Improvement of phytoremediation of an aged petroleum hydrocarbon-contaminated soil by Rhodococcus erythropolis CD 106 strain

The aim of this study was to assess the impact of soil inoculation with the Rhodococcus erythropolis CD 106 strain on the effectiveness of the phytoremediation of an aged hydrocarbon-contaminated [approx. 1% total petroleum hydrocarbon (TPH)] soil using ryegrass (Lolium perenne). The introduction of CD 106 into the soil significantly increased the biomass of ryegrass and the removal of hydrocarbons in planted soil. The fresh weight of the shoots and roots of plants inoculated with CD 106 increased by 49% and 30%, respectively. After 210 days of the experiment, the concentration of TPH was reduced by 31.2%, whereas in the planted, non-inoculated soil, it was reduced by 16.8%. By contrast, the concentration of petroleum hydrocarbon decreased by 18.7% in non-planted soil bioaugmented with the CD 106 strain. The rifampicin-resistant CD 106 strain survived after inoculation into soil and was detected in the soil during the entire experimental period, but the number of CD 106 cells decreased constantly during the enhanced phytoremediation and bioaugmentation experiments.

The plant growth-promoting and hydrocarbon-degrading properties of CD 106, which are connected with its long-term survival and limited impact on autochthonous microflora, make this strain a good candidate for improving the phytoremediation efficiency of soil contaminated with hydrocarbons.     

Supercritical Fluid Extraction of a Light PAH Contaminated Sand

This work was aimed at evaluating the feasibility of a remediation treatment performed by means of a supercritical carbon dioxide extraction on a sandy soil recently contaminated by light polycyclic aromatic hydrocarbons.

The soil utilized in this study was artificially contaminated by naphthalene and anthracene. The artificial contamination process was intended to simulate a recent accidental spillage of hydrocarbon fuels.

Several extractions, aimed at singling out the operating parameters (pressure, temperature, supercritical fluid mass flow rate) that are able to obtain the residual required concentration (50 mg/kg dry soil) in the shortest time, were carried out on a on-purpose made system.

The best extraction conditions were 120 bar and 40°C for a naphthalene contaminated soil and 200 bar and 80–100°C for an anthracene contaminated soil.

The results obtained in the experimental tests made it possible to build an analytical model able to correlate, for the given soil, the extraction length to the operating parameters such as supercritical fluid density, temperature and mass flow rate.

In order to evaluate the economic feasibility of the process, a unit treatment cost was evaluated for the case of an extraction carried out in a 10 m³ reactor in the presence of the best extraction conditions that were previously determined. The extraction unit cost was therefore equal to 35 000–65 000 €/t for a soil with a starting contaminant concentration equal to 1000 mg/kg of dry soil.     

Application of Diffusive Gradient in Thin Film to Estimate Available Copper in Soil Solution

In Chile, there are several agricultural areas with soils containing high levels of copper of both anthropic and geochemical origin. The diffusive gradient in thin film (DGT) technique is a promising tool for the evaluation of the bioavailability of metals in situ in different environmental systems. The objective of this study was the preparation, validation, and application of DGT to soil solutions and soil containing copper over 1000 mg kg^?1.

The results show that a resin gel thickness of 0.3 mm gives the best reproducibility and response in the absorption of copper by DGT. The amount of copper extracted in a period of 4 h by the devices from the soil solution corresponds to 13% of the total metal present in the solution.

The DGT allowed a more representative estimation of the amount of Cu available in the soil, more in agreement with the absence of symptoms of phytotoxicity in cultivated species. This shows that the determination of available Cu by DTPA must be handled cautiously because in soils with high Cu content the amount of metal that can have direct influence on absorption by the plant is overestimated.     

The Potential of the Ni-Resistant TCE-Degrading Pseudomonas putida W619-TCE to Reduce Phytotoxicity and Improve Phytoremediation Efficiency of Poplar Cuttings on A Ni-TCE Co-Contamination

To examine the potential of Pseudomonas putida W619-TCE to improve phytoremediation of Ni-TCE co-contamination, the effects of inoculation of a Ni-resistant, TCE-degrading root endophyte on Ni-TCE phytotoxicity, Ni uptake and trichloroethylene (TCE) degradation of Ni-TCE-exposed poplar cuttings are evaluated.

