Fate of prions in soil: Interaction of a recombinant ovine prion protein with synthetic humic-like mineral complexes

Prion proteins are regarded as the main agents of transmissible spongiform encephalopathies. Understanding their fate in soil may be crucial to elucidate the dissemination of the prion in the environment, associated with a possible transmission of infectivity. Studies were performed with simplified model systems, derived by the birnessite-mediated oxidative polymerization of catechol, which simulate processes naturally occurring in soil. A benign full-length recombinant purified ovine protein (PrP) (residues 23-234), as well as a truncated-form ovPrP (tPrP) (103-234) were utilized. Catechol and prion protein interacted under experimental conditions that reproduced the interaction of PrP with soluble organic matter or with insoluble organic matter during or after formation of catechol polymers. PrP stability in all buffers and chemicals was preliminarily monitored by circular dicroism (CD) measurements. The disappearance of protein molecules from the solution, the decrease of UV-Visible absorbance of supernatants, and the FT-IR spectra and the elemental analyses of solid-phase residues indicated that both PrP and tPrP were involved in catechol polymerization by birnessite. Furthermore, a clear flocculation of soluble catechol-protein polymeric products in solid aggregates was observed when PrP was added to the supernatants. Different kinds of extracting agents were not able to desorb/extract PrP as well as tPrP from the formed solid aggregates, thereby highlighting the high stability of protein-organic and -organo-mineral complexes.     

Aggregate breakdown during tillage in a Mediterranean loamy soil

Long-term tillage negatively affects soil aggregation, but little is known about the short-term effects of tillage. We investigated the effects of intensive tillage (moldboard plowing) and conservation tillage (chisel plowing) on aggregate breakage during tillage in a long-term study located in the semiarid Ebro river valley (NE Spain). The type of tillage resulted in different soil aggregate distributions. In the 0–5-cm and 5–10-cm soil layers, chisel plowing decreased dry mean weight diameter (DMWD) 29% and 35%, respectively, while moldboard plowing decreased DMWD by only 2% and 16%, respectively. The decrease in DMWD was mainly due to breaking of large aggregates ranging (2–8 mm) into small aggregates (<0.5 mm). Tillage method had no effect on water stability of 1–2 mm aggregates. The differences in DMWD demonstrate that the choice of the tillage implement can be a key factor in improving soil management and productivity. The surprising result that aggregate breakdown was greater with chisel than moldboard plowing needs further research to determine the mechanisms controlling aggregate breaking during tillage.     

Measuring the CO2 production from maize‐straw‐amended soil columns— a comparison of four methods

A soil‐column experiment with maize‐straw application at different depths was carried out to investigate the accuracy of CO₂‐measurement systems in a greenhouse experiment with sandy and loamy soils. The classical approach of CO₂ absorption in NaOH solution was compared with three other methods using dynamic chambers. These methods were gas chromatography (GC), a portable infrared analyzer (IR), and a portable photo‐acoustic system (PAS). The cumulative CO₂ production over the 57‐day incubation period was significantly affected by the method and soil‐specifically by the treatments. The NaOH and GC method always formed a pair of lowest cumulative CO₂ production in all treatments with maize‐straw addition. In the treatments with bottom application of the maize straw, IR and PAS methods gave values at identical levels in both soils. In the treatments with top application of the maize straw, the IR method gave significantly highest values in the sandy soil and the PAS method in the loamy soil. The correlation coefficients between the cumulative CO₂ production of the three dynamic‐chamber methods (GC, IR, and PAS) and the static NaOH method were all significant, with r values between 0.90 and 0.93. The C balance can be used for testing the plausibility of CO₂‐production data. Roughly 102% (NaOH and GC) and 114% (IR and PAS) were recovered, including the CO₂‐production data in the C balance of the sandy soil. The respective data were 97% (NaOH and GC) and 104% (IR and PAS) for the loamy soil.     

