The response of soil microbial diversity and abundance to long-term application of biosolids

The disposal of biosolids poses a major environmental and economic problem. Agricultural use is generally regarded as the best means of disposal. However, its impact on soil ecosystems remains uncertain. Biosolids can improve soil properties by supplying nutrients and increasing organic matter content but there is also a potentially detrimental effect arising from the introduction of heavy metals into soils. To assess the balance between these competing effects on soil health, we investigated soil bacterial and fungal diversity and community structure at a site that has been dedicated to the disposal of sewage sludge for over 100 years. Terminal restriction fragment length polymorphism (T-RFLP) was used to characterize the soil microbial communities. The most important contaminants at the site were Ni, Cu, Zn, Cd, and Pb. Concentrations were highly correlated and Zn concentration was adopted as a good indicator of the overall (historical) biosolids loading. A biosolids loading, equivalent to 700–1000 mg kg−1 Zn appeared to be optimal for maximum bacterial and fungal diversity. This markedly exceeds the maximum soil Zn concentration of 300 mg kg−1permitted under the current UK Sludge (use in agriculture) Regulations. Redundancy analysis (RDA) suggested that the soil microbial communities had been altered in response to the accumulation of trace metals, especially Zn, Cd, and Cu. We believe this is the first time the trade-off between positive and negative effects of long term (>100 years) biosolids disposal on soil microorganisms have been observed in the field situation

Three-dimensional quantification of soil hydraulic properties using X-ray computed tomography and image-based modeling

We demonstrate the application of a high-resolution X-ray Computed Tomography (CT) method to quantify water distribution in soil pores under successive reductive drying. We focus on the wet end of the water release characteristic (WRC) (0 to −75 kPa) to investigate changes in soil water distribution in contrasting soil textures (sand and clay) and structures (sieved and field structured) and to determine the impact of soil structure on hydraulic behavior. The 3-D structure of each soil was obtained from the CT images (at a 10 μm resolution). Stokes equations for flow were solved computationally for each measured structure to estimate hydraulic conductivity. The simulated values obtained compared extremely well with the measured saturated hydraulic conductivity values. By considering different sample sizes we were able to identify the smallest possible representative sample size which is required to determine a globally valid hydraulic conductivity

SNi from SN2: a front-face mechanism ‘synthase’ engineered from a retaining hydrolase

SNi or SNi-like mechanisms, in which leaving group departure and nucleophile approach occur on the same ‘front’ face, have been observed previously experimentally and computationally in both the chemical and enzymatic (glycosyltransferase) substitution reactions of α-glycosyl electrophiles. Given the availability of often energetically comparable competing pathways for substitution (SNi vs SN1 vs SN2) the precise modulation of this archetypal reaction type should be feasible. Here, we show that the drastic engineering of a protein that catalyzes substitution, a retaining β-glycosidase (from Sulfolobus solfataricus SSβG), apparently changes the mode of reaction from “SN2” to “SNi”. Destruction of the nucleophilic Glu387 of SSβG-WT through Glu387Tyr mutation (E387Y) created a catalyst (SSβG-E387Y) with lowered but clear transglycosylation substitution activity with activated substrates, altered substrate and reaction preferences and hence useful synthetic (‘synthase’) utility by virtue of its low hydrolytic activity with unactivated substrates. Strikingly, the catalyst still displayed retaining β stereoselectivity, despite lacking a suitable nucleophile; pH-activity profile, mechanism-based inactivators and mutational analyses suggest that SSβG-E387Y operates without either the use of nucleophile or general acid/base residues, consistent with a SNi or SNi-like mechanism. An x-ray structure of SSβG-E387Y and subsequent metadynamics simulation suggest recruitment of substrates aided by a π-sugar interaction with the introduced Tyr387 and reveal a QM/MM free energy landscape for the substitution reaction catalyzed by this unnatural enzyme similar to those of known natural, SNi-like glycosyltransferase (GT) enzymes. Proton flight from the putative hydroxyl nucleophile to the developing p-nitrophenoxide leaving group of the substituted molecule in the reactant complex creates a hydrogen bond that appears to crucially facilitate the mechanism, mimicking the natural mechanism of SNi-GTs. An oxocarbenium ion-pair minimum along the reaction pathway suggests a step-wise SNi-like DN*ANss rather than a concerted SNi DNAN mechanism. This first observation of a front face mechanism in a β-retaining glycosyl transfer enzyme highlights, not only that unusual SNi reaction pathways may be accessed through direct engineering of catalysts with suitable environments, but also suggests that ‘β-SNi’ reactions are also feasible for glycosyl transfer enzymes and the more widespread existence of SNi or SNi-like mechanism in nature

Measuring alcohol consumption for genomic meta-analyses of alcohol intake: opportunities and challenges

Whereas moderate drinking may have health benefits, excessive alcohol consumption causes many important acute and chronic diseases and is the third leading contributor to preventable death in the United States. Twin studies suggest that alcohol-consumption patterns are heritable (50%); however, multiple genetic variants of modest effect size are likely to contribute to this heritable variation. Genome-wide association studies provide a tool for discovering genetic loci that contribute to variations in alcohol consumption. Opportunities exist to identify susceptibility loci with modest effect by meta-analyzing together multiple studies. However, existing studies assessed many different aspects of alcohol use, such as typical compared with heavy drinking, and these different assessments can be difficult to reconcile. In addition, many studies lack the ability to distinguish between lifetime and recent abstention or to assess the pattern of drinking during the week, and a variety of such concerns surround the appropriateness of developing a common summary measure of alcohol intake. Combining such measures of alcohol intake can cause heterogeneity and exposure misclassification, cause a reduction in power, and affect the magnitude of genetic association signals. In this review, we discuss the challenges associated with harmonizing alcohol-consumption data from studies with widely different assessment instruments, with a particular focus on large-scale genetic studies

Have missing markets for ecological goods and services affected modelling of terrestrial C and N fluxes?

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Time-dependent sorption of Cd2+ on CaX zeolite : experimental observations and model predictions.

The effect of prolonged contact time (up to 130 days) on the immobilization of Cd by sorption to calcium exchanged zeolite-X (CaX), under environmentally relevant conditions, was studied using both isotopic exchange and extended X-ray absorption fine structure spectroscopy (EXAFS). Sorption and isotopic exchange measurements revealed time-dependent Cd sorption and indicated the movement of Cd2+ ions into less accessible sites due to ageing. EXAFS suggested progressive fixation of Cd in the double six-ring (D6R) unit of the CaX structure. Proportional allocation of the apparent Cd–Si bond distance to two ‘end-members’, across all contact times, indicated that the bond distance for labile Cd was 3.41 Å and for non-labile (or fixed) Cd was 3.47 Å

Kinetics of Cd sorption, desorption and fixation by calcite : a long-term radiotracer study.

Time-dependent sorption and desorption of Cd on calcite was studied over 210 days utilizing 109Cd as a tracer to distinguish between ‘labile’ and ‘non-labile’ forms of sorbed Cd. Stabilizing the calcite suspensions for 12 months under atmospheric PCO2 and controlled temperature was necessary to reliably follow Cd dynamics following initial sorption. Results revealed time-dependant Cd sorption and marked desorption hysteresis by calcite under environmentally relevant conditions. Data obtained were fitted to a first-order kinetic model and a concentric shell diffusion model. Both models described the progressive transfer of Cd2+ to a less reactive form within calcite and subsequent desorption of Cd subject to different initial contact times. The kinetic model provided a better fit to the combined sorption and desorption data (R2 = 0.992). It differentiates between two ‘pools’ of sorbed Cd2+ on calcite, ‘labile’ and ‘non-labile’, in which labile sorbed Cd is in immediate equilibrium with the free Cd2+ ion activity in solution whereas non-labile Cd is kinetically restricted. For the diffusion model (R2 = 0.959), the rate constants describing Cd dynamics in calcite produced a half-life for Cd desorption of 175 d, for release to a ‘zero-sink’ solution. Results from this study allow comment on the likely mechanisms occurring at the calcite surface following long-term Cd sorption

Kinetics of zinc and cadmium release in freshly contaminated soils.

The kinetics of metal release from the solid phase to solution was measured on two sets of 14 freshly contaminated soils with diverse properties. From measurements of metal concentrations in extracted soil pore water, the amount accumulated from the soil by diffusive gradients in thin-film (DGT) devices, and the distribution coefficient for labile metal, Kdl, estimated by isotopic exchange, we calculated the response time, Tc, of the soil-solution system to the removal of metal by DGT and the rate constant for release from the solid phase, k−1. Resupply was so fast for Zn that Tc (and k−1) could be measured only in three of the soils, with either a silty or a sandy loam texture and low to intermediate pH (4.84–5.66). In only six clay soils was resupply of Cd too fast to measure. The generally slower release rates of Cd compared to Zn may reflect the 100-fold lower concentration of Cd, which allowed a greater proportion of it to occupy stronger binding sites with slower release rates. The rate constants derived indicate that supply from the solid phase to solution will not limit uptake of Cd or Zn by plants in clay soils, but it could be a factor in sandy or silty soils with a low pH. These findings suggest that risk assessment of clay soils could be undertaken using measurements of metals in soil solution. However, devices such as DGT, which respond to the kinetics of supply, are necessary to assess available metal in low pH, sandy, and silty soils

Transfer of cadmium and mercury to sheep tissues

Toxic heavy metals such as cadmium and mercury can enter the diet of farm animals by a variety of environmental exposure routes and, hence, contaminate food products derived from those animals. Therefore, there is a need to be able to predict the likely levels of contamination in animal tissues if exposed to a contaminated diet and also to estimate how rapidly an animal will decontaminate once the source of contamination is removed from the diet. Data on the transfer and excretion rates of Cd and Hg from tissues have previously been inadequate to allow the development of dynamic models to predict changes in the degree of contamination of different tissues of ruminants. A study is described during which a group of sheep were given a single oral administration of 109Cd and 203Hg. Measurements of the concentrations of the radioisotopes in tissue samples were subsequently made over a period of 1 year. The resultant data were used to develop compartment models to describe the behavior of the two metals in sheep tissues. To our knowledge the models developed are the first to allow the time-dependent prediction of the potential Cd and Hg contamination of animal-derived food products. Previously only advised transfer coefficients were available; we demonstrate that these are of little value for cadmium and mercury due to their slow rates of accumulation and excretion