After inoculation with P. putida W619-TCE, root weight of non-exposed poplar cuttings significantly increased. Further, inoculation induced a mitigation of the Ni-TCE phytotoxicity, which was illustrated by a diminished exposure-induced increase in activity of antioxidative enzymes. Considering phytoremediation efficiency, inoculation with P. putida W619-TCE resulted in a 45% increased Ni uptake in roots as well as a slightly significant reduction in TCE concentration in leaves and TCE evapotranspiration to the atmosphere.

These results indicate that endophytes equipped with the appropriate characteristics can assist their host plant to deal with co-contamination of toxic metals and organic contaminants during phytoremediation. Furthermore, as poplar is an excellent plant for biomass production as well as for phytoremediation, the obtained results can be exploited to produce biomass for energy and industrial feedstock applications in a highly productive manner on contaminated land that is not suited for normal agriculture. Exploiting this land for biomass production could contribute to diminish the conflict between food and bioenergy production.     

The utility of saliva for the assessment of anti-pneumococcal antibodies: investigation of saliva as a marker of antibody status in serum

Context: Salivary antibodies may act as non-invasive marker of systemic immunity enabling assessment of vaccination and protection against bacterial infections.

Objective: To assess if levels of anti-pneumococcal (Pn) antibodies in saliva reflect concentrations in serum and determine whether saliva can accurately identify protective concentrations in serum.

Methods: IgG, IgA and IgM antibody levels in paired saliva and serum samples were measured against 12 Pn polysaccharide antigens in 72 healthy adults.

Results: Antibody levels in saliva correlated positively with serum across immunoglobulin classes, most strongly for IgA. Individuals who had protective antibody levels in serum demonstrated significantly higher IgG and IgA salivary antibody concentrations/secretion rates. Salivary IgG and IgA Pn antibodies were able to distinguish between those with/without protective levels in serum for the majority of serotypes. Salivary IgM antibodies were not able to differentiate protective status. Median IgG and IgA Pn salivary parameters were able to identify individuals who had protective levels in serum on ≥8/12 serotypes with moderate accuracy: median IgA secretion rates provided the best sensitivity (73%) and specificity (71%).

Conclusions: These findings suggest that IgG and IgA Pn specific antibodies in saliva may be useful surrogate markers of antibody status in serum.     

Feasibility of Phytoextraction to Clean Up Low-Level Uranium-Contaminated Soil

The potential to phytoextract uranium (U) from a sandy soil contaminated at low levels was tested in the greenhouse. Two soils were tested: a control soil (317 Bq ²³⁸U kg^-1) and the same soil washed with bicarbonate (69 Bq ²³⁸U kg^-1). Ryegrass (Lolium perenne cv. Melvina), Indian mustard (Brassica juncea cv. Vitasso), and Redroot Pigweed (Amarathus retroflexus) were used as test plants.

The annual removal of the soil activity with the biomass was less than 0.1%. The addition of citric acid (25 mmol kg^-1) 1 week before the harvest increased U uptake up to 500-fold. With a ryegrass and mustard yield of 15000 kg ha^-1 and 10000 kg ha^-1, respectively, up to 3.5% and 4.6% of the soil activity could annually be removed with the biomass.

With a desired activity reduction level of 1.5 and 5 for the bicarbonate washed and control soil, respectively, it would take 10 to 50 years to attain the release limit.

A linear relationship between the plant ²³⁸U concentration and the ²³⁸U concentration in the soil solution of the control, bicarbonate-washed, or citric acid-treated soil points to the importance of the soil solution activity concentration in determining U uptake and hence to the importance of solubilising agents to increase plant uptake.

However, citric acid addition resulted in a decreased dry weight production (all plants tested) and crop regrowth (in case of ryegrass).     

Mineral Nitrogen in Plant Physiology and Plant Nutrition

Nitrogen (N) nutrition enhances metabolic processes that influences the physicochemical environment at the soil-root interface, modifies rhizosphere conditions, interferes with the uptake of cations and anions, and enhances or represses the activity of several enzyme systems. Also, it affects growth patterns, protein content, and protein quality of seeds.

Ammonium (NH₄)-N nutrition increases anion uptake, free amino-N/protein ratios, and acidity of root free space; it reduces carbohydrate levels in plant tissues. NO₃-N nutrition results in higher cation uptake, higher carbohydrate content in tissues, and alkalinization of root free space. N-Assimilation interferes with the allocation of dry matter and energy, which causes different growth rates of plant parts.