Nutrient availability and corn growth in a poultry litter biochar‐amended loam soil in a greenhouse experiment

Nutrient‐rich biochar produced from animal wastes, such as poultry litter, may increase plant growth and nutrient uptake although the role of direct and indirect mechanisms, such as stimulation of the activity of mycorrhizal fungi and plant infection, remains unclear. The effects of poultry litter biochar in combination with fertilizer on mycorrhizal infection, soil nutrient availability and corn (Zea mays L.) growth were investigated by growing corn in a loam soil in a greenhouse with biochar (0, 5 and 10 Mg/ha) and nitrogen (N) and phosphorus (P) fertilizer (0, half and full rates). Biochar did not affect microbial biomass C or N, mycorrhizal infection, or alkaline phosphomonoesterase activities, but acid phosphomonoesterase activities, water‐soluble P, Mehlich‐3 Mg, plant height, aboveground and root biomass, and root diameter were greater with 10 Mg/ha than with no biochar. Root length, volume, root tips and surface area were greatest in the fully fertilized soil receiving 10 Mg/ha biochar compared to all other treatments. The 10 Mg/ha biochar application may have improved plant access to soil nutrients by promoting plant growth and root structural features, rather than by enhancing mycorrhizal infection rates.     

Location and stability of a recombinant ovine prion protein in synthetic humic-like mineral complexes

Location and stability of a recombinant prion protein (recPrP) and its interaction with humic-like complexes were investigated by low-temperature ashing (LTA), thermal gravimetric (TG), and scanning electron microscopy (SEM) analyses. Humic-like complexes were obtained by abiotic polymerization of catechol, one of the possible precursors of soil humic matter, through the catalysis of birnessite, a manganese oxide common in soil environment. The recPrP was immobilized in organomineral complexes via sorption or entrapment. Complexes were treated by LTA, allowing the controlled removal of organic matter layer by layer, from the external to the internal side, with minimal disturbance of mineral constituents. Thermal gravimetric and SEM analyses were performed on specimens before and after LTA treatment. Entrapped recPrP, compared with sorbed, resulted less easily accessible to LTA treatment and showed a higher thermal stability by TGA analyses. On the basis of these findings, we hypothesize that the processes leading to newly formed organic complexes can enhance prion stability in soil and thus influence the environmental diffusion of infectivity.     

Effects of bentonite on water infiltration in a loamy sand soil

Water loss as deep percolation is considerable in furrow irrigation in light soils due to the high infiltration rate. Application of soil conditioners such as bentonite reduces the infiltration rate and improves irrigation application efficiency (E_a) in these soils. The effects of bentonite application rates (BAR) of 0, 2, 4 and 6 g L^?1 on infiltration of a loamy sand soil were determined in a soil column in the laboratory. The exponent of the Kostiakov infiltration equation was not influenced by BAR. Maximum reduction in infiltration equation coefficient and final infiltration rate (i _f) occurred with 2 g bentonite L^?1 and this reduction was lower on increasing BAR from 2 to 4 and 4 to 6 g L^?1 compared with control. The effect of 2 g L^?1 BAR on infiltration and its effect on the design of furrow irrigation in a field with a loamy sand soil indicated that in the first irrigation after field ploughing and seed planting, longer furrow length, lower deep percolation and higher E_a are obtained.     

Measured and simulated denitrification activity in a cropped sandy and loamy soil

Summary Denitrification activities were measured over a 3-year period in a coarse sandy soil and a sandy loam soil. In all years the crops were spring barley in combination with Italian ryegrass as a catch crop. The denitrification loss was measured using the acetylene inhibition technique on soil cores. Furthermore, a simple model was developed, based on daily values of soil moisture and soil temperature, to calculate the denitrification loss. Soil temperatures for the model were measured, whereas soil moisture was derived from a water-balance model. Measurements of denitrification gave an annual loss of 0.6 kg N ha^-1, and the model calculated a loss of 1–2 kg N ha^-1 in the coarse sandy soil. In the sandy loam soil annual losses were measured as 1.5, 3.0, and 13.0 kg N ha^-1 in 1988, 1989, and 1990, respectively. The corresponding values from the model simulation were 14, 9 and 14 kg N ha^-1.     

