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The aim of this study was to assess the effects of soil fumigation with methyl bromide (MeBr; CH(3)Br) and methyl iodide (MeI, iodomethane; CH(3)I) on the microbial community structure and diversity in two soils and determine the effects of microbial diversity on the survival of Escherichia coli O157:H7 from contaminated irrigation water. Polymerase chain reaction (PCR) was used to amplify 16S rRNA from total bacterial community composition and the products were subjected to denaturing gradient gel electrophoresis (DGGE). The Shannon-Weaver index of diversity (H') was used to determine the effects of both fumigants on soil microbial diversity. The effect was more severe in sandy soil than in clay soil at the normal application rate of MeBr and MeI. Our results showed that MeBr and MeI have about the same effects on soil microbial diversity. The two fumigants had greater impact on microbial diversity in sandy soil than in clay soil and this resulted in higher survival of E. coli O157:H7 in sandy soil than in clay soil during the 50 days that the study was conducted. MeBr has been used as soil fumigant for >40 years with no serious detrimental effects on agricultural production and our research also suggests that the use of MeI may also produce no long-term detrimental effects on agricultural production since both fumigants had about the same effects on soil microbial communities. Therefore, soil systems with reduced microbial diversity may offer greater opportunities for the survival of pathogenic bacteria such as E. coli O157:H7.

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AIMS: The major objective of this study was to determine the effects of low levels of Escherichia coli O157:H7 contamination on plant by monitoring the survival of the pathogen on the rhizosphere and leaf surfaces of lettuce during the growth process. METHODS AND RESULTS: Real-time PCR and plate counts were used to quantify the survival of E. coli O157:H7 in the rhizosphere and leaf surfaces after planting. Real-time PCR assays were designed to amplify the stx1, stx2 and the eae genes of E. coli O157:H7. The detection limit for E. coli O157:H7 quantification by real-time PCR was 2.4 x 10(3) CFU g(-1) of starting DNA in rhizosphere and phyllosphere samples and about 10(2) CFU g(-1) by plate count. The time for pathogens to reach detection limits on the leaf surface by plate counts was 7 days after planting in comparison with 21 days in the rhizosphere. However, real-time PCR continued to detect stx1, stx2 and the eae genes throughout the experimental period. CONCLUSION: Escherichia coli O157:H7 survived throughout the growth period as was determined by real-time PCR and by subsequent enrichment and immunomagnetic separation of edible part of plants. SIGNIFICANCE AND IMPACT OF THE STUDY: The potential presence of human pathogens in vegetables grown in soils contaminated with E. coli O157:H7 is a serious problem to our national food supply as the pathogen may survive on the leaf surface as they come in contact with contaminated soil during germination.

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In arid irrigated regions, the proportion of crop production under deficit irrigation with poorer quality water is increasing as demand for fresh water soars and efforts to prevent saline water table development occur. Remote sensing technology to quantify salinity and water stress effects on forage yield can be an important tool to address yield loss potential when deficit irrigating with poor water quality. Two important forages, alfalfa (Medicago sativa L.) and tall wheatgrass (Agropyron elongatum L.), were grown in a volumetric lysimeter facility where rootzone salinity and water content were varied and monitored. Ground-based hyperspectral canopy reflectance in the visible and near infrared (NIR) were related to forage yields from a broad range of salinity and water stress conditions. Canopy reflectance spectra were obtained in the 350- to 1000-nm region from two viewing angles (nadir view, 45 degrees from nadir). Nadir view vegetation indices (VI) were not as strongly correlated with leaf area index changes attributed to water and salinity stress treatments for both alfalfa and wheatgrass. From a list of 71 VIs, two were selected for a multiple linear-regression model that estimated yield under varying salinity and water stress conditions. With data obtained during the second harvest of a three-harvest 100-d growing period, regression coefficients for each crop were developed and then used with the model to estimate fresh weights for preceding and succeeding harvests during the same 100-d interval. The model accounted for 72% of the variation in yields in wheatgrass and 94% in yields of alfalfa within the same salinity and water stress treatment period. The model successfully predicted yield in three out of four cases when applied to the first and third harvest yields. Correlations between indices and yield increased as canopy development progressed. Growth reductions attributed to simultaneous salinity and water stress were well characterized, but the corrections for effects of varying tissue nitrogen (N) and very low leaf area index (LAI) are necessary.

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The effects of sand and clay soils and water contaminated by Escherichia coli O157:H7 on the development of rhizosphere and phyllosphere microbial communities were analyzed to determine the influence of plant age on microbial community structure and composition. Community bacterial nucleic acids were extracted from lettuce rhizosphere and phyllosphere samples at different stages of plant development after the soils were irrigated with water contaminated with E. coli O157:H7 at planting and 15 days after planting. PCR was used to amplify 16S ribosomal RNA (rRNA) for total bacterial community composition and the products were subjected to denaturing gradient gel electrophoresis (DGGE). Prominent DGGE bands were excised and sequenced to gain insight into the identities of predominant bacterial populations. The majority of DGGE band sequences were related to bacterial genera previously associated with the rhizosphere and phyllosphere, such as Pseudomonas, Acidobacterium, Bacillus and Agrobacterium. The PCR-DGGE patterns observed for rhizosphere samples were more complex than those obtained from the bulk soil and the phyllosphere. The Shannon index of diversity (H) was used to determine the complexity of the DGGE bands from the phyllosphere, rhizosphere and the bulk soils at different growth stages. A higher diversity was observed in the clay soil than sandy soil during the first week. Few changes in diversity were observed after the first week. The results show that microbial community development in lettuce may take about 7-12 days and this may be the most likely period for maximum pathogen contamination in plants.