In this article we review the effects of mineral-N nutrition on uptake of cations and anions, activity of enzymes, growth patterns of roots and shoots, and water use efficiency, protein content, and protein quality of seeds.     

Phytochemicals,antioxidant activity and hepatoprotective effect of ginger (Zingiber officinale) on diethylnitrosamine toxicity in rats

Context: Chronic liver damage has serious medical consequences.

Objective: To investigate the hepatoprotective effect of dry Zingiber officinale (ginger) and its essential (volatile) oil against diethylnitrosamine (DEN) toxicity in rats.

Materials and methods: Phenols and flavonoids components were characterized in dry ginger using HPLC-UV instrument while ginger essential oil (E.O.) was investigated via GC-MS technique. Antioxidant activity was determined in vitro. In rat model, ginger was administrated for 2 months. Lipid profile, antioxidant biomarkers, liver functions and histopathology were assessed.

Results: Chlorogenic acid (63.85?ppm) and hesperidin (156.91?ppm) are among the major phenolic and flavonoid constituents in dry ginger. Curcumene (15.21%) and linalool (13.47%) represent the main E.O. constituents. In rats treated with ginger E.O., a significant elevation in serum HDL (31.14%) was accompanied by a decrease in LDL (55.14%). A significant decrease in serum ALT and ALP was reported (56.85% and 53.84%, respectively). Serum GSH-Px activity has significantly increased 75.06%. Meanwhile, E.O. showed anticancer potential against HepG2 cell line (IC₅₀?=?40?µg/mL). Liver histopathological examinations confirmed the protective effect against abnormalities.

Conclusion: Ginger was able to reduce the severity of DEN-cytotoxicity in rats, which suggests a novel antioxidant role originating from this medicinal plant.     

Eggshell speckling in a passerine bird reveals chronic long-term decline in soil calcium

Capsule: Long-term changes in eggshell speckling correlated temporally and spatially with declining soil calcium in an English Great Tit Parus major population.

Aims: Eggshell speckling in the Great Tit correlates with eggshell thickness and calcium availability. We investigated whether eggshell speckling changed in a Great Tit population during a period when soil calcium declined, and estimated changes in eggshell thickness.

Methods: Eggshell pigmentation of 2313 Great Tit clutches was recorded in 1988–2007 across a geological gradient in Wytham Woods, UK. Soil surveys conducted in 1974 and 1991 were repeated in 2008. Temporal and spatial changes in eggshell speckling and soil calcium were examined using generalized linear mixed models. We also estimated the change in eggshell thickness over this period.

Results: Soil-calcium availability declined 1974–2008 especially in calcium-rich limestone areas. A systematic change in eggshell speckling, approximating to a 6.5% reduction in eggshell thickness, occurred between 1988 and 2007. The change was greatest in parts of Wytham that experienced the greatest decline in soil calcium. Hatching success was unaffected.

Conclusion: Soil-calcium availability has declined in Wytham Woods, affecting Great Tit eggshell characteristics. This is the first evidence that declining soil calcium affects birds nesting in calcium-rich areas. Practical applications of these findings are considered.     

Soil depth shapes plant functional diversity in granite outcrops vegetation of Southwestern Australia

Background: The arid and nutrient-poor Southwestern Australia is one of the global biodiversity hotspots. Embedded in this landscape, granite outcrops are considered terrestrial insular habitats supporting habitat heterogeneity when compared to the more homogenous surrounds. Ecology of plant species and communities on granite outcrops has been addressed in numerous studies. However, functional diversity (FD) in context of the environmental heterogeneity remained unexplored.

Aims: We tested whether mesic deep-soil habitats on granite outcrops can sustain larger FD than dry shallow-soil habitats.

Methods: We calculated FD for dominant species for five single traits (leaf dry matter content, foliar δ¹³C, foliar C:N ratio, plant height and specific leaf area) and their combinations. We employed Generalized Additive Mixed Models to quantify the relationship between selected climate and soil depth variables, and FD.

Results: More benign (deep-soil) habitats supported larger FD for foliar C:N, plant height and for multiple traits than did shallow-soil habitats.

