From Scattering and Recoiling Spectrometry to Scattering and Recoiling Imaging

A new ion scattering technique, called scattering and recoiling imaging spectrometry (SARIS), is being developed. The SARIS technique uses a large, position sensitive microchannel plate (MCP) and time-of-flight methods to capture images of scattered and recoiled particles from a pulsed ke V ion beam. These images combine the advantage of atomic scale microscopy and spatial averaging simultaneously since they are created from a macroscopic surface area but they are directly related to the atomic arrangement of the surface. This paper de-scribes the basis of the SARIS technique, the instrument which is under development, and the scattering and recoiling imaging code (SARIC) for simulation of the classical ion trajectories. Time-of-flight scattering and recoiling spectrometry (TOF-SARS) data are used to emulate the SARIS images for the case of 4 keV Ne+ scattering from a Pt{111} surface. The observed scattering intensity patterns are characterized by their complex and rich structure. These experimental images are simulated by use of the SARIC program. The abundance of information contained in the images can be used to identify the type of surface being studied and its structure. The extraction of numerical values for the interatomic spacings, relaxations, reconstructions, and adsorbate site positions is accomplished by comparing the experimental and simulated images. Quantitative comparisons are made through the use of a reliability, or R, factor, which is based on the differences between the two images. The SARIS development will move low energy ion scattering into the realm of surface imaging techniques

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".

This is the final version of the article. Available from American Society for Microbiology via the DOI in this record.Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments-Parcubacteria (OD1) and Peregrinibacteria Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.IMPORTANCE Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon-many of which occur in bacterioplankton from poorly understood lineages-have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these "microbial dark matter" taxa during hypoxia

The Impact of Accelerating Land-Use Change on the N-Cycle of Tropical Aquatic Ecosystems: Current Conditions and Projected Changes

Published data and analyses from temperate and tropical aquatic systems are used to summarize knowledge about the potential impact of land-use alteration on the nitrogen biogeochemistry of tropical aquatic ecosystems, identify important patterns and recommend key needs for research. The tropical N-cycle is traced from pre-disturbance conditions through the phases of disturbance, highlighting major differences between tropical and temperate systems that might influence development strategies in the tropics. Analyses suggest that tropical freshwaters are more frequently N-limited than temperate zones, while tropical marine systems may show more frequent P limitation. These analyses indicate that disturbances to pristine tropical lands will lead to greatly increased primary production in freshwaters and large changes in tropical freshwater communities. Increased freshwater nutrient flux will also lead to an expansion of the high production, N- and light-limited zones around river deltas, a switch from P- to N-limitation in calcareous marine systems, with large changes in the community composition of fragile mangrove and reef systems. Key information gaps are highlighted, including data on mechanisms of nutrient transport and atmospheric deposition in the tropics, nutrient and material retention capacities of tropical impoundments, and N/P coupling and stoichiometric impacts of nutrient supplies on tropical aquatic communities. The current base of biogeochemical data suggests that alterations in the N-cycle will have greater impacts on tropical aquatic ecosystems than those already observed in the temperate zone

Simulations of energetic beam deposition: from picoseconds to seconds

We present a new method for simulating crystal growth by energetic beam deposition. The method combines a Kinetic Monte-Carlo simulation for the thermal surface diffusion with a small scale molecular dynamics simulation of every single deposition event. We have implemented the method using the effective medium theory as a model potential for the atomic interactions, and present simulations for Ag/Ag(111) and Pt/Pt(111) for incoming energies up to 35 eV. The method is capable of following the growth of several monolayers at realistic growth rates of 1 monolayer per second, correctly accounting for both energy-induced atomic mobility and thermal surface diffusion. We find that the energy influences island and step densities and can induce layer-by-layer growth. We find an optimal energy for layer-by-layer growth (25 eV for Ag), which correlates with where the net impact-induced downward interlayer transport is at a maximum. A high step density is needed for energy induced layer-by-layer growth, hence the effect dies away at increased temperatures, where thermal surface diffusion reduces the step density. As part of the development of the method, we present molecular dynamics simulations of single atom-surface collisions on flat parts of the surface and near straight steps, we identify microscopic mechanisms by which the energy influences the growth, and we discuss the nature of the energy-induced atomic mobility

