Peat Formation Concentrates Arsenic Within Sediment Deposits of the Mekong Delta

Mekong River Delta sediment bears arsenic that is released to groundwater under anaerobic conditions over the past several thousand years. The oxidation state, speciation, and distribution of arsenic and the associated iron bearing phases are crucial determinants of As reactivity in sediments. Peat from buried mangrove swamps in particular may be an important host, source, or sink of arsenic in the Mekong Delta. The total concentration, speciation, and reactivity of arsenic and iron were examined in sediments in a Mekong Delta wetland by X-ray fluorescence spectrometry (XRF), X-ray absorption spectroscopy (XAS), and selective chemical extractions. Total solid-phase arsenic concentrations in a peat layer at a depth of 6 m below ground increased 10-fold relative to the overlying sediment. Extended X-ray absorption fine structure (EXAFS) spectroscopy revealed that arsenic in the peat was predominantly in the form of arsenian pyrite. Arsenic speciation in the peat was examined further at the micron-scale using μXRF and μX-ray absorption near-edge structure (XANES) spectroscopy coupled with principal component analysis. The multiple energy μXRF mapping and μXANES routine was repeated for both iron and sulfur phase analyses. Our μXRF/μXANES analyses confirm arsenic association with pyrite – a less reactive host phase than iron (hydr)oxides under anaerobic conditions. The arsenian pyrite likely formed upon deposition/formation of the peat in a past estuarine environment (∼ 5.5 ka BP), a process that is not expected under current geochemical conditions. Presently, arsenian pyrite is neither a source nor a sink for aqueous arsenic in our sediment profile, and under present geochemical conditions represents a stable host of As under the reducing aquifer conditions of the Mekong Delta. Furthermore, organic carbon within the peat is unable to fuel Fe(III) reduction, as noted by the persistence of goethite which can be reduced microbially with the addition of glucose

Human and mouse essentiality screens as a resource for disease gene discovery

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery. Discovery of causal variants for monogenic disorders has been facilitated by whole exome and genome sequencing, but does not provide a diagnosis for all patients. Here, the authors propose a Full Spectrum of Intolerance to Loss-of-Function (FUSIL) categorization that integrates gene essentiality information to aid disease gene discovery

Reactivity and Speciation of Mineral-Associated Arsenic in Seasonal and Permanent Wetlands of the Mekong Delta

Millions of people in the deltaic regions of S/SE Asia regularly consume As contaminated groundwater. Arsenic persists within these groundwaters despite being flushed by several pore volumes of recharge, indicative of an in situ solid phase source. Despite the importance of this solid phase source, the identity and reactivity of the minerals hosting and releasing As in the deltaic aquifers remain poorly constrained. Here we seek to define the chemistry and reactivity of As and its host minerals in aquifer sediments recharged by both seasonally saturated and permanent wetlands in the Mekong Delta of Cambodia. Sediment cores were retrieved to depths of up to 30 m. Selective extractions on near-surface sediments (to depths of 4–6 m) indicate that more than a third (27–50%) of the Fe in the profile is ‘‘reducible” (citrate–bicarbonate–dithionite–extractable) – nominally consisting of Fe(III) oxides. The Fe(III) oxide fraction was approximately the same under seasonal wetlands (mean = 39%) compared with sediments from beneath permanent wetlands (mean = 37%). Correspondingly, Fe K-edge extended X-ray absorption fine structure (EXAFS) spectra analysis indicates that the Fe mineral phases are predominantly goethite and hematite (30–50%). Analysis of solid phase As speciation by X-ray absorption near edge structure (XANES) spectroscopy showed arsenate in the shallowest sediments (upper 1 and 4 m of seasonal and permanent wetlands), and arsenite and/or As sulfides as the dominant phases in the deeper sediments. The reducible As fraction ranged from 17% to 42% of the total As at both sites. The exception was found in a peat layer at 6 m beneath the seasonal wetland, in which only 1% of the total As was reducible. Arsenian pyrite was the predominant form of As in the peat. Thus, a pool of As hosted by reducible mineral phases persists in sediments below both the seasonal and permanently saturated wetland sites

Impacts of hydrous manganese oxide on the retention and lability of dissolved organic matter