Conclusions: We suggest that: (1) functional diversification, likely aimed at avoiding intra- and interspecific competition for light and nutrients acquisition, might be the important factor in deep-soil habitats; (2) deep-soils patches on and around granite outcrops may serve as ecological microrefugia for biota associated with resource-rich environments.     

Quantification of 1-hydroxypyrene, 1- and 2-hydroxynaphthalene, 3-hydroxybenzo[a]pyrene and 6-hydroxynitropyrene by HPLC-MS/MS in human urine as exposure biomarkers for environmental and occupational surveys

Context: Several urinary PAHs metabolites can be detected by HPLC-MS/MS for individual exposure assessment.

Objective: Quantitation of urinary metabolites of four PAHs, selected on the basis of their significance, with reduced costs and high sensitivity.

Materials and methods: HPLC-MS/MS was used and pure standards and isotope-labeled internal analogs of the analytes. Two hundred samples were tested after enzymatic hydrolysis.

Results: Accuracy was higher than 90% and variability lower than 19%; LODs permit to measure 1-hydroxypyrene, 1 and 2-hydroxynaphthalene in all subjects, 6-hydroxynitropyrene in the 65% and 3-hydroxybenzo[a]pyrene in the 70%.

Discussion and conclusion: The method is suitable both for occupational and for environmental studies. This is the first paper reporting urinary levels of 6-hydroxynitropyrene in European subjects, nonoccupationally exposed to nitro-PAHs.     

Association of IL-10 (-819T/C, -592A/C and -1082A/G) and IL-6 -174G/C gene polymorphism and the risk of pneumonia-induced sepsis

Context: Association between inherited variants and the risks of sepsis is controversial.

Objective: To evaluate the risk of pneumonia-induced sepsis by examining its linkage with polymorphisms of IL-6 and IL-10.

Materials and methods: Samples were obtained from 188 pneumonia-induced sepsis patients, 162 pneumonia patients and 200 healthy controls.

Results: Subjects with IL-10 -1082 AA genotypes and IL-6 -174?CC genotype had a higher risk of sepsis and increased mRNA levels.

Conclusion: The variants of IL-10 -1082 A allele and IL-6 -174 C allele contributed to an increased risk of pneumonia-induced sepsis.     

Growth and Cadmium Phytoextraction by Swiss Chard,Maize, Rice,Noccaea caerulescens,and Alyssum murale in pH Adjusted Biosolids Amended Soils

Past applications of biosolids to soils at some locations added higher Cd levels than presently permitted. Cadmium phytoextraction would alleviate current land use constraints. Unamended farm soil, and biosolids amended farm and mine soils were obtained from a Fulton Co., IL biosolids management facility. Soils contained 0.16, 22.8, 45.3 mg Cd kg^–1 and 43.1, 482, 812 mg Zn kg^–1 respectively with initial pH 6.0, 6.1, 6.4. In greenhouse studies, Swiss chard (Beta vulgaris var. cicla), a Cd-accumulator maize (inbred B37 Zea mays) and a southern France Cd-hyperaccumulator genotype of Noccaea caerulescens were tested for Cd accumulation and phytoextraction. Soil pH was adjusted from ～5.5–7.0. Additionally 100 rice (Oryza sativa) genotypes and the Ni-hyperaccumulator Alyssum murale were screened for potential phytoextraction use.

Chard suffered phytotoxicity at low pH and accumulated up to 90 mg Cd kg^–1 on the biosolids amended mine soil. The maize inbred accumulated up to 45 mg Cd kg^–1 with only mild phytotoxicity symptoms during early growth at pH > 6.0. N. caerulescens did not exhibit phytotoxicity symptoms at any pH, and accumulated up to 235 mg Cd kg^–1 in 3 months. Reharvested N. caerulescens accumulated up to 900 mg Cd kg^–1 after 10 months. Neither Alyssum nor 90% of rice genotypes survived acceptably.

Both N. caerulescens and B37 maize show promise for Cd phytoextraction in IL and require field evaluation; both plants could be utilized for nearly continuous Cd removal. Other maize inbreds may offer higher Cd phytoextraction at lower pH, and mono-cross hybrids higher shoot biomass yields. Further, maize grown only for biomass Cd maximum removal could be double-cropped.     

