DE). Advanced Light Source analyses at the Lawrence Berkeley National Lab are supported by the Office of Science, Basic Energy Sciences, Division of Materials Science of the United States Department of Energy (DE-AC02-05CH11231).

Description: © 2010 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 5 (2010): e8537, doi:10.1371/journal.pone.0008537.

Description: Despite the profound variation among marine consumers in tolerance for allelochemically-rich foods, few studies have examined the biochemical adaptations underlying diet choice. Here we examine the role of glutathione S-transferases (GSTs) in the detoxification of dietary allelochemicals in the digestive gland of the predatory gastropod Cyphoma gibbosum, a generalist consumer of gorgonian corals. Controlled laboratory feeding experiments were used to investigate the influence of gorgonian diet on Cyphoma GST activity and isoform expression. Gorgonian extracts and semi-purified fractions were also screened to identify inhibitors and possible substrates of Cyphoma GSTs. In addition, we investigated the inhibitory properties of prostaglandins (PGs) structurally similar to antipredatory PGs found in high concentrations in the Caribbean gorgonian Plexaura homomalla. Cyphoma GST subunit composition was invariant and activity was constitutively high regardless of gorgonian diet. Bioassay-guided fractionation of gorgonian extracts revealed that moderately hydrophobic fractions from all eight gorgonian species examined contained putative GST substrates/inhibitors. LC-MS and NMR spectral analysis of the most inhibitory fraction from P. homomalla subsequently identified prostaglandin A2 (PGA2) as the dominant component. A similar screening of commercially available prostaglandins in series A, E, and F revealed that those prostaglandins most abundant in gorgonian tissues (e.g., PGA2) were also the most potent inhibitors. In vivo estimates of PGA2 concentration in digestive gland tissues calculated from snail grazing rates revealed that Cyphoma GSTs would be saturated with respect to PGA2 and operating at or near physiological capacity. The high, constitutive activity of Cyphoma GSTs is likely necessitated by the ubiquitous presence of GST substrates and/or inhibitors in this consumer's gorgonian diet. This generalist's GSTs may operate as ‘all-purpose’ detoxification enzymes, capable of conjugating or sequestering a broad range of lipophilic gorgonian compounds, thereby allowing this predator to exploit a range of chemically-defended prey, resulting in a competitive dietary advantage for this species.

Description: Financial support for this work was provided by the Ocean Life Institute Tropical Research Initiative Grant (WHOI) to KEW and MEH; the Robert H. Cole Endowed Ocean Ventures Fund (WHOI) to KEW; the National Undersea Research Center - Program Development Proposal (CMRC-03PRMN0103A) to KEW; Walter A. and Hope Noyes Smith, and a National Science Foundation Graduate Research Fellowship to KEW.

Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 5 (2010): e12805, doi:10.1371/journal.pone.0012805.

Description: Circadian rhythms in behavior and physiology are the observable phenotypes from cycles in expression of, interactions between, and degradation of the underlying molecular components. In bilaterian animals, the core molecular components include Timeless-Timeout, photoreceptive cryptochromes, and several members of the basic-loop-helix-Per-ARNT-Sim (bHLH-PAS) family. While many of core circadian genes are conserved throughout the Bilateria, their specific roles vary among species. Here, we identify and experimentally study the rhythmic gene expression of conserved circadian clock members in a sea anemone in order to characterize this gene network in a member of the phylum Cnidaria and to infer critical components of the clockwork used in the last common ancestor of cnidarians and bilaterians. We identified homologs of circadian regulatory genes in the sea anemone Nematostella vectensis, including a gene most similar to Timeout, three cryptochromes, and several key bHLH-PAS transcription factors. We then maintained N. vectensis either in complete darkness or in a 12 hour light: 12 hour dark cycle in three different light treatments (blue only, full spectrum, blue-depleted). Gene expression varied in response to light cycle and light treatment, with a particularly strong pattern observed for NvClock. The cryptochromes more closely related to the light-sensitive clade of cryptochromes were upregulated in light treatments that included blue wavelengths. With co-immunoprecipitation, we determined that heterodimerization between CLOCK and CYCLE is conserved within N. vectensis. Additionally, we identified E-box motifs, DNA sequences recognized by the CLOCK:CYCLE heterodimer, upstream of genes showing rhythmic expression. This study reveals conserved molecular and functional components of the circadian clock that were in place at the divergence of the Cnidaria and Bilateria, suggesting the animal circadian clockwork is more ancient than previous data suggest. Characterizing circadian regulation in a cnidarian provides insight into the early origins of animal circadian rhythms and molecular regulation of environmentally cued behaviors.

Description: The project described was supported by Award Number F32HD062178 to AMR from the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the Tropical Research Initiative of the Woods Hole Oceanographic Institution.

Description: This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS ONE 5 (2010): e9597, doi:10.1371/journal.pone.0009597.

Description: The objective of this study was to enhance removal of fishing gear from right whales (Eubalaena glacialis) at sea that evade disentanglement boat approaches. Titrated intra muscular injections to achieve sedation were undertaken on two free swimming right whales. Following initial trials with beached whales, a sedation protocol was developed for right whales. Mass was estimated from sighting and necropsy data from comparable right whales. Midazolam (0.01 to 0.025 mg/kg) was first given alone or with meperidine (0.17 to 0.25 mg/kg) either once or four times over two hours to whale #1102 by cantilevered pole syringe. In the last attempt on whale #1102 there appeared to be a mild effect in 20–30 minutes, with duration of less than 2 hours that included exhalation before the blowhole fully cleared the water. Boat avoidance, used as a measure of sedation depth, was not reduced. A second severely entangled animal in 2009, whale #3311, received midazolam (0.03 mg/kg) followed by butorphanol (0.03 mg/kg) an hour later, delivered ballistically. Two months later it was then given midazolam (0.07 mg/kg) and butorphanol (0.07 mg/kg) simultaneously. The next day both drugs at 0.1 mg/kg were given as a mixture in two darts 10 minutes apart. The first attempt on whale #3311 showed increased swimming speed and boat avoidance was observed after a further 20 minutes. The second attempt on whale #3311 showed respiration increasing mildly in frequency and decreasing in strength. The third attempt on whale #3311 gave a statistically significant increase in respiratory frequency an hour after injection, with increased swimming speed and marked reduction of boat evasion that enabled decisive cuts to entangling gear. We conclude that butorphanol and midazolam delivered ballistically in appropriate dosages and combinations may have merit in future refractory free swimming entangled right whale cases until other entanglement solutions are developed.

Description: This work was funded by Cecil H. and Ida M. Green Technology Innovation Program (WHOI), North Pond Foundation, Sloan and Wick Simmonds, Northeast Consortium, National Oceanic Atmospheric Administration (NOAA), Georgia Department of Natural Resources, Florida Fish and Wildlife Conservation Commission, Provincetown Center for Coastal Studies, Coastwise Consulting, the Atlantic Large Whale Disentanglement Network, and Aquatic Animal Health Program, University of Florida.

Description: The work is made available under the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS Computational Biology 7 (2011): e1002089, doi:10.1371/journal.pcbi.1002089.

Description: An important problem in neuronal computation is to discern how features of stimuli control the timing of action potentials. One aspect of this problem is to determine how an action potential, or spike, can be elicited with the least energy cost, e.g., a minimal amount of applied current. Here we show in the Hodgkin & Huxley model of the action potential and in experiments on squid giant axons that: 1) spike generation in a neuron can be highly discriminatory for stimulus shape and 2) the optimal stimulus shape is dependent upon inputs to the neuron. We show how polarity and time course of post-synaptic currents determine which of these optimal stimulus shapes best excites the neuron. These results are obtained mathematically using the calculus of variations and experimentally using a stochastic search methodology. Our findings reveal a surprising complexity of computation at the single cell level that may be relevant for understanding optimization of signaling in neurons and neuronal networks.

Description: This work was supported by the Intramural Research Program of the National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892 and NIH grant R01 HL718884 to DP. DBF is an AFOSR Young Investigator (FA 9550-08-01-0076).

Description: This article is distributed under the terms of the Creative Commons Public Domain. The definitive version was published in PLoS One 6 (2011): e16153, doi:10.1371/journal.pone.0016153.

Description: Seamounts are unique deep-sea features that create habitats thought to have high levels of endemic fauna, productive fisheries and benthic communities vulnerable to anthropogenic impacts. Many seamounts are isolated features, occurring in the high seas, where access is limited and thus biological data scarce. There are numerous seamounts within the Drake Passage (Southern Ocean), yet high winds, frequent storms and strong currents make seafloor sampling particularly difficult. As a result, few attempts to collect biological data have been made, leading to a paucity of information on benthic habitats or fauna in this area, particularly those on primarily hard-bottom seamounts and ridges. During a research cruise in 2008 six locations were examined (two on the Antarctic margin, one on the Shackleton Fracture Zone, and three on seamounts within the Drake Passage), using a towed camera with onboard instruments to measure conductivity, temperature, depth and turbidity. Dominant fauna and bottom type were categorized from 200 randomized photos from each location. Cold-water corals were present in high numbers in habitats both on the Antarctic margin and on the current swept seamounts of the Drake Passage, though the diversity of orders varied. Though the Scleractinia (hard corals) were abundant on the sedimented margin, they were poorly represented in the primarily hard-bottom areas of the central Drake Passage. The two seamount sites and the Shackleton Fracture Zone showed high numbers of stylasterid (lace) and alcyonacean (soft) corals, as well as large numbers of sponges. Though data are preliminary, the geological and environmental variability (particularly in temperature) between sample sites may be influencing cold-water coral biogeography in this region. Each area observed also showed little similarity in faunal diversity with other sites examined for this study within all phyla counted. This manuscript highlights how little is understood of these isolated features, particularly in Polar regions.

Description: This work was funded by the National Science Foundation’s Antarctic Earth Sciences Program (ANT0636787 awarded to LFR and RGW) and a CenSeam minigrant (awarded to RGW), and RGW is supported by a SOEST Young Investigator Fellowship from the University of Hawaii at Manoa.

Description: This article is distributed under the terms of the Creative Commons Public Domain declaration. The definitive version was published in PLoS One 6 (2011): e17009, doi:10.1371/journal.pone.0017009.

Description: Beaked whales have mass stranded during some naval sonar exercises, but the cause is unknown. They are difficult to sight but can reliably be detected by listening for echolocation clicks produced during deep foraging dives. Listening for these clicks, we documented Blainville's beaked whales, Mesoplodon densirostris, in a naval underwater range where sonars are in regular use near Andros Island, Bahamas. An array of bottom-mounted hydrophones can detect beaked whales when they click anywhere within the range. We used two complementary methods to investigate behavioral responses of beaked whales to sonar: an opportunistic approach that monitored whale responses to multi-day naval exercises involving tactical mid-frequency sonars, and an experimental approach using playbacks of simulated sonar and control sounds to whales tagged with a device that records sound, movement, and orientation. Here we show that in both exposure conditions beaked whales stopped echolocating during deep foraging dives and moved away. During actual sonar exercises, beaked whales were primarily detected near the periphery of the range, on average 16 km away from the sonar transmissions. Once the exercise stopped, beaked whales gradually filled in the center of the range over 2–3 days. A satellite tagged whale moved outside the range during an exercise, returning over 2–3 days post-exercise. The experimental approach used tags to measure acoustic exposure and behavioral reactions of beaked whales to one controlled exposure each of simulated military sonar, killer whale calls, and band-limited noise. The beaked whales reacted to these three sound playbacks at sound pressure levels below 142 dB re 1 µPa by stopping echolocation followed by unusually long and slow ascents from their foraging dives. The combined results indicate similar disruption of foraging behavior and avoidance by beaked whales in the two different contexts, at exposures well below those used by regulators to define disturbance.

Description: The research reported here was financially supported by the United States (U.S.) Office of Naval Research (www.onr.navy.mil) Grants N00014-07-10988, N00014-07-11023, N00014-08-10990; the U.S. Strategic Environmental Research and Development Program (www.serdp.org) Grant SI-1539, the Environmental Readiness Division of the U.S. Navy (http://www.navy.mil/local/n45/), the U.S. Chief of Naval Operations Submarine Warfare Division (Undersea Surveillance), the U.S. National Oceanic and Atmospheric Administration (National Marine Fisheries Service, Office of Science and Technology) (http://www.st.nmfs.noaa.gov/), U.S. National Oceanic and Atmospheric Administration Ocean Acoustics Program (http://www.nmfs.noaa.gov/pr/acoustics/), and the Joint Industry Program on Sound and Marine Life of the International Association of Oil and Gas Producers (www.soundandmarinelife.org).

Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 6(2011): e18046, doi:10.1371/journal.pone.0018046.

Description: The domestic cat (Felis catus) shows remarkable sensitivity to the adverse effects of phenolic drugs, including acetaminophen and aspirin, as well as structurally-related toxicants found in the diet and environment. This idiosyncrasy results from pseudogenization of the gene encoding UDP-glucuronosyltransferase (UGT) 1A6, the major species-conserved phenol detoxification enzyme. Here, we established the phylogenetic timing of disruptive UGT1A6 mutations and explored the hypothesis that gene inactivation in cats was enabled by minimal exposure to plant-derived toxicants. Fixation of the UGT1A6 pseudogene was estimated to have occurred between 35 and 11 million years ago with all extant Felidae having dysfunctional UGT1A6. Out of 22 additional taxa sampled, representative of most Carnivora families, only brown hyena (Parahyaena brunnea) and northern elephant seal (Mirounga angustirostris) showed inactivating UGT1A6 mutations. A comprehensive literature review of the natural diet of the sampled taxa indicated that all species with defective UGT1A6 were hypercarnivores (〉70% dietary animal matter). Furthermore those species with UGT1A6 defects showed evidence for reduced amino acid constraint (increased dN/dS ratios approaching the neutral selection value of 1.0) as compared with species with intact UGT1A6. In contrast, there was no evidence for reduced amino acid constraint for these same species within UGT1A1, the gene encoding the enzyme responsible for detoxification of endogenously generated bilirubin. Our results provide the first evidence suggesting that diet may have played a permissive role in the devolution of a mammalian drug metabolizing enzyme. Further work is needed to establish whether these preliminary findings can be generalized to all Carnivora.

Description: Binu Shrestha was supported by a Fulbright scholarship from the United States Department of State. This project was funded by grant R01GM061834 from the National Institute of General Medical Sciences, contract N01-CO-12400 from the National Cancer Institute (NCI), and by the Intramural Research Program, NCI Center for Cancer Research, National Institutes of Health (NIH).

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22965, doi:10.1371/journal.pone.0022965.

Description: Historically, cosmopolitan phytoplankton species were presumed to represent largely unstructured populations. However, the recent development of molecular tools to examine genetic diversity have revealed differences in phytoplankton taxa across geographic scales and provided insight into the physiology and ecology of blooms. Here we describe the genetic analysis of an extensive bloom of the toxic dinoflagellate Alexandrium fundyense that occurred in the Gulf of Maine in 2005. This bloom was notable for its intensity and duration, covering hundreds of kilometers and persisting for almost two months. Genotypic analyses based on microsatellite marker data indicate that the open waters of the northeastern U.S. harbor a single regional population of A. fundyense comprising two genetically distinct sub-populations. These subpopulations were characteristic of early- and late-bloom samples and were derived from the northern and southern areas of the bloom, respectively. The temporal changes observed during this study provide clear evidence of succession during a continuous bloom and show that selection can act on the timescale of weeks to significantly alter the representation of genotypes within a population. The effects of selection on population composition and turnover would be magnified if sexual reproduction were likewise influenced by environmental conditions. We hypothesize that the combined effects of differential growth and reproduction rates serves to reduce gene flow between the sub-populations, reinforcing population structure while maintaining the diversity of the overall regional population.

Description: This work was supported by the National Institute of Environmental Health Sciences (1-P50-ES012742 to DMA and DLE), by the National Science Foundation through the Woods Hole Center for Oceans and Human Health (OCE-0430724), and by the ECOHAB program (NOAA Grant NA06NOS4780245).

Description: © The Authors, 2007. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 2 (2007): e667, doi:10.1371/journal.pone.0000667.

Description: For decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano. Using gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe0 were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the Proteobacteria. The most similar sequence (85.3% similarity) from a cultivated isolate came from Methylophaga marina. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the Proteobacteria. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi. On the basis of phylogenetic and physiological data, it is proposed that isolate PV-1T ( = 1ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, Mariprofundus ferrooxydans gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the Proteobacteria that is widely distributed in deep-sea environments, Candidatus ζ (zeta)-Proteobacteria cl. nov.

Description: Funding was provided to DE and CLM by the National Science Foundation (0348330) and to DE through the NASA Astobiology Institute.

Description: © The Authors, 2008. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 3 (2008): e2581, doi:10.1371/journal.pone.0002581.

Description: Birdsong is a widely used model for vocal learning and human speech, which exhibits high temporal and acoustic diversity. Rapid acoustic modulations are thought to arise from the vocal organ, the syrinx, by passive interactions between the two independent sound generators or intrinsic nonlinear dynamics of sound generating structures. Additionally, direct neuromuscular control could produce such rapid and precisely timed acoustic features if syringeal muscles exhibit rare superfast muscle contractile kinetics. However, no direct evidence exists that avian vocal muscles can produce modulations at such high rates. Here, we show that 1) syringeal muscles are active in phase with sound modulations during song over 200 Hz, 2) direct stimulation of the muscles in situ produces sound modulations at the frequency observed during singing, and that 3) syringeal muscles produce mechanical work at the required frequencies and up to 250 Hz in vitro. The twitch kinematics of these so-called superfast muscles are the fastest measured in any vertebrate muscle. Superfast vocal muscles enable birds to directly control the generation of many observed rapid acoustic changes and to actuate the millisecond precision of neural activity into precise temporal vocal control. Furthermore, birds now join the list of vertebrate classes in which superfast muscle kinetics evolved independently for acoustic communication.