Water repellence and soil aggregate dynamics in a loamy grassland soil as affected by texture

It has been hypothesized that aggregate stability is partly caused by subcritical (i.e. mild) water repellence. We conducted both a field study at a pasture site and an incubation experiment in the laboratory to characterize the relationship between aggregate dynamics and water repellence. In the field study, we investigated 53 samples from a natural texture gradient for water repellence and aggregation. In the 3‐week incubation experiment, we added wheat straw to crushed soil material from five of the 53 soils representative of the texture gradient (a sandy loam, two loams, a silt loam and a clay loam), and followed changes in aggregate formation and water repellence. Although there was a dramatic increase (P < 0.0001) in aggregation in all the soils during incubation (the mean weight diameter increased from about 300 μm to at least 900 μm), we observed a concomitant increase in water repellence only in the clay loam soil (P = 0.0003). We found no significant correlations between water repellence and aggregation (n = 53, P > 0.05) in the field. Whereas correlation between aggregate formation and texture was weak in the incubation experiment, we found a significant correlation between aggregation and textural parameters in the field. The amount of large macro‐aggregates (> 2000 μm) was positively correlated with clay content (n = 53, r = 0.53, P < 0.001), and negatively with sand content (n = 53, r = ?0.46, P < 0.001). These results indicate that (i) microbially induced water repellence might only become apparent when enough easily decomposable substrate is available, (ii) soil texture affects aggregate stabilization rather than aggregate formation, and (iii) aggregate formation is not necessarily associated with an increase in water repellence.     

Co-selection for antibiotic resistance genes is induced in a soil amended with zinc

The likelihood of co-selection for antibiotic resistance induced by heavy metals is a potential threat to human health, however, direct evidence of heavy metal-induced co-selection of antibiotic resistance is lacking in soil. By using a metagenomic sequencing approach, zinc (Zn) driven co-selection of antibiotic resistance genes (ARGs) in soil was investigated through a microcosm experiment where Zn salts were added at different levels. The results showed that the abundance and diversity of ARGs had a tendency to increase along the gradient of increasing Zn contents, with the maximum values recorded in the soil amended with 800 mg Zn kg⁻¹. The abundance of mobile genetic elements (MGEs) such as integrons and insertion sequences was significantly increased by Zn exposure. Network analysis demonstrated significant associations between ARGs and MGEs, suggesting that Zn treatment might enhance the potential for horizontal transfer of ARGs. Furthermore, structural equation models revealed that the types of ARGs were primarily driven by variations in bacterial compositions and Zn exposure, followed by integrons. Thus, these results indicate that added Zn salts considerably changed the diversity, abundance and mobility potential of antibiotic resistance, and imply that application of amendments containing high levels of Zn to soil could be causing the emergence and release of ARGs to the environment, and should be carefully monitored.     

N2O and CH4 emission from soil amended with steam‐activated biochar

Steam‐activation increased CH₄ emission of stover biochar but decreased it for wood biochar by 14%^–70%. Biochar generally increased CH₄ emission but reduced N₂O emission by 10%–41%. Emission of N₂O was 17% lower for maize‐stover biochar compared to Eucalyptus‐wood biochar, and 3% lower for 350°C compared to 550°C pyrolysis temperature. Emission of CH₄ was 21% higher for activated stover biochar compared to Eucalyptus‐wood biochar and 10% lower for 350°C compared to 550°C pyrolysis temperature. No difference in net CO₂ equivalent was observed among biochar grades.     

