Compositional data analysis of Holocene sediments from the West Bengal Sundarbans, India: Geochemical proxies for grain-size variability in a delta environment

This paper is part of a special issue of Applied Geochemistry focusing on reliable applications of compositional multivariate statistical methods. This study outlines the application of compositional data analysis (CoDa) to calibration of geochemical data and multivariate statistical modelling of geochemistry and grain-size data from a set of Holocene sedimentary cores from the Ganges-Brahmaputra (G-B) delta. Over the last two decades, understanding near-continuous records of sedimentary sequences has required the use of core-scanning X-ray fluorescence (XRF) spectrometry, for both terrestrial and marine sedimentary sequences. Initial XRF data are generally unusable in ‘raw-format’, requiring data processing in order to remove instrument bias, as well as informed sequence interpretation. The applicability of these conventional calibration equations to core-scanning XRF data are further limited by the constraints posed by unknown measurement geometry and specimen homogeneity, as well as matrix effects. Log-ratio based calibration schemes have been developed and applied to clastic sedimentary sequences focusing mainly on energy dispersive-XRF (ED-XRF) core-scanning. This study has applied high resolution core-scanning XRF to Holocene sedimentary sequences from the tidal-dominated Indian Sundarbans, (Ganges-Brahmaputra delta plain). The Log-Ratio Calibration Equation (LRCE) was applied to a sub-set of core-scan and conventional ED-XRF data to quantify elemental composition. This provides a robust calibration scheme using reduced major axis regression of log-ratio transformed geochemical data. Through partial least squares (PLS) modelling of geochemical and grain-size data, it is possible to derive robust proxy information for the Sundarbans depositional environment. The application of these techniques to Holocene sedimentary data offers an improved methodological framework for unravelling Holocene sedimentation patterns.

Physico-geochemical and mineral composition of neem tree soils and relation to organic properties

The Neem tree, the oil of which has a long history of pesticide, fertilizer and medicinal use in India, has been studied extensively for its organic compounds. Here we present a physical, mineralogical and geochemical database resulting from the analyses of two Neem soil profiles (epipedons) in India. Neem tree derivatives are used in the manufacture of a variety of products, from anti-bacterial drugs and insecticides to fertilizers and animal feeds. A preliminary geochemical and mineralogical analysis of Neem soils is made to explore the potential for chemical links between Neem tree derivatives and soils. Physical soil characteristics, including colour, texture and clay mineralogy, suggest the two pedons formed under different hydrological regimes, and hence, are products of different leaching environments, one well-drained site, the other poorly drained. Geochemically, the two Neem soils exhibit similarities, with elevated concentrations of Th and rare earth elements. These elements are of interest because of their association with phosphates, especially monazite and apatite, and the potential link to fertilizer derivatives. Higher concentrations of trace elements in the soils may be linked to nutritional derivatives and to cell growth in the Neem tree.

Geochemical analysis at ODP Site 207-1261 from the Demerara Rise in the western equatorial Atlantic