Abstract Minerals constitute a primary ecosystem control on organic C decomposition in soils, and therefore on greenhouse gas fluxes to the atmosphere. Secondary minerals, in particular, Fe and Al (oxyhydr)oxides—collectively referred to as “oxides” hereafter—are prominent protectors of organic C against microbial decomposition through sorption and complexation reactions. However, the impacts of Mn oxides on organic C retention and lability in soils are poorly understood. Here we show that hydrous Mn oxide (HMO), a poorly crystalline δ-MnO2, has a greater maximum sorption capacity for dissolved organic matter (DOM) derived from a deciduous forest composite Oi, Oe, and Oa horizon leachate (“O horizon leachate” hereafter) than does goethite under acidic (pH 5) conditions. Nonetheless, goethite has a stronger sorption capacity for DOM at low initial C:(Mn or Fe) molar ratios compared to HMO, probably due to ligand exchange with carboxylate groups as revealed by attenuated total reflectance-Fourier transform infrared spectroscopy. X-ray photoelectron spectroscopy and scanning transmission X-ray microscopy–near-edge X-ray absorption fine structure spectroscopy coupled with Mn mass balance calculations reveal that DOM sorption onto HMO induces partial Mn reductive dissolution and Mn reduction of the residual HMO. X-ray photoelectron spectroscopy further shows increasing Mn(II) concentrations are correlated with increasing oxidized C (C=O) content (r = 0.78, P < 0.0006) on the DOM–HMO complexes. We posit that DOM is the more probable reductant of HMO, as Mn(II)-induced HMO dissolution does not alter the Mn speciation of the residual HMO at pH 5. At a lower C loading (2 × 102 μg C m−2), DOM desorption—assessed by 0.1 M NaH2PO4 extraction—is lower for HMO than for goethite, whereas the extent of desorption is the same at a higher C loading (4 × 102 μg C m−2). No significant differences are observed in the impacts of HMO and goethite on the biodegradability of the DOM remaining in solution after DOM sorption reaches steady state. Overall, HMO shows a relatively strong capacity to sorb DOM and resist phosphate-induced desorption, but DOM–HMO complexes may be more vulnerable to reductive dissolution than DOM–goethite complexes

MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography.

BACKGROUND: A central tenet of structural biology is that related proteins of common function share structural similarity. This has key practical consequences for the derivation and analysis of protein structures, and is exploited by the process of "molecular sieving" whereby a common core is progressively distilled from a comparison of two or more protein structures. This paper reports a novel web server for "sieving" of protein structures, based on the multiple structural alignment program MUSTANG. METHODOLOGY/PRINCIPAL FINDINGS: "Sieved" models are generated from MUSTANG-generated multiple alignment and superpositions by iteratively filtering out noisy residue-residue correspondences, until the resultant correspondences in the models are optimally "superposable" under a threshold of RMSD. This residue-level sieving is also accompanied by iterative elimination of the poorly fitting structures from the input ensemble. Therefore, by varying the thresholds of RMSD and the cardinality of the ensemble, multiple sieved models are generated for a given multiple alignment and superposition from MUSTANG. To aid the identification of structurally conserved regions of functional importance in an ensemble of protein structures, Lesk-Hubbard graphs are generated, plotting the number of residue correspondences in a superposition as a function of its corresponding RMSD. The conserved "core" (or typically active site) shows a linear trend, which becomes exponential as divergent parts of the structure are included into the superposition. CONCLUSIONS: The application addresses two fundamental problems in structural biology: first, the identification of common substructures among structurally related proteins--an important problem in characterization and prediction of function; second, generation of sieved models with demonstrated uses in protein crystallographic structure determination using the technique of Molecular Replacement

Sea Level Rise Induced Arsenic Release from Historically Contaminated Coastal Soils

Climate change-induced perturbations in the hydrologic regime are expected to impact biogeochemical processes, including contaminant mobility and cycling. Elevated levels of geogenic and anthropogenic arsenic are found along many coasts around the world, most notably in south and southeast Asia but also in the United States, particularly along the Mid-Atlantic coast. The mechanism by and the extent to which arsenic may be released in contaminated coastal soils due to sea level rise are unknown. Here we show a series of data from a coastal arsenic-contaminated soil exposed to sea and river waters in biogeochemical microcosm reactors across field-validated redox conditions. We find that reducing conditions lead to arsenic release from historically contaminated coastal soils through reductive dissolution of arsenic-bearing mineral oxides in both sea and river water inundations, with less arsenic release from seawater scenarios than river water due to inhibition of oxide dissolution. For the first time, we systematically display gradation of solid phase soil-arsenic speciation across defined redox windows from reducing to oxidizing conditions in natural waters by combining biogeochemical microcosm experiments and X-ray absorption spectroscopy. Our results demonstrate the threat of sea level rise stands to impact arsenic release from contaminated coastal soils by changing redox conditions