Description: This study was funded by NIH DC04390 and DC06876 to FG, and NIH AR38404-20 and NIH AR46125 to LCR. The work was also supported by a grant from the Pennsylvania Department of Health to LCR.

Description: © The Authors, 2007. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 2 (2007): e671, doi:10.1371/journal.pone.0000671.

Description: Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking. We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy. Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu.

Description: This research was supported by the Nagasaki Prefecture Collaboration of Regional Entities for the Advancement of Technological Excellence, Japan Science and Technology Agency to KS, YT, YS and AH, and US NSF grants EF-0412674 and MCB-0544199 to DMW.

Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 5 (2010): e9688, doi:10.1371/journal.pone.0009688.

Description: Dinoflagellates are unicellular, often photosynthetic protists that play a major role in the dynamics of the Earth's oceans and climate. Sequencing of dinoflagellate nuclear DNA is thwarted by their massive genome sizes that are often several times that in humans. However, modern transcriptomic methods offer promising approaches to tackle this challenging system. Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions. We generated more than 40,000 unique short expression signatures gathered from the four conditions. Of these, about 11,000 signatures did not display detectable differential expression patterns. At a p-value 〈 1E-10, 1,124 signatures were differentially expressed in the three treatments, xenic, nitrogen-limited, and phosphorus-limited, compared to the nutrient-replete control, with the presence of bacteria explaining the largest set of these differentially expressed signatures. Among microbial eukaryotes, dinoflagellates contain the largest number of genes in their nuclear genomes. These genes occur in complex families, many of which have evolved via recent gene duplication events. Our expression data suggest that about 73% of the Alexandrium transcriptome shows no significant change in gene expression under the experimental conditions used here and may comprise a “core” component for this species. We report a fundamental shift in expression patterns in response to the presence of bacteria, highlighting the impact of biotic interaction on gene expression in dinoflagellates.

Description: This work was primarily funded by a collaborative grant from the National Institutes of Health (R01 ES 013679-01A2) awarded to DB, DMA, and M. Bento Soares. Funding support for DMA and DLE was also provided from the Woods Hole Center for Oceans and Human Health from the NSF/NIEHS Centers for Oceans and Human Health program, NIEHS (P50 ES 012742) and (NSF OCE-043072). Additional support came from the National Science Foundation (EF-0732440) in a grant awarded to F. Gerald Plumley, DB, JDH, and DMA. AM was supported by an Institutional NRSA (T 32 GM98629).

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e18849, doi:10.1371/journal.pone.0018849.

Description: Oysters play important roles in estuarine ecosystems but have suffered recently due to overfishing, pollution, and habitat loss. A tradeoff between growth rate and disease prevalence as a function of salinity makes the estuarine salinity transition of special concern for oyster survival and restoration. Estuarine salinity varies with discharge, so increases or decreases in precipitation with climate change may shift regions of low salinity and disease refuge away from optimal oyster bottom habitat, negatively impacting reproduction and survival. Temperature is an additional factor for oyster survival, and recent temperature increases have increased vulnerability to disease in higher salinity regions. We examined growth, reproduction, and survival of oysters in the New York Harbor-Hudson River region, focusing on a low-salinity refuge in the estuary. Observations were during two years when rainfall was above average and comparable to projected future increases in precipitation in the region and a past period of about 15 years with high precipitation. We found a clear tradeoff between oyster growth and vulnerability to disease. Oysters survived well when exposed to intermediate salinities during two summers (2008, 2010) with moderate discharge conditions. However, increased precipitation and discharge in 2009 reduced salinities in the region with suitable benthic habitat, greatly increasing oyster mortality. To evaluate the estuarine conditions over longer periods, we applied a numerical model of the Hudson to simulate salinities over the past century. Model results suggest that much of the region with suitable benthic habitat that historically had been a low salinity refuge region may be vulnerable to higher mortality under projected increases in precipitation and discharge. Predicted increases in precipitation in the northeastern United States due to climate change may lower salinities past important thresholds for oyster survival in estuarine regions with appropriate substrate, potentially disrupting metapopulation dynamics and impeding oyster restoration efforts, especially in the Hudson estuary where a large basin constitutes an excellent refuge from disease.

Description: Funding was provided by the Hudson River Foundation, grant number 00607A, and the New York State Department of Environmental Conservation (MOU 2008).

Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 4 (2009): e6372, doi:10.1371/journal.pone.0006372.

Description: Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations. Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments. Massively parallel pyrosequencing of eukaryotic V9 hypervariable regions of SSU rRNA genes provides a means of estimating species richness from deeply-sampled populations and for discovering novel species from the environment.

Description: This work was supported by grants from the W.M. Keck Foundation and the Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J) (LAZ and SH).

Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 5 (2010): e15545, doi:10.1371/journal.pone.0015545.

Description: How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial ‘multi-omic’ study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.

Description: Funding for this work was provided by a Natural Environmental Research Council (www.nerc.ac.uk) grant, NE/F00138X/1.

Description: This article is distributed under the terms of the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 6 (2011): e19269, doi:10.1371/journal.pone.0019269.

Description: Beaked whales, specifically Blainville's (Mesoplodon densirostris) and Cuvier's (Ziphius cavirostris), are known to feed in the Tongue of the Ocean, Bahamas. These whales can be reliably detected and often localized within the Atlantic Undersea Test and Evaluation Center (AUTEC) acoustic sensor system. The AUTEC range is a regularly spaced bottom mounted hydrophone array covering 〉350 nm2 providing a valuable network to record anthropogenic noise and marine mammal vocalizations. Assessments of the potential risks of noise exposure to beaked whales have historically occurred in the absence of information about the physical and biological environments in which these animals are distributed. In the fall of 2008, we used a downward looking 38 kHz SIMRAD EK60 echosounder to measure prey scattering layers concurrent with fine scale turbulence measurements from an autonomous turbulence profiler. Using an 8 km, 4-leaf clover sampling pattern, we completed a total of 7.5 repeat surveys with concurrently measured physical and biological oceanographic parameters, so as to examine the spatiotemporal scales and relationships among turbulence levels, biological scattering layers, and beaked whale foraging activity. We found a strong correlation among increased prey density and ocean vertical structure relative to increased click densities. Understanding the habitats of these whales and their utilization patterns will improve future models of beaked whale habitat as well as allowing more comprehensive assessments of exposure risk to anthropogenic sound.

Description: The data collection and analysis was funded by the Office of Naval Research as N00014-08-1-1162.

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 9 (2011): e1001088, doi:10.1371/journal.pbio.1001088.

Description: A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

Description: NERC International Opportunities Fund Award NE/3521773/1 and NE/E007325/1 (http://www.nerc. ac.uk/funding/) and National Science Foundation grant RCN4GSC, DBI-0840989 (http://www.nsf.gov/funding/).

Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e26732, doi:10.1371/journal.pone.0026732.

Description: Bacterial vaginosis (BV) is an enigmatic disease of unknown origin that affects a large percentage of women. The vaginal microbiota of women with BV is associated with serious sequelae, including abnormal pregnancies. The etiology of BV is not fully understood, however, it has been suggested that it is transmissible, and that G. vaginalis may be an etiological agent. Studies using enzymatic assays to define G. vaginalis biotypes, as well as more recent genomic comparisons of G. vaginalis isolates from symptomatic and asymptomatic women, suggest that particular G. vaginalis strains may play a key role in the pathogenesis of BV. To explore G. vaginalis diversity, distribution and sexual transmission, we developed a Shannon entropy-based method to analyze low-level sequence variation in 65,710 G. vaginalis 16S rRNA gene segments that were PCR-amplified from vaginal samples of 53 monogamous women and from urethral and penile skin samples of their male partners. We observed a high degree of low-level diversity among G. vaginalis sequences with a total of 46 unique sequence variants (oligotypes), and also found strong correlations of these oligotypes between sexual partners. Even though Gram stain-defined normal and some Gram stain-defined intermediate oligotype profiles clustered together in UniFrac analysis, no single G. vaginalis oligotype was found to be specific to BV or normal vaginal samples. This study describes a novel method for investigating G. vaginalis diversity at a low level of taxonomic discrimination. The findings support cultivation-based studies that indicate sexual partners harbor the same strains of G. vaginalis. This study also highlights the fact that a few, reproducible nucleotide variations within the 16S rRNA gene can reveal clinical or epidemiological associations that would be missed by genus-level or species-level categorization of 16S rRNA data.

Description: This work is supported by funding from the Research Institute for Children in New Orleans and NIH grant 5RO1AI79071-2.

Description: Kinematics of a mass movement constrained by sparse and inhomogeneous data Natural Hazards and Earth System Science, 11, 1609-1618, 2011 Author(s): M. Karbon, E. Brückl, E. Hegedüs, and A. Preh On 12 February 2008, a landslide occurred along a 50 m high bank of the Danube river near Dunaszekcsö, Hungary. The initial state is only incompletely documented and the geodetic data acquired after the mass movement are sparse. A generalized 3-D topographic model of the landslide and its surrounding area was assembled and a representative longitudinal profile extracted. The reconstruction of the original surface is based on an orthophoto as well as on morphological considerations. Recorded observations include the locations of the outcrops of basal sliding surfaces, displacements at the main scarp and in the lower part of the slide, and a value to describe the total mass transport. Such sparse and inhomogeneous data were insufficient to derive a comprehensive documentation of the landslide or obtain adequate constraints for an accurate numerical analysis. Therefore, slider block models were fitted to the field data, which have only a small number of free parameters. A general view on the morphology of the mass movement justifies its classification as a rotational slide. A double slider block model fits all observational parameters within their error margin and supplies valuable information on the geometry of the slide. Estimates of the residual friction angles were derived and the question of reactivation was addressed. Finite Difference (FD) modelling and the application of conventional stability analysis support the geometry of the slider blocks and the computed average residual friction angles. Generally, the results are assumed to represent preliminary information, which could only be attained by the combination of the thinly distributed geodetic data with qualitative morphological observations and the implementation of a model. This type of information can be gained quickly and may be valuable for preliminary hazard mitigation measures or the planning of a comprehensive exploration and monitoring program.

Description: North Atlantic 20th century multidecadal variability in coupled climate models: sea surface temperature and ocean overturning circulation Ocean Science, 7, 389-404, 2011 Author(s): I. Medhaug and T. Furevik Output from a total of 24 state-of-the-art Atmosphere-Ocean General Circulation Models is analyzed. The models were integrated with observed forcing for the period 1850–2000 as part of the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report. All models show enhanced variability at multi-decadal time scales in the North Atlantic sector similar to the observations, but with a large intermodel spread in amplitudes and frequencies for both the Atlantic Multidecadal Oscillation (AMO) and the Atlantic Meridional Overturning Circulation (AMOC). The models, in general, are able to reproduce the observed geographical patterns of warm and cold episodes, but not the phasing such as the early warming (1930s–1950s) and the following colder period (1960s–1980s). This indicates that the observed 20th century extreme in temperatures are due to primarily a fortuitous phasing of intrinsic climate variability and not dominated by external forcing. Most models show a realistic structure in the overturning circulation, where more than half of the available models have a mean overturning transport within the observed estimated range of 13–24 Sverdrup. Associated with a stronger than normal AMOC, the surface temperature is increased and the sea ice extent slightly reduced in the North Atlantic. Individual models show potential for decadal prediction based on the relationship between the AMO and AMOC, but the models strongly disagree both in phasing and strength of the covariability. This makes it difficult to identify common mechanisms and to assess the applicability for predictions.

Description: Sensitivity analysis of an ocean carbon cycle model in the North Atlantic: an investigation of parameters affecting the air-sea CO 2 flux, primary production and export of detritus Ocean Science, 7, 405-419, 2011 Author(s): V. Scott, H. Kettle, and C. J. Merchant The sensitivity of the biological parameters in a nutrient-phytoplankton-zooplankton-detritus (NPZD) model in the calculation of the air-sea CO 2 flux, primary production and detrital export is analysed. We explore the effect on these outputs of variation in the values of the twenty parameters that control ocean ecosystem growth in a 1-D formulation of the UK Met Office HadOCC NPZD model used in GCMs. We use and compare the results from one-at-a-time and all-at-a-time perturbations performed at three sites in the EuroSITES European Ocean Observatory Network: the Central Irminger Sea (60° N 40° W), the Porcupine Abyssal Plain (49° N 16° W) and the European Station for Time series in the Ocean Canary Islands (29° N 15° W). Reasonable changes to the values of key parameters are shown to have a large effect on the calculation of the air-sea CO 2 flux, primary production, and export of biological detritus to the deep ocean. Changes in the values of key parameters have a greater effect in more productive regions than in less productive areas. The most sensitive parameters are generally found to be those controlling well-established ocean ecosystem parameterisations widely used in many NPZD-type models. The air-sea CO 2 flux is most influenced by variation in the parameters that control phytoplankton growth, detrital sinking and carbonate production by phytoplankton (the rain ratio). Primary production is most sensitive to the parameters that define the shape of the photosynthesis-irradiance curve. Export production is most sensitive to the parameters that control the rate of detrital sinking and the remineralisation of detritus.

Description: Theoretical basis for convective invigoration due to increased aerosol concentration Atmospheric Chemistry and Physics, 11, 5407-5429, 2011 Author(s): Z. J. Lebo and J. H. Seinfeld The potential effects of increased aerosol loading on the development of deep convective clouds and resulting precipitation amounts are studied by employing the Weather Research and Forecasting (WRF) model as a detailed high-resolution cloud resolving model (CRM) with both detailed bulk and bin microphysics schemes. Both models include a physically-based activation scheme that incorporates a size-resolved aerosol population. We demonstrate that the aerosol-induced effect is controlled by the balance between latent heating and the increase in condensed water aloft, each having opposing effects on buoyancy. It is also shown that under polluted conditions, increases in the CCN number concentration reduce the cumulative precipitation due to the competition between the sedimentation and evaporation/sublimation timescales. The effect of an increase in the IN number concentration on the dynamics of deep convective clouds is small and the resulting decrease in domain-averaged cumulative precipitation is shown not to be statistically significant, but may act to suppress precipitation. It is also shown that even in the presence of a decrease in the domain-averaged cumulative precipitation, an increase in the precipitation variance, or in other words, andincrease in rainfall intensity, may be expected in more polluted environments, especially in moist environments. A significant difference exists between the predictions based on the bin and bulk microphysics schemes of precipitation and the influence of aerosol perturbations on updraft velocity within the convective core. The bulk microphysics scheme shows little change in the latent heating rates due to an increase in the CCN number concentration, while the bin microphysics scheme demonstrates significant increases in the latent heating aloft with increasing CCN number concentration. This suggests that even a detailed two-bulk microphysics scheme, coupled to a detailed activation scheme, may not be sufficient to predict small changes that result from perturbations in aerosol loading.

Description: Analysis of HCl and ClO time series in the upper stratosphere using satellite data sets Atmospheric Chemistry and Physics, 11, 5321-5333, 2011 Author(s): A. Jones, J. Urban, D. P. Murtagh, C. Sanchez, K. A. Walker, N. J. Livesey, L. Froidevaux, and M. L. Santee Previous analyses of satellite and ground-based measurements of hydrogen chloride (HCl) and chlorine monoxide (ClO) have suggested that total inorganic chlorine in the upper stratosphere is on the decline. We create HCl and ClO time series using satellite data sets extended to November 2008, so that an update can be made on the long term evolution of these two species. We use the HALogen Occultation Experiment (HALOE) and the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) data for the HCl analysis, and the Odin Sub-Millimetre Radiometer (SMR) and the Aura Microwave Limb Sounder (Aura-MLS) measurements for the study of ClO. Altitudes between 35 and 45 km and two mid-latitude bands: 30° S–50° S and 30° N–50° N, for HCl, and 20° S–20° N for ClO and HCl are studied. ACE-FTS and HALOE HCl anomaly time series (with QBO and seasonal contributions removed) are combined to produce all instrument average time series, which show HCl to be reducing from peak 1997 values at a linear estimated rate of −5.1 % decade −1 in the Northern Hemisphere and −5.2 % decade −1 in the Southern Hemisphere, while the tropics show a linear trend of −5.8 % per decade (although we do not remove the QBO contribution there due to sparse data). Trend values are significantly different from a zero trend at the 2 sigma level. ClO is decreasing in the tropics by −7.1 % ± 7.8 % decade −1 based on measurements made from December 2001 to November 2008. The statistically significant downward trend found in HCl after 1997 and the apparent downward ClO trend since 2001 (although not statistically significant) confirm how effective the 1987 Montreal protocol objectives and its amendments have been in reducing the total amount of inorganic chlorine.

Description: Bayesian statistical modeling of spatially correlated error structure in atmospheric tracer inverse analysis Atmospheric Chemistry and Physics, 11, 5365-5382, 2011 Author(s): C. Mukherjee, P. S. Kasibhatla, and M. West We present and discuss the use of Bayesian modeling and computational methods for atmospheric chemistry inverse analyses that incorporate evaluation of spatial structure in model-data residuals. Motivated by problems of refining bottom-up estimates of source/sink fluxes of trace gas and aerosols based on satellite retrievals of atmospheric chemical concentrations, we address the need for formal modeling of spatial residual error structure in global scale inversion models. We do this using analytically and computationally tractable conditional autoregressive (CAR) spatial models as components of a global inversion framework. We develop Markov chain Monte Carlo methods to explore and fit these spatial structures in an overall statistical framework that simultaneously estimates source fluxes. Additional aspects of the study extend the statistical framework to utilize priors on source fluxes in a physically realistic manner, and to formally address and deal with missing data in satellite retrievals. We demonstrate the analysis in the context of inferring carbon monoxide (CO) sources constrained by satellite retrievals of column CO from the Measurement of Pollution in the Troposphere (MOPITT) instrument on the TERRA satellite, paying special attention to evaluating performance of the inverse approach using various statistical diagnostic metrics. This is developed using synthetic data generated to resemble MOPITT data to define a proof-of-concept and model assessment, and then in analysis of real MOPITT data. These studies demonstrate the ability of these simple spatial models to substantially improve over standard non-spatial models in terms of statistical fit, ability to recover sources in synthetic examples, and predictive match with real data.

