An emulation-based approach for interrogating reactive transport models

We present a new approach to understand the interactions among different chemical and biological processes modelled in environmental reactive transport models (RTMs) and explore how the parameterisation of these processes influences the results of multi-component RTMs. We utilize a previously published RTM consisting of 20 primary species, 20 secondary complexes, 17 mineral reactions and 2 biologically-mediated reactions which describes bio-stimulation using sediment from a contaminated aquifer. We choose a subset of the input parameters to vary over a range of values. The result is the construction of a new dataset that describes the model behaviour over a range of environmental conditions. Using this dataset to train a statistical model creates an emulator of the underlying RTM. This is a condensed representation of the original RTM that facilitates rapid exploration of a broad range of environmental conditions and sensitivities. As an illustration of this approach, we use the emulator to explore how varying the boundary conditions in the RTM describing the aquifer impacts the rates and volumes of mineral precipitation. A key result of this work is the recognition of an unanticipated dependency of pyrite precipitation on pCO2 in the injection fluid due to the stoichiometry of the microbially-mediated sulphate reduction reaction. This complex relationship was made apparent by the emulator, while the underlying RTM was not specifically constructed to create such a feedback. We argue that this emulation approach to sensitivity analysis for RTMs may be useful in discovering such new coupled sensitives in geochemical systems and for designing experiments to optimise environmental remediation. Finally, we demonstrate that this approach can maximise specific mineral precipitation or dissolution reactions by using the emulator to find local maxima, which can be widely applied in environmental systems.</p

Calcium isotope fractionation in sedimentary pore fluids from ODP Leg 175: Resolving carbonate recrystallization

We present calcium isotope data from pore fluids and solids from Ocean Drilling Program Leg 175: Sites 1081 and 1086 (off the coast of West Africa). These sites are similar with respect to geographic location, sediment age (from modern to 8 Myr), and water depth (800 m), but Site 1081 is carbonate-poor, whereas Site 1086 is carbonate-rich. Therefore, these sites are suited for the exploration of the influence of sediment type on carbonate dissolution, precipitation, and recrystallization. We use two numerical modelling approaches to explore the rates of carbonate dissolution and precipitation in the sediment column. The first is the standard diffusion-reaction approach, using the strontium concentration within the pore fluid to ascertain a dissolution rate for the carbonate, which is then applied to a second model of calcium isotopes within the pore fluid to calculate precipitation rates. Given the high sedimentation rates we also apply an advection-reaction model (Huber et al., 2017) which results in the same depth distribution of carbonate precipitation but significantly higher overall rates, which is discussed. Calcium isotope ratios in pore fluid calcium increase in zones where our model predicts carbonate precipitation, and approach isotopic equilibrium with the solid in zones where our model predicts equivalent rates of dissolution and precipitation, similar to previous findings. Contrary to previous findings in marine sediments, our model requires a calcium isotope fractionation on carbonate precipitation to fit the data, as there is an offset between the δ44Ca of the fluid and the solid. Using the zones of carbonate precipitation determined from the models and previously published carbon isotope profiles of the dissolved inorganic carbon from these sites, we suggest that the δ13C of the authigenic carbonate is uniformly lower than biogenic carbonate but by a wider range than was previously suggested

The calcium isotopic composition of carbonate hardground cements: A new record of changes in ocean chemistry?

Reconstructing changes in the calcium isotopic composition (δ44Ca) of the ocean over Earth history has been challenging. This difficulty is due to the large range of calcium isotope fractionation factors during mineral precipitation and the potential for overwriting the initial δ44Ca of minerals during shallow marine diagenesis. We present a new δ44Ca record measured in carbonate hardground cements, an inorganic carbonate-mineral precipitate that rapidly forms at or near the sediment-water interface. The range in the δ44Ca for any particular carbonate hardground cements is between 0.05 and 0.56‰. In some cases, the progressive increase in the δ44Ca during precipitation can be observed, consistent with precipitation in a ‘closed-system’. Our data show an average calcium isotope fractionation during carbonate hardground cement precipitation that is −0.57 ± 0.27‰, similar to the calcium isotope fractionation factor for inorganic calcite precipitates in previous laboratory and modelling studies, and closer to what is considered a kinetic end member calcium isotope fractionation than growth at equilibrium. This is consistent with the rapid carbonate mineral precipitation expected for carbonate hardground cements. Our δ44Ca record over the Phanerozoic is similar to other calcium-bearing mineral records over the same time interval, with average δ44Ca becoming lower going back in time by about 0.5 to 0.7‰. Our results add further support for the evolution of seawater δ44Ca over time, and we discuss the possible causes of these changes with suggestions for future studies

Calcium isotope fractionation during microbially induced carbonate mineral precipitation

We report the calcium isotope fractionation during the microbially-induced precipitation of calcium carbonate minerals in pure cultures of the marine sulfate-reducing bacterium Desulfovibrio bizertensis. These data are used to explore how the calcium isotope fractionation factor during microbially-induced carbonate mineral precipitation differs from the better-constrained calcium isotope fractionation factors during biogenic or abiotic carbonate mineral precipitation. Bacterial growth was then modulated with antibiotics, and the evolution of δ44Ca in solution was monitored under different microbial growth rates. The faster the microbial growth rate, the larger the calcium isotope fractionation during carbonate mineral precipitation, with Δ44Ca(s-f) ranging from −1.07‰ to −0.48‰. The reported calcium isotope fractionation can help us understand the link between calcium isotope fractionation and microbial metabolism in carbonate minerals precipitated during sedimentary diagenesis

