Quantification of Mirafiori lettuce big‐vein virus and its vector,Olpidium virulentus,from soil using real‐time PCR

Big vein disease of lettuce (Lactuca sativa) is an economically important disease transmitted through soil by Olpidium virulentus, and has occurred in most production areas worldwide. The disease is assumed to be caused by Mirafiori lettuce big‐vein virus (MiLBVV). To understand the dynamics of the virus and its vector, MiLBVV and O. virulentus were directly detected in soil. DNA and RNA were extracted from 5 g soil using a bead beating method, followed by purification using adsorption to a column. Detection and quantification were performed using real‐time PCR and a TaqMan probe that was prepared based on the CP region of MiLBVV and the rDNA‐ITS region of O. virulentus, respectively. Furthermore, using a visual assessment of the incidence rate of big vein disease on lettuce in agricultural fields, the C_t values of MiLBVV and O. virulentus from soil were also determined using real‐time PCR. The results showed that MiLBVV concentrations in the soil were high in the field, as also determined by a visual assessment of the incidence rate of big vein disease on lettuce. However, the amount of O. virulentus in soil was not directly correlated with the incidence of MiLBVV. From these results, it is suggested that the risk of lettuce crops developing big vein disease can be estimated using an index of the amount of MiLBVV in the soil.     

Hydrolysis of triasulfuron,metsulfuron‐methyl and chlorsulfuron in alkaline soil and aqueous solutions

The hydrolysis of triasulfuron, metsulfuron‐methyl and chlorsulfuron in aqueous buffer solutions and in soil suspensions at pH values ranging from 5.2 to 11.2 was investigated. Hydrolysis of all three compounds in both aqueous buffer and soil suspensions was highly pH‐sensitive. The rate of hydrolysis was much faster in the acidic pH range (5.2–6.2) than under neutral and moderately alkaline conditions (8.2–9.4), but it increased rapidly as the pH exceeded 10.2. All three compounds degraded faster at pH 5.2 than at pH 11.2. Hydrolysis rates of all three compounds could be described well with pseudo‐first‐order kinetics. There were no significant differences (P = 0.05) in the rate constants (k, day⁻¹) of the three compounds in soil suspensions from those in buffer solutions within the pH ranges studied. A functional relationship based on the propensity of nonionic and anionic species of the herbicides to hydrolyse was used to describe the dependence of the ‘rate constant’ on pH. The hydrolysis involving attack by neutral water was at least 100‐fold faster when the sulfonylurea herbicides were undissociated (acidic conditions) than when they were present as the anion at near neutral pH. In aqueous buffer solution at pH > 11, a prominent degradation pathway involved O‐demethylation of metsulfuron‐methyl to yield a highly polar degradate, and hydrolytic opening of the triazine ring. It is concluded that these herbicides are not likely to degrade substantially through hydrolysis in most agricultural alkaline soils. © 2000 Society of Chemical Industry     

Severity of phytophthora root rot and pre‐emergence damping‐off in subterranean clover influenced by moisture,temperature, nutrition,soil type,cultivar and their interactions

Studies were carried out in controlled environment rooms reflecting field situations. In the presence of the devastating soilborne pathogen Phytophthora clandestina, subterranean clover (Trifolium subterraneum) seedling emergence was significantly affected by moisture, soil type, temperature and cultivar. The level of rotting of tap and lateral roots was significantly affected by nutrition, soil type, temperature and cultivar. There were significant interactions involving temperature, moisture, soil type and cultivar; cultivar resistance, high moisture, high or medium temperature, high nutrition and sand soil all contributed towards less pre‐emergence damping‐off and tap and lateral root disease and to greater clover productivity. Host resistance of subterranean clover cultivars was critical for reducing disease severity and increasing productivity, even when favourable environmental conditions for severe disease occurred. In the presence of P. clandestina, the most resistant cultivar, Seaton Park, performed best under a high temperature, high nutrition and high moisture combination, but showed lower productivity under conditions of low nutrition or lower temperature, even when moisture level was high. In contrast, less resistant cultivars Riverina and Meteora had less disease and greater productivity under low moisture conditions. Findings reflect field observations that pre‐emergence damping‐off and root disease from P. clandestina in subterranean clover is particularly severe under colder conditions and in nutritionally impoverished sandy soils, and demonstrate how variations in soil type, nutrition, moisture, temperature and cultivar have profound effects on the expression and severity of phytophthora pre‐emergence damping‐off and root disease and the productivity of subterranean clover forages.     

