A laboratory study to estimate pore geometric parameters of sandstones using complex conductivity and nuclear magnetic resonance for permeability prediction

We estimate parameters from the Katz and Thompson permeability model using laboratory complex electrical conductivity (CC) and nuclear magnetic resonance (NMR) data to build permeability models parameterized with geophysical measurements. We use the Katz and Thompson model based on the characteristic hydraulic length scale, determined from mercury injection capillary pressure estimates of pore throat size, and the intrinsic formation factor, determined from multi-salinity conductivity measurements, for this purpose. Two new permeability models are tested, one based on CC data and another that incorporates CC and NMR data. From measurements made on forty-five sandstone cores collected from fifteen different formations, we evaluate how well the CC relaxation time and the NMR transverse relaxation times compare to the characteristic hydraulic length scale and how well the formation factor estimated from CC parameters compares to the intrinsic formation factor. We find: (1) the NMR transverse relaxation time models the characteristic hydraulic length scale more accurately than the CC relaxation time (R2 of 0.69 and 0.39 and normalized root mean square errors (NRMSE) of 0.16 and 0.20, respectively); (2) the CC estimated formation factor is well correlated with the intrinsic formation factor (NRMSE=0.23). We demonstrate that that permeability estimates from the joint-NMR-CC model (NRMSE=0.13) compare favorably to estimates from the Katz and Thompson model (NRMSE=0.074). This model advances the capability of the Katz and Thompson model by employing parameters measureable in the field giving it the potential to more accurately estimate permeability using geophysical measurements than are currently possible

Simulation of soil water flow and heat transport in drip irrigated potato field with raised beds and full plastic-film mulch in a semiarid area

Surface drip irrigation with full plastic-film mulch can increase crop yield and save water by regulating soil water and heat conditions for potato (Solanum tuberosum L.) production with raised beds in semiarid area where the rainfall is scarce and evaporation is high. For efficient use of plastic film mulch an understanding of the soil water flow and heat transport is needed. Here we use a model (HYRUS-2D) which is calibrated with field experiments to simulate soil water movement and heat transport. The field experiments were conducted with three treatments, characterized as wetted soil percentages: 35% (P1), 55% (P2), and 75% (P3). Furthermore, the effects of the uncertainty of key soil hydraulic parameters on soil water contents were evaluated using three approaches: (1) soil hydraulic parameters estimated from measured soil textural information (S1); (2) from experimentally measured soil water retention curve (S2); and (3) from inverse modeling (S3). The performance of S2 was the worst in all treatments; the root mean square error (RMSE) was > 0.05 cm3 cm-3. The performance of S3 was the best with RMSE ranged from 0.015 to 0.038 cm3 cm-3 at 10-50 cm soil depth. The simulated soil water in the raised bed decreased quickly after irrigation, maintaining adequate aeration for potato growth, irrespective of the wetted soil percentage. The downward transport of soil water still existed during the second and third days after irrigation in the simulations of the P2 and P3 treatments. The soil temperatures between the P1 and P3 treatments were similar. In conclusion, the HYDRUS-2D simulations could be used to estimate the soil hydraulic and thermal parameters with inverse modeling. The calibrated model can be used in the design and management of surface drip irrigation with raised beds and full plastic-film mulch to provide favorable soil water and heat conditions for potato growth

The interplay between transport and reaction rates as controls on nitrate attenuation in permeable, streambed sediments

Anthropogenic nitrogen fixation and subsequent use of this nitrogen as fertilizer has greatly disturbed the global nitrogen cycle. Rivers are recognized hotspots of nitrogen removal in the landscape as interaction between surface water and sediments creates heterogeneous redox environments conducive for nitrogen transformations. Our understanding of riverbed nitrogen dynamics to date comes mainly from shallow sediments or hyporheic exchange flow pathways with comparatively little attention paid to groundwater-fed, gaining reaches. We have used 15N techniques to quantify in situ rates of nitrate removal to 1m depth within a groundwater-fed riverbed where subsurface hydrology ranged from strong upwelling to predominantly horizontal water fluxes. We combine these rates with detailed hydrologic measurements to investigate the interplay between biogeochemical activity and water transport in controlling nitrogen attenuation along upwelling flow pathways. Nitrate attenuation occurred via denitrification rather than dissimilatory nitrate reduction to ammonium or anammox (range = 12 to >17000 nmol 15N L-1 h-1). Overall, nitrate removal within the upwelling groundwater was controlled by water flux rather than reaction rate (i.e. Damköhler numbers 80% of nitrate removal occurs within sediments not exposed to hyporheic exchange flows under baseflow conditions, illustrating the importance of deep sediments as nitrate sinks in upwelling systems