Yield variability related to landscape properties of a loamy soil in central Belgium

A field was investigated with precision farming techniques to delineate zones with different yield potential due to previous soil erosion. Winter wheat (Triticum aestivum L.) grain yield, straw yield, biomass and harvest index were measured with a combine harvester. Fuzzy clustering of grain and straw yield provided good delineation of zones in the field with different yield potential. Entropy and fuzziness calculations for different number of classes resulted in a division of the field into five clearly differentiated yield potential zones. Straw yield, biomass and harvest index were significantly different among zones. Grain yield was significantly different for all zones, except for two. Elevation and slope of the field were measured from a global positioning system (GPS) unit on the combine. Both were related to yield variability in the field. Average elevation, slope and soil type were calculated per cluster class. High grain yield, straw yield and biomass could be related to flat, high places in the field with little erosion. Good grain yield, low straw yield and high harvest index were found on relatively steep slopes subjected to erosion. High straw yield and low grain yield were found at low places in the field on relatively steep slopes. Lowest grain yield, straw yield and biomass were located on steepest slopes with high erosion and in depressions where accumulation of eroded soil took place and slumping and crusting of the soil were present. This information suggests that variable management on a site-specific basis would optimize yield and inputs.     

Modifications to atrazine degradation pathways in a loamy soil after addition of organic amendments

The effects of two organic amendments, a municipal solid waste compost and a composted straw, on [U-ring- ]atrazine degradation pathways in a loamy soil (Grignon, Yvelines, France) were studied during laboratory incubations under controlled conditions. Three month conditionings were conducted under sterile or non-sterile conditions, with soil plus atrazine, organic amendment plus atrazine, or soil plus organic amendment. Then either an organic amendment or soil or atrazine was added, respectively, to these three treatments and incubated for an additional 3 months under non-sterile conditions. Both organic amendments modified the behaviour of atrazine in soil but via different processes. The addition of municipal compost increased atrazine sorption and decreased its availability for degradation by soil microorganisms. The effect of the composted straw was mainly related to its high enzymatic activity, which appeared to be responsible for the production of large amounts of hydroxyatrazine. This hydroxylation favoured the opening of the triazine ring and its subsequent mineralization in the soil. At the end of the incubations, less atrazine was mineralized in the presence of the two types of organic amendment, which both increased the formation of non-extractable residues of atrazine. The addition of municipal compost preserved larger amounts of extractable atrazine, while the addition of composted straw enhanced hydroxyatrazine production. In all cases, the greatest effects were found when atrazine was directly in contact with the organic amendment during conditioning.     

Fate of prions in soil: Degradation of recombinant prion in aqueous extracts from soil and casts of two earthworm species

Prions represent the active agent in transmissible spongiform encephalopathy (TSE) diseases and can remain infective to mammals even after prolonged periods in soil. The influence of mesofauna on prion dispersal and degradation in soil, however, remains unknown. In this study the effect of earthworms on the retention/dissemination of TSEs in soil was evaluated using a model recombinant prion protein (recPrP) and aqueous extracts from soil and fresh casts of two earthworm species, Lumbricus terrestris and Aporrectodea caliginosa. Our results showed that earthworm gut-derived enzymes did not enhance the degradation of recPrP in comparison to soil, even though non-prion related proteolytic activity was higher in fresh worm excrements than in soil samples. Complete degradation of recPrP occurred in the aqueous extracts from all samples within up to 6 days at +15 °C. The proteolytic enzymes responsible for degrading recPrP were inhibited by aprotinin and leupeptin and studies in pure cultures suggested these were most probably of soil microbial origin.     

Influence of soil solution Ca concentration on short-term K release and fixation of a loamy soil

