Total organic carbon, delta13C, biomarker, gas compilations and hopanoids analysis from IODP Sites 307-U1317 and 307-U1318

During the Integrated Ocean Drilling Program (IODP) Expedition 307 for the first time a cold-water coral carbonate mound was drilled down through its base into the underlying sediments. In the current study, sample material from within and below Challenger Mound, located in the Belgica carbonate mound province in the Porcupine Basin offshore Ireland, was investigated for its distribution of microbial communities and gas composition using biogeochemical and geochemical approaches to elucidate the question on the initiation of carbonate mounds. Past and living microbial populations are lower in the mound section compared to the underlying sediments or sediments of an upslope reference site. A reason for this might be a reduced substrate feedstock, reflected by low total organic carbon (TOC) contents, in the once coral dominated mound sequence. In contrast, in the reference site a lithostratigraphic sequence with comparatively high TOC contents shows higher abundances of both past and present microbial communities, indicating favourable living conditions from time of sedimentation until today. Composition and isotopic values of gases below the mound base seem to point to a mixed gas of biogenic and thermogenic origin with a higher proportion of biogenic gas. Oil-derived hydrocarbons were not detected at the mound site. This suggests that at least in the investigated part of the mound base the upward flow of fossil hydrocarbons, being one hypothesis for the initiation of the formation of carbonate mounds, seems to be only of minor significance.

Global database of surface ocean particulate organic carbon export fluxes diagnosed from the 234Th technique

Through the processes of the biological pump, carbon is exported to the deep ocean in the form of dissolved and particulate organic matter. There are several ways by which downward export fluxes can be estimated. The great attraction of the 234Th technique is that its fundamental operation allows a downward flux rate to be determined from a single water column profile of thorium coupled to an estimate of POC/234Th ratio in sinking matter. We present a database of 723 estimates of organic carbon export from the surface ocean derived from the 234Th technique. Data were collected from tables in papers published between 1985 and 2013 only. We also present sampling dates, publication dates and sampling areas. Most of the open ocean Longhurst provinces are represented by several measurements. However, the Western Pacific, the Atlantic Arctic, South Pacific and the South Indian Ocean are not well represented. There is a variety of integration depths ranging from surface to 220m. Globally the fluxes ranged from -22 to 125 mmol of C/m**2/d. We believe that this database is important for providing new global estimate of the magnitude of the biological carbon pump.

Organic and inorganic geochemistry and archaeal community composition of hypersaline sediments from Orca Basin, RV Atlantis Expedition AT18-02

Among the most extreme habitats on Earth, dark, deep, anoxic brines host unique microbial ecosystems that remain largely unexplored. As the terminal step of anaerobic degradation of organic matter, methanogenesis is a potentially significant but poorly constrained process in deep-sea hypersaline environments. We combined biogeochemical and phylogenetic analyses as well as incubation experiments to unravel the origin of methane in hypersaline sediments of Orca Basin in the northern Gulf of Mexico. Substantial concentrations of methane (up to 3.4 mM) coexisted with high concentrations of sulfate (16-43 mM) in two sediment cores retrieved from the northern and southern parts of Orca Basin. The strong depletion of 13C in methane (-77 to -89 per mill) pointed towards a biological source. While low concentrations of competitive substrates limited the significance of hydrogenotrophic and acetoclastic methanogenesis, the presence of non-competitive methylated substrates (methanol, trimethylamine, dimethyl sulfide, dimethylsulfoniopropionate) supported the potential for methane generation through methylotrophic methanogenesis. Thermodynamic calculations demonstrated that hydrogenotrophic and acetoclastic methanogenesis were unlikely to occur under in situ conditions, while methylotrophic methanogenesis from a variety of substrates was highly favorable. Likewise, carbon isotope relationships between methylated substrates and methane supported methylotrophic methanogenesis as the major source of methane. Stable isotope tracer and radiotracer experiments with 13C bicarbonate, acetate and methanol as well as 14C-labeled methylamine indicated that methylotrophic methanogenesis was the predominant methanogenic pathway. Based on 16S rRNA gene sequences, halophilic methylotrophic methanogens related to the genus Methanohalophilus dominated the benthic archaeal community in the northern basin but also occurred in the southern basin. High abundances of methanogen lipid biomarkers such as intact polar and polyunsaturated hydroxyarchaeols were detected in sediments from the northern basin, with lower abundances in the southern basin. Strong 13C-depletion of saturated and monounsaturated hydroxyarchaeol were consistent with methylotrophic methanogenesis as the major methanogenic pathway. Collectively, the availability of methylated substrates, thermodynamic calculations, experimentally determined methanogenic activity as well as lipid and gene biomarkers strongly suggested methylotrophic methanogenesis as predominant pathway of methane formation in the presence of sulfate in Orca Basin sediments.