Laboratory spectral induced polarisation signatures associated with iron and manganese oxide dissolution because of anaerobic degradation

Degradation of organic chemicals in natural soils depends on oxidation-reduction conditions. To protect our groundwater resources we need to understand the degradation processes under anaerobic conditions. Available iron and manganese oxides are used as electron acceptors for anaerobic degradation and are reduced to the dissolved form of metallic cations in pore water. To monitor this process is a challenge, because anaerobic conditions are difficult to sample directly without introducing oxygen. A few studies have shown an impact of iron reduction on spectral induced polarisation (SIP) signature, often associated with bacterial growth. Our objective is to study the impact of iron and manganese oxide dissolution, caused by degradation of an organic compound, with spectral induced polarisation signatures. Twenty-six vertical columns (30cm high, inner diameter 4.6cm) were filled with a sand rich in oxides (manganese and iron) with a static water table in the middle. In half of the columns, a 2cm high contaminated layer was installed just above the water table. As the contaminant degrades, the initial oxygen is consumed and anaerobic conditions form Every three days over a period of one month, spectral induced polarisation (twenty frequencies between 5mHz and 10kHz) data were collected on six columns: three contaminated replicates and three control replicates. Chemical analysis was done on twenty columns assigned for destructive water sampling, ten contaminated columns and ten control. The results show an increase of the real conductivity associated with the degradation processes, independent of frequency. Compared with the pore water electrical conductivity in the saturated zone, the real conductivity measurement revealed the formation of surface conductivity before iron was released in the pore water. In parallel, we also observed an evolution of the imaginary conductivity in both saturated and unsaturated zones at frequencies below 1Hz. Overall, the anaerobic reduction of iron and manganese oxide during the organic degradation increased both the conductive and polarisation component of the complex conductivity

Diffusive equilibrium in thin films provides evidence of suppression of hyporheic exchange and large-scale nitrate transformation in a groundwater-fed river

The hyporheic zone of riverbed sediments has the potential to attenuate nitrate from upwelling, polluted groundwater. However, the coarse-scale (5–10 cm) measurement of nitrogen biogeochemistry in the hyporheic zone can often mask fine-scale (<1 cm) biogeochemical patterns, especially in near-surface sediments, leading to incomplete or inaccurate representation of the capacity of the hyporheic zone to transform upwelling NO3−. In this study, we utilised diffusive equilibrium in thin-films samplers to capture high resolution (cm-scale) vertical concentration profiles of NO3−, SO42−, Fe and Mn in the upper 15 cm of armoured and permeable riverbed sediments. The goal was to test whether nitrate attenuation was occurring in a sub-reach characterised by strong vertical (upwelling) water fluxes. The vertical concentration profiles obtained from diffusive equilibrium in thin-films samplers indicate considerable cm-scale variability in NO3− (4.4 ± 2.9 mg N/L), SO42− (9.9 ± 3.1 mg/l) and dissolved Fe (1.6 ± 2.1 mg/l) and Mn (0.2 ± 0.2 mg/l). However, the overall trend suggests the absence of substantial net chemical transformations and surface-subsurface water mixing in the shallow sediments of our sub-reach under baseflow conditions. The significance of this is that upwelling NO3−-rich groundwater does not appear to be attenuated in the riverbed sediments at <15 cm depth as might occur where hyporheic exchange flows deliver organic matter to the sediments for metabolic processes. It would appear that the chemical patterns observed in the shallow sediments of our sub-reach are not controlled exclusively by redox processes and/or hyporheic exchange flows. Deeper-seated groundwater fluxes and hydro-stratigraphy may be additional important drivers of chemical patterns in the shallow sediments of our study sub-reach. Copyright © 2014 John Wiley & Sons, Ltd

Characterizing the heterogeneity of karst critical zone and its hydrological function:an integrated approach