Description: Understanding evolution of product composition and volatility distribution through in-situ GC × GC analysis: a case study of longifolene ozonolysis Atmospheric Chemistry and Physics, 11, 5335-5346, 2011 Author(s): G. Isaacman, D. R. Worton, N. M. Kreisberg, C. J. Hennigan, A. P. Teng, S. V. Hering, A. L. Robinson, N. M. Donahue, and A. H. Goldstein A method for predicting volatility and polarity based on chromatographic information was developed and applied to the smog chamber ozonolysis of the sesquiterpene longifolene. The products were collected and analyzed using a GC × GC Thermal Desorption Aerosol Gas Chromatograph/Mass Spectrometer (2D-TAG) and a quadrupole Aerodyne Aerosol Mass Spectrometer (AMS). All the secondary organic aerosol (SOA) was produced within the first half hour of the experiment. However, the oxidation level of the organic aerosol, as inferred from the fraction of ion m/z 44, suggested continued evolution of the SOA over the subsequent hours. Measurements of speciated organic compounds using 2D-TAG confirm that the composition of the particles changed over the course of the experiment. Nearly 200 oxidation products (thought to be mostly ketones and acids) were observed with 2D-TAG, but most could not be identified definitively due to a lack of standards and the absence of likely sesquiterpene oxidation products in available mass spectral databases. To categorize the observed products, the vapor pressure and oxygen-to-carbon ratio (O/C) of observed compounds were estimated based on their two-dimensional chromatographic retention times relative to those of known standards, establishing a retention time correlation (RTC) method for using 2D-TAG to better constrain important modelling parameters. The product distribution continuously evolved in volatility and oxygenation during 5 h of oxidation. Using peak area as the best available proxy for mass, we conclude that the product mixture includes many non-negligible products; the most abundant 3 compounds accounted for only half of the total observed peak area and 80 % of peak area was spread across 15 compounds. The data provide evidence for three conclusions: (1) 2D-TAG provides valuable volatility and oxygenation information even in the absence of definitive species identification, (2) complex particle-phase chemistry causes continued evolution of particle composition after new particles formation, and (3) minor products contribute significantly to SOA from the ozonolysis of longifolene.

Description: The Level 2 research product algorithms for the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) Atmospheric Measurement Techniques Discussions, 4, 3593-3645, 2011 Author(s): P. Baron, J. Urban, H. Sagawa, J. Möller, D. P. Murtagh, J. Mendrok, E. Dupuy, T. O. Sato, S. Ochiai, K. Suzuki, T. Manabe, T. Nishibori, K. Kikuchi, R. Sato, M. Takayanagi, Y. Murayama, M. Shiotani, and Y. Kasai This paper describes the algorithms of the level-2 research (L2r) processing chain developed for the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES). The chain has been developed in parallel to the operational chain for conducting researches on calibration and retrieval algorithms. L2r chain products are available to the scientific community. The objective of version 2 is the retrieval of the vertical distribution of trace gases in the altitude range of 18–90 km. An theoretical error analysis is conducted to estimate the retrieval feasibility of key parameters of the processing: line-of-sight elevation tangent altitudes (or angles), temperature and O 3 profiles. The line-of-sight tangent altitudes are retrieved between 20 and 50 km from the strong ozone (O 3 ) line at 625.371 GHz, with low correlation with the O 3 volume-mixing ratio and temperature retrieved profiles. Neglecting the non-linearity of the radiometric gain in the calibration procedure is the main systematic error. It is large for the retrieved temperature (between 5–10 K). Therefore, atmospheric pressure can not be derived from the retrieved temperature, and, then, in the altitude range where the line-of-sight tangent altitudes are retrieved, the retrieved trace gases profiles are found to be better represented on pressure levels than on altitude levels. The error analysis for the retrieved HOCl profile demonstrates that best results for inverting weak lines can be obtained by using narrow spectral windows. Future versions of the L2r algorithms will improve the temperature/pressure retrievals and also provide information in the upper tropospheric/lower stratospheric region (e.g., water vapor, ice content, O 3 ) and on stratospheric and mesospheric line-of-sight winds.

Description: Deciphering the spatio-temporal complexity of climate change of the last deglaciation: a model analysis Climate of the Past, 7, 591-602, 2011 Author(s): D. M. Roche, H. Renssen, D. Paillard, and G. Levavasseur Understanding the sequence of events occuring during the last major glacial to interglacial transition (21 ka BP to 9 ka BP) is a challenging task that has the potential to unveil the mechanisms behind large scale climate changes. Though many studies have focused on the understanding of the complex sequence of rapid climatic change that accompanied or interrupted the deglaciation, few have analysed it in a more theoretical framework with simple forcings. In the following, we address when and where the first significant temperature anomalies appeared when using slow varying forcing of the last deglaciation. We used here coupled transient simulations of the last deglaciation, including ocean, atmosphere and vegetation components to analyse the spatial timing of the deglaciation. To keep the analysis in a simple framework, we did not include freshwater forcings that potentially cause rapid climate shifts during that time period. We aimed to disentangle the direct and subsequent response of the climate system to slow forcing and moreover, the location where those changes are more clearly expressed. In a data – modelling comparison perspective, this could help understand the physically plausible phasing between known forcings and recorded climatic changes. Our analysis of climate variability could also help to distinguish deglacial warming signals from internal climate variability. We thus are able to better pinpoint the onset of local deglaciation, as defined by the first significant local warming and further show that there is a large regional variability associated with it, even with the set of slow forcings used here. In our model, the first significant hemispheric warming occurred simultaneously in the North and in the South and is a direct response to the obliquity forcing.

Description: Impact of changes in grain size and pore space on the hydraulic conductivity and spectral induced polarization response of sand Hydrology and Earth System Sciences, 15, 1785-1794, 2011 Author(s): K. Koch, A. Kemna, J. Irving, and K. Holliger Understanding the influence of pore space characteristics on the hydraulic conductivity and spectral induced polarization (SIP) response is critical for establishing relationships between the electrical and hydrological properties of surficial unconsolidated sedimentary deposits, which host the bulk of the world's readily accessible groundwater resources. Here, we present the results of laboratory SIP measurements on industrial-grade, saturated quartz samples with granulometric characteristics ranging from fine sand to fine gravel. We altered the pore space characteristics by changing (i) the grain size spectra, (ii) the degree of compaction, and (iii) the level of sorting. We then examined how these changes affect the SIP response, the hydraulic conductivity, and the specific surface area of the considered samples. In general, the results indicate a clear connection between the SIP response and the granulometric as well as pore space characteristics. In particular, we observe a systematic correlation between the hydraulic conductivity and the relaxation time of the Cole-Cole model describing the observed SIP effect for the entire range of considered grain sizes. The results do, however, also indicate that the detailed nature of these relations depends strongly on variations in the pore space characteristics, such as, for example, the degree of compaction. This underlines the complexity of the origin of the SIP signal as well as the difficulty to relate it to a single structural factor of a studied sample, and hence raises some fundamental questions with regard to the practical use of SIP measurements as site- and/or sample-independent predictors of the hydraulic conductivity.

Description: WRF simulation of a precipitation event over the Tibetan Plateau, China – an assessment using remote sensing and ground observations Hydrology and Earth System Sciences, 15, 1795-1817, 2011 Author(s): F. Maussion, D. Scherer, R. Finkelnburg, J. Richters, W. Yang, and T. Yao Meteorological observations over the Tibetan Plateau (TiP) are scarce, and precipitation estimations over this remote region are difficult. The constantly improving capabilities of numerical weather prediction (NWP) models offer the opportunity to reduce this problem by providing precipitation fields and other meteorological variables of high spatial and temporal resolution. Longer time periods of years to decades can be simulated by NWP models by successive model runs of shorter periods, which can be described by the term "regional atmospheric reanalysis". In this paper, we assess the Weather Research and Forecasting (WRF) models capacity in retrieving rain- and snowfall on the TiP in such a configuration using a nested approach: the simulations are conducted with three nested domains at spatial resolutions of 30, 10, and 2 km. A validation study is carried out for a one-month period with a special focus on one-week (22–28 October 2008), during which strong rain- and snowfall was observed on the TiP. The output of the model in each resolution is compared to the Tropical Rainfall Measuring Mission (TRMM) data set for precipitation and to the Moderate Resolution Imaging Spectroradiometer (MODIS) data set for snow extent. TRMM and WRF data are then compared to weather-station measurements. Our results suggest an overall improvement from WRF over TRMM with respect to weather-station measurements. Various configurations of the model with different nesting and forcing strategies, as well as physical parameterisation schemes are compared to propose a suitable design for a regional atmospheric reanalysis over the TiP. The WRF model showed good accuracy in simulating snow- and rainfall on the TiP for a one-month simulation period. Our study reveals that there is nothing like an optimal model strategy applicable for the high-altitude TiP, its fringing high-mountain areas of extremely complex topography and the low-altitude land and sea regions from which much of the precipitation on the TiP is originating. The choice of the physical parameterisation scheme will thus be always a compromise depending on the specific purpose of a model simulation. Our study demonstrates the high importance of orographic precipitation, but the problem of the orographic bias remains unsolved since reliable observational data are still missing. The results are relevant for anyone interested in carrying out a regional atmospheric reanalysis. Many hydrological analyses and applications like rainfall-runoff modelling or the analysis of flood events require precipitation rates at daily or even hourly intervals. Thus, our study offers a process-oriented alternative for retrieving precipitation fields of high spatio-temporal resolution in regions like the TiP, where other data sources are limited.

Description: Near infrared nadir sounding of vertical column densities: methodology and application to SCIAMACHY Atmospheric Measurement Techniques Discussions, 4, 3685-3737, 2011 Author(s): S. Gimeno García, F. Schreier, G. Lichtenberg, and S. Slijkhuis Nadir observations with the shortwave infrared channels of SCIAMACHY onboard the ENVISAT satellite can be used to derive information on atmospheric gases such as CO, CH 4 , N 2 O, CO 2 , and H 2 O. For the operational level 1b–2 processing of SCIAMACHY data a new retrieval code BIRRA (Beer InfraRed Retrieval Algorithm) has been developed: BIRRA performs a nonlinear least squares fit of the measured radiance, where molecular concentration vertical profiles are scaled to fit the observed data. Here we present the forward modeling (radiative transfer) and inversion (least squares optimization) fundamentals of the code along with the further processing steps required to generate higher level products such as global distributions and time series. Moreover, various aspects of level 1 (observed spectra) and auxiliary input data relevant for successful retrievals are discussed. BIRRA is currently used for operational analysis of carbon monoxide vertical column densities from SCIAMACHY channel 8 observations, and is being prepared for methane retrievals using channel 6 spectra. A set of representative CO retrievals and first CH 4 results are presented to demonstrate BIRRA's capabilities.

Description: Volatilizable biogenic organic compounds (VBOCs) with two dimensional gas chromatography-time of flight mass spectrometry (GC × GC-TOFMS): sampling methods, VBOC complexity, and chromatographic retention data Atmospheric Measurement Techniques Discussions, 4, 3647-3684, 2011 Author(s): J. F. Pankow, W. Luo, A. N. Melnychenko, K. C. Barsanti, L. M. Isabelle, C. Chen, A. B. Guenther, and T. N. Rosenstiel Two dimensional gas chromatography (GC × GC) with detection by time-of-flight mass spectrometry (TOFMS) was applied in the rapid analysis of air samples containing highly complex mixtures of volatilizable biogenic organic compounds (VBOCs). VBOC analytical methodologies are briefly reviewed, and optimal conditions are discussed for sampling with both adsorption/thermal desorption (ATD) cartridges and solid-phase microextraction (SPME) fibers. Air samples containing VBOC emissions from leaves of two tree species ( Cedrus atlantica and Calycolpus moritzianus ) were obtained by both ATD and SPME. The optimized gas chromatographic conditions utilized a 45 m, 0.25 mm I.D. low-polarity primary column (DB-VRX, 1.4 μm film) and a 1.5 m, 0.25 mm I.D. polar secondary column (Stabilwax® 0.25 μm film). Excellent separation was achieved in a 36 min temperature programmed GC × GC chromatogram. Thousands of VBOC peaks were present in the sample chromatograms; hundreds of tentative identifications by NIST mass spectral matching are provided. Very few of the tentatively identified compounds are currently available as authentic standards. Method detection limit values for a 5 l ATD sample were 3.5 pptv (10 ng m −3 ) for isoprene, methyl vinyl ketone, and methacrolein, and ~1.5 pptv (~10 ng m −3 ) for monoterpenes and sesquiterpenes. Kovats-type chromatographic retention index values on the primary column and relative retention time values on the secondary column are provided for 21 standard compounds and for 417 tentatively identified VBOCs. 19 of the 21 authentic standard compounds were found in one of the Cedrus atlantica SPME samples. In addition, easily quantifiable levels of at least 13 sesquiterpenes were found in an ATD sample obtained from a branch enclosure of Calycolpus moritzianus . Overall, the results obtained via GC × GC-TOFMS highlight an extreme, and largely uncharacterized diversity of VBOCs, consistent with the hypothesis that sesquiterpenes and other compounds beyond the current list of typically determined VBOC analytes may well be important contributors to global atmospheric levels of organic particulate matter.

Description: The influence of land cover change in the Asian monsoon region on present-day and mid-Holocene climate Biogeosciences, 8, 1499-1519, 2011 Author(s): A. Dallmeyer and M. Claussen Using the general circulation model ECHAM5/JSBACH, we investigate the biogeophysical effect of large-scale afforestation and deforestation in the Asian monsoon domain on present-day and mid-Holocene climate. We demonstrate that the applied land cover change does not only modify the local climate but also change the climate in North Africa and the Middle East via teleconnections. Deforestation in the Asian monsoon domain enhances the rainfall in North Africa. In parts of the Sahara summer precipitation is more than doubled. In contrast, afforestation strongly decreases summer rainfall in the Middle East and even leads to the cessation of the rainfall-activity in some parts of this region. Regarding the local climate, deforestation results in a reduction of precipitation and a cooler climate as grass mostly has a higher albedo than forests. However, in the core region of the Asian monsoon the decrease in evaporative cooling in the monsoon season overcompensates this signal and results in a net warming. Afforestation has mainly the opposite effect, although the pattern of change is less clear. It leads to more precipitation in most parts of the Asian monsoon domain and a warmer climate except for the southern regions where a stronger evaporation decreases near-surface temperatures in the monsoon season. When prescribing mid-Holocene insolation, the pattern of local precipitation change differs. Afforestation particularly increases monsoon rainfall in the region along the Yellow River which was the settlement area of major prehistoric cultures. In this region, the effect of land cover change on precipitation is half as large as the orbitally-induced precipitation change. Thus, our model results reveal that mid- to late-Holocene land cover change could strongly have contributed to the decreasing Asian monsoon precipitation during the Holocene known from reconstructions.

Description: Sensing Hadley cell with space lidar Atmospheric Chemistry and Physics Discussions, 11, 16599-16610, 2011 Author(s): W. Sun and B. Lin This letter shows that the extent of the Hadley cell could reliably be estimated by measuring the height of the uppermost super-thin clouds in the troposphere with space-borne lidar. Through consecutive multi-year measurements of the height of the uppermost super-thin clouds, a good estimation of the expansion of the Hadley cell could be obtained.

Description: Looking for evidence of climate change impacts in the eastern Irish Sea Natural Hazards and Earth System Science, 11, 1641-1656, 2011 Author(s): L. S. Esteves, J. J. Williams, and J. M. Brown Although storminess is often cited as a driver of long-term coastal erosion, a lack of suitable datasets has only allowed objective assessment of this claim in a handful of case studies. This reduces our ability to understand and predict how the coastline may respond to an increase in "storminess" as suggested by global and regional climate models. With focus on 16 km of the Sefton coastline bordering the eastern Irish Sea (UK), this paper analyses available measured datasets of water level, surge level, wave height, wind speed and barometric pressure with the objective of finding trends in metocean climate that are consistent with predictions. The paper then examines rates of change in shoreline position over the period 1894 to 2005 with the aim of establishing relationships with climatic variability using a range of measured and modelled metocean parameters (with time spans varying from two to eight decades). With the exception of the mean monthly wind speed, available metocean data do not indicate any statistically significant changes outside seasonal and decadal cycles. No clear relationship was found between changes in metocean conditions and rates of shoreline change along the Sefton coast. High interannual variability and the lack of long-term measurements make unambiguous correlations between climate change and shoreline evolution problematic. However, comparison between the North Atlantic Oscillation winter index (NAOw) and coastline changes suggest increased erosion at times of decreasing NAOw values and reduced erosion at times of increasing NAOw values. Erosion tends to be more pronounced when decreasing NAOw values lead to a strong negative NAO phase. At present, anthropogenic changes in the local sediment budget and the short-term impact of extreme events are still the largest threat likely to affect coastal flooding and erosion risk in the short- and medium-term. Nevertheless, the potential impacts of climate change in the long-term should not be ignored.