Modelling the fate of chromated copper arsenate in a sandy soil

A pulse of chromated copper arsenate (CCA, a timber preservative) was applied in irrigation water to an undisturbed field soil in a laboratory column. Concentrations of various elements in the leachate from the column were measured during the experiment. Also, the remnants within the soil were measured at the end of the experiment. The geochemical modelling package, PHREEQC-2, was used to simulate the experimental data. Processes included in the CCA transport modelling were advection, dispersion, non-specific adsorption (cation exchange) and specific adsorption by clay minerals and organic matter, as well as other possible chemical reactions such as precipitation/dissolution. The modelling effort highlighted the possible complexities in CCA transport and reaction experiments. For example, the uneven dosing of CCA as well as incomplete knowledge of the soil properties resulted in simulations that gave only partial, although reasonable, agreement with the experimental data. Both the experimental data and simulations show that As and Cu are strongly adsorbed and therefore, will mostly remain at the top of the soil profile, with a small proportion appearing in leachate. On the other hand, Cr is more mobile and thus it is present in the soil column leachate. Further simulations show that both the quantity of CCA added to the soil and the pH of the irrigation water will influence CCA transport. Simulations suggest that application of larger doses of CCA to the soil will result in higher leachate concentrations, especially for Cu and As. Irrigation water with a lower pH will dramatically increase leaching of Cu. These results indicate that acidic rainfall or significant accidental spillage of CCA will increase the risk of groundwater pollution.

The use of enzymes in organic solvents in polytransesterification reactions

The aim of this research project was to identify the factors affecting the porcine pancreatic lipase (PPL.)-catalysed polytransesterification of a diester and a diol in organic solvents. It was hoped that by modifying reaction conditions a commercially acceptable polymer molecular weight (Mn) of 20,000 daltons might be attained. Exploratory investigations were carried out using 1,4-butanediolibis(2,2,2- trichloroethyl) adipate and glutarate systems in diethyl ether, with and without molecular sieves. It was found that molecular sieves promoted the reaction by reducing hydrolysis of the ester end-groups, resulting in polymer molecular weights between 1.2 and 2.2 times greater than those obtainable without molecular sieves. Investigations were then concentrated on the PPL-catalysed polytransesterification of 1,4-butanediol with divinyl adipate. The particular advantage of this system is that the reaction is irreversible. The effects of varying substrate concentration, mass of drying agent, reaction solvent, reaction temperature, mass of enzyme and also enzyme immobilisation on the 1,4-butanediolidivinyl adipate system were investigated. The highest molecular weight polymer obtained for the PPL-catalysed polytransesterification of 1,4-butanedial with divinyl adipate in diethyl ether was Mn -8,000. In higher boiling ether solvents molecular weights as high as Mn -9,200 were obtained for this system at elevated temperatures. It was found that the major factor limiting polymerisation was the low solubility of the polymer in the solvent which resulted in precipitation of the polymer onto the surface of the enzyme.