A high-resolution geochemical record of a 120 cm black shale interval deposited during the Coniacian-Santonian Oceanic Anoxic Event 3 (ODP Leg 207, Site 1261, Demerara Rise) has been constructed to provide detailed insight into rapid changes in deep ocean and sediment paleo-redox conditions. High contents of organic matter, sulfur and redox-sensitive trace metals (Cd, Mo, V, Zn), as well as continuous lamination, point to deposition under consistently oxygen-free and largely sulfidic bottom water conditions. However, rapid and cyclic changes in deep ocean redox are documented by short-term (~15-20 ka) intervals with decreased total organic carbon (TOC), S and redox-sensitive trace metal contents, and in particular pronounced phosphorus peaks (up to 2.5 wt% P) associated with elevated Fe oxide contents. Sequential iron and phosphate extractions confirm that P is dominantly bound to iron oxides and incorporated into authigenic apatite. Preservation of this Fe-P coupling in an otherwise sulfidic depositional environment (as indicated by Fe speciation and high amounts of sulfurized organic matter) may be unexpected, and provides evidence for temporarily non-sulfidic bottom waters. However, there is no evidence for deposition under oxic conditions. Instead, sulfidic conditions were punctuated by periods of anoxic, non-sulfidic bottom waters. During these periods, phosphate was effectively scavenged during precipitation of iron (oxyhydr)oxides in the upper water column, and was subsequently deposited and largely preserved at the sea floor. After ~15-25 ka, sulfidic bottom water conditions were re-established, leading to the initial precipitation of CdS, ZnS and pyrite. Subsequently, increasing concentrations of H2S in the water column led to extensive formation of sulfurized organic matter, which effectively scavenged particle-reactive Mo complexes (thiomolybdates). At Site 1261, sulfidic bottom waters lasted for ?90-100 ka, followed by another period of anoxic, non-sulfidic conditions lasting for ~15-20 ka. The observed cyclicity at the lower end of the redox scale may have been triggered by repeated incursions of more oxygenated surface- to mid-waters from the South Atlantic resulting in a lowering of the oxic-anoxic chemocline in the water column. Alternatively, sea water sulfate might have been stripped by long-lasting high rates of sulfate reduction, removing the ultimate source for HS**- production.

Coupled Ge/Si and Ge isotope ratios as geochemical tracers of seafloor hydrothermal systems: Case studies at Loihi Seamount and East Pacific Rise 9°50’N

Germanium (Ge) and Silicon (Si) exhibit similar geochemical behaviour in marine environments but are variably enriched in seafloor hydrothermal fluids relative to seawater. In this study, Ge isotope and Ge/Si ratio systematics were investigated in low temperature hydrothermal vents from Loihi Seamount (Pacific Ocean, 18°54’N, 155°15’W) and results were compared to high-temperature vents from the East Pacific Rise (EPR) at 9°50’N. Loihi offers the opportunity to understand contrasting Ge and Si behaviour in low temperature seafloor hydrothermal systems characterized by abundant Fe oxyhydroxide deposition at the seafloor. The results show that both Ge/Si and δ74/70Ge in hydrothermal fluids are fractionated relative to the basaltic host rocks. The enrichment in Ge vs. Si relative to fresh basalts, together with Ge isotope fractionation (Δ74/70Ge fluid-basalt up to 1.15 ‰ at EPR 9°50’N and 1.64 ‰ at Loihi) are best explained by the precipitation of minerals (e.g. quartz and Fe-sulfides) during higher temperature seawater-rock reactions in the subsurface. The study of Fe-rich hydrothermal deposits at Loihi, largely composed of Fe-oxyhydroxides, shows that Ge isotopes are also fractionated upon mineral precipitation at the seafloor. We obtained an average Ge isotope fractionation factor between Fe-oxyhydroxide (ferrihydrite) and dissolved Ge in the fluid of -2.0 ± 0.6 ‰ (2sd), and a maximum value of -3.6 ± 0.6 ‰ (2sd), which is consistent with recent theoretical and experimental studies. The study of a hydrothermal chimney at Bio 9 vent at EPR 9°50’N also demonstrates that Ge isotopes are fractionated by approximately -5.6 ± 0.6 ‰ (2sd) during precipitation of metal sulfides under hydrothermal conditions. Using combined Ge/Si and estimated Ge isotope signatures of Ge sinks and sources in seawater, we propose a preliminary oceanic budget of Ge which reveals that an important sink, referred as the “missing Ge sink”, may correspond to Ge sequestration into authigenic Fe-oxyhydroxides in marine sediments. This study shows that combining Ge/Si and δ74/70Ge systematics provides a useful tool to trace hydrothermal Ge and Si sources in marine environments and to understand formation processes of seafloor hydrothermal deposits.