The effect of initial concentration of carbofuran on the development and stability of its enhanced biodegradation in top‐soil and sub‐soil

Carbofuran was incubated in top‐soil and sub‐soil samples from a pesticide‐free site at a range of initial concentrations from 0.1 to 10 mg kg⁻¹. Amounts of the incubated soils were removed at intervals over the subsequent 12 months, and the rate of degradation of a second carbofuran dose at 10 mg kg⁻¹ was assessed. An applied concentration as low as 0.1 mg kg⁻¹ to top‐soil resulted in more rapid degradation of the fresh addition of carbofuran for at least 12 months. The degree of enhancement was generally more pronounced with the higher initial concentrations. When the same study was conducted in sub‐soil samples from the same site, an initial dose of carbofuran at 0.1 mg kg⁻¹ resulted in only small increases in rates of degradation of a second carbofuran dose. However, degradation rates in the sub‐soil samples were, in many instances, considerably greater than in the corresponding top‐soil samples, irrespective of pre‐treatment concentration or pre‐incubation period. Initial doses of 0.5 mg kg⁻¹ and higher applied to sub‐soil successfully activated the sub‐soil microflora. Application of the VARLEACH model to simulate carbofuran movement through the soil profile indicated that approximately 0.01 mg kg⁻¹ of carbofuran may reach a depth of 70 cm 400 days after a standard field application. The results therefore imply that adaptation of the sub‐soil microflora (c 1 m depth) by normal field rate applications of carbofuran is unlikely to occur. In experiments to investigate this in soils exposed to carbofuran in the field, there was no apparent relationship between top‐soil exposure and degradation rates in the corresponding sub‐soils. The results further confirmed that some sub‐soil samples have an inherent capacity for rapid biodegradation of carbofuran. The high levels of variability observed between replicates in some of the sub‐soil samples were attributed to the uneven distribution of a low population of carbofuran‐degrading micro‐organisms in sub‐surface soil. There was no apparent relationship between soil microbial biomass and degradation rates within or between top‐soil and sub‐soil samples. © 2001 Society of Chemical Industry     

In situ bioremediation of organochlorine‐pesticide‐contaminated microcosm soil and evaluation by gene probe

BACKGROUND: Pesticide‐formulating industries are contaminating the environment through various activities. Bioremediation is the best method for decontamination, as chemical and physical methods are not only costly but also not very effective in open field systems. In the present study, in situ bioremediation of organochlorine‐contaminated soil was demonstrated by combined biostimulation and bioaugmentation strategies, followed by evaluation using a molecular method. RESULTS: Three parameters were monitored: microbial biomass (colony‐forming units (CFU) g^?1 soil), residual pesticides after treatment and catabolic genes from microcosm soil. Both the biostimulation and the bioaugmentation treatments showed an initial lag phase of 80 days towards colony‐forming units. Gas chromatography of soil samples showed that concentrations of residual pesticides in the soil declined by up to 85–90% after 80 days, indicating their utilisation with time. On dot‐blot hybridisation of the total DNA from the same soil samples, it was observed that catabolic genes tfdC (catechol 1,2‐dioxygenase) and cm genes (chlorophenol monoxygenase) were predominant, whereas other catabolic genes such as catechol 2,3‐dioxygenase (xylE) were negligible. CONCLUSION: The strategy of in situ bioremediation and its evaluation by gene probe and also by conventional methods was demonstrated for organochlorine‐pesticide‐contaminated soil in open microcosms. It showed that bioaugmentation along with biostimulation was effective, although initial acclimatisation for a period of almost 2–3 months was required in the open field systems. Copyright © 2009 Society of Chemical Industry     

Applicability of ELISA for determination of metsulfuron‐methyl in soil samples

An immunoassay (ELISA) for analysis of metsulfuron‐methyl was evaluated as a method for quantifying residues in soil. Soil samples were extracted with phosphate buffered saline (PBS), PBS + acetone (80 + 20 by volume) or ammonium carbonate and were analyzed with both ELISA and LC‐MS. A tendency for the ELISA to overstimate the metsulfuron‐methyl content was noted and matrix effects were pronounced, particularly in PBS + acetone or ammonium carbonate extracts. Dilution of extracts before analysis improved the situation but reduced the sensitivity of the assay. Using light standard concentrations it was shown that the extracts in PBS on dilutions exhibited a curve parallel with the standard curve, indicating no significant interference due to matrix effects. A working range of 10–250 ng litre⁻¹ was found for ELISA on this type of extracts. © 2000 Society of Chemical Industry     