Description: Calculating the water and heat balances of the Eastern Mediterranean basin using ocean modelling and available meteorological, hydrological, and ocean data Ocean Science Discussions, 8, 1301-1338, 2011 Author(s): M. Shaltout and A. Omstedt This paper analyses the Eastern Mediterranean water and heat balances over a 52-yr period. The modelling uses a process-oriented approach resolving the one-dimensional equations of momentum, heat, and salt conservation, with turbulence modelled using a two-equation model. The exchange through the Sicily Channel connecting the Eastern and Western basins is calculated from satellite altimeter data. The results illustrates that calculated surface temperature and salinity follow the reanalysed data well and with biases of −0.4 °C and −0.004, respectively. Monthly and yearly temperature and salinity cycles are also satisfactory simulated. Reanalysed data and calculated water mass structure and heat balance components are in good agreement, indicating that the air-sea interaction and the turbulent mixing are realistically simulated. The study illustrates that the water balance in the Eastern Mediterranean basin is controlled by the difference between inflows/outflows through the Sicily Channel and by the net precipitation rates. The heat balance is controlled by the heat loss from the water surface, sun radiation into the sea, and heat flow through the Sicily Channel, the first two displaying both climate trends. An annual net heat loss of approximately 9 W m −2 was balanced by net heat in flow through the Sicily Channel.

Description: Extraction of spatial-temporal rules from mesoscale eddies in the South China Sea Based on rough set theory Ocean Science Discussions, 8, 1261-1300, 2011 Author(s): Y. Du, X. Fan, Z. He, F. Su, C. Zhou, H. Mao, and D. Wang In this paper, a rough set theory is introduced to represent spatial-temporal relationships and extract the corresponding rules from typical mesoscale-eddy states in the South China Sea (SCS). Three decision attributes are adopted in this study, which make the approach flexible in retrieving spatial-temporal rules with different features. Spatial-temporal rules of typical states in the SCS are extracted as three decision attributes, which then are confirmed by the previous works. The results demonstrate that this approach is effective in extracting spatial-temporal rules from typical mesoscale-eddy states, and therefore provides a powerful approach to forecasts in the future. Spatial-temporal rules in the SCS indicate that warm eddies following the rules are generally in the southeastern and central SCS around 2000 m isobaths in winter. Their intensity and vorticity are weaker than those of cold eddies. They usually move a shorter distance. By contrast, cold eddies are in 2000 m-deeper regions of the southwestern and northeastern SCS in spring and fall. Their intensity and vorticity are strong. Usually they move a long distance. In winter, a few rules are followed by cold eddies in the northern tip of the basin and southwest of Taiwan Island rather than warm eddies, indicating cold eddies may be well-regulated in the region. Several warm-eddy rules are achieved west of Luzon Island, indicating warm eddies may be well-regulated in the region as well. Otherwise, warm and cold eddies are distributed not only in the jet flow off southern Vietnam induced by intraseasonal wind stress in summer-fall, but also in the northern shallow water, which should be a focus of future study.

Description: Comparing historical-hydrogeomorphological reconstitution and hydrological-hydraulic modelling in the estimation of flood-prone areas – a case study in Central Portugal Natural Hazards and Earth System Science, 11, 1669-1681, 2011 Author(s): P. P. Santos, A. O. Tavares, and A. I. A. S. S. Andrade The Arunca River basin in Central Portugal has a historical record of hazardous events related to floods, causing widespread disturbance. This article describes the application of two approaches based on well-known methods for the estimation of flood-prone areas: (i) historical-hydrogeomorphological reconstitution, applied to the entire Arunca River basin, and (ii) hydrological-hydraulic modelling, applied to four sections selected from different (upper, middle and lower) sectors of the basin and including urban and rural areas along the Arunca River. The mapping of the flood-prone areas obtained by these two methods was compared in order to identify the main differences and similarities. Human interventions (river channel and floodplain morphological changes) were found to be the main factor explaining the differences and similarities between the results obtained by both methods. The application of hydrological-hydraulic modelling proved important in reinforcing the results of the historical-hydrogeomorphological method; it also helped in complementing the results produced by the latter method in urban areas and in areas with insufficient historical records. The application of the historical-hydrogeomorphological method, in turn, allowed for the size of the flood-prone areas to be determined where the primary data (e.g. geometry, roughness and flow) was not accurate enough for hydrological-hydraulic modelling. The methodological approach adopted demonstrates the strong complementary relationship between the different existing methods for estimating flood-prone areas, and may be reproduced for other drainage basins.

Description: On the influence of CMEs on the global 3-D coronal electron density Annales Geophysicae, 29, 1019-1028, 2011 Author(s): M. Kramar, J. Davila, H. Xie, and S. Antiochos In order to analize the influence of a Coronal Mass Ejection (CME) on the coronal streamer belt, we made 3-D reconstructions of the electron density in the corona at heliospheric distances from 1.5 to 4 R ⊙ for periods before and after a CME occured. The reconstructions were performed using a tomography technique. We studied two CME cases: (i) a slow CME on 1 June 2008; (ii) two fast CMEs on 31 December 2007 and 2 January 2008. For the first case of slow CME, it was found: (i) the potential magnetic field configuration in the CME initiation region before the CME does not agree with the coronal density structure while after the CME the agreement between the field and density is much better. This could be manifistation of that that the field was non-potential before the CME and after the CME the field relaxes towards a more potential state. (ii) It was shown that the dimming caused by the slow CME is not due to rotation of the corona and a line-of-sight (LOS) effect but a streamer blow out effect took place.

Description: Seasonal variations and vertical features of aerosol particles in the Antarctic troposphere Atmospheric Chemistry and Physics, 11, 5471-5484, 2011 Author(s): K. Hara, K. Osada, C. Nishita-Hara, and T. Yamanouchi Tethered balloon-borne aerosol measurements were conducted at Syowa Station, Antarctica during the 46th Japanese Antarctic expedition (2005–2006). The CN concentration reached a maximum in the summer, although the number concentrations of fine particles ( D p 〉0.3 μm) and coarse particles ( D p 〉2.0 μm) increased during the winter–spring. The CN concentration was 30–2200 cm −3 near the surface (surface – 500 m) and 7–7250 cm −3 in the lower free troposphere (〉1500 m). During the austral summer, higher CN concentration was often observed in the lower free troposphere, where the number concentrations in fine and coarse modes were remarkably lower. The frequent appearance of higher CN concentrations in the free troposphere relative to continuous aerosol measurements at the ground strongly suggests that new particle formation is more likely to occur in the lower free troposphere in Antarctic regions. Seasonal variations of size distribution of fine-coarse particles show that the contribution of the coarse mode was greater in the winter–spring than in summer because of the dominance of sea-salt particles in the winter–spring. The number concentrations of fine and coarse particles were high in air masses from the ocean and mid-latitudes. Particularly, aerosol enhancement was observed not only in the boundary layer, but also in the lower free troposphere during and immediately after Antarctic haze events occurring in May, July and September.

Description: The fluorescence properties of aerosol larger than 0.8 μm in urban and tropical rainforest locations Atmospheric Chemistry and Physics, 11, 5491-5504, 2011 Author(s): A. M. Gabey, W. R. Stanley, M. W. Gallagher, and P. H. Kaye UV-LIF measurements were performed on ambient aerosol in Manchester, UK (urban city centre, winter) and Borneo, Malaysia (remote, tropical) using a Wide Issue Bioaerosol Spectrometer, version 3 (WIBS3). These sites are taken to represent environments with minor and significant primary biological aerosol (PBA) influences respectively, and the urban dataset describes the fluorescent background aerosol against which PBA must be identified by researchers using LIF. The ensemble aerosol at both sites was characterised over 2–3 weeks by measuring the fluorescence intensity and optical equivalent diameter ( D P ) of single particles sized 0.8 ≤ D P ≤ 20 μm. Filter samples were also collected for a subset of the Manchester campaign and analysed using energy dispersive X-Ray (EDX) spectroscopy and environmental scanning electron microscopy (ESEM), which revealed mostly non-PBA at D ≤ 1 μm. The WIBS3 features three fluorescence channels: the emission following a 280 nm excitation is recorded at 310–400 nm (channel F1) and 400–600 nm (F2), and fluorescence excited at 350 nm is detected at 400–600 nm (F3). In Manchester the primary size mode of fluorescent and non-fluorescent material was present at 0.8–1.2 μm, with a secondary fluorescent mode at 2–4 μm. In Borneo non-fluorescent material peaked at 0.8–1.2 μm and fluorescent at 3–4 μm. Agreement between fluorescent number concentrations in each channel differed at the two sites, with F1 and F3 reporting similar concentrations in Borneo but F3 outnumbering F1 by a factor of 2–3 across the size spectrum in Manchester. The fluorescence intensity in each channel generally rose with D P at both sites with the exception of F1 intensity in Manchester, which peaked at D P = 4 μm, causing a divergence between F1 and F3 intensity at larger D P . This divergence and the differing fluorescent particle concentrations demonstrate the additional discrimination provided by the F1 channel in Manchester. The relationships between fluorescence intensities in different pairs of channels were also investigated as a function of D P . Differences between these metrics were apparent at each site and provide some distinction between the two datasets. Finally, particle selection criteria based on the Borneo dataset were applied to identify a median concentration of 10 "Borneo-like" fluorescent particles per litre in Manchester.

Description: Domestic wells have high probability of pumping septic tank leachate Hydrology and Earth System Sciences Discussions, 8, 5701-5732, 2011 Author(s): J. E. Horn and T. Harter Onsite wastewater treatment systems such as septic systems are common in rural and semi-rural areas around the world; in the US, about 25–30 % of households are served by a septic system and a private drinking water well. Site-specific conditions and local groundwater flow are often ignored when installing septic systems and wells. Particularly in areas with small lots, thus a high septic system density, these typically shallow wells are prone to contamination by septic system leachate. Typically, mass balance approaches are used to determine a maximum septic system density that would prevent contamination of the aquifer. In this study, we estimate the probability of a well pumping partially septic system leachate. A detailed groundwater and transport model is used to calculate the capture zone of a typical drinking water well. A spatial probability analysis is performed to assess the probability that a capture zone overlaps with a septic system drainfield depending on aquifer properties, lot and drainfield size. We show that a high septic system density poses a high probability of pumping septic system leachate. The hydraulic conductivity of the aquifer has a strong influence on the intersection probability. We conclude that mass balances calculations applied on a regional scale underestimate the contamination risk of individual drinking water wells by septic systems. This is particularly relevant for contaminants released at high concentrations, for substances which experience limited attenuation, and those being harmful even in low concentrations.

Description: Tropopause height at 78° N 16° E: average seasonal variation 2007–2010 Atmospheric Chemistry and Physics, 11, 5485-5490, 2011 Author(s): C. M. Hall, G. Hansen, F. Sigernes, and K. M. Kuyeng Ruiz We present a seasonal climatology of tropopause altitude for 78° N 16° E derived from observations 2007–2010 by the SOUSY VHF radar on Svalbard. The spring minimum occurs one month later than that of surface air temperature and instead coincides with the maximum in ozone column density. This confirms similar studies based on radiosonde measurements in the arctic and demonstrates downward control by the stratosphere. If one is to exploit the potential of tropopause height as a metric for climate change at high latitude and elsewhere, it is imperative to observe and understand the processes which establish the tropopause – an understanding to which this study contributes.

Description: Radio occultation bending angle anomalies during tropical cyclones Atmospheric Measurement Techniques, 4, 1053-1060, 2011 Author(s): R. Biondi, T. Neubert, S. Syndergaard, and J. K. Nielsen The tropical deep convection affects the radiation balance of the atmosphere changing the water vapor mixing ratio and the temperature of the upper troposphere lower stratosphere. The aim of this work is to better understand these processes and to investigate if severe storms leave a significant signature in radio occultation profiles in the tropical tropopause layer. Using tropical cyclone best track database and data from different GPS radio occultation missions (COSMIC, GRACE, CHAMP, SACC and GPSMET), we selected 1194 profiles in a time window of 3 h and a space window of 300 km from the eye of the cyclone. We show that the bending angle anomaly of a GPS radio occultation signal is typically larger than the climatology in the upper troposphere and lower stratosphere and that a double tropopause during deep convection can easily be detected using this technique. Comparisons with co-located radiosondes, climatology of tropopause altitudes and GOES analyses are also shown to support the hypothesis that the bending angle anomaly can be used as an indicator of convective towers. The results are discussed in connection to the GPS radio occultation receiver which will be part of the Atomic Clock Ensemble in Space (ACES) payload on the International Space Station.

Description: An algorithm for detecting Trichodesmium surface blooms in the South Western Tropical Pacific Biogeosciences Discussions, 8, 5653-5689, 2011 Author(s): C. Dupouy, D. Benielli-Gary, J. Neveux, Y. Dandonneau, and T. K. Westberry Trichodesmium , a major colonial cyanobacterial nitrogen fixer, forms large blooms in NO 3 -depleted tropical oceans and enhances CO 2 sequestration by the ocean due to its ability to fix dissolved dinitrogen. Thus, its importance in C and N cycles requires better estimates of its distribution at basin to global scales. However, existing algorithms to detect them from satellite have not yet been successful in the South Western Tropical Pacific (SWTP). Here, a novel approach based on radiance anomaly spectra (RAS) observed in SeaWiFS imagery is used to detect Trichodesmium during the austral summertime in the SWTP. Selected pixels are characterized by a restricted range of parameters quantifying RAS spectra quantitative parameters (e.g. slope, intercept, curvature). The fraction of valid pixels identified as Trichodesmium surface blooms in the region 5° S–25° S 160° E–190° E is low (between 0.01 and 0.2 %), but is about 100 times higher than suggested by previous algorithms. This represents a total surface area which varies from 1500 to 20 000 km 2 . A monthly distribution of Trichodesmium surface accumulations in the SWTP is presented which demonstrates that the number of selected pixels peaks in November–February each year, consistent with field observations. This approach was validated with in situ observations of Trichodesmium surface accumulations for the period 1998–2010.

Description: CARIBIC aircraft measurements of Eyjafjallajökull volcanic plumes in April/May 2010 Atmospheric Chemistry and Physics Discussions, 11, 16693-16744, 2011 Author(s): A. Rauthe-Schöch, A. Weigelt, M. Hermann, B. G. Martinsson, A. K. Baker, K.-P. Heue, C. A. M. Brenninkmeijer, A. Zahn, D. Scharffe, S. Eckhardt, A. Stohl, and P. F. J. van Velthoven The Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container (CARIBIC) project investigates physical and chemical processes in the Earth's atmosphere using a Lufthansa Airbus long-distance passenger aircraft. After the beginning of the explosive eruption of the Eyjafjallajökull volcano on Iceland on 14 April 2010, the first CARIBIC volcano-specific measurement flight was carried out over the Baltic Sea and Southern Sweden on 20 April. Two more flights followed: one over Ireland and the Irish Sea on 16 May and the other over the Norwegian Sea on 19 May 2010. During these three special mission flights the CARIBIC container proved its merits as a versatile and comprehensive flying laboratory. The elemental composition of particles collected over the Baltic Sea during the first flight (20 April) indicated the presence of volcanic ash. Over Northern Ireland and the Irish Sea (16 May), the DOAS system detected SO 2 and BrO co-located with volcanic ash particles that increased the aerosol optical depth. Over the Norwegian Sea (19 May), the optical particle counter detected a strong increase of particles larger than 400 nm diameter in a region where ash clouds were predicted by aerosol dispersion models. Aerosol particle samples collected over the Irish Sea and the Norwegian Sea showed large relative enhancements of the elements silicon, iron, titanium and calcium. Non-methane hydrocarbon concentrations in whole air samples collected on 16 May and 19 May 2010 showed a pattern of removal of several hydrocarbons that is typical for chlorine chemistry in the plumes. Comparisons of measured ash concentrations and simulations with the FLEXPART dispersion model demonstrate the difficulty of detailed volcanic ash dispersion modelling due to the large variability of the volcanic plume sources, extent and patchiness as well as the thin ash layers formed in the volcanic plumes.

Description: Corrigendum to "Breeding and predictability in the baroclinic rotating annulus using a perfect model" published in Nonlin. Processes Geophys., 15, 469–487, 2008 Nonlinear Processes in Geophysics, 18, 359-359, 2011 Author(s): R. M. B. Young and P. L. Read No abstract available.

Description: Validation of cloud property retrievals with simulated satellite radiances: a case study for SEVIRI Atmospheric Chemistry and Physics, 11, 5603-5624, 2011 Author(s): L. Bugliaro, T. Zinner, C. Keil, B. Mayer, R. Hollmann, M. Reuter, and W. Thomas Validation of cloud properties retrieved from passive spaceborne imagers is essential for cloud and climate applications but complicated due to the large differences in scale and observation geometry between the satellite footprint and the independent ground based or airborne observations. Here we illustrate and demonstrate an alternative approach: starting from the output of the COSMO-EU weather model of the German Weather Service realistic three-dimensional cloud structures at a spatial scale of 2.33 km are produced by statistical downscaling and microphysical properties are associated to them. The resulting data sets are used as input to the one-dimensional radiative transfer model libRadtran to simulate radiance observations for all eleven low resolution channels of MET-8/SEVIRI. At this point, both cloud properties and satellite radiances are known such that cloud property retrieval results can be tested and tuned against the objective input "truth". As an example, we validate a cloud property retrieval of the Institute of Atmospheric Physics of DLR and that of EUMETSAT's Climate Monitoring Science Application Facility CMSAF. Cloud detection and cloud phase assignment perform well. By both retrievals 88% of the pixels are correctly classified as clear or cloudy. The DLR algorithm assigns the correct thermodynamic phase to 95% of the cloudy pixels and the CMSAF retrieval to 84%. Cloud top temperature is slightly overestimated by the DLR code (+3.1 K mean difference with a standard deviation of 10.6 K) and to a very low extent by the CMSAF code (−0.12 K with a standard deviation of 7.6 K). Both retrievals account reasonably well for the distribution of optical thickness for both water and ice clouds, with a tendency to underestimation. Cloud effective radii are most difficult to evaluate but the APICS algorithm shows that realistic histograms of occurrences can be derived (CMSAF was not evaluated in this context). Cloud water path, which is a combination of the last two quantities, is slightly underestimated by APICS, while CMSAF shows a larger scattering.