Multiple roles of charged amino acids in cytoplasmic loop 7 for expression and function of the multidrug and organic anion transporter MRP1 (ABCC1)

Multidrug resistance protein MRP1 mediates the ATP-dependent efflux of many chemotherapeutic agents and organic anions. MRP1 has two nucleotide binding sites (NBSs) and three membrane spanning domains (MSDs) containing 17 transmembrane helices linked by extracellular and cytoplasmic loops (CL). Homology models suggest that CL7 (amino acids 1141-1195) is in a position where it could participate in signaling between the MSDs and NBSs during the transport process. We have individually replaced eight charged residues in CL7 with Ala, and in some cases, an amino acid with the same charge, and then investigated the effects on MRP1 expression, transport activity, and nucleotide and substrate interactions. A triple mutant in which Glu(1169), Glu(1170), and Glu(1172) were all replaced with Ala was also examined. The properties of R1173A and E1184A were comparable with those of wild-type MRP1, whereas the remaining mutants were either poorly expressed (R1166A, D1183A) or exhibited reduced transport of one or more organic anions (E1144A, D1179A, K1181A, (1169)AAQA). Same charge mutant D1183E was also not expressed, whereas expression and activity of R1166K were similar to wild-type MRP1. The moderate substrate-selective changes in transport activity displayed by mutants E1144A, D1179A, K1181A, and (1169)AAQA were accompanied by changes in orthovanadate-induced trapping of [alpha-(32)P]azidoADP by NBS2 indicating changes in ATP hydrolysis or release of ADP. In the case of E1144A, estradiol glucuronide no longer inhibited trapping of azidoADP. Together, our results demonstrate the extreme sensitivity of CL7 to mutation, consistent with its critical and complex dual role in both the proper folding and transport activity of MRP1.

Interdigitating organic bilayers direct the short interlayer spacing in hybrid organic–inorganic layered vanadium oxide nanostructures

Layered metal oxides provide a single-step route to sheathed superlattices of atomic layers of a variety of inorganic materials, where the interlayer spacing and overall layered structure forms the most critical feature in the nanomaterials’ growth and application in electronics, health, and energy storage. We use a combination of computer simulations and experiments to describe the atomic-scale structure, dynamics and energetics of alkanethiol-intercalated layered vanadium oxide-based nanostructures. Molecular dynamics (MD) simulations identify the unusual substrate-constrained packing of the alkanethiol surfactant chains along each V2O5 (010) face that combines with extensive interdigitation between chains on opposing faces to maximize three-dimensional packing in the interlayer regions. The findings are supported by high resolution electron microscopy analyses of synthesized alkanethiol-intercalated vanadium oxide nanostructures, and the preference for this new interdigitated model is clarified using a large set of MD simulations. This dependency stresses the importance of organic–inorganic interactions in layered material systems, the control of which is central to technological applications of flexible hybrid nanomaterials.

Atomic nanolithography patterning of submicron features: writing an organic self-assembled monolayer with cold bright Cs atom beams

Cs atom beams, transversely collimated and cooled, passing through material masks in the form of arrays of reactive-ion-etched hollow Si pyramidal tips and optical masks formed by intense standing light waves, write submicron features on self-assembled monolayers (SAMs). Features with widths as narrow as 43 ± 6 nm and spatial resolution limited only by the grain boundaries of the substrate have been realized in SAMs of alkanethiols. The material masks write two-dimensional arrays of submicron holes; the optical masks result in parallel lines spaced by half the optical wavelength. Both types of feature are written to the substrate by exposure of the masked SAM to the Cs flux and a subsequent wet chemical etch. For the arrays of pyramidal tips, acting as passive shadow masks, the resolution and size of the resultant feature depends on the distance of the mask array from the SAM, an effect caused by the residual divergence of the Cs atom beam. The standing wave optical mask acts as an array of microlenses focusing the atom flux onto the substrate. Atom 'pencils' writing on SAMs have the potential to create arbitrary submicron figures in massively parallel arrays. The smallest features and highest resolutions were realized with SAMs grown on smooth, sputtered gold substrates.

The Effects of Organic Matter Amendments and Migratory Waterfowl on Greenhouse Gas and Nutrient Dynamics in Managed Coastal Plain Wetlands

Wetland ecosystems provide many valuable ecosystem services, including carbon (C) storage and improvement of water quality. Yet, restored and managed wetlands are not frequently evaluated for their capacity to function in order to deliver on these values. Specific restoration or management practices designed to meet one set of criteria may yield unrecognized biogeochemical costs or co-benefits. The goal of this dissertation is to improve scientific understanding of how wetland restoration practices and waterfowl habitat management affect critical wetland biogeochemical processes related to greenhouse gas emissions and nutrient cycling. I met this goal through field and laboratory research experiments in which I tested for relationships between management factors and the biogeochemical responses of wetland soil, water, plants and trace gas emissions. Specifically, I quantified: (1) the effect of organic matter amendments on the carbon balance of a restored wetland; (2) the effectiveness of two static chamber designs in measuring methane (CH4) emissions from wetlands; (3) the impact of waterfowl herbivory on the oxygen-sensitive processes of methane emission and coupled nitrification-denitrification; and (4) nitrogen (N) exports caused by prescribed draw down of a waterfowl impoundment.