The Carbon-Sulfur Link in the Remineralization of Organic Carbon in Surface Sediments

Here we present the carbon isotopic composition of dissolved inorganic carbon (DIC) and the sulfur isotopic composition of sulfate, along with changes in sulfate concentrations, of the pore fluid collected from a series of sediment cores located along a depth transect on the Iberian Margin. We use these data to explore the coupling of microbial sulfate reduction (MSR) to organic carbon oxidation in the uppermost (up to nine meters) sediment. We argue that the combined use of the carbon and sulfur isotopic composition, of DIC and sulfate respectively, in sedimentary pore fluids, viewed through a δ13CDIC vs. δ34SSO4 cross plot, reveals significant insight into the nature of carbon-sulfur coupling in marine sedimentary pore fluids on continental margins. Our data show systemic changes in the carbon and sulfur isotopic composition of DIC and sulfate (respectively) where, at all sites, the carbon isotopic composition of the DIC decreases before the sulfur isotopic composition of sulfate increases. We compare our results to global data and show that this behavior persists over a range of sediment types, locations and water depths. We use a reactive-transport model to show how changes in the amount of DIC in seawater, the carbon isotopic composition of organic matter, the amount of organic carbon oxidation by early diagenetic reactions, and the presence and source of methane influence the carbon and sulfur isotopic composition of sedimentary pore fluids and the shape of the δ13CDIC vs. δ34SSO4 cross plot. The δ13C of the DIC released during sulfate reduction and sulfate-driven anaerobic oxidation of methane is a major control on the minimum δ13CDIC value in the δ13CDIC vs. δ34SSO4 cross plot, with the δ13C of the organic carbon being important during both MSR and combined sulfate reduction, sulfate-driven AOM and methanogenesis

Assessing Sedimentary Boundary Layer Calcium Carbonate Precipitation and Dissolution Using the Calcium Isotopic Composition of Pore Fluids

We present pore fluid geochemistry, including major ion and trace metal concentrations and the isotopic composition of pore fluid calcium and sulfate, from the uppermost meter of sediments from the Gulf of Aqaba (Northeast Red Sea) and the Iberian Margin (North Atlantic Ocean). In both the locations, we observe strong correlations among calcium, magnesium, strontium, and sulfate concentrations as well as the sulfur isotopic composition of sulfate and alkalinity, suggestive of active changes in the redox state and pH that should lead to carbonate mineral precipitation and dissolution. The calcium isotope composition of pore fluid calcium (δ44Ca) is, however, relatively invariant in our measured profiles, suggesting that carbonate mineral precipitation is not occurring within the boundary layer at these sites. We explore several reasons why the pore fluid δ44Ca might not be changing in the studied profiles, despite changes in other major ions and their isotopic composition, including mixing between the surface and deep precipitation of carbonate minerals below the boundary layer, the possibility that active iron and manganese cycling inhibits carbonate mineral precipitation, and that mineral precipitation may be slow enough to preclude calcium isotope fractionation during carbonate mineral precipitation. Our results suggest that active carbonate dissolution and precipitation, particularly in the diffusive boundary layer, may elicit a more complex response in the pore fluid δ44Ca than previously thought

Creek Dynamics Determine Pond Subsurface Geochemical Heterogeneity in East Anglian (UK) Salt Marshes

Salt marshes are complex systems comprising ephemerally flooded, vegetated platforms hydraulically fed by tidal creeks. Where drainage is poor, formation of saline-water ponds can occur. Within East Anglian (UK) salt marshes, two types of sediment chemistries can be found beneath these ponds; iron-rich sediment, which is characterized by high ferrous iron concentration in subsurface porewaters (up to 2 mM in the upper 30 cm); and sulfide-rich sediment, which is characterized by high porewater sulfide concentrations (up to 8 mM). We present 5 years of push-core sampling to explore the geochemistry of the porewater in these two types of sediment. We suggest that when organic carbon is present in quantities sufficient to exhaust the oxygen and iron content within pond sediments, conditions favor the presence of sulfide-rich sediments. In contrast, in pond sediments where oxygen is present, primarily through bioirrigation, reduced iron can be reoxidised and thus recycled for further reduction, favoring the perpetuation of iron-rich sedimentary conditions. We find these pond sediments can alter significantly over an annual timescale. We carried out a drone survey, with ground-truthed measurements, to explore the spatial distribution of geochemistry in these ponds. Our results suggest that a pond’s proximity to a creek partially determines the pond subsurface geochemistry, with iron-rich ponds tending to be closer to large creeks than sulfide-rich ponds. We suggest differences in surface delivery of organic carbon, due to differences in the energy of the ebb flow, or the surface/subsurface delivery of iron may control the distribution. This could be amplified if tidal inundations flush ponds closer to creeks more frequently, removing carbon and flushing with oxygen. These results suggest that anthropogenic creation of drainage ditches could shift the distribution of iron- and sulfide-rich ponds and thus have an impact on nutrient, trace metal and carbon cycling in salt marsh ecosystems.This work was funded partially by an ERC starting investigator grant (CARBONSINK – 307582) to AVT as well as NERC RG94667 to AVT. Funding for AH was provided by a NERC DTP grant (LBAG/199.02.RG91292)

The USDA Barley Core Collection:Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections