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

Forage grasses with lower uptake of casesium and strontium could provide 'safer' crops for radiologically contaminated areas

Substitution of a species or cultivar with higher uptake of an element by one with lower uptake has been proposed as a remediation strategy following accidental releases of radioactivity. However, despite the importance of pasture systems for radiological dose, species/cultivar substitution has not been thoroughly investigated for forage grasses. 397 cultivars from four forage grass species; hybrid ryegrass (Lolium perenne L. x Lolium multiflorum Lam.), perennial ryegrass (Lolium perenne L.), Italian ryegrass (Lolium multiflorum Lam.) and tall fescue (Festuca arundinacea Shreb.); were sampled from 19 field-based breeding experiments in Aberystwyth and Edinburgh (UK) in spring 2013 and analysed for caesium (Cs) and strontium (Sr) concentrations. In order to calculate concentration ratios (CRs; the concentration of an element in a plant in relation to the concentration in the soil), soils from the experiments were also analysed to calculate extractable concentrations of Cs and Sr. To test if cultivars have consistently low Cs and Sr concentration ratios, 17 hybrid ryegrass cultivars were sampled from both sites again in summer 2013 and spring and summer 2014. Tall fescue cultivars had lower Cs and Sr CRs than the other species. Three of the selected 17 hybrid ryegrass cultivars had consistently low Cs CRs, two had consistently low Sr CRs and one had consistently low Cs and Sr CRs. Cultivar substitution could reduce Cs CRs by up to 14-fold and Sr CRs by 4-fold in hybrid ryegrass. The identification of species and cultivars with consistently low CRs suggests that species or cultivar substitution could be an effective remediation strategy for contaminated areas

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

Overview of selected soil pore water extraction methods for the determination of potentially toxic elements in contaminated soils : operational and technical aspects

Chemical elements that are either present naturally in the soil or introduced by pollution are more usefully estimated in terms of ‘availability’ of the element, because this property can be related to mobility and uptake by plants. A good estimation of ‘availability’ can be achieved by measuring the concentration of the element in soil pore water. Recent achievements in analytical techniques allowed to expand the range of interest to trace elements, which play a crucial role both in contaminated and uncontaminated soils and include those defined as potentially toxic elements (PTE) in environmental studies. A complete chemical analysis of soil pore water represents a powerful diagnostic tool for the interpretation of many soil chemical phenomena relating to soil fertility, mineralogy and environmental fate. This chapter describes some of the current methodologies used to extract soil pore water. In particular, four laboratory-based methods, (1) high-speed centrifugation-filtration, (2) low (negative-)-pressure Rhizon™ samplers, (3) high-pressure soil squeezing and (4) equilibration of dilute soil suspensions, are described and discussed in detail. A number of operational factors are presented: pressure applicable (i.e. pore size involved), moisture prerequisites of the soil, pore water yielding, efficiency, duration of extraction, materials and possible contaminations for PTE studies. Some consideration is then taken to assess advantages and disadvantages of the methods, including costs and materials availability

Assessing potential risk of heavy metal exposure from consumption of home-produced vegetables by urban populations

We performed a risk assessment of metal exposure to population subgroups living on, and growing food on, urban sites. We modeled uptake of cadmium, copper, nickel, lead, and zinc for a selection of commonly grown allotment and garden vegetables. Generalized linear cross-validation showed that final predictions of Cd, Cu, Ni, and Zn content of food crops were satisfactory, whereas the Pb uptake models were less robust. We used predicted concentrations of metals in the vegetables to assess the risk of exposure to human populations from homegrown food sources. Risks from other exposure pathways (consumption of commercially produced foodstuffs, dust inhalation, and soil ingestion) were also estimated. These models were applied to a geochemical database of an urban conurbation in the West Midlands, United Kingdom. Risk, defined as a "hazard index," was mapped for three population subgroups: average person, highly exposed person, and the highly exposed infant (assumed to be a 2-year-old child). The results showed that food grown on 92% of the urban area presented minimal risk to the average person subgroup. However, more vulnerable population subgroups (highly exposed person and the highly exposed infant) were subject to hazard index values greater than unity. This study highlights the importance of site-specific risk assessment and the "suitable for use" approach to urban redevelopment

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