A territory scale analysis of habitat preferences of the declining Ortolan Bunting Emberiza hortulana

Capsule Ortolan Bunting occurrence is associated with bare ground, Lucerne, shrub cover and hedgerows/tree rows.

Aims To assess the habitat features selected by Ortolan Buntings at the territory level in semi-open landscapes, in the northern Apennines of Italy.

Methods We mapped territories in ten different plots and built a habitat selection model comparing 52 occupied cells with 52 unoccupied ones (cell size: 1?ha). We built multivariate adaptive regression splines models based on ground-measured variables.

Results The model revealed an association with intermediate Lucerne cover (50% of the cell), high shrub cover, bare ground (≥5%) and hedgerows/tree rows (≥25?m/ha). The most important driver of occurrence was bare ground (optimum at 5–20%).

Conclusion The maintenance of the mosaic and low-intensity farmed landscape, the promotion of Lucerne and the conservation/restoration of hedgerows/tree rows, may be promoted through the Rural Development Programme. The conservation of bare soil, grassland and shrubs at optimum amount at fine-scale could be the object of an agri-environment scheme targeted specifically at the Ortolan Bunting.     

The role of elevation and soil chemistry in the distribution and ion accumulation of floral morphs of Streptanthus polygaloides Gray (Brassicaceae), a Californian nickel hyperaccumulator

Background: The flora of serpentine/ultramafic soils provides an excellent model system for the study of natural selection in plant populations. Streptanthus polygaloides is a nickel hyperaccumulator that is endemic to serpentine soils in the Sierra Nevada of California, and has four floral morphs (yellow, purple, yellow-to-purple and undulate).

Aims: We investigate three hypotheses: (1) the purple morph occurs in colder, wetter climates than the yellow morph; (2) tissue–soil ionic relationships differ among morphs; and (3) morphs occur on soils with differing elemental concentrations.

Methods: We queried herbarium records to investigate patterns of occurrence among the yellow and purple floral morphs, and analysed soil and tissue samples from wild populations of all four morphs.

Results: The purple morph inhabited serpentine outcrops with colder temperatures and greater precipitation levels than the yellow morph. Concentrations of elements in leaf tissue and rhizosphere soil differed little among populations of the morphs, but showed substantial within-site variation.

Conclusions: Our results suggest that a climatic gradient may be responsible for divergence in floral colour among populations of S. polygaloides. Because of the large within-site variation in soil and tissue elemental concentrations, plants appear to have a varied physiological response to edaphic factors, regardless of morph membership.     

Effect of confounding factors on a phospho-flow assay of ribosomal S6 protein for therapeutic drug monitoring of the mTOR-inhibitor everolimus in heart transplanted patients

Context: Several assays of monitoring immune cell function have been developed to enhance therapeutic drug monitoring.

Objective: An in vitro-validated whole-blood assay of phosphorylated ribosomal protein S6 (pS6RP) was evaluated for confounders to monitor the mTOR-inhibitor everolimus (ERL).

Materials and methods: Whole blood samples from 87 heart transplant recipients were analyzed for pS6RP-expression in CD3-positive T-cells by phospho-flow analysis.

Results: ERL blood concentration, laboratory parameters, co-medications, demographic and clinical data were reviewed.

Conclusion: Evaluating the pS6RP-assay revealed that pS6RP is influenced by cyclosporine A (CsA) blood concentration, duration of ERL treatment, co-medication with thiazide diuretics and different metabolic parameters.     

Solubilization and Plant Uptake of Zinc and Cadmium from Soils Treated with Elemental Sulfur

In growth chamber experiments we studied the potential use of elemental sulfur (S₈) as an acidifying agent to enhance the uptake of Cd and Zn from three different polluted soils by candidate phytoremediation plants (Brassica juncea, Helianthus annuus, Salix viminalis). Two of the three soils were calcareous, the other slightly acidic. One of the calcareous soils had been contaminated by dust emissions from a nearby brass smelter. The pollution of the other two soils had resulted from sewage sludge applications.

Sulfur was added to soils in quantities of 20 to 400 mmol sulfur kg^-1 soil. Plants were grown under fluorescent light in 1.5 l ($OS 13 cm) pots for 28 d.