Description: Assimilation of GPS radio occultation data at DWD Atmospheric Measurement Techniques, 4, 1105-1113, 2011 Author(s): H. Anlauf, D. Pingel, and A. Rhodin We describe the status of the assimilation of bending angles from GPS radio occultations in the 3D-Var for DWD's operational global forecast model GME ("Global Model for Europe"). Experiments show that the assimilation of GPSRO data leads to a significant reduction of biases in the analyses of temperature, humidity and wind in the upper troposphere and the stratosphere, as well as a better r. m. s. fit in the comparison to radiosondes. The impact on forecasts is most prominent in the data sparse Southern Hemisphere, but is also quite notable in the Northern Hemisphere extra-tropics. The positive results found in the impact experiments lead to the implementation of the assimilation of GPS radio occultations from GRACE-A, FORMOSAT-3/COSMIC and GRAS/MetOp-A into the operational suite on 3 August 2010. We also show some initial results from assimilation experiments using radio occultation data from the German research satellite TerraSAR-X.

Description: Longitudinal study of the ionospheric response to the geomagnetic storm of 15 May 2005 and manifestation of TADs Annales Geophysicae, 29, 1063-1070, 2011 Author(s): S. Sharma, P. Galav, N. Dashora, and R. Pandey Response of low latitude ionosphere to the geomagnetic storm of 15 May 2005 has been studied using total electron content (TEC) data, obtained from three GPS stations namely, Yibal, Udaipur and Kunming situated near the northern crest of equatorial ionization anomaly at different longitudes. Solar wind parameters, north-south component of the interplanetary magnetic field (IMF B z ) and AE index data have been used to infer the strength of the geomagnetic storm. A large value of eastward interplanetary electric field at 06:15 UT, during the time of maximum southward IMF B z has been used to infer the transmission of an eastward prompt penetration electric field (PPEF) which resulted in a peak in TEC at 07:45 UT due to the local uplift of plasma in the low latitudes near the anomaly crest over a wide range of longitudes. Wave-like modulations superposed over the second enhancement in TEC between 09:15 UT to 10:30 UT have been observed at all the three stations. The second enhancement in TEC along with the modulations of up to 5 TECU have been attributed to the combined effect of super plasma fountain and traveling atmospheric disturbances (TAD). Observed large enhancements in TEC are a cause of concern for satellite based navigation and ground positioning. Increased [O/N 2 ] ratio between 09:15 UT to 10:15 UT when modulations in TEC have been also observed, confirms the presence of TADs over a wide range of longitudes.

Description: The contribution of engineering surveys by means of GPS to the determination of crustal movements in Istanbul Natural Hazards and Earth System Science, 11, 1705-1713, 2011 Author(s): M. Özyaşar and M. T. Özlüdemir Global Navigation Satellite Systems (GNSS) are space based positioning techniques and widely used in geodetic applications. Geodetic networking accomplished by engineering surveys constitutes one of these tasks. Geodetic networks are used as the base of all kinds of geodetic implementations, Co from the cadastral plans to the relevant surveying processes during the realization of engineering applications. Geodetic networks consist of control points positioned in a defined reference frame. In fact, such positional information could be useful for other studies as well. One of such fields is geodynamic studies that use the changes of positions of control stations within a network in a certain time period to understand the characteristics of tectonic movements. In Turkey, which is located in tectonically active zones and struck by major earthquakes quite frequently, the positional information obtained in engineering surveys could be very useful for earthquake related studies. For this purpose, a GPS (Global Positioning System) network of 650 stations distributed over Istanbul (Istanbul GPS Triangulation Network; abbreviated IGNA) covering the northern part of the North Anatolian Fault Zone (NAFZ) was established in 1997 and measured in 1999. From 1998 to 2004, the IGNA network was extended to 1888 stations covering an area of about 6000 km 2 , the whole administration area of Istanbul. All 1888 stations within the IGNA network were remeasured in 2005. In these two campaigns there existed 452 common points, and between these two campaigns two major earthquakes took place, on 17 August and 12 November 1999 with a Richter scale magnitude of 7.4 and 7.2, respectively. Several studies conducted for estimating the horizontal and vertical displacements as a result of these earthquakes on NAFZ are discussed in this paper. In geodynamic projects carried out before the earthquakes in 1999, an annual average velocity of 2–2.5 cm for the stations along the NAFZ were estimated. Studies carried out using GPS observations in the same area after these earthquakes indicated that point displacements vary depending on their distance to the epicentres of the earthquakes. But the directions of point displacements are similar. The results obtained through the analysis of the IGNA network also show that there is a common trend in the directions of point displacements in the study area. In this paper, the past studies about the tectonics of Marmara region are summarised and the results of the displacement analysis on the IGNA network are discussed.

Description: Origin and fate of the secondary nitrite maximum in the Arabian Sea Biogeosciences, 8, 1565-1577, 2011 Author(s): P. Lam, M. M. Jensen, A. Kock, K. A. Lettmann, Y. Plancherel, G. Lavik, H. W. Bange, and M. M. M. Kuypers The Arabian Sea harbours one of the three major oxygen minimum zones (OMZs) in the world's oceans, and it alone is estimated to account for ~10–20 % of global oceanic nitrogen (N) loss. While actual rate measurements have been few, the consistently high accumulation of nitrite (NO 2 − ) coinciding with suboxic conditions in the central-northeastern part of the Arabian Sea has led to the general belief that this is the region where active N-loss takes place. Most subsequent field studies on N-loss have thus been drawn almost exclusively to the central-NE. However, a recent study measured only low to undetectable N-loss activities in this region, compared to orders of magnitude higher rates measured towards the Omani Shelf where little NO 2 − accumulated (Jensen et al., 2011). In this paper, we further explore this discrepancy by comparing the NO 2 − -producing and consuming processes, and examining the relationship between the overall NO 2 − balance and active N-loss in the Arabian Sea. Based on a combination of 15 N-incubation experiments, functional gene expression analyses, nutrient profiling and flux modeling, our results showed that NO 2 − accumulated in the central-NE Arabian Sea due to a net production via primarily active nitrate (NO 3 − ) reduction and to a certain extent ammonia oxidation. Meanwhile, NO 2 − consumption via anammox, denitrification and dissimilatory nitrate/nitrite reduction to ammonium (NH 4 + ) were hardly detectable in this region, though some loss to NO 2 − oxidation was predicted from modeled NO 3 − changes. No significant correlation was found between NO 2 − and N-loss rates ( p 〉0.05). This discrepancy between NO 2 − accumulation and lack of active N-loss in the central-NE Arabian Sea is best explained by the deficiency of labile organic matter that is directly needed for further NO 2 − reduction to N 2 O, N 2 and NH 4 + , and indirectly for the remineralized NH 4 + required by anammox. Altogether, our data do not support the long-held view that NO 2 − accumulation is a direct activity indicator of N-loss in the Arabian Sea or other OMZs. Instead, NO 2 − accumulation more likely corresponds to long-term integrated N-loss that has passed the prime of high and/or consistent in situ activities.

Description: Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume Atmospheric Chemistry and Physics Discussions, 11, 17013-17070, 2011 Author(s): J. Lee-Taylor, S. Madronich, B. Aumont, M. Camredon, A. Hodzic, G. S. Tyndall, E. Apel, and R. A. Zaveri The evolution of organic aerosols (OA) in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere), wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3–10 alkanes, alkenes, and light aromatics, as well as larger n -alkanes (up to C25) not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO). The model successfully reproduces the magnitude and diurnal shape for both primary (POA) and secondary (SOA) organic aerosols, with POA peaking in the early morning at 15–20 μg m −3 , and SOA peaking at 10–15 μg m −3 during mid-day. The majority (≥75 %) of the model SOA stems from the large n -alkanes, with the remainder mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by δ-hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NO x is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of 〉3. These results suggest significant regional radiative impacts of SOA.

Description: Variability and budget of CO 2 in Europe: analysis of the CAATER airborne campaigns – Part 1: Observed variability Atmospheric Chemistry and Physics, 11, 5655-5672, 2011 Author(s): I. Xueref-Remy, C. Messager, D. Filippi, M. Pastel, P. Nedelec, M. Ramonet, J. D. Paris, and P. Ciais Atmospheric airborne measurements of CO 2 are very well suited for estimating the time-varying distribution of carbon sources and sinks at the regional scale due to the large geographical area covered over a short time. We present here an analysis of two cross-European airborne campaigns carried out on 23–26 May 2001 (CAATER-1) and 2–3 October 2002 (CAATER-2) over Western Europe. The area covered during CAATER-1 and CAATER-2 was 4° W to 14° E long; 44° N to 52° N lat and 1° E to 17° E long; 46° N to 52° N lat respectively. High precision in situ CO 2 , CO and Radon 222 measurements were recorded. Flask samples were collected during both campaigns to cross-validate the in situ data. During CAATER-1 and CAATER-2, the mean CO 2 concentration was 370.1 ± 4.0 (1-σ standard deviation) ppm and 371.7 ± 5.0 (1-σ) ppm respectively. A HYSPLIT back-trajectories analysis shows that during CAATER 1, northwesterly winds prevailed. In the planetary boundary layer (PBL) air masses became contaminated over Benelux and Western Germany by emissions from these highly urbanized areas, reaching about 380 ppm. Air masses passing over rural areas were depleted in CO 2 because of the photosynthesis activity of the vegetation, with observations as low as 355 ppm. During CAATER-2, the back-trajectory analysis showed that air masses were distributed among the 4 sectors. Air masses were enriched in CO 2 and CO over anthropogenic emission spots in Germany but also in Poland, as these countries have part of the most CO 2 -emitting coal-based plants in Europe. Simultaneous measurements of in situ CO 2 and CO combined with back-trajectories helped us to distinguish between fossil fuel emissions and other CO 2 sources. The ΔCO/ΔCO 2 ratios ( R 2 = 0.33 to 0.88, slopes = 2.42 to 10.37), calculated for anthropogenic-influenced air masses over different countries/regions matched national inventories quite well, showing that airborne measurements can help to identify the origin of fossil fuel emissions in the PBL even when distanced by several days/hundreds of kms from their sources. We have compared airborne CO 2 observations to nearby ground station measurements and thereby, confirmed that measurements taken in the lower few meters of the PBL (low-level ground stations) are representative of the local scale, while those located in the free troposphere (FT) (moutain stations) are representative of atmospheric CO 2 regionally on a scale of a few hundred kilometers. Stations located several 100 km away from each other differ from a few ppm in their measurements indicating the existence of a gradient within the free troposphere. Observations at stations located on top of small mountains may match the airborne data if the sampled air comes from the FT rather than coming up from the valley. Finally, the analysis of the CO 2 vertical variability conducted on the 14 profiles recorded in each campaign shows a variability at least 5 to 8 times higher in the PBL (the 1-σ standard deviation associated to the CO 2 mean of all profiles within the PBL is 4.0 ppm and 5.7 ppm for CAATER-1 and CAATER-2, respectively) than in the FT (within the FT, 1-σ is 0.5 ppm and 1.1 ppm for CAATER-1 and CAATER-2, respectively). The CO 2 jump between the PBL and the FT equals 3.7 ppm for the first campaign and −0.3 ppm for the second campaign. A very striking zonal CO 2 gradient of about 11 ppm was observed in the mid-PBL during CAATER-2, with higher concentrations in the west than in the east. This gradient may originate from differences in atmospheric mixing, ground emission rates or Autumn's earlier start in the west. More airborne campaigns are currently under analysis in the framework of the CARBOEUROPE-IP project to better assess the likelihood of these different hypotheses. In a companion paper (Xueref-Remy et al., 2011, Part 2), a comparison of vertical profiles from observations and several modeling frameworks was conducted for both campaigns.

Description: Variability and budget of CO 2 in Europe: analysis of the CAATER airborne campaigns – Part 2: Comparison of CO 2 vertical variability and fluxes between observations and a modeling framework Atmospheric Chemistry and Physics, 11, 5673-5684, 2011 Author(s): I. Xueref-Remy, P. Bousquet, C. Carouge, L. Rivier, and P. Ciais Our ability to predict future climate change relies on our understanding of current and future CO 2 fluxes, particularly on a regional scale (100–1000 km). CO 2 regional sources and sinks are still poorly understood. Inverse transport modeling, a method often used to quantify these fluxes, relies on atmospheric CO 2 measurements. One of the main challenges for the transport models used in the inversions is to properly reproduce CO 2 vertical gradients between the boundary layer and the free troposphere, as these gradients impact on the partitioning of the calculated fluxes between the different model regions. Vertical CO 2 profiles are very well suited to assess the performances of the models. In this paper, we conduct a comparison between observed and modeled CO 2 profiles recorded during two CAATER campaigns that occurred in May 2001 and October 2002 over Western Europe, as described in a companion paper. We test different combinations between a global transport model (LMDZt), a mesoscale transport model (CHIMERE), and different sets of biospheric fluxes, all chosen with a diurnal cycle (CASA, SiB2 and ORCHIDEE). The vertical profile comparison shows that: 1) in most cases the influence of the biospheric flux is small but sometimes not negligible, ORCHIDEE giving the best results in the present study; 2) LMDZt is most of the time too diffuse, as it simulates a too high boundary layer height; 3) CHIMERE better reproduces the observed gradients between the boundary layer and the free troposphere, but is sometimes too variable and gives rise to incoherent structures. We conclude there is a need for more vertical profiles to conduct further studies to improve the parameterization of vertical transport in the models used for CO 2 flux inversions. Furthermore, we use a modeling method to quantify CO 2 fluxes at the regional scale from a chosen observing point, coupling influence functions from the transport model LMDZt (that works quite well at the synoptic scale) with information on the space-time distribution of fluxes. This modeling method is compared to a dual tracer method (the so-called Radon method) for a case study on 25 May 2001 during which simultaneous well-correlated in situ CO 2 and Radon 222 measurements have been collected. Both methods give a similar result: a flux within the Radon 222 method uncertainty (35%), that is an atmospheric CO 2 sink of −4.2 to −4.4 gC m −2 day −1 . We have estimated the uncertainty of the modeling method to be at least 33% on average, and even more for specific individual events. This method allows the determination of the area that contributed to the CO 2 observed concentration. In our case, the observation point located at 1700 m a.s.l. in the north of France, is influenced by an area of 1500×700 km 2 that covers the Benelux region, part of Germany and western Poland. Furthermore, this method allows deconvolution between the different contributing fluxes. In this case study, the biospheric sink contributes 73% of the total flux, fossil fuel emissions for 27%, the oceanic flux being negligible. However, the uncertainties of the influence function method need to be better assessed. This could be possible by applying it to other cases where the calculated fluxes can be checked independently, for example at tall towers where simultaneous CO 2 and Radon 222 measurements can be conducted. The use of optimized fluxes (from atmospheric inversions) and of mesoscale models for atmospheric transport may also significantly reduce the uncertainties.

Description: Nudging technique for scale bridging in air quality/climate atmospheric composition modelling Atmospheric Chemistry and Physics Discussions, 11, 17177-17199, 2011 Author(s): A. Maurizi, F. Russo, M. D'Isidoro, and F. Tampieri The interaction between air quality and climate involves dynamical scales that cover an immensely wide range. Bridging these scales in numerical simulations is fundamental in studies devoted to megacity/hot-spot impacts on climate. The nudging technique is proposed as a bridging method that can couple different models at different scales. Here, nudging is used to force low resolution chemical composition models using a high resolution run on critical areas. A one-year numerical experiment focused on the Po Valley hot spot is performed using the BOLCHEM model to asses the method. The results show that the model response is stable to perturbation induced by the nudging and that, if a high resolution run is taken as a reference, there is an increase in model skills of low resolution run when the technique is applied. This improvement depends on the species and the season. The effect spreads outside the forcing area and remains noticeable over an extension about 9 times larger.

Description: Better constraints on sources of carbonaceous aerosols using a combined 14 C – macro tracer analysis in a European rural background site Atmospheric Chemistry and Physics, 11, 5685-5700, 2011 Author(s): S. Gilardoni, E. Vignati, F. Cavalli, J. P. Putaud, B. R. Larsen, M. Karl, K. Stenström, J. Genberg, S. Henne, and F. Dentener The source contributions to carbonaceous PM 2.5 aerosol were investigated at a European background site at the edge of the Po Valley, in Northern Italy, during the period January–December 2007. Carbonaceous aerosol was described as the sum of 8 source components: primary (1) and secondary (2) biomass burning organic carbon, biomass burning elemental carbon (3), primary (4) and secondary (5) fossil organic carbon, fossil fuel burning elemental carbon (6), primary (7) and secondary (8) biogenic organic carbon. The mass concentration of each component was quantified using a set of macro tracers (organic carbon OC, elemental carbon EC, and levoglucosan), micro tracers (arabitol and mannitol), and 14 C measurements. This was the first time that 14 C measurements covered a full annual cycle with daily resolution. This set of 6 tracers, together with assumed uncertainty ranges of the ratios of OC-to-EC, and the reference fraction of modern carbon in the 8 source categories, provides strong constraints to the source contributions to carbonaceous aerosol. The uncertainty of contributions was assessed with a Quasi-Monte Carlo (QMC) method accounting for the variability of OC and EC emission factors, the uncertainty of reference fractions of modern carbon, and the measurement uncertainty. During winter, biomass burning composed 64 % (±15 %) of the total carbon (TC) concentration, while in summer secondary biogenic OC accounted for 50 % (±16 %) of TC. The contribution of primary biogenic aerosol particles was negligible during the entire year. Moreover, aerosol associated with fossil sources represented 27 % (±16 %) and 41 % (±26 %) of TC in winter and summer, respectively. The contribution of secondary organic aerosol (SOA) to the organic mass (OM) was significant during the entire year. SOA accounted for 30 % (±16 %) and 85 % (±12 %) of OM during winter and summer, respectively. While the summer SOA was dominated by biogenic sources, winter SOA was mainly due to biomass burning and fossil sources. This indicates that the oxidation of semi-volatile and intermediate volatility organic compounds co-emitted with primary organics is a significant source of SOA, as suggested by recent model results and Aerosol Mass Spectrometer measurements. Comparison with previous global model simulations, indicates a strong underestimate of wintertime primary aerosol emissions in this region. The comparison of source apportionment results in different urban and rural areas showed that the sampling site was mainly affected by local aerosol sources during winter and regional air masses from the nearby Po Valley in summer. This observation was further confirmed by back-trajectory analysis applying the Potential Source Contribution Function method to identify potential source regions.