Spatial heterogeneity in the subsurface of karst environments is high, as evidenced by the multi‐phase porosity of carbonate rocks and complex landform features that result in marked variability of hydrological processes in space and time. This includes complex exchange of various flows (e.g. fast conduit flows and slow fracture flows) in different locations. Here, we integrate various “state‐of‐the‐art” methods to understand the structure and function of this poorly‐constrained critical zone environment. Geophysical, hydrometric and tracer tools are used to characterize the hydrological functions of the cockpit karst critical zone in the small catchment of Chenqi, Guizhou province, China. Geophysical surveys, using electrical resistivity tomography (ERT), inferred the spatial heterogeneity of permeability in the epikarst and underlying aquifer. Water tables in depression wells in valley bottom areas, as well as discharge from springs on steeper hillslopes and at the catchment outlet, showed different hydrodynamic responses to storm event rainwater recharge and hillslope flows. Tracer studies using water temperatures and stable water isotopes (δD and δ18O) could be used alongside insights into aquifer permeability from ERT surveys to explain site‐ and depth‐dependent variability in the groundwater response in terms of the degree to which “new” water from storm rainfall recharges and mixes with “old” pre‐event water in karst aquifers. This integrated approach reveals spatial structure in the karst critical zone and provides a conceptual framework of hydrological functions across spatial and temporal scales

Deep roots and soil structure

In this opinion article we examine the relationship between penetrometer resistance and soil depth in the field. Assuming that root growth is inhibited at penetrometer resistances > 2.5 MPa, we conclude that in most circumstances the increases in penetrometer resistance with depth are sufficiently great to confine most deep roots to elongating in existing structural pores. We suggest that deep rooting is more likely related to the interaction between root architecture and soil structure than it is to the ability of a root to deform strong soil. Although the ability of roots to deform strong soil is an important trait, we propose it is more closely related to root exploration of surface layers than deep rooting

Stoichiometric constraints on the microbial processing of carbon with soil depth along a riparian hillslope

Soil organic matter (SOM) content is a key indicator of riparian soil functioning and in the provision of ecosystem services such as water retention, flood alleviation, pollutant attenuation and carbon (C) sequestration for climate change mitigation. Here, we studied the importance of microbial biomass and nutrient availability in regulating SOM turnover rates. C stabilisation in soil is expected to vary both vertically, down the soil profile and laterally across the riparian zone. In this study, we evaluated the influence of five factors on C mineralization (Cmin): (i) substrate quantity, (ii) substrate quality, (iii) nutrient (C, N and P) stoichiometry, (iv) soil microbial activity with proximity to the river (2 to 75 m), and (v) as a function of soil depth (0 – 3 m). Substrate quality, quantity and nutrient stoichiometry were evaluated using high and low molecular weight 14C-labelled dissolved organic (DOC) along with different nutrient additions. Differences in soil microbial activity with proximity to the river and soil depth were assessed by comparing initial (immediate) Cmin rates and cumulative C mineralized at the end of the incubation period. Overall, microbial biomass C (MBC), organic matter (OM) and soil moisture content (MC) proved to be the major factors controlling rates of Cmin at depth. Differences in the immediate and medium-term response (42 days) of Cmin suggested that microbial growth increased and carbon use efficiency (CUE) decreased down the soil profile. Inorganic N and/or P availability had little or no effect on Cmin suggesting that microbial community growth and activity is predominantly C limited. Similarly, proximity to the watercourse also had relatively little effect on Cmin. This work challenges current theories suggesting that areas adjacent to watercourse process C differently from upslope areas. In contrast, our results suggest that substrate quality and microbial biomass are more important in regulating C processing rates rather than proximity to a river

Fine-Scale in Situ Measurement of Riverbed Nitrate Production and Consumption in an Armored Permeable Riverbed

Alteration of the global nitrogen cycle by man has increased nitrogen loading in waterways considerably, often with harmful consequences for aquatic ecosystems. Dynamic redox conditions within riverbeds support a variety of nitrogen transformations, some of which can attenuate this burden. In reality, however, assessing the importance of processes besides perhaps denitrification is difficult, due to a sparseness of data, especially in situ, where sediment structure and hydrologic pathways are intact. Here we show in situ within a permeable riverbed, through injections of 15N-labeled substrates, that nitrate can be either consumed through denitrification or produced through nitrification, at a previously unresolved fine (centimeter) scale. Nitrification and denitrification occupy different niches in the riverbed, with denitrification occurring across a broad chemical gradient while nitrification is restricted to more oxic sediments. The narrow niche width for nitrification is in effect a break point, with the switch from activity “on” to activity “off” regulated by interactions between subsurface chemistry and hydrology. Although maxima for denitrification and nitrification occur at opposing ends of a chemical gradient, high potentials for both nitrate production and consumption can overlap when groundwater upwelling is strong

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies.

CAPRISA, 2014.Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development