Preliminary geochemical data of the 2014 erupted lavas and pyroclasts at Fogo Island (Cape Verde Archipelago)

Resumo alargado

The estuarine geochemical reactivity of Zn isotopes and its relevance for the biomonitoring of anthropogenic Zn and Cd contaminations from metallurgical activities: Example of the Gironde fluvial-estuarine system, France

Zinc stable isotopes measurements by MC-ICP-MS, validated by laboratory intercalibrations, were performed on wild oysters, suspended particles and filtered river/estuarine water samples to provide new constraints for the use of Zn isotopes as environmental tracers. The samples selected were representative of the long range (400 km) transport of metal (Zn, Cd, etc.) contamination from former Zn-refining activities at Decazeville (i.e. δ66Zn > 1 ‰) and its phasing out, recorded during 30 years in wild oysters from the Gironde Estuary mouth (RNO/ROCCH sample bank). The study also addresses additional anthropogenic sources (urban and viticulture) and focuses on geochemical reactivity of Zn in the turbidity gradient and the maximum turbidity zone (MTZ) of the fluvial Gironde Estuary. In this area, dissolved Zn showed a strong removal onto suspended particulate matter (SPM) and progressive enrichment in heavy isotopes with increasing SPM concentrations varying from δ66Zn = -0.02 ‰ at 2 mg/L to +0.90 ‰ at 1310 mg/L. These signatures were attributed to kinetically driven adsorption due to strongly increasing sorption sites in the turbidity gradient and MTZ of the estuary. Oysters from the estuary mouth, contaminated sediments from the Lot River and SPM entering the estuary showed parallel historical evolutions (1979-2010) for Zn/Cd ratios but not for δ66Zn values. Oysters had signatures varying from δ66Zn = 1.43 ‰ in 1983 to 1.18 ‰ in 2010 and were offset by δ66Zn = 0.6 - 0.7 ‰ compared to past (1988) and present SPM from the salinity gradient. Isotopic signatures in river-borne particles entering the Gironde Estuary under contrasting freshwater discharge regimes during 2003-2011 showed similar values (δ66Zn ≈ 0.35 ± 0.03 ‰; 1SD, n=15), i.e. they were neither related to former metal refining activities at least for the past decade nor clearly affected by other anthropogenic sources. Therefore, the Zn isotopic signatures in Gironde oysters reflect the geochemical reactivity of Zn in the estuary rather than signatures of past metallurgical contaminations in the watershed as recorded in contaminated river sediments. The study also shows that the isotopic composition of Zn is strongly fractionated by its geochemical reactivity in the Gironde Estuary, representative of meso-macrotidal estuarine systems.

Migration, prospecting, dispersal? What host movement matters for infectious agent circulation?

Spatial disease ecology is emerging as a new field that requires the integration of complementary approaches to address how the distribution and movements of hosts and parasites may condition the dynamics of their interactions. In this context, migration, the seasonal movement of animals to different zones of their distribution, is assumed to play a key role in the broad scale circulation of parasites and pathogens. Nevertheless, migration is not the only type of host movement that can influence the spatial ecology, evolution, and epidemiology of infectious diseases. Dispersal, the movement of individuals between the location where they were born or bred to a location where they breed, has attracted attention as another important type of movement for the spatial dynamics of infectious diseases. Host dispersal has notably been identified as a key factor for the evolution of host-parasite interactions as it implies gene flow among local host populations and thus can alter patterns of coevolution with infectious agents across spatial scales. However, not all movements between host populations lead to dispersal per se. One type of host movement that has been neglected, but that may also play a role in parasite spread is prospecting, i.e., movements targeted at selecting and securing new habitat for future breeding. Prospecting movements, which have been studied in detail in certain social species, could result in the dispersal of infectious agents among different host populations without necessarily involving host dispersal. In this article, we outline how these various types of host movements might influence the circulation of infectious disease agents and discuss methodological approaches that could be used to assess their importance. We specifically focus on examples from work on colonial seabirds, ticks, and tick-borne infectious agents. These are convenient biological models because they are strongly spatially structured and involve relatively simple communities of interacting species. Overall, this review emphasizes that explicit consideration of the behavioral and population ecology of hosts and parasites is required to disentangle the relative roles of different types of movement for the spread of infectious diseases.