The Ca concentration of the soil solution influences K plant nutrition by its influence on K concentration of the soil solution and on soil buffer power through ion exchange and K release or fixation. The effects of the imposed solution Ca concentration on the estimates of these parameters and on these two phenomena were studied on a loamy soil. Potassium sorption and desorption experiments were conducted for 16 h at five initial Ca concentrations (from 0 to 10^?1 M) and followed by the measurement of soil exchangeable K (ammonium acetate extraction). Soil K-Ca exchange properties and the contributions of exchangeable K and non-exchangeable K to K dynamics of the soil-solution system were estimated. The‘Ratio Law’ applied for the medium range of Ca concentrations, i.e. 10^?1 M to 10^?3 M. But, it failed for some experiments at small initial Ca concentrations (0 M and 10^?4 M). This failure went with a decrease of the number of sites of great affinity for K in K-Ca ion exchange and/or a decrease of the amount of K not in exchange equilibrium with Ca but extracted by M ammonium acetate. Release of K increased and fixation of K decreased when Ca concentration increased. The relation between the change in the amount of non-exchangeable K during the experiment and the initial constraint (ø) was curvilinear on the large range of ø investigated. But, this relation was independent of Ca concentration. The K concentration of the solution for which neither sorption of K by the soil nor desorption of K from the soil occurred decreased and the slope of the sorption-desorption curve at this K concentration increased when the solution Ca concentration decreased. These two parameters can be considered the K concentration of the soil solution of the soil and the buffer power of the soil, respectively, only if the initial Ca concentration imposed during the sorption-desorption experiments is close to the Ca concentration of the soil solution of the soil. A predictive model of the soil buffer power based on ion exchange and release-fixation properties is proposed. Despite some discrepancies at very low Ca concentrations (<0·5 mM Ca) when‘Ratio Law’did not apply the agreement between calculated and observed values was good. The model permits the correction of the experimentally obtained buffer power for the bias related to the great solution volume: soil weight ratio commonly used during the sorption-desorption experiments.     

Degradation kinetics of manure-derived sulfadimethoxine in amended soil

Spreading of contaminated manure into agricultural lands as fertilizer is one of the major routes through which veterinary antibiotics enter the environment. In this study, the degradation of manure-derived sulfadimethoxine, a widely used veterinary sulfonamide antibiotic, in manure-amended soil was investigated. A kinetic model, called the availability-adjusted first-order model based on the first-order kinetics and an assumption of the availability of target compound during the degradation process, was developed and was found to fit sulfadimethoxine degradation well. The effect of initial sulfadimethoxine concentration showed that the degradation rate constant increased with decreasing initial concentration, indicating that the bioactivity of the degrading microorganisms in manure-amended soil was sensitive to sulfadimethoxine concentration. Sulfadimethoxine degradation was accelerated with increasing manure content in amended soil. Degradation in nonamended soil was significantly slower than in manure-amended soil. This indicated that sulfadimethoxine may become more persistent once it reaches soil after leaching from manure and that storage of manure for a certain period before application is needed to diminish sulfadimethoxine contamination. Sulfadimethoxine degradation was effectively enhanced with increasing moisture of amended soil. No adverse effect was observed with manure storage on the degradation of manure-derived sulfadimethoxine in amended soil.     

碱茅根际土壤盐分动态变化研究

A glasshouse experiment using a rhizobox technique was conducted to examine salt dynamics in the rhizosphere of a salt-tolerant grass, Puccinellia ciliata Bor. ‘Irwin Hunter', grown in a loamy soil, and to study the effect of rainfall flush on salt accumulation in the rhizosphere. The rhizobox (10 × 5.5 × 50 cm) had a nylon mesh (1 μm) positioned vertically in the middle to create two compartments filled with soil amended with 1 g NaCl kg^-1. The plants were grown in one compartment only. Flushed treatments received 275 mL of deionized water two days before harvest. In the plant-growing compartment, soils were sectioned vertically at 5 cm intervals. Significant differences in soil electrical conductivity (EC) (P < 0.05) and pH (P < 0.05) were observed for depths, but not between flushed and non-flushed treatments. In the no-plant compartment (rhizosphere), soil cores were taken horizontally at depths of 5, 20 and 40 cm and sliced at 1, 2, 3, 4, 5, 7, 10, 15 and 20 mm away from the roots. Soil EC and Cl^- concentration at the 5 and 20 cm depths, and Na⁺ concentration at the 5 cm depth significantly decreased (P < 0.05) with the distance away from the root, but no significant differences were observed in soil pH and concentrations of the K⁺ and Ca²⁺. The flush treatment only had significant influence on soil EC, pH, and Cl^- concentration at the 20 cm depth. Thus, salt accumulation could occur in the rhizosphere of salt-tolerant species on saline soils, and the periodic low rainfall might not have a strong influence on salt distribution in the rhizosphere and/or root zone.     