Application of bispyribac‐sodium provides effective weed control in direct‐planted rice on a sandy loam soil

An increasing water crisis, as well as the unavailability and high cost of labor, in Pakistan has forced rice‐growers to plant rice directly into the field. However, severe weed infestation causes disastrous effects on the productivity of this rice system. In this study, three herbicides (pendimethalin, penoxsulam and bispyribac‐sodium) were evaluated for weed control in direct‐planted rice on a sandy loam soil. Weedy check and weed‐free plots were established for comparison. Weed infestation decreased the rice yield by 75.2%. However, the application of herbicides suppressed the weed infestation, with a simultaneous increase in the rice yield. The postemergence application of bispyribac‐sodium was the most effective herbicide in reducing the total weed density and dry weight over the weedy check, followed by penoxsulam and pendimethalin, respectively. Bispyribac‐sodium increased the number of productive tillers, 1000‐grain weight, number of grains per panicle and grain yield over the control, as well as improved the water productivity and economic returns of direct‐planted rice. The weeds' proliferation increased the number of unproductive tillers and decreased the plant height. In conclusion, the postemergence application of bispyribac‐sodium can be used effectively to control weeds, increase water productivity and improve the economic returns and yield of direct‐planted rice on a sandy loam soil in Pakistan.     

Potential of barnyard grass to remediate arsenic‐contaminated soil

The present study investigated the arsenic (As) remediation potential of barnyard grass (Echinochloa crus‐galli L. Beauv. var. formosensis Ohwi), with a special focus on the behavior of As in the soil in comparison with rice (Oryza sativa L. cv. Nipponbare). For both plants, very little growth inhibition was observed in the As‐contaminated soil. The amount of As in the soil was reduced by the plant's uptake and the level of As in the soil water from the rice‐growing pots was remarkably lower than that in the plant‐free soil water. In the soil with the barnyard grass, the amount of As in the soil water was higher than that in the plant‐free soil water, but the amount of As in the soil and the amount of As that was adsorbed on the soil solid were reduced by the plant's uptake. At the highest As level in the soil (100 mg kg^?1), 249.60 and 101.26 µg As pot^?1 were taken up by the rice shoot and barnyard grass shoot, respectively, and total amounts of 1468.65 and 1060.57 µg As pot^?1 were taken up by the barnyard grass and rice seedlings, respectively. At the same As level in the soil, the As concentrations were 14.99 and 37.76 µg g^?1 in the shoot of barnyard grass and rice, respectively, and 486.61 and 339.32 µg g^?1 in the root of barnyard grass and rice, respectively. Barnyard grass took up more As than rice, but the As concentration in the shoot of barnyard grass was lower than that in the shoot of rice. A considerable amount of As was taken up by both barnyard grass and rice, suggesting that the plant species have the potential to remediate As‐contaminated soil.     

Germination rates of weedy radish populations (Raphanus spp.) altered by crop‐wild hybridisation,not human‐mediated changes to soil moisture

Cultivated plants are known to readily hybridise with their wild relatives, sometimes forming populations with weedier life‐history strategies than their progenitors. Due to altered precipitation patterns from human‐induced global climate change, crop‐wild hybrid populations may have new and unpredictable environmental tolerances relative to parental populations, which would further challenge farming and land‐management weed control strategies. To recognise the role of seed dormancy variation in weed invasion, we compared seedbank dynamics of two cross‐type populations (wild radish, Raphanus raphanistrum, and crop‐wild hybrid radish, R. raphanistrum × R. sativus) across a soil moisture gradient. In a seed‐burial experiment, we assessed relative rates of seed germination, dormancy and seed mortality over two years across cross types (crop‐wild hybrid or wild) and watering treatments (where water was withheld, equal to annual rainfall, or double annual rainfall). Weekly population censuses in 2012 and 2013 assessed the frequency and timing of seedling emergence within a growing season. Generally, germination rates were two times higher and seed dormancy was 58% lower in hybrid versus wild populations. Surprisingly, experimental soil moisture conditions did not determine seedbank dynamics over time. Yet, seed bank dynamics changed between years, potentially related to different amounts of annual rainfall. Thus, variation in seedbank dynamics may be driven by crop‐wild hybridisation rates and, potentially, annual variation in soil moisture conditions.     