Within 700 h soil pH decreased significantly in all soils, depending on S₈ dosage. In the acid soil, pH decreased from pH 6.5 to about 4 at the highest treatment level, while pH in one of the calcareous soils dropped even below pH 4. The effect was smaller in the second calcareous soil.

NaNO₃-extractable Cd and Zn increased up to 26-and 13-fold, respectively, in the acid soil, while in the calcareous soils, maximum increases were 9-and 11-fold, respectively.

Increased NaNO₃-extractable concentrations translated well into shoot concentrations (dry matter) in plants. Shoot Zn concentrations in H. annuus, for example, increased from 930 in the controls to 4300 mg kg^-1 in the highest S₈ treatment. However, effects observed in the plants were generally smaller than in the soils. In addition, in some variants growth was negatively affected, resulting in reduced metal removal from the soils.     

The effect of harsh abiotic conditions on the diversity of serpentine plant communities on Lesbos,an eastern Mediterranean island

Background: Diversity patterns of plant communities are related to the environment, including productivity and patchiness of habitat.

Aims: To determine differences in diversity patterns between serpentine and non-serpentine communities.

Methods: A two-year study was conducted in native eastern Mediterranean grasslands. For each year 40 0.25 m² plots were sampled across four pairs of sites, each of which contained a serpentine and an adjacent non-serpentine plant community. Alpha and beta diversity (variation in species composition among plots within localities), species composition and biomass production were determined. Total soil elemental concentrations and pH were also measured.

Results: Serpentine habitats were shown to support a lower alpha diversity relative to non-serpentine habitatas on a per plot basis. Differences in alpha diversity between the two substrates were associated with variation in soil chemistry rather than above-ground biomass production. Serpentine habitats also exhibited lower beta diversity, which was unrelated to variation in biomass production. The two contrasting communities presented distinct species composition.

Conclusions: Differences in diversity patterns between serpentine and non-serpentine communities in the eastern Mediterranean are influenced by soil chemistry rather than biomass production.     

Evaluation of Heavy Metals Pollution Loadings in the Sediments of the Ave River Basin (Portugal)

Sediment samples from the Ave river basin were collected with the aim of determining metal total pollution contents. Cr, Cu, Fe, Mn, Pb, Zn and VM at 550 °C were determined. Some physico-chemical parameters were also quantified in water samples collected in the water column just above the sediments.

Metal contamination factors (CF) indicated that sediments were not contaminated with Cu and Pb, slightly with Zn and moderately with Cr.

For sediments with high metal pollution loadings, the original BCR (Community Bureau of Reference) metal speciation protocol was also applied. Speciation studies showed that chromium was mainly associated with the oxidisable plus residual fractions (>85%). These results suggest that changes in the physico-chemical properties of the river water (e.g. pH, Eh) should not be accompanied by a significative release of chromium from sediments.

The relationships between chromium speciation fractions, physic-chemical parameters of the sediments and water samples were studied by Principal Component Analysis, and allowed to reduce the dimensionality of the data matrix from 14 to 3 significant components accounting for 89% of the variance. It was found that hydrous Fe/Mn oxides and organic matter are the “carriers” of chromium associated to fractions exchangeable and oxidable.     

Advances,challenges and tools in characterizing bacterial serine,threonine and tyrosine kinases and phosphorylation target sites.

Introduction: The cellular response to infection by bacterial pathogens involves a complex and highly regulated series of pathways that carry messages to various parts of the cell. These messages are transferred using post-translational modifications including phosphorylation by kinases. Understanding the host’s signaling pathways is valuable in identifying potential treatment targets, but the bacterial signaling pathways and host-pathogen crosstalk are equally important to the development of therapeutics.

Areas covered: This review summarizes some of the recent findings related to the bacterial phosphoproteome and especially serine/threonine/tyrosine sites, including methods and considerations for identifying novel phosphosites. We also consider the bioinformatics tools that have been developed to sift through the large volume of data in these studies and connect them to biologically relevant knowledge about pathways and function. Literature databases used include PubMed and Google Scholar from April 2018 to December 2018.

Expert opinion: While the field has developed significantly in the past decade of research, high-quality experimental sequence data remains the limiting factor to future research into bacterial phosphoproteomics. As more proteomes are explored, it will be easier to tailor tools and techniques to prokaryotes. It will be necessary to consider the phosphoproteome in the broader biological context, through interdisciplinary collaborations.