Physical characterization of a soil amended with organic residues in a rice–wheat cropping system using a single value soil physical index

The effect of soil incorporations of lantana (Lantana spp.) biomass, an obnoxious weed, on physical environment of a silty clay loam soil (Typic Hapludalf) under rice (Oryza sativa L.)–wheat (Triticum aestivum L.) cropping was studied in a long-term field experiment conducted in a wet temperate region of north India. Fresh lantana biomass was incorporated into the plough layer at 10, 20 and 30 Mg ha⁻¹ annually, 7–10 days before puddling. Plant-available water capacity (PAWC), non-limiting water range (NLWR) and NLWR:PAWC ratio were determined to characterize soil physical environment during wheat crop in the tenth cropping cycle.

Ten annual applications of lantana at 10, 20 and 30 Mg ha⁻¹, increased organic carbon (OC) content over control by 12.6, 17.6 and 27.9% in 0–15 cm soil layer, and 17.1, 26.3 and 39.5% in 15–30 cm soil layer, respectively. The OC content in 0–15 and 15–30 cm soil layer of control plots was 11.1 and 7.6 g kg⁻¹ soil. Bulk density decreased by 3–14% in 7.5–10.5 cm layer and 1–6% in 15–18 cm layer. Volumetric moisture contents at 10% air-filled porosity were 38.4, 40.0, 54.5 and 55.7% at 7.5–10.5 cm depth, and 31.4, 32.2, 33.9 and 34.6% at 15–18 cm depth corresponding to 0, 10, 20 and 30 Mg ha⁻¹ lantana treatment, respectively. At 15–18 cm soil depth, volumetric moisture contents at 2 MPa soil penetration resistance were 26.9, 24.8, 23.0 and 19.6% in zero, 10, 20 and 30 Mg ha⁻¹ lantana-treated plots, respectively. Lower soil water contents associated with 10% air-filled porosity and greater soil water contents associated with a limiting penetration resistance of 2 MPa resulted in a lower NLWR (4.3%) for control as compared to lantana-treated soil (7.4–15.1%). The PAWC showed slight increase from 12.9 to 13.4–14.9% due to lantana additions. The NLWR:PAWC ratio was also lower in control (0.33) as compared to lantana-treated soil (0.55–1.01). The NLWR was significantly and positively correlated with wheat grain yield (r=0.858^**).     

Response of soil structure and hydraulic conductivity to reduced tillage and animal manure in a temperate loamy soil

We studied the combined effects of reduced tillage and animal manure on soil structure and hydraulic conductivity (K) in the 2–10 and 12–20 cm layers in a loamy soil. The study was performed at the end of a 7‐yr field trial and included three tillage treatments (mouldboard ploughing until 25 cm depth: MP, shallow tillage until 12 cm depth: ST, no‐till: NT) and two fertilizer application treatments (mineral or poultry manure). Soil structure was assessed through bulk density (ρ_b), micromorphological and macropore‐space characteristics. K was measured in situ at ?0.6, ?0.2 and ?0.05 kPa. Untilled layers had a vermicular microstructure resulting from earthworm activity, whereas tilled layers displayed a mixture of crumb and channel microstructures. Untilled layers had the highest ρ_b and twice as much lower total macroporosity area (pores > 240 μm in equivalent diameter) than tilled layers, reflected by the smallest area of macropores 310–2000 μm in diameter and the smallest area of large complex macropores. K under untilled layers was 12–62% lower than that under tilled layers, but differences were statistically significant only at ?0.05 kPa in the 2–10 cm. No significant interaction between tillage and nutrient application treatments was detected for all properties. Compared with mineral fertilizer, poultry manure resulted in a similar ρ_b but 20% greater total macroporosity area and 30% higher K at ?0.2 kPa. Overall, the sensitivity of soil structure and K to poultry manure were relatively small compared with tillage. We suggest that cultivation practices other than animal manure application are needed to improve physical properties under reduced tillage.