Effect of long‐term field application of pendimethalin: enhanced degradation in soil

The effect of long‐term application of pendimethalin in a maize–wheat rotation on herbicide persistence was investigated. Pendimethalin was applied at 1.5 kg AI ha⁻¹ separately as one or two annual applications for five consecutive years in the same plots. Residues of pendimethalin were determined by gas chromatography. Harvest‐time residues of the herbicide decreased gradually over the years and at the end of five years less than 3% of applied pendimethalin was recovered from soil as against 18% in the first year. Residues were found distributed in the soil profile up to 90 cm depth at the end of the experiment with peak distribution of 0.03 µg g⁻¹ in the surface layer of soil treated with 10 herbicide applications. The minimum distribution was, however, in the deepest soil (75–90 cm) profile. Some of the metabolites of pendimethalin ie dealkylated pendimethalin derivative, partially reduced derivative and cyclized product were also traced in surface and sub‐surface soils up to 90 cm. A study of the rate of degradation of pendimethalin in field‐treated soils under laboratory conditions revealed faster degradation compared to control soils. Only the surface soil (0–15 cm) showed this enhanced degradation of the herbicide, which could be due to the adaptability of the aerobic micro‐organisms to degrade pendimethalin. Microbes capable of degrading herbicide were isolated, identified and pendimethalin degradation was confirmed in nutrient broth. © 2000 Society of Chemical Industry     

Effect of temperature,organic amendment rate and moisture content on the degradation of 1,3‐dichloropropene in soil

1,3‐Dichloropropene (1,3‐D), which consists of two isomers, (Z)‐ and (E)‐1,3‐D, is considered to be a viable alternative to methyl bromide, but atmospheric emission of 1,3‐D is often associated with deterioration of air quality. To minimize environmental impacts of 1,3‐D, emission control strategies are in need of investigation. One approach to reduce 1,3‐D emissions is to accelerate its degradation by incorporating organic amendments into the soil surface. In this study, we investigated the ability of four organic amendments to enhance the rate of degradation of (Z)‐ and (E)‐1,3‐D in a sandy loam soil. Degradation of (Z)‐ and (E)‐1,3‐D was well described by first‐order kinetics, and rates of degradation for the two isomers were similar. Composted steer manure (SM) was the most reactive of the organic amendments tested. The half‐life of both the (Z)‐ and (E)‐isomers in unamended soil at 20 °C was 6.3 days; those in 5% SM‐amended soil were 1.8 and 1.9 days, respectively. At 40 °C, the half‐life of both isomers in 5% SM‐amended soil was 0.5 day. Activation energy values for amended soil at 2, 5 and 10% SM were 56.5, 53.4 and 64.5 kJ mol^?1, respectively. At 20 °C, the contribution of degradation from biological mechanisms was largest in soil amended with SM, but chemical mechanisms still accounted for more than 58% of the (Z)‐ and (E)‐1,3‐D degradation. The effect of temperature and amendment rate upon degradation should be considered when describing the fate and transport of 1,3‐D isomers in soil. Use of organic soil amendments appears to be a promising method to enhance fumigant degradation and reduce volatile emissions. Published in 2001 for SCI by John Wiley & Sons, Ltd     

Night‐time tillage revisited: the delayed soil desiccation process in night‐time tilled plots may promote unexpected weed germination

Night‐time tillage and sowing (photocontrol of weeds, soil cultivation in darkness) can reduce the germination and subsequent density of light‐sensitive weeds by excluding the short light flash during soil disturbance. In most experiments conducted from 1990 to 2004 worldwide, total weed density was reduced in night‐time tilled plots as expected. However, in a few field experiments, total weed density was significantly increased in night‐time compared with daytime tilled plots. We hypothesise that the desiccation process of the upper soil layer (roughly about 0–30 mm), from where most small seeded weeds emerge, may have been delayed in night‐time compared with daytime tilled plots, with significant effects on early seed germination processes. Daytime tillage was usually performed around noon, to capture high light intensities during soil tillage. However, around noon soil desiccation can be much higher than during the night. A few hours of relatively higher water availability for seeds in the upper soil layer during the night, before the next morning when soil desiccation usually increases again, may have favoured seed germination and subsequent weed emergence compared with daytime tillage, finally resulting in higher weed density in night‐time tilled plots. On the other hand, crop germination and emergence may also be higher under such conditions.