Description: Use of ENVISAT ASAR Global Monitoring Mode to complement optical data in the mapping of rapid broad-scale flooding in Pakistan Hydrology and Earth System Sciences Discussions, 8, 5769-5809, 2011 Author(s): D. O'Grady, M. Leblanc, and D. Gillieson Envisat ASAR Global Monitoring Mode (GM) data are used to produce maps of the extent of the flooding in Pakistan which are made available to the rapid response effort within 24 h of acquisition. The high temporal frequency and independence of the data from cloud-free skies makes GM data a viable tool for mapping flood waters during those periods where optical satellite data is unavailable, which may be crucial to rapid response disaster planning, where thousands of lives are affected. Image differencing techniques are used, with pre-flood baseline image backscatter values being deducted from target values to eliminate regions with a permanent flood-like radar response due to volume scattering and attenuation, and to highlight the low response caused by specular reflection by open flood water. The effect of local incidence angle on the received signal is mitigated by ensuring that the deducted image is acquired from the same orbit track as the target image. Poor separability of the water class with land in areas beyond the river channels is tackled using a region-growing algorithm which seeks threshold-conformance from seed pixels at the center of the river channels. The resultant mapped extents are tested against MODIS SWIR data where available, with encouraging results.

Description: Soil weathering rates in 21 catchments of the Canadian Shield Hydrology and Earth System Sciences Discussions, 8, 5743-5768, 2011 Author(s): D. Houle, P. Lamoureux, N. Bélanger, M. Bouchard, C. Gagnon, S. Couture, and A. Bouffard Soil mineral weathering represents an essential source of nutrient base cation (Ca, Mg and K) for forest growth in addition to provide a buffering power against precipitation acidity for soils and surface waters. Weathering rates of base cations were obtained for 21 catchments located within the temperate and the boreal forest of the Canadian Shield with the geochemical model PROFILE. Weathering rates ranged from 0.58 to 4.46 kmol c ha −1 yr −1 and their spatial variation within the studied area was mostly in agreement with spatial variations in soil mineralogy. Weathering rates of Ca and Mg were significantly correlated ( r = 0.80 and 0.64) with their respective lake concentrations. Weathering rates of K and Na did not correlate with lake concentrations of K and Na. The modeled weathering rates for each catchment were also compared with estimations of net catchment exportations. The result show that modeled weathering rates of Ca were not significantly different than the net catchment exportations while modeled weathering rates of Mg were higher by 51 %. Larger differences were observed for K and Na weathering rates that were significantly different than net catchment exportations being 6.9 and 2.2 times higher than net exportations, respectively. The results for K were expected given its high reactivity with biotic compartments and suggest that most of the K produced by weathering reactions was retained within soil catchments and/or above ground biomass. This explanation does not apply to Na, however, which is a conservative element in forest ecosystems because of the insignificant needs of Na for soil microorganisms and above ground vegetations. It raises concern about the liability of the PROFILE model to provide reliable values of Na weathering rates. Overall, we concluded that the PROFILE model is powerful enough to reproduce spatial geographical gradients in weathering rates for relatively large areas as well as adequately predict absolute weathering rates values for the sum of base cations, Ca and Mg.

Description: Spatio-temporal variations in soil moisture and physicochemical properties of a typical semiarid sand-meadow-desert landscape as influenced by land use Hydrology and Earth System Sciences, 15, 1865-1877, 2011 Author(s): L. Duan, T. Liu, X. Wang, G. Wang, L. Ma, and Y. Luo A good understanding of the interrelations between land cover alteration and changes in hydrologic conditions (e.g., soil moisture) as well as soil physicochemical properties (e.g., fine soil particles and nutrients) is crucial for maintaining the fragile hydrologic and environmental conditions of semiarid land, such as the Horqin Sandy Land in China, but is lacking in existing literature. The objectives of this study were to examine: (1) spatio-temporal variations of soil moisture and physicochemical properties in semiarid land; and (2) how those variations are influenced by land cover alteration. Using the data collected in a 9.71 km 2 well-instrumented area of the Horqin Sandy Land, this study examined by visual examination and statistical analyses the spatio-temporal variations of soil moisture and physicochemical properties. The results indicated that for the study area, the soil moisture and physicochemical properties were dependent on local topography, soil texture, vegetation density, and human activity. Long-term reclamation for agriculture was found to reduce soil moisture by over 23 % and significantly (p-value 〈 0.05) lower the contents of soil organic matter, fine soil particles, and nutrients.

Description: A new tide model for the Mediterranean Sea based on altimetry and tide gauge assimilation Ocean Science, 7, 429-444, 2011 Author(s): D. N. Arabelos, D. Z. Papazachariou, M. E. Contadakis, and S. D. Spatalas The tides for the Mediterranean Sea are described through a high resolution model (MEDI10) developed by assimilation of tide-gauge data and T/P data into a barotropic ocean tide model. Tidal parameters from 56 coastal tide-gauge stations around the Mediterranean for eight principal constituents: M2, S2, N2, K2, K1, O1, P1 and Q1 and from 20 stations for M2, S2, K1, O1 are included in the model. TOPEX/Poseidon data with all corrections applied except for the ocean tides and bathymetry from TOPO 13.1 were used for development of the model. Numerical experiments were carried out for the estimation of the friction velocity and of the decorrelation length scale. The experiments related to the friction velocity showed that the use of spatially varying friction velocity, estimated as a function of position in the model domain, gives better results than a constant value. The experiments related to the estimation of the decorrelation length suggest that the results are not sensitive for lengths close to ten times the length of the grid cell. The assessment of the model is based on ten tide-gauge observations that are not used for the assimilation. Comparisons were carried out with contemporary published global or regional models. The final solution is computed using 76 selected coastal tide-gauge stations. The comparison between the observed and the model constituents results in a Root Sum of Squares (RSS) equal to 1.3 cm.

Description: Diurnally resolved particulate and VOC measurements at a rural site: indication of significant biogenic secondary organic aerosol formation Atmospheric Chemistry and Physics, 11, 5745-5760, 2011 Author(s): S. J. Sjostedt, J. G. Slowik, J. R. Brook, R. Y.-W. Chang, C. Mihele, C. A. Stroud, A. Vlasenko, and J. P. D. Abbatt We report simultaneous measurements of volatile organic compound (VOC) mixing ratios including C 6 to C 8 aromatics, isoprene, monoterpenes, acetone and organic aerosol mass loadings at a rural location in southwestern Ontario, Canada by Proton-Transfer-Reaction Mass Spectrometry (PTR-MS) and Aerosol Mass Spectrometry (AMS), respectively. During the three-week-long Border Air Quality and Meteorology Study in June–July 2007, air was sampled from a range of sources, including aged air from the polluted US Midwest, direct outflow from Detroit 50 km away, and clean air with higher biogenic input. After normalization to the diurnal profile of CO, a long-lived tracer, diurnal analyses show clear photochemical loss of reactive aromatics and production of oxygenated VOCs and secondary organic aerosol (SOA) during the daytime. Biogenic VOC mixing ratios increase during the daytime in accord with their light- and temperature-dependent sources. Long-lived species, such as hydrocarbon-like organic aerosol and benzene show little to no photochemical reactivity on this timescale. From the normalized diurnal profiles of VOCs, an estimate of OH concentrations during the daytime, measured O 3 concentrations, and laboratory SOA yields, we calculate integrated local organic aerosol production amounts associated with each measured SOA precursor. Under the assumption that biogenic precursors are uniformly distributed across the southwestern Ontario location, we conclude that such precursors contribute significantly to the total amount of SOA formation, even during the period of Detroit outflow. The importance of aromatic precursors is more difficult to assess given that their sources are likely to be localized and thus of variable impact at the sampling location.

Description: An investigation of methods for injecting emissions from boreal wildfires using WRF-Chem during ARCTAS Atmospheric Chemistry and Physics, 11, 5719-5744, 2011 Author(s): W. R. Sessions, H. E. Fuelberg, R. A. Kahn, and D. M. Winker The Weather Research and Forecasting Model (WRF) is considered a "next generation" mesoscale meteorology model. The inclusion of a chemistry module (WRF-Chem) allows transport simulations of chemical and aerosol species such as those observed during NASA's Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) in 2008. The ARCTAS summer deployment phase during June and July coincided with large boreal wildfires in Saskatchewan and Eastern Russia. One of the most important aspects of simulating wildfire plume transport is the height at which emissions are injected. WRF-Chem contains an integrated one-dimensional plume rise model to determine the appropriate injection layer. The plume rise model accounts for thermal buoyancy associated with fires and local atmospheric stability. This paper describes a case study of a 10 day period during the Spring phase of ARCTAS. It compares results from the plume model against those of two more traditional injection methods: Injecting within the planetary boundary layer, and in a layer 3–5 km above ground level. Fire locations are satellite derived from the GOES Wildfire Automated Biomass Burning Algorithm (WF_ABBA) and the MODIS thermal hotspot detection. Two methods for preprocessing these fire data are compared: The prep_chem_sources method included with WRF-Chem, and the Naval Research Laboratory's Fire Locating and Monitoring of Burning Emissions (FLAMBE). Results from the simulations are compared with satellite-derived products from the AIRS, MISR and CALIOP sensors. When FLAMBE provides input to the 1-D plume rise model, the resulting injection heights exhibit the best agreement with satellite-observed injection heights. The FLAMBE-derived heights are more realistic than those utilizing prep_chem_sources. Conversely, when the planetary boundary layer or the 3–5 km a.g.l. layer were filled with emissions, the resulting injection heights exhibit less agreement with observed plume heights. Results indicate that differences in injection heights produce different transport pathways. These differences are especially pronounced in area of strong vertical wind shear and when the integration period is long.

Description: Measurements of ozone and its precursors in Beijing during summertime: impact of urban plumes on ozone pollution in downwind rural areas Atmospheric Chemistry and Physics Discussions, 11, 17337-17373, 2011 Author(s): J. Xu, J. Z. Ma, X. L. Zhang, X. B. Xu, X. F. Xu, W. L. Lin, Y. Wang, W. Meng, and Z. Q. Ma Sea-land and mount-valley circulations are the dominant mesoscale synoptic systems affecting the Beijing area during summertime. Under the influence of these two circulations, the prevailing wind is southwesterly from afternoon to midnight, and then changes to northeasterly till forenoon. In this study, surface ozone (O 3 ), carbon monoxide (CO), nitric oxide (NO), nitrogen dioxide (NO 2 ), nitrogen oxide (NO x ) and non-methane hydrocarbons (NMHCs) were measured at four sites located along the route of prevailing wind, including two upwind urban sites (Fengtai (FT) and Baolian (BL)), an upwind suburban site (Shunyi (SY)) and a downwind rural site (Shangdianzi (SDZ)) during 20 June–16 September 2007. The purpose is to improve our understanding of ozone photochemistry in urban and rural areas of Beijing and the influence of urban plumes on ozone pollution in downwind rural areas. It is found that ozone pollution was synchronism in the urban and rural areas of Beijing, coinciding with the regional-scale synoptic processes. Due to the high traffic density and local emissions, the average levels of reactive gases NO x and NMHCs at the non-rural sites were much higher than those at SDZ. The level of long-lived gas CO at SDZ was comparable to and slightly lower than it was at other sites. The daily-averaged ozone concentration at SDZ was much higher than at other sites due to weak titration. Ranking by OH loss rate coefficient ( L OH ), alkenes played a dominant role in total NMHCs reactivity at both urban and rural sites during the experiment, accounting for 48.6 % and 52.1 % of total L OH , respectively. The NMHCs data were also used to estimate the ozone potential formation (OFP) in Beijing. The leading contributors to ozone formation were aromatics at both urban and rural sites during the experiment, which accounts for 55.5 % and 49.4 % of total OFP, respectively. The ozone peak values are found to lag behind one site after another along the route of prevailing wind from SW to NE. Intersection analyses of trace gases reveal that polluted air masses arriving at SDZ were more aged with both higher O 3 and O x concentrations than those at BL. The results indicate that urban plume can transport not only O 3 but its precursors, the latter leading more photochemical O 3 production when being mixed with background atmosphere in the downwind rural area.

Description: Correcting orbital drift signal in the time series of AVHRR derived convective cloud fraction using rotated empirical orthogonal function Atmospheric Measurement Techniques Discussions, 4, 3877-3890, 2011 Author(s): A. Devasthale, K. Karlsson, J. Quaas, and H. Grassl The AVHRRs instruments onboard the series of NOAA satellites offer the longest available meteorological data records from space. These satellites have drifted in orbit resulting in shifts in the local time sampling during the life span of sensors onboard. Depending on the amplitude of a diurnal cycle of the geophysical parameters derived, orbital drift may cause spurious trends in their time series. We investigate tropical deep convective clouds, which show pronounced diurnal cycle amplitude, to bracket an upper bound of the impact of orbital drift on their time series. We carry out a rotated empirical orthogonal function analysis and show that the REOFs are useful in delineating orbital drift signal and, more importantly, in correcting this signal in the time series of convective cloud amount. These results will help facilitate the derivation of homogenized data series of cloud amount from NOAA satellite sensors and ultimately analyzing trends from them. However, we suggest detailed comparison of various methods and their rigorous testing before applying final orbital drift corrections.

Description: Ice nucleation properties of volcanic ash from Eyjafjallajökull Atmospheric Chemistry and Physics Discussions, 11, 17201-17243, 2011 Author(s): C. R. Hoyle, V. Pinti, A. Welti, B. Zobrist, C. Marcolli, B. Luo, Á. Höskuldsson, H. B. Mattsson, T. Thorsteinsson, G. Larsen, and T. Peter The ice nucleation ability of volcanic ash particles collected close to the Icelandic volcano Eyjafjallajökull during its eruptions in April and May 2010 is investigated experimentally, in the immersion and deposition modes, and applied to atmospheric conditions by comparison with airborne measurements and microphysical model calculations. The number of ash particles which are active as ice nuclei (IN) is strongly temperature dependent, with a very small minority being active in the immersion mode at temperatures of 250–263 K. Average ash particles show only a moderate effect on ice nucleation, by inducing freezing at temperatures between 236 K and 240 K (i.e. approximately 3–4 K higher than temperatures required for homogeneous ice nucleation, measured with the same instrument). By scaling the results to aircraft and lidar measurements of the conditions in the ash plume days down wind of the eruption and by applying a simple microphysical model, it was found that the IN active in the immersion mode in the range 250–263 K generally occurred in atmospheric number densities at the lower end of those required to have an impact on ice cloud formation. However, 3–4 K above the homogeneous freezing point, immersion mode IN number densities a few days down wind of the eruption were sufficiently high to have a moderate influence on ice cloud formation. The efficiency of IN in the deposition mode was found to be poor except at very cold conditions ( 〈 238 K), when they reach an efficiency similar to that of mineral dust with the onset of freezing at 10 % supersaturation with respect to ice, and with the frozen fraction nearing its maximum value at a supersaturation 20 %. In summary, these investigations suggest volcanic ash particles to have only moderate effects on atmospheric ice formation.

Description: Carbon dioxide fluxes over an ancient broadleaved deciduous woodland in southern England Biogeosciences, 8, 1595-1613, 2011 Author(s): M. V. Thomas, Y. Malhi, K. M. Fenn, J. B. Fisher, M. D. Morecroft, C. R. Lloyd, M. E. Taylor, and D. D. McNeil We present results from a study of canopy-atmosphere fluxes of carbon dioxide from 2007 to 2009 above a site in Wytham Woods, an ancient temperate broadleaved deciduous forest in southern England. Gap-filled net ecosystem exchange (NEE) data were partitioned into gross primary productivity (GPP) and ecosystem respiration ( R e ) and analysed on daily, monthly and annual timescales. Over the continuous 24 month study period annual GPP was estimated to be 21.1 Mg C ha −1 yr −1 and R e to be 19.8 Mg C ha −1 yr −1 ; net ecosystem productivity (NEP) was 1.2 Mg C ha −1 yr −1 . These estimates were compared with independent bottom-up estimates derived from net primary productivity (NPP) and flux chamber measurements recorded at a plot within the flux footprint in 2008 (GPP = 26.5 ± 6.8 Mg C ha −1 yr −1 , R e = 24.8 ± 6.8 Mg C ha −1 yr −1 , biomass increment = ~1.7 Mg C ha −1 yr −1 ). Over the two years the difference in seasonal NEP was predominantly caused by changes in ecosystem respiration, whereas GPP remained similar for equivalent months in different years. Although solar radiation was the largest influence on daily values of CO 2 fluxes ( R 2 = 0.53 for the summer months for a linear regression), variation in R e appeared to be driven by temperature. Our findings suggest that this ancient woodland site is currently a substantial sink for carbon, resulting from continued growth that is probably a legacy of past management practices abandoned over 40 years ago. Our GPP and R e values are generally higher than other broadleaved temperate deciduous woodlands and may represent the influence of the UK's maritime climate, or the particular species composition of this site. The carbon sink value of Wytham Woods supports the protection and management of temperate deciduous woodlands (including those managed for conservation rather than silvicultural objectives) as a strategy to mitigate atmospheric carbon dioxide increases.