The potency of CH4 emissions from wetlands raises the concern that widespread restoration and/or creation of freshwater wetlands may present a radiative forcing hazard. Yet data on greenhouse gas emissions from restored wetlands are sparse and there has been little investigation into the greenhouse gas effects of amending wetland soils with organic matter, a recent practice used to improve function of mitigation wetlands in the Eastern United States. I measured trace gas emissions across an organic matter gradient at a restored wetland in the coastal plain of Virginia to test the hypothesis that added C substrate would increase the emission of CH4. I found soils heavily loaded with organic matter emitted significantly more carbon dioxide than those that have received little or no organic matter. CH4 emissions from the wetland were low compared to reference wetlands and contrary to my hypothesis, showed no relationship with the loading rate of added organic matter or total soil C. The addition of moderate amounts of organic matter (< 11.2 kg m-2) to the wetland did not greatly increase greenhouse gas emissions, while the addition of high amounts produced additional carbon dioxide, but not CH4.

I found that the static chambers I used for sampling CH4 in wetlands were highly sensitive to soil disturbance. Temporary compression around chambers during sampling inflated the initial chamber CH4 headspace concentration and/or lead to generation of nonlinear, unreliable flux estimates that had to be discarded. I tested an often-used rubber-gasket sealed static chamber against a water-filled-gutter seal chamber I designed that could be set up and sampled from a distance of 2 m with a remote rod sampling system to reduce soil disturbance. Compared to the conventional design, the remotely-sampled static chambers reduced the chance of detecting inflated initial CH4 concentrations from 66 to 6%, and nearly doubled the proportion of robust linear regressions from 45 to 86%. The new system I developed allows for more accurate and reliable CH4 sampling without costly boardwalk construction.

I explored the relationship between CH4 emissions and aquatic herbivores, which are recognized for imposing top-down control on the structure of wetland ecosystems. The biogeochemical consequences of herbivore-driven disruption of plant growth, and in turn, mediated oxygen transport into wetland sediments, were not previously known. Two growing seasons of herbivore exclusion experiments in a major waterfowl overwintering wetland in the Southeastern U.S. demonstrate that waterfowl herbivory had a strong impact on the oxygen-sensitive processes of CH4 emission and nitrification. Denudation by herbivorous birds increased cumulative CH4 flux by 233% (a mean of 63 g CH4 m-2 y-1) and inhibited coupled nitrification-denitrification, as indicated by nitrate availability and emissions of nitrous oxide. The recognition that large populations of aquatic herbivores may influence the capacity for wetlands to emit greenhouse gases and cycle nitrogen is particularly salient in the context of climate change and nutrient pollution mitigation goals. For example, our results suggest that annual emissions of 23 Gg of CH4 y-1 from ~55,000 ha of publicly owned waterfowl impoundments in the Southeastern U.S. could be tripled by overgrazing.

Hydrologically controlled moist-soil impoundment wetlands provide critical habitat for high densities of migratory bird populations, thus their potential to export nitrogen (N) to downstream waters may contribute to the eutrophication of aquatic ecosystems. To investigate the relative importance of N export from these built and managed habitats, I conducted a field study at an impoundment wetland that drains into hypereutrophic Lake Mattamuskeet. I found that prescribed hydrologic drawdowns of the impoundment exported roughly the same amount of N (14 to 22 kg ha-1) as adjacent fertilized agricultural fields (16 to 31 kg ha-1), and contributed approximately one-fifth of total N load (~45 Mg N y-1) to Lake Mattamuskeet. Ironically, the prescribed drawdown regime, designed to maximize waterfowl production in impoundments, may be exacerbating the degradation of habitat quality in the downstream lake. Few studies of wetland N dynamics have targeted impoundments managed to provide wildlife habitat, but a similar phenomenon may occur in some of the 36,000 ha of similarly-managed moist-soil impoundments on National Wildlife Refuges in the southeastern U.S. I suggest early drawdown as a potential method to mitigate impoundment N pollution and estimate it could reduce N export from our study impoundment by more than 70%.