Geochemical analysis at ODP Site 207-1259 from the Demerara Rise in the western equatorial Atlantic

Organic carbon-rich shales deposited during the Coniacian-Santonian Oceanic Anoxic Event 3 were drilled during ODP Leg 207 at Demerara Rise. We present integrated high-resolution geochemical records of core intervals from ODP Sites 1259 and 1261 both from nannofossil biozone CC14. Our results reveal systematic variations in marine and detrital sediment contribution, depositional processes, and bottom water redox conditions during black shale formation at two locations on Demerara Rise in different paleo-water depths. A combination of redox proxies (Fe/S, P/Al, C/P, redox-sensitive/sulfide-forming trace metals Mn, Cd, Mo, Ni, V, Zn) and other analytical approaches (bulk sediment composition, P speciation, electron microscopy, X-ray diffraction) evidence anoxic to sulfidic bottom water and sediment conditions throughout the deposition of black shale. These extreme redox conditions persisted and were periodically punctuated by short-termed periods with less reducing bottom waters irrespective of paleo-water depth. Sediment supply at both sites was generally dominated by marine material (carbonate, organic matter, opal) although relationships of detrital proxies as well as glauconitic horizons support some influence of turbidites, winnowing bottom currents and/or variable detritus sources, along with less reducing bottom water at the proposed shallower location (ODP Site 1259). At Site 1261, located at greater paleo-depth, redox fluctuations were more regular, and steady hemipelagic sedimentation sustained the development of mostly undisturbed lamination in the sedimentary record. Strong similarities of the studied deposits exist with the stratigraphic older Cenomanian-Turonian OAE2 black shale sections at Demerara Rise, suggesting that the primary mechanisms controlling continental supply and ocean redox state were time-invariant and kept the western equatorial Atlantic margin widely anoxic over millions of years.

(Appendix A) Sedimentation rate, geochemical and environmental magnetic proxies of the samples of the Metochia section, on the island of Gavdos, south of Crete

The upper Tortonian Metochia marls on the island of Gavdos provide an ideal geological archive to trace variations in Aegean sediment supply as well as changes in the North African monsoon system. A fuzzy-cluster analysis on the multiproxy geochemical and rock magnetic dataset of the astronomically tuned sedimentary succession shows a dramatic shift in the dominance of 'Aegean tectonic' clusters to 'North African climate' clusters. The tectonic signature, traced by the starvation of the Cretan sediment, now enables to date the late Tortonian basin foundering on Crete, related to the tectonic break-up of the Aegean landmass, at c. 8.2 Ma. The synchronous decrease in the North African climate proxies is interpreted to indicate a change in the depositional conditions of the sink rather than a climatic change in the African source. This illustrates that interpretations of climate proxies require a multiproxy approach which also assesses possible contributions of regional tectonism.

Geochemical Assessment and Separation of Source Waters in the Upper Boulder River Watershed Near Boulder, MT

Environmental samples were collected at three surface water sites between 5/21/2011 and 11/21/2014 along the Upper Boulder River near Boulder Montana. The sites were located at Bernice (within the mountain block), near the High Ore drainage (near the mountain block/basin transition), and at the USGS Gauging Station near Boulder, Montana (within the basin). The parameters measured in the field were SC, temperature, and alkalinity with occasional pH measurements. We collected samples for anions, cations, and stable isotopes in the catchment. We identified endmembers by sampling snow and groundwater and determined from available data an approximate endmember for rain, snow, and groundwater. We used temporal and spatial variations of water chemistry and isotopes to generate an endmember mixing model. Groundwater was found to always be an important contributor to river flow and could increase by nearly an order of magnitude during large snowmelt events. This resulted in groundwater comprising ~20% of total river flow during snowmelt at all sites. At peak snowmelt we observed that near surface water contributions to the river were from a mixture of rain and snow. Soil water, though not sampled, was hypothesized to be an important part of the hydrologic story. If so, the endmember contributions determined in this study may be different. Groundwater may have the highest variation depending on water chemistry of shallow soil water.