Description: Novel application of satellite and in-situ measurements to map surface-level NO 2 in the Great Lakes region Atmospheric Chemistry and Physics Discussions, 11, 17245-17287, 2011 Author(s): C. J. Lee, J. R. Brook, G. J. Evans, R. V. Martin, and C. Mihele Ozone Monitoring Instrument (OMI) tropospheric NO 2 vertical column density data were used in conjunction with in-situ NO 2 concentrations collected by permanently installed monitoring stations to infer 24 h surface-level NO 2 concentrations at 0.1° (~ 11 km) resolution. The region examined included rural and suburban areas, and the highly industrialised area of Windsor, Ontario, which is situated directly across the US-Canada border from Detroit, MI. Photolytic NO 2 monitors were collocated with standard NO 2 monitors to provide qualitative data regarding NO z interference during the campaign. To test the accuracy of the OMI-inferred concentrations, two-week integrative NO 2 measurements were collected using passive monitors at 18 locations, approximating a 15 km grid across the region, for 7 consecutive two-week periods. When compared with these passive results, satellite-inferred concentrations showed an 18 % positive bias. The correlation of the passive monitor and OMI-inferred concentrations ( R = 0.69, n = 115) was stronger than that for the passive monitor concentrations and OMI column densities ( R = 0.52), indicating that using a sparse network of monitoring sites to estimate concentrations improves the direct utility of the OMI observations. OMI-inferred concentrations were then calculated for four years to show an overall declining trend in surface NO 2 concentrations in the region. Additionally, by separating OMI-inferred surface concentrations by wind direction, clear patterns in emissions and affected down-wind regions, in particular around the US-Canada border, were revealed.

Description: Rainfall patterns after fire differentially affect the recruitment of three Mediterranean shrubs Biogeosciences Discussions, 8, 5761-5786, 2011 Author(s): J. M. Moreno, E. Zuazua, B. Pérez, B. Luna, A. Velasco, and V. Resco de Dios In fire-prone environments, the "event-dependent hypothesis" states that plant population changes are driven by the unique set of conditions of a fire (e.g., fire season, climate). Climate variability, in particular changes in rainfall patterns, can be most important for seeder species, since they must regenerate after fire from seeds, and for Mediterranean shrublands, given the high yearly variability of rainfall in these ecosystems. Yet, the role of rainfall variability and its interaction with fire characteristics (e.g., fire season) on plant populations has received little attention. Here we investigated the changes in seedling emergence and recruitment of three seeder species ( Cistus ladanifer , Erica umbellata and Rosmarinus officinalis ) after fires lit during three different years and at two times during the fire season (early and late in the fire season) to account for potential changes in the soil seed-bank during the year. Three plots were burned at each season, for a total of 18 plots burned during the three years. After fire, emerged seedlings were tallied, tagged and monitored during three years (two the last burning year). Rainfall during the study period was rather variable, and in some years was well below average. Seedling emergence after fire varied by a factor of 3 to 10, depending on the species and on the burning year. The bulk of seedling emergence occurred in the first year after fire, and seedling recruitment at the end of the study period was tightly correlated with this early emergence. Seedling emergence in E umbellata and R officinalis , but not in C ladanifer , were correlated with precipitation in the fall and winter immediately after the fire, being E umbellata most sensitive to low rainfall. Fire season was generally not an important factor in controlling emergence and recruitment. We discuss how projected changes in rainfall patterns with global warming can alter the balance of species in this shrubland, and can drive some species to near local extinction.

Description: Tropical climate and vegetation changes during Heinrich Event 1: comparing climate model output to pollen-based vegetation reconstructions with emphasis on the region around the tropical Atlantic Ocean Climate of the Past Discussions, 7, 1973-2019, 2011 Author(s): D. Handiani, A. Paul, and L. Dupont Abrupt climate changes associated with Heinrich Event 1 (HE1) about 18 to 15 thousand years before present (ka BP) strongly affected climate and vegetation patterns not only in the Northern Hemisphere, but also in tropical regions in the South Atlantic Ocean. We used the University of Victoria (UVic) Earth System-Climate Model (ESCM) with dynamical vegetation and land surface components to simulate four scenarios of climate-vegetation interaction: the pre-industrial era (PI), the Last Glacial Maximum (LGM), and a Heinrich-like event with two different climate backgrounds (interglacial and glacial). The HE1-like simulation with a glacial climate background produced sea surface temperature patterns and enhanced interhemispheric thermal gradients in accordance with the "bipolar seesaw" hypothesis. It allowed us to investigate the vegetation changes that result from a transition to a drier climate as predicted for northern tropical Africa due to a southward shift of the Intertropical Convergence Zone (ITCZ). We found that a cooling of the Northern Hemisphere caused a southward shift of those plant-functional types (PFTs) in Northern Tropical Africa that are indicative of an increased desertification, and a retreat of broadleaf forests in Western Africa and Northern South America. We used the PFTs generated by the model to calculate mega-biomes to allow for a direct comparison between paleodata and palynological vegetation reconstructions. Our calculated mega-biomes for the pre-industrial period and the LGM corresponded well to the modern and LGM sites of the BIOME6000 (v.4.2) reconstruction, except that our present-day simulation predicted the dominance of grassland in Southern Europe and our LGM simulation simulated more forest cover in tropical and sub-tropical South America. The mega-biomes from the HE1 simulation with glacial background climate were in agreement with paleovegetation data from land and ocean proxies in West, Central, and Northern Tropical Africa as well as Northeast South America. However, our model did not agree well with predicted biome distributions in Eastern South America.

Description: Quantitative estimation of landslide risk from rapid debris slides on natural slopes in the Nilgiri hills, India Natural Hazards and Earth System Science, 11, 1723-1743, 2011 Author(s): P. Jaiswal, C. J. van Westen, and V. Jetten A quantitative procedure for estimating landslide risk to life and property is presented and applied in a mountainous area in the Nilgiri hills of southern India. Risk is estimated for elements at risk located in both initiation zones and run-out paths of potential landslides. Loss of life is expressed as individual risk and as societal risk using F-N curves, whereas the direct loss of properties is expressed in monetary terms. An inventory of 1084 landslides was prepared from historical records available for the period between 1987 and 2009. A substantially complete inventory was obtained for landslides on cut slopes (1042 landslides), while for natural slopes information on only 42 landslides was available. Most landslides were shallow translational debris slides and debris flowslides triggered by rainfall. On natural slopes most landslides occurred as first-time failures. For landslide hazard assessment the following information was derived: (1) landslides on natural slopes grouped into three landslide magnitude classes, based on landslide volumes, (2) the number of future landslides on natural slopes, obtained by establishing a relationship between the number of landslides on natural slopes and cut slopes for different return periods using a Gumbel distribution model, (3) landslide susceptible zones, obtained using a logistic regression model, and (4) distribution of landslides in the susceptible zones, obtained from the model fitting performance (success rate curve). The run-out distance of landslides was assessed empirically using landslide volumes, and the vulnerability of elements at risk was subjectively assessed based on limited historic incidents. Direct specific risk was estimated individually for tea/coffee and horticulture plantations, transport infrastructures, buildings, and people both in initiation and run-out areas. Risks were calculated by considering the minimum, average, and maximum landslide volumes in each magnitude class and the corresponding minimum, average, and maximum run-out distances and vulnerability values, thus obtaining a range of risk values per return period. The results indicate that the total annual minimum, average, and maximum losses are about US$ 44 000, US$ 136 000 and US$ 268 000, respectively. The maximum risk to population varies from 2.1 × 10 −1 for one or more lives lost to 6.0 × 10 −2 yr −1 for 100 or more lives lost. The obtained results will provide a basis for planning risk reduction strategies in the Nilgiri area.

Description: Tracer distribution in the Pacific Ocean following a release off Japan – what does an oceanic general circulation model tell us? Ocean Science Discussions, 8, 1441-1466, 2011 Author(s): H. Dietze and I. Kriest In the aftermath of an earthquake and tsunami on 11 March 2011 considerable amounts of radioactive materials were accidentally released into the sea off Fukushima-Daiichi, Japan. This study uses a three-dimensional eddy-resolving oceanic general circulation model to explore potential pathways of a tracer, similar to 137 Cs, from the coast to the open ocean. Results indicate that enhanced concentrations meet a receding spring bloom offshore and that the area of enhanced concentrations offshore is strongly determined by surface mixed layer dynamics. However, huge uncertainties remain. Among them are the realism of the simulated cross-shelf transport and apparently inconsistent estimates of the particle reactivity of 137 Cs which are discussed in a brief literature review. We argue that a comprehensive set of 137 Cs measurements, including sites offshore, could be a unique opportunity to both evaluate and advance the evaluation of oceanic general circulation models.

Description: The energetics response to a warmer climate: relative contributions from the transient and stationary eddies Earth System Dynamics, 2, 105-120, 2011 Author(s): D. Hernández-Deckers and J.-S. von Storch We use the Lorenz Energy Cycle (LEC) to evaluate changes in global energetic activity due to CO 2 -doubling in the coupled atmosphere-ocean ECHAM5/MPI-OM model. Globally, the energetic activity – measured as the total conversion rate of available potential energy into kinetic energy – decreases by about 4 %. This weakening results from a dual response that consists of a strengthening of the LEC in the upper-troposphere and a weakening in the lower and middle troposphere. This is fully consistent with results from a coarser resolution version of the same coupled model. We further use our experiments to investigate the individual contributions of the transient and stationary eddy components to the main energetics response. The transient eddy terms have a larger contribution to the total energetic activity than the stationary ones. We find that this is also true in terms of their 2 × CO 2 -response. Changes in the transient eddy components determine the main energetics response, whereas the stationary eddy components have very small contributions. Hence, the dual response – strengthening in the upper troposphere and weakening below – concerns mainly the transient eddy terms. We can relate qualitatively this response to the two main features of the 2 × CO 2 warming pattern: (a) the tropical upper-tropospheric warming increases the pole-to-equator temperature gradient – strengthening the energetic activity above – and enhances static stability – weakening the energetic activity below; and (b) the high-latitude surface warming decreases the pole-to-equator temperature gradient in the lower troposphere – weakening the energetic activity below. Despite the small contribution from the stationary eddies to the main energetics response, changes in stationary eddy available potential energy ( P se ) reflect some features of the warming pattern: stronger land-sea contrasts at the subtropics and weaker land-sea contrasts at the high northern latitudes affect P se regionally, but do not affect the global energetics response.

Description: Exploring the potentials and limitations of the time-reversal imaging of finite seismic sources Solid Earth, 2, 95-105, 2011 Author(s): S. Kremers, A. Fichtner, G. B. Brietzke, H. Igel, C. Larmat, L. Huang, and M. Käser The characterisation of seismic sources with time-reversed wave fields is developing into a standard technique that has already been successful in numerous applications. While the time-reversal imaging of effective point sources is now well-understood, little work has been done to extend this technique to the study of finite rupture processes. This is despite the pronounced non-uniqueness in classic finite source inversions. The need to better constrain the details of finite rupture processes motivates the series of synthetic and real-data time reversal experiments described in this paper. We address questions concerning the quality of focussing in the source area, the localisation of the fault plane, the estimation of the slip distribution and the source complexity up to which time-reversal imaging can be applied successfully. The frequency band for the synthetic experiments is chosen such that it is comparable to the band usually employed for finite source inversion. Contrary to our expectations, we find that time-reversal imaging is useful only for effective point sources, where it yields good estimates of both the source location and the origin time. In the case of finite sources, however, the time-reversed field does not provide meaningful characterisations of the fault location and the rupture process. This result cannot be improved sufficiently with the help of different imaging fields, realistic modifications of the receiver geometry or weights applied to the time-reversed sources. The reasons for this failure are manifold. They include the choice of the frequency band, the incomplete recording of wave field information at the surface, the excitation of large-amplitude surface waves that deteriorate the depth resolution, the absence of a sink that should absorb energy radiated during the later stages of the rupture process, the invisibility of small slip and the neglect of prior information concerning the fault geometry and the inherent smoothness of seismologically inferred Earth models that prevents the beneficial occurrence of strong multiple-scattering. The condensed conclusion of our study is that the limitations of time-reversal imaging – at least in the frequency band considered here – start where the seismic source stops being effectively point-localised.

Description: Volume cross section of auroral radar backscatter and RMS plasma fluctuations inferred from coherent and incoherent scatter data: a response on backscatter volume parameters Annales Geophysicae, 29, 1081-1092, 2011 Author(s): M. V. Uspensky, P. Janhunen, A. V. Koustov, and K. Kauristie Norway and Finland STARE radar measurements in the eastward auroral electrojet are combined with EISCAT CP-1 measurements of the electron density and electric field vector in the common scattering volume to investigate the variation of the auroral radar volume cross section (VCS) with the flow angle of observations (radar look direction with respect to the E × B electron drift). The data set available consists of ~6000 points for flow angles of 40–85° and electron drifts between 500 and 2000 m s −1 . The EISCAT electron density N(h) -profile data are used to estimate the effective electron density, aspect angle and thickness of the backscattering layer. It is shown that the flow angle variation of the VCS is rather weak, only ~5 dB within the range of the considered flow angles. The VCS values themselves respond almost linearly to the square of both the electron drift velocity magnitude and the effective electron density. By adopting the inferred shape of the VCS variation with the flow angle and the VCS dependence upon wavelength, the relative amplitude of electrostatic electron density fluctuations over all scales is estimated. Inferred values of 2–4 percent react nearly linearly to the electron drift velocity in the range of 500–1000 m s −1 but the rate of increase slows down at electron drifts 〉1000 m s −1 and density fluctuations of ~5.5 percent due to, perhaps, progressively growing nonlinear wave losses.

Description: Development and evaluation of the aerosol dynamics and gas phase chemistry model ADCHEM Atmospheric Chemistry and Physics, 11, 5867-5896, 2011 Author(s): P. Roldin, E. Swietlicki, G. Schurgers, A. Arneth, K. E. J. Lehtinen, M. Boy, and M. Kulmala The aim of this work was to develop a model suited for detailed studies of aerosol dynamics, gas and particle phase chemistry within urban plumes, from local scale (1 × 1 km 2 ) to regional scale. This article describes and evaluates the trajectory model for Aerosol Dynamics, gas and particle phase CHEMistry and radiative transfer (ADCHEM). The model treats both vertical and horizontal dispersion perpendicular to an air mass trajectory (2-space dimensions). The Lagrangian approach enables a more detailed representation of the aerosol dynamics, gas and particle phase chemistry and a finer spatial and temporal resolution compared to that of available regional 3D-CTMs. These features make it among others well suited for urban plume studies. The aerosol dynamics model includes Brownian coagulation, dry deposition, wet deposition, in-cloud processing, condensation, evaporation, primary particle emissions and homogeneous nucleation. The organic mass partitioning was either modeled with a 2-dimensional volatility basis set (2D-VBS) or with the traditional two-product model approach. In ADCHEM these models consider the diffusion limited and particle size dependent condensation and evaporation of 110 and 40 different organic compounds respectively. The gas phase chemistry model calculates the gas phase concentrations of 61 different species, using 130 different chemical reactions. Daily isoprene and monoterpene emissions from European forests were simulated separately with the vegetation model LPJ-GUESS, and included as input to ADCHEM. ADCHEM was used to simulate the ageing of the urban plumes from the city of Malmö in southern Sweden (280 000 inhabitants). Several sensitivity tests were performed concerning the number of size bins, size structure method, aerosol dynamic processes, vertical and horizontal mixing, coupled or uncoupled condensation and the secondary organic aerosol formation. The simulations show that the full-stationary size structure gives accurate results with little numerical diffusion when more than 50 size bins are used between 1.5 and 2500 nm, while the moving-center method is preferable when only a few size bins are selected. The particle number size distribution in the center of the urban plume from Malmö was mainly affected by dry deposition, coagulation and vertical dilution. The modeled PM2.5 mass was dominated by organic material, nitrate, sulfate and ammonium. If the condensation of HNO 3 and NH 3 was treated as a coupled process (pH independent) the model gave lower nitrate PM2.5 mass than if considering uncoupled condensation. Although the time of ageing from that SOA precursors are emitted until condensable products are formed is substantially different with the 2D-VBS and two product model, the models gave similar total organic mass concentrations.

Description: Global multi-year O 3 -CO correlation patterns from models and TES satellite observations Atmospheric Chemistry and Physics, 11, 5819-5838, 2011 Author(s): A. Voulgarakis, P. J. Telford, A. M. Aghedo, P. Braesicke, G. Faluvegi, N. L. Abraham, K. W. Bowman, J. A. Pyle, and D. T. Shindell The correlation between measured tropospheric ozone (O 3 ) and carbon monoxide (CO) has been used extensively in tropospheric chemistry studies to explore the photochemical characteristics of different regions and to evaluate the ability of models to capture these characteristics. Here, we present the first study that uses multi-year, global, vertically resolved, simultaneous and collocated O 3 and CO satellite (Tropospheric Emission Spectrometer) measurements, to determine this correlation in the middle/lower free troposphere for two different seasons, and to evaluate two chemistry-climate models. We find results that are fairly robust across different years, altitudes and timescales considered, which indicates that the correlation maps presented here could be used in future model evaluations. The highest positive correlations (around 0.8) are found in the northern Pacific during summer, which is a common feature in the observations and the G-PUCCINI model. We make quantitative comparisons between the models using a single-figure metric ( C ), which we define as the correlation coefficient between the modeled and the observed O 3 -CO correlations for different regions of the globe. On a global scale, the G-PUCCINI model shows a good performance in the summer ( C =0.71) and a satisfactory performance in the winter ( C =0.52). It captures midlatitude features very well, especially in the summer, whereas the performance in regions like South America or Central Africa is weaker. The UKCA model ( C =0.46/0.15 for July–August/December–January on a global scale) performs better in certain regions, such as the tropics in winter, and it captures some of the broad characteristics of summer extratropical correlations, but it systematically underestimates the O 3 -CO correlations over much of the globe. It is noteworthy that the correlations look very different in the two models, even though the ozone distributions are similar. This demonstrates that this technique provides a powerful global constraint for understanding modeled tropospheric chemical processes. We investigated the sources of the correlations by performing a series of sensitivity experiments. In these, the sign of the correlation is, in most cases, insensitive to removing different individual emissions, but its magnitude changes downwind of emission regions when applying such perturbations. Interestingly, we find that the O 3 -CO correlation does not solely reflect the strength of O 3 photochemical production, as often assumed by earlier studies, but is more complicated and may reflect a mixture of different processes such as transport.