In this dissertation research I found direct relationships between wetland restoration and impoundment management practices, and biogeochemical responses of greenhouse gas emission and nutrient cycling. Elevated soil C at a restored wetland increased CO2 losses even ten years after the organic matter was originally added and intensive herbivory impact on emergent aquatic vegetation resulted in a ~230% increase in CH4 emissions and impaired N cycling and removal. These findings have important implications for the basic understanding of the biogeochemical functioning of wetlands and practical importance for wetland restoration and impoundment management in the face of pressure to mitigate the environmental challenges of global warming and aquatic eutrophication.

Benthic cyanobacterial mat (BCM) abundance on samples from the coast of Curacao

Benthic cyanobacterial mats (BCMs) are impacting coral reefs worldwide. However, the factors and mechanisms driving their proliferation are unclear. We conducted a multi-year survey around the Caribbean island of Curaçao, which revealed highest BCM abundance on sheltered reefs close to urbanised areas. Reefs with high BCM abundance were also characterised by high benthic cover of macroalgae and low cover of corals. Nutrient concentrations in the water-column were consistently low, but markedly increased just above substrata (both sandy and hard) covered with BCMs. This was true for sites with both high and low BCM coverage, suggesting that BCM growth is stimulated by a localised, substrate-linked release of nutrients from the microbial degradation of organic matter. This hypothesis was supported by a higher organic content in sediments on reefs with high BCM coverage, and by an in situ experiment which showed that BCMs grew within days on sediments enriched with organic matter (Spirulina). We propose that nutrient runoff from urbanised areas stimulates phototrophic blooms and enhances organic matter concentrations on the reef. This organic matter is transported by currents and settles on the seabed at sites with low hydrodynamics. Subsequently, nutrients released from the organic matter degradation fuel the growth of BCMs. Improved management of nutrients generated on land should lower organic loading of sediments and other benthos (e.g. turf and macroalgae) to reduce BCM proliferation on coral reefs.

Granulometry, mineralogy and organic matter content of permafrost core 5011-3

The combination of permafrost history and dynamics, lake level changes and the tectonical framework is considered to play a crucial role for sediment delivery to El'gygytgyn Crater Lake, NE Russian Arctic. The purpose of this study is to propose a depositional framework based on analyses of the core strata from the lake margin and historical reconstructions from various studies at the site. A sedimentological program has been conducted using frozen core samples from the 141.5 m long El'gygytgyn 5011-3 permafrost well. The drill site is located in sedimentary permafrost west of the lake that partly fills the El'gygytgyn Crater. The total core sequence is interpreted as strata building up a progradational alluvial fan delta. Four macroscopically distinct sedimentary units are identified. Unit 1 (141.5-117.0 m) is comprised of ice-cemented, matrix-supported sandy gravel and intercalated sandy layers. Sandy layers represent sediments which rained out as particles in the deeper part of the water column under highly energetic conditions. Unit 2 (117.0-24.25 m) is dominated by ice-cemented, matrix-supported sandy gravel with individual gravel layers. Most of the Unit 2 diamicton is understood to result from alluvial wash and subsequent gravitational sliding of coarse-grained (sandy gravel) material on the basin slope. Unit 3 (24.25-8.5 m) has ice-cemented, matrix-supported sandy gravel that is interrupted by sand beds. These sandy beds are associated with flooding events and represent near-shore sandy shoals. Unit 4 (8.5-0.0 m) is ice-cemented, matrix-supported sandy gravel with varying ice content, mostly higher than below. It consists of slope material and creek fill deposits. The uppermost metre is the active layer (i.e. the top layer of soil with seasonal freeze and thaw) into which modern soil organic matter has been incorporated. The nature of the progradational sediment transport taking place from the western and northern crater margins may be related to the complementary occurrence of frequent turbiditic layers in the central lake basin, as is known from the lake sediment record. Slope processes such as gravitational sliding and sheet flooding occur especially during spring melt and promote mass wasting into the basin. Tectonics are inferred to have initiated the fan accumulation in the first place and possibly the off-centre displacement of the crater lake.