Nutrient Enrichment Drives Gulf of Mexico Hypoxia

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95312/1/eost16763.pd

Spatial extent and historical context of North Sea oxygen depletion in August 2010

Prompted by recent observations of seasonal low dissolved oxygen from two moorings in the North Sea, a hydrographic survey in August 2010 mapped the spatial extent of summer oxygen depletion. Typical near-bed dissolved oxygen saturations in the stratified regions of the North Sea were 75–80 % while the well-mixed regions of the southern North Sea reached 90 %. Two regions of strong thermal stratification, the area between the Dooley and Central North Sea Currents and the area known as the Oyster Grounds, had oxygen saturations as low as 65 and 70 % (200 and 180 µmol dm-3) respectively. Low dissolved oxygen was apparent in regions characterised by low advection, high stratification, elevated organic matter production from the spring bloom and a deep chlorophyll maximum. Historical data over the last century from the International Council for the Exploration of the Sea oceanographic database highlight an increase in seasonal oxygen depletion and a warming over the past 20 years. The 2010 survey is consistent with, and reinforces, the signal of recent depleted oxygen at key locations seen in the (albeit sparse) historical data

Can biodiversity of preexisting and created salt marshes match across scales? An assessment from microbes to predators

Coastal wetlands are rapidly disappearing worldwide due to a variety of processes, including climate change and flood control. The rate of loss in the Mississippi River Delta is among the highest in the world and billions of dollars have been allocated to build and restore coastal wetlands. A key question guiding assessment is whether created coastal salt marshes have similar biodiversity to preexisting, reference marshes. However, the numerous biodiversity metrics used to make these determinations are typically scale dependent and often conflicting. Here, we applied ecological theory to compare the diversity of different assemblages (surface and below-surface soil microbes, plants, macroinfauna, spiders, and on-marsh and off-marsh nekton) between two created marshes (4–6 years old) and four reference marshes. We also quantified the scale-dependent effects of species abundance distribution, aggregation, and density on richness differences and explored differences in species composition. Total, between-sample, and within-sample diversity (γ, β, and α, respectively) were not consistently lower at created marshes. Richness decomposition varied greatly among assemblages and marshes (e.g., soil microbes showed high equitability and α diversity, but plant diversity was restricted to a few dominant species with high aggregation). However, species abundance distribution, aggregation, and density patterns were not directly associated with differences between created and reference marshes. One exception was considerably lower density for macroinfauna at one of the created marshes, which was drier because of being at a higher elevation and having coarser substrate compared with the other marshes. The community compositions of created marshes were more dissimilar than reference marshes for microbe and macroinfauna assemblages. However, differences were small, particularly for microbes. Together, our results suggest generally similar taxonomic diversity and composition between created and reference marshes. This provides support for the creation of marsh habitat as tools for the maintenance and restoration of coastal biodiversity. However, caution is needed when creating marshes because specific building and restoration plans may lead to different colonization patterns

Transits across a Cyclopentadienyl: Organic and Organometallic Haptotropic Shifts