Paleoenvironments and Geochemical Signals from the Late Barremian to the Middle Aptian in a Tethyan Marginal Basin, Northeast Spain: Implications for Carbon Sequestration in Restricted Basins

The hallmark of oceanic anoxic event 1a (OAE1a) (early Aptian ~125 Ma) corresponds to worldwide deposition of black shales with total organic carbon (TOC) content > 2% and a d13C positive excursion up to ~5‰. OAE1a has been related to large igneous province volcanism and dissociation of methane hydrates during the Lower Cretaceous. However, the occurrence of atypical, coeval and diachronous organic-rich deposits associated with OAE1a, which are also characterized by positive spikes of the d13C in epicontinental to restricted marine environments of the Tethys Ocean, indicates localized responses decoupled from complex global forcing factors. The present research is a high-resolution, multiproxy approach to assess the paleoenvironmental conditions that led to enhanced carbon sequestration from the late Barremian to the middle Aptian in a restricted, Tethyan marginal basin prior to and during OAE1a. I studied the lower 240 m of the El Pui section, Organyà Basin, Spanish Pyrenees. The basin developed as the result of extensional tectonism linked to the opening of the Atlantic Ocean. At the field scale the section consists of a sequence of alternating beds of cm – m-scale, medium-gray to grayish-black limestones and marlstones with TOC up to ~4%. The results indicate that the lowest 85 m of the section, from latest Barremian –earliest Aptian, characterize a deepening phase of the basin concomitant with sustained riverine flux and intensified primary productivity. These changes induced a shift in the sedimentation pattern and decreased the oxygen levels in the water column through organic matter respiration and limited ventilation of the basin. The upper 155 m comprising the earliest – late-early Aptian document the occurrence of OAE1a and its associated geochemical signatures (TOC up to 3% and a positive shift in d13C of ~5‰). However, a low enrichment of redox-sensitive trace elements indicates that the basin did not achieve anoxic conditions. The results also suggest that a shallower-phase of the basin, coeval with platform progradation, may have increased ventilation of the basin at the same time that heightened sedimentation rates and additional input of organic matter from terrestrial sources increased the burial and preservation rate of TOC in the sediment.

Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins.

In this study, we carried out a comparative analysis between two classical methodologies to prospect residue contacts in proteins: the traditional cutoff dependent (CD) approach and cutoff free Delaunay tessellation (DT). In addition, two alternative coarse-grained forms to represent residues were tested: using alpha carbon (CA) and side chain geometric center (GC). A database was built, comprising three top classes: all alpha, all beta, and alpha/beta. We found that the cutoff value? at about 7.0 A emerges as an important distance parameter.? Up to 7.0 A, CD and DT properties are unified, which implies that at this distance all contacts are complete and legitimate (not occluded). We also have shown that DT has an intrinsic missing edges problem when mapping the first layer of neighbors. In proteins, it may produce systematic errors affecting mainly the contact network in beta chains with CA. The almost-Delaunay (AD) approach has been proposed to solve this DT problem. We found that even AD may not be an advantageous solution. As a consequence, in the strict range up ? to 7.0 A, the CD approach revealed to be a simpler, more complete, and reliable technique than DT or AD. Finally, we have shown that coarse-grained residue representations may introduce bias in the analysis of neighbors in cutoffs up to ? 6.8 A, with CA favoring alpha proteins and GC favoring beta proteins. This provides an additional argument pointing to ? the value of 7.0 A as an important lower bound cutoff to be used in contact analysis of proteins.