Description: In-cloud oxalate formation in the global troposphere: a 3-D modeling study Atmospheric Chemistry and Physics, 11, 5761-5782, 2011 Author(s): S. Myriokefalitakis, K. Tsigaridis, N. Mihalopoulos, J. Sciare, A. Nenes, K. Kawamura, A. Segers, and M. Kanakidou Organic acids attract increasing attention as contributors to atmospheric acidity, secondary organic aerosol mass and aerosol hygroscopicity. Oxalic acid is globally the most abundant dicarboxylic acid, formed via chemical oxidation of gas-phase precursors in the aqueous phase of aerosols and droplets. Its lifecycle and atmospheric global distribution remain highly uncertain and are the focus of this study. The first global spatial and temporal distribution of oxalate, simulated using a state-of-the-art aqueous-phase chemical scheme embedded within the global 3-dimensional chemistry/transport model TM4-ECPL, is here presented. The model accounts for comprehensive gas-phase chemistry and its coupling with major aerosol constituents (including secondary organic aerosol). Model results are consistent with ambient observations of oxalate at rural and remote locations (slope = 1.16 ± 0.14, r 2 = 0.36, N = 114) and suggest that aqueous-phase chemistry contributes significantly to the global atmospheric burden of secondary organic aerosol. In TM4-ECPL most oxalate is formed in-cloud and less than 5 % is produced in aerosol water. About 62 % of the oxalate is removed via wet deposition, 30 % by in-cloud reaction with hydroxyl radical, 4 % by in-cloud reaction with nitrate radical and 4 % by dry deposition. The in-cloud global oxalate net chemical production is calculated to be about 21–37 Tg yr −1 with almost 79 % originating from biogenic hydrocarbons, mainly isoprene. This condensed phase net source of oxalate in conjunction with a global mean turnover time against deposition of about 5 days, maintain oxalate's global tropospheric burden of 0.2–0.3 Tg, i.e. 0.05–0.1 Tg-C that is about 5–9 % of model-calculated water soluble organic carbon burden.

Description: Bridging the Faraoni and Selli oceanic anoxic events: short and repetitive dys- and anaerobic episodes during the late Hauterivian to early Aptian in the central Tethys Climate of the Past Discussions, 7, 2021-2059, 2011 Author(s): K. B. Föllmi, M. Bôle, N. Jammet, P. Froidevaux, A. Godet, S. Bodin, T. Adatte, V. Matera, D. Fleitmann, and J. E. Spangenberg A detailed stratigraphical and geochemical analysis was performed on the upper part of the Maiolica Formation outcropping in the Breggia (southern Switzerland) and Capriolo sections (northern Italy). In these localities, the Maiolica Formation consists of well-bedded, partly siliceous, pelagic, micritic carbonate, which lodges numerous thin, dark and organic-rich layers. Stable-isotope, phosphorus, organic-carbon and a suite of redox-sensitive trace-metal contents (RSTE: Mo, U, Co, V and As) were measured. Higher densities of organic-rich layers were identified in the uppermost Hauterivian, lower Barremian and the Barremian-Aptian boundary intervals, whereas the upper Barremian interval and the interval immediately following the Barremian-Aptian boundary interval are characterized by lower densities of organic-rich layers. TOC contents, RSTE pattern and C org :P tot ratios indicate that most layers were deposited under dysaerobic rather than anaerobic conditions and that latter conditions were likely restricted to short intervals in the latest Hauterivian, the early Barremian and the pre-Selli early Aptian. Correlations are possible with organic-rich intervals in central Italy (the Gorgo a Cerbara section) and the Boreal northwest German Basin, and with the facies and drowning pattern in the evolution of the Helvetic segment of the northern Tethyan carbonate platform. Our data and correlations suggest that the latest Hauterivian witnessed the progressive installation of dysaerobic conditions in the Tethys, which went along with the onset in sediment condensation, phosphogenesis and platform drowning on the northern Tethyan margin, and which culminated in the Faraoni anoxic episode. This brief episode is followed by further episodes of dysaerobic conditions in the Tethys and the northwest German Basin, which became more frequent and progressively stronger in the late early Barremian. Platform drowning persisted and did not halt before the latest early Barremian. The late Barremian witnessed diminishing frequencies and intensities in dysaerobic conditions, which went along with the progressive installation of the Urgonian carbonate platform. Near the Barremian-Aptian boundary, the increasing density in dysaerobic episodes in the Tethyan and northwest German Basins is paralleled by a change towards heterozoan carbonate production on the northern Tethyan shelf. The following return to more oxygenated conditions is correlated with the second phase of Urgonian platform growth and the period immediately preceding and corresponding to the Selli anoxic episode is characterized by renewed platform drowning and the change to heterozoan carbonate production. Changes towards more humid climate conditions were likely the cause for the repetitive installation of dys- to anaerobic conditions in the Tethyan and Boreal basins and the accompanying changes in the evolution of the carbonate platform towards heterozoan carbonate-producing ecosystems and platform drowning.

Description: Usefulness of high resolution coastal models for operational oil spill forecast: the Full City accident Ocean Science Discussions, 8, 1467-1504, 2011 Author(s): G. Broström, A. Carrasco, L. R. Hole, S. Dick, F. Janssen, J. Mattsson, and S. Berger Oil spill modeling is considered to be an important decision support system (DeSS) useful for remedial action in case of accidents, as well as for designing the environmental monitoring system that is frequently set up after major accidents. Many accidents take place in coastal areas implying that low resolution basin scale ocean models is of limited use for predicting the trajectories of an oil spill. In this study, we target the oil spill in connection with the Full City accident on the Norwegian south coast and compare three different oil spill models for the area. The result of the analysis is that all models do a satisfactory job. The "standard" operational model for the area is shown to have severe flaws but including an analysis based on a higher resolution model (1.5 km resolution) for the area the model system show results that compare well with observations. The study also shows that an ensemble using three different models is useful when predicting/analyzing oil spill in coastal areas.

Description: Brief communication "Snow profile associated measurements (SPAM) – a new instrument for quick snow profile measurements" The Cryosphere Discussions, 5, 1737-1748, 2011 Author(s): P. Lahtinen A new instrument concept (SPAM) for snow profile associated measurements is presented. The potential of the concept is demonstrated by presenting preliminary results obtained with the prototype instrument. With this concept it is possible to retrieve rapid snow profiles of e.g. light extinction, reflectance, temperature and snow layer structure with high vertical resolution. As a side-product, also snow depth is retrieved.

Description: Variable lifetimes and loss mechanisms for NO 3 and N 2 O 5 during the DOMINO campaign: contrasts between marine, urban and continental air Atmospheric Chemistry and Physics Discussions, 11, 17825-17877, 2011 Author(s): J. N. Crowley, J. Thieser, M. Tang, G. Schuster, H. Bozem, Z. Hosaynali Beygi, H. Fischer, J. Diesch, F. Drewnick, S. Borrmann, W. Song, N. Yassaa, J. Williams, D. Pöhler, U. Platt, and J. Lelieveld Nighttime mixing ratios of boundary layer N 2 O 5 were determined using cavity-ring-down spectroscopy during the DOMINO campaign. Observation of N 2 O 5 was intermittent, with mixing ratios ranging from below the detection limit (~5 ppt) to ~500 ppt. A steady-state analysis constrained by measured mixing ratios of NO 2 and O 3 was used to derive NO 3 lifetimes and compare them to calculated rates of loss via gas-phase and heterogeneous reactions of both NO 3 and N 2 O 5 . Three distinct types of air masses were encountered, which were largely marine (Atlantic), continental or urban-industrial in origin. NO 3 lifetimes were longest in the Atlantic sector (up to ~30 min) but were very short (a few seconds) in polluted, air masses from the local city and petroleum-related industrial complex of Huelva. Air from the continental sector was an intermediate case. The high reactivity to NO 3 of the urban air mass was not accounted for by gas-phase and heterogeneous reactions, rates of which were constrained by measurements of NO, volatile organic species and aerosol surface area. In general, high NO 2 mixing ratios resulted in low NO 3 lifetimes, though heterogeneous processes (e.g. reaction of N 2 O 5 on aerosol) were generally less important than direct gas-phase losses of NO 3 . The presence of SO 2 at levels above ~2 ppb in the urban air sector was always associated with very low N 2 O 5 mixing ratios indicating either very short NO 3 lifetimes in the presence of combustion-related emissions or an important role for reduced sulphur species in urban, nighttime chemistry. High production rates coupled with low lifetimes of NO 3 imply an important contribution of nighttime chemistry to removal of both NO x and VOC.

Description: Constraining global methane emissions and uptake by ecosystems Biogeosciences, 8, 1643-1665, 2011 Author(s): R. Spahni, R. Wania, L. Neef, M. van Weele, I. Pison, P. Bousquet, C. Frankenberg, P. N. Foster, F. Joos, I. C. Prentice, and P. van Velthoven Natural methane (CH 4 ) emissions from wet ecosystems are an important part of today's global CH 4 budget. Climate affects the exchange of CH 4 between ecosystems and the atmosphere by influencing CH 4 production, oxidation, and transport in the soil. The net CH 4 exchange depends on ecosystem hydrology, soil and vegetation characteristics. Here, the LPJ-WHyMe global dynamical vegetation model is used to simulate global net CH 4 emissions for different ecosystems: northern peatlands (45°–90° N), naturally inundated wetlands (60° S–45° N), rice agriculture and wet mineral soils. Mineral soils are a potential CH 4 sink, but can also be a source with the direction of the net exchange depending on soil moisture content. The geographical and seasonal distributions are evaluated against multi-dimensional atmospheric inversions for 2003–2005, using two independent four-dimensional variational assimilation systems. The atmospheric inversions are constrained by the atmospheric CH 4 observations of the SCIAMACHY satellite instrument and global surface networks. Compared to LPJ-WHyMe the inversions result in a~significant reduction in the emissions from northern peatlands and suggest that LPJ-WHyMe maximum annual emissions peak about one month late. The inversions do not put strong constraints on the division of sources between inundated wetlands and wet mineral soils in the tropics. Based on the inversion results we diagnose model parameters in LPJ-WHyMe and simulate the surface exchange of CH 4 over the period 1990–2008. Over the whole period we infer an increase of global ecosystem CH 4 emissions of +1.11 Tg CH 4 yr −1 , not considering potential additional changes in wetland extent. The increase in simulated CH 4 emissions is attributed to enhanced soil respiration resulting from the observed rise in land temperature and in atmospheric carbon dioxide that were used as input. The long-term decline of the atmospheric CH 4 growth rate from 1990 to 2006 cannot be fully explained with the simulated ecosystem emissions. However, these emissions show an increasing trend of +3.62 Tg CH 4 yr −1 over 2005–2008 which can partly explain the renewed increase in atmospheric CH 4 concentration during recent years.

Description: The role of catchment classification in rainfall-runoff modeling Hydrology and Earth System Sciences Discussions, 8, 6113-6153, 2011 Author(s): Y. He, A. Bárdossy, and E. Zehe A sound catchment classification scheme is a fundamental step towards improved catchment hydrology science and prediction in ungauged basins. Two categories of catchment classification methods are presented in the paper. The first one is based directly on physiographic properties and climatic conditions over a catchment and regarded as a Linnaean type or natural classification scheme. The second one is based on numerical clustering and regionalization methods and considered as a statistical or arbitrary classification scheme. This paper reviews each category including what has been done since recognition of the intrinsic value of catchment classification, what is being done in the current research, as well as what is to be done in the future.

Description: Inverse modeling of CO 2 sources and sinks using satellite observations of CO 2 from TES and surface flask measurements Atmospheric Chemistry and Physics, 11, 6029-6047, 2011 Author(s): R. Nassar, D. B. A. Jones, S. S. Kulawik, J. R. Worden, K. W. Bowman, R. J. Andres, P. Suntharalingam, J. M. Chen, C. A. M. Brenninkmeijer, T. J. Schuck, T. J. Conway, and D. E. Worthy We infer CO 2 surface fluxes using satellite observations of mid-tropospheric CO 2 from the Tropospheric Emission Spectrometer (TES) and measurements of CO 2 from surface flasks in a time-independent inversion analysis based on the GEOS-Chem model. Using TES CO 2 observations over oceans, spanning 40° S–40° N, we find that the horizontal and vertical coverage of the TES and flask data are complementary. This complementarity is demonstrated by combining the datasets in a joint inversion, which provides better constraints than from either dataset alone, when a posteriori CO 2 distributions are evaluated against independent ship and aircraft CO 2 data. In particular, the joint inversion offers improved constraints in the tropics where surface measurements are sparse, such as the tropical forests of South America. Aggregating the annual surface-to-atmosphere fluxes from the joint inversion for the year 2006 yields −1.13±0.21 Pg C for the global ocean, −2.77±0.20 Pg C for the global land biosphere and −3.90±0.29 Pg C for the total global natural flux (defined as the sum of all biospheric, oceanic, and biomass burning contributions but excluding CO 2 emissions from fossil fuel combustion). These global ocean and global land fluxes are shown to be near the median of the broad range of values from other inversion results for 2006. To achieve these results, a bias in TES CO 2 in the Southern Hemisphere was assessed and corrected using aircraft flask data, and we demonstrate that our results have low sensitivity to variations in the bias correction approach. Overall, this analysis suggests that future carbon data assimilation systems can benefit by integrating in situ and satellite observations of CO 2 and that the vertical information provided by satellite observations of mid-tropospheric CO 2 combined with measurements of surface CO 2 , provides an important additional constraint for flux inversions.

Description: General overview: European Integrated project on Aerosol Cloud Climate and Air Quality interactions (EUCAARI) – integrating aerosol research from nano to global scales Atmospheric Chemistry and Physics Discussions, 11, 17941-18160, 2011 Author(s): M. Kulmala, A. Asmi, H. K. Lappalainen, U. Baltensperger, J.-L. Brenguier, M. C. Facchini, H.-C. Hansson, Ø. Hov, C. D. O'Dowd, U. Pöschl, A. Wiedensohler, R. Boers, O. Boucher, G. de Leeuw, H. Denier van den Gon, J. Feichter, R. Krejci, P. Laj, H. Lihavainen, U. Lohmann, G. McFiggans, T. Mentel, C. Pilinis, I. Riipinen, M. Schulz, A. Stohl, E. Swietlicki, E. Vignati, M. Amann, M. Amann, C. Alves, S. Arabas, P. Artaxo, D. C. S. Beddows, R. Bergström, J. P. Beukes, M. Bilde, J. F. Burkhart, F. Canonaco, S. Clegg, H. Coe, S. Crumeyrolle, B. D'Anna, S. Decesari, S. Gilardoni, M. Fischer, A. M. Fjæraa, C. Fountoukis, C. George, L. Gomes, P. Halloran, T. Hamburger, R. M. Harrison, H. Herrmann, T. Hoffmann, C. Hoose, M. Hu, U. Hõrrak, Y. Iinuma, T. Iversen, M. Josipovic, M. Kanakidou, A. Kiendler-Scharr, A. Kirkevåg, G. Kiss, Z. Klimont, P. Kolmonen, M. Komppula, J.-E. Kristjánsson, L. Laakso, A. Laaksonen, L. Labonnote, V. A. Lanz, K. E. J. Lehtinen, R. Makkonen, G. McMeeking, J. Merikanto, A. Minikin, S. Mirme, W. T. Morgan, E. Nemitz, D. O'Donnell, T. S. Panwar, H. Pawlowska, A. Petzold, J. J. Pienaar, C. Pio, C. Plass-Duelmer, A. S. H. Prévôt, S. Pryor, C. L. Reddington, G. Roberts, D. Rosenfeld, J. Schwarz, Ø. Seland, K. Sellegri, X. J. Shen, M. Shiraiwa, H. Siebert, B. Sierau, D. Simpson, J. Y. Sun, D. Topping, P. Tunved, P. Vaattovaara, V. Vakkari, J. P. Veefkind, A. Visschedijk, H. Vuollekoski, R. Vuolo, B. Wehner, J. Wildt, S. Woodward, D. R. Worsnop, G.-J. van Zadelhoff, A. A. Zardini, K. Zhang, P. G. van Zyl, V.-M. Kerminen, K. S. Carslaw, and S. N. Pandis In this paper we describe and summarize the main achievements of the European Aerosol Cloud Climate and Air Quality Interactions project (EUCAARI). EUCAARI started on 1 January 2007 and ended on 31 December 2010 leaving a rich legacy including: (a) a comprehensive database with a year of observations of the physical, chemical and optical properties of aerosol particles over Europe, (b) the first comprehensive aerosol measurements in four developing countries, (c) a database of airborne measurements of aerosols and clouds over Europe during May 2008, (d) comprehensive modeling tools to study aerosol processes fron nano to global scale and their effects on climate and air quality. In addition a new Pan-European aerosol emissions inventory was developed and evaluated, a new cluster spectrometer was built and tested in the field and several new aerosol parameterizations and computations modules for chemical transport and global climate models were developed and evaluated. This work enabled EUCAARI to improve our understanding of aerosol radiative forcing and air quality-climate interactions. The EUCAARI results can be utilized in European and global environmental policy to assess the aerosol impacts and the corresponding abatement strategies.