references cited therein. (13) Electron acceptors which are also conjugated with the alkene r system will polarize the HOMO in the same directions as, but to a smaller extent than, Inductive acceptors.8 (14) There has been a suggestion that Me is an acceptor relative to H when attached to an sp3 carbon [C. A. Grob, Angew. Chem. lnt. Ed. Engl., 15, 569 (1976), and references cited therein]. The product ratio discussed here reflect this, but the IP changes do not. A subtle role of solvent may be involved. (15) J. Bastideand J. P. Maier, Chem. Phys., 12, 144 (1976 Li+, CUR+), the e component of which greatly stabilizes the most symmetrical q5 coordination. The lower the energy of the e acceptor set and the better the overlap with its Cp counterpart, the more are q2 and q5 stabilized relative to 7'. In the case of XH3+ (X = C, Si, Ge, Sn) an e acceptor orbital moves to lower energy as one proceeds down the group, and this is responsible for the decreasing barrier for sigmatropic shifts in CpXH3. The XH2 case, which yields a number of interesting collapse structures, is analyzed in detail for X, a main group center. Contrast the interaction of a cyclopentadienide anion and a proton with the interaction of the same anion and a Mn(CO)3+ fragment. Both result in stable molecules: cyclopentadiene (1) and V~-C~M~( C O )~ (2). But what a difference in the equilibrium geometries of these end products of the interaction! If we focus our attention on the cyclopentadienide site where the interacting partner settles down, then the proton chooses a position near to one carbon of the ring, but the Mn(C0)3+ fragment sits directly over the center of the ring. The ramifications of this differential are the concern of this paper. We will examine the interaction of a cyclopentadienide (CsHs-, Cp) ion with an interacting group X, X = H+, CH3+, SiR3+, Mn(C0)3+, CH22f, CH2. The result will consist of some conclusions concerning the equilibrium geometry of CpX as well as the relative energetics of the various haptotropic reactions of this Consider the passage of the interacting group X across the face of a Cp molecule, moving as indicated in 3 in a plane parallel to the Cp ring. Let the distance d be a separation at which there is sizable interaction between the frontier orbitals of X and the Cp a system. For a surface so constrained the asymmetric unit that need be calculated consists of the shaded area in 4, and two of the three boundaries of that area are contained in a transit along a line shown in projection in 5. Mirror symmetry is maintained at all points. The numbers nq shown along that line are convenient labels invoking a connection to the inorganic 7" notation* for denoting an approximate coordination geometry. In order to avoid confusion with structure numbers and ring carbon numbers, we have labeled the various sites along the transit line as 17, 217, . . . , 57. The site labeled 17, or some geometry near it, corresponds to or simple u interaction, such as we have in the collapse product cyclopentadiene. The 7IS site 57 is where one better come up with maximum stabilization for X = Mn(C0)3+. The site labeled 27 positions X over the center of a bond, and obviously will describe the important transition state region for a sigmatropic shift of a system like cyclopentadiene. 37 and 47 are not so easily defined. Experimentally, slippage of Cp rings from q5 coordination is often observed and q3 or q4 coordination may or may not be invoked. Somewhat arbitrarily we define 317 at the intersection of the transit line with the line joining C-2 and C-5 projected on the transit plane. The tetrahapto coordination site is most ambiguous (it could be near 37 or near 57), and SO we will not label any position as such. The analysis will consist of an inspection of interaction diagrams for the orbitals of Cp and X, as the ligand X and its position along the transit are varied. The qualitative arguments based on symmetry and overlap are supported by extended Huckel calculations whose details are given in the Appendix. The reader should be aware that this is an approximate metho

Securing ocean benefits for society in the face of climate change

Benefits humans rely on from the ocean - marine ecosystem services - are increasingly vulnerable under future climate. This paper reviews how three valued services have, and will continue to, shift under climate change: (1) capture fisheries, (2) food from aquaculture, and (3) protection from coastal hazards such as storms and sea-level rise. Climate adaptation planning is just beginning for fisheries, aquaculture production, and risk mitigation for coastal erosion and inundation. A few examples are highlighted, showing the promise of considering multiple ecosystem services in developing approaches to adapt to sea-level rise, ocean acidification, and rising sea temperatures. Ecosystem-based adaptation in fisheries and along coastlines and changes in aquaculture practices can improve resilience of species and habitats to future environmental challenges. Opportunities to use market incentives - such as compensation for services or nutrient trading schemes - are relatively untested in marine systems. Relocation of communities in response to rising sea levels illustrates the urgent need to manage human activities and investments in ecosystems to provide a sustainable flow of benefits in the face of future climate change. (C) 2013 Elsevier Ltd. All rights reserved