(Table 1) Organic petrography and Rock-Eval pyrolysis at DSDP Hole 79-547B

A lenticle of organic matter in a piece of dolomite rock embedded in Triassic sandy mudstone of Core 547B-35 (DSDP Leg 79) was identified as inertinite-rich coal by organic petrography and analytical pyrolysis. About 95% of the organic matter recognized under the microscope consists of pyrofusinite, degradofusinite, and inertodetrinite. Gaseous hydrocarbons evolved during pyrolysis are rich in methane and are characteristic of inertinitic material. The organic matter is suggested to be a piece of redeposited Permian Gondwana coal.

Potential Shifts in Canadian High Arctic Sedimentary Organic Matter Composition With Permafrost Active Layer Detachments

Increased temperature and precipitation in Arctic regions have led to deeper thawing and structural instability in permafrost soil. The resulting localized disturbances, referred to as active layer detachments (ALDs), may transport organic matter (OM) to more biogeochemically active zones. To examine this further, solid state cross polarization magic angle spinning 13C nuclear magnetic resonance (CPMAS NMR) and biomarker analysis were used to evaluate potential shifts in riverine sediment OM composition due to nearby ALDs within the Cape Bounty Arctic Watershed Observatory, Nunavut, Canada. In sedimentary OM near ALDs, NMR analysis revealed signals indicative of unaltered plant-derived material, likely derived from permafrost. Long chain acyclic aliphatic lipids, steroids, cutin, suberin and lignin occurred in the sediments, consistent with a dominance of plant-derived compounds, some of which may have originated from permafrost-derived OM released by ALDs. OM degradation proxies for sediments near ALDs revealed less alteration in acyclic aliphatic lipids, while constituents such as steroids, cutin, suberin and lignin were found at a relatively advanced stage of degradation. Phospholipid fatty acid analysis indicated that microbial activity was higher near ALDs than downstream but microbial substrate limitation was prevalent within disturbed regions. Our study suggests that, as these systems recover from disturbance, ALDs likely provide permafrost-derived OM to sedimentary environments. This source of OM, which is enriched in labile OM, may alter biogeochemical patterns and enhance microbial respiration within these ecosystems.

Ultrafast charge-transfer in organic photovoltaic interfaces: geometrical and functionalization effects

Understanding the microscopic mechanisms of electronic excitation in organic photovoltaic cells is a challenging problem in the design of efficient devices capable of performing sunlight harvesting. Here we develop and apply an ab initio approach based on time-dependent density functional theory and Ehrenfest dynamics to investigate photoinduced charge transfer in small organic molecules. Our calculations include mixed quantum–classical dynamics with ions moving classically and electrons quantum mechanically, where no experimental external parameter other than the material geometry is required. We show that the behavior of photocarriers in zinc phthalocyanine (ZnPc) and C60 systems, an effective prototype system for organic solar cells, is sensitive to the atomic orientation of the donor and the acceptor units as well as the functionalization of covalent molecules at the interface. In particular, configurations with the ZnPc molecules facing on C60 facilitate charge transfer between substrate and molecules that occurs within 200 fs. In contrast, configurations where ZnPc is tilted above C60 present extremely low carrier injection efficiency even at longer times as an effect of the larger interfacial potential level offset and higher energetic barrier between the donor and acceptor molecules. An enhancement of charge injection into C60 at shorter times is observed as binding groups connect ZnPc and C60 in a dyad system. Our results demonstrate a promising way of designing and controlling photoinduced charge transfer on the atomic level in organic devices that would lead to efficient carrier separation and maximize device performance.

Few-layer, large-area, 2D covalent organic framework semiconductor thin films.

In this work, we synthesize large-area thin films of a conjugated, imine-based, two-dimensional covalent organic framework at the solution/air interface. Thicknesses between ∼2-200 nm are achieved. Films can be transferred to any desired substrate by lifting from underneath, enabling their use as the semiconducting active layer in field-effect transistors.