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AIMS: To apply the real-time Polymerase chain reaction (PCR) method to detect and quantify Escherichia coli O157:H7 in soil, manure, faeces and dairy waste washwater. METHODS AND RESULTS: Soil samples were spiked with E. coli O157:H7 and subjected to a single enrichment step prior to multiplex PCR. Other environmental samples suspected of harbouring E.coli O157:H7 were also analysed. The sensitivity of the primers was confirmed with DNA from E.coli O157:H7 strain 3081 spiked into soil by multiplex PCR assay. A linear relationship was measured between the fluorescence threshold cycle (C T ) value and colony counts (CFU ml(-1)) in spiked soil and other environmental samples. The detection limit for E.coli O157:H7 in the real-time PCR assay was 3.5 x 10(3) CFU ml(-1) in pure culture and 2.6 x 10(4) CFU g(-1) in the environmental samples. Use of a 16-h enrichment step for spiked samples enabled detection of <10 CFU g(-1) soil. E. coli colony counts as determined by the real-time PCR assay, were in the range of 2.0 x 10(2) to 6.0 x 10(5) CFU PCR (-1) in manure, faeces and waste washwater. CONCLUSIONS: The real-time PCR-based assay enabled sensitive and rapid quantification of E. coli O157:H7 in soil and other environmental samples. SIGNIFICANCE AND IMPACT OF THE STUDY: The ability to quantitatively determine cell counts of E.coli O157:H7 in large numbers of environmental samples, represents considerable advancement in the area of pathogen quantification for risk assessment and transport studies.

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Thirty Atriplex lines were examined for potential habitat improvement and phytoremediation of selenium (Se) contaminated sites. Studies were conducted to determine the biomass production, Se accumulation, and resistance of each line to the beet armyworm, Spodoptera exigua, an agriculturally important insect. Plants were tested using three salinity treatments: (1) control, no Se; (2) NaCl and CaCl2 salts and 1 mg l(-1) Se (12.7 microM) added as sodium selenate; and (3) iso-osmotic to treatment 2 containing high concentrations of sulfate and I mg l(-1) Se added as sodium selenate. Insect bioassays measured survival, growth, and development. Atriplex patula. A. spongiosa 415862, A. hortensis, A. hortensis 379088 and A. hortensis 379092 were among the top biomass producers and Se accumulators, yet they exhibited significantly reduced insect growth, development, and survival. High background sulfate strongly reduced Se accumulation, suggesting that phytoremediation potential is greatest in saline areas having low to moderate sulfate levels. However, these lines grew well in high salinity soils, indicating possible use as a self-seeding cover crop to improve habitat. All plant lines grown in control and high sulfate salinity treatments are acceptable oviposition sites for S. exigua, indicating that these plants would help reduce populations of this key agricultural pest.

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Soil and water resources can be severely degraded by salinity when total salt input exceeds output in irrigated agriculture. This study was conducted to examine partitioning of Ca2+, Na+, and Cl- between soil and soybean [Glycine max (L.) Merr.] plants under different irrigation regimes with both field and modeling assessments. In drip and sprinkler treatments, the irrigation water was salinized with NaCl and CaCl2 salts to simulate a Cl- and Na+ dominant saline drainage water. In the furrow irrigation treatment, the soil was salinized, prior to planting, with NaCl and CaCl2 salts to simulate a Cl- and Na+ dominant saline soil. A total of 756 soil and 864 plant samples were collected and analyzed for the salt ions to obtain ion partitioning and mass balance assessments. Modeling of salt ion uptake by plants and distribution in the soil profile was performed with a two-dimensional solute transport model for the three irrigation regimes. Results indicated that about 20% of the applied Ca2+ was recovered in harvested soybean biomass in all treatments. Plant uptake of either Na+ or Cl- was less than 0.5% in the drip and furrow, and about 2% in the sprinkler irrigation treatment. Significant increases in soil salinity were found in the sprinkler plot that received the highest cumulative amount of salts. Simulated ion distributions in the soil were comparable with the measurements. Compared with the total seasonal salt input, mass balances between 65 and 108% were obtained. Most salt inputs accumulate in the soil, and need to be removed periodically to prevent soil salinization.

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Saplings of Eucalyptus camaldulensis Dehn. Clone 4544, irrigated with water of differing salinities (2 to 28 dS m-1) and boron concentrations (1 to 30 mg l-1), integrated the history of these stresses through the discrimination of stable isotopes of carbon in leaf and woody tissues. Carbon isotope discrimination (delta) was reduced primarily by salinity. Decreases in discrimination in response to boron stress were detected in the absence of salinity stress, but the decreases were significant only in leaf tissues with visible boron injury. Sapwood core samples indicated that salinity- and boron-induced reductions in delta increased with increasing tree age. Absolute values of delta varied with location of leaf or wood tissue, but relative effects of salinity on the relationship between delta and transpiration efficiency (W) were similar. In response to increasing salinity stress, relative decreases in delta paralleled relative decreases in biomass and both indices yielded similar salt tolerance model parameters. The strong correlations between delta, tree fresh weight, leaf area and W suggest that delta is a useful parameter for evaluating salt tolerance of eucalyptus

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Mesophyll cells from leaves of cowpea (Vigna unquiculata [L.] Walp.) plants grown under saline conditions were isolated and used for the determination of photosynthetic CO(2) fixation. Maximal CO(2) fixation rate was obtained when the osmotic potential of both cell isolation and CO(2) fixation assay media were close to leaf osmotic potential, yielding a zero turgor pressure. Hypotonic and hypertonic media decreased the rate of photosynthesis regardless of the salinity level during plant growth. No decrease in photosynthesis was obtained for NaCl concentrations up to 87 moles per cubic meter in the plant growing media and only a 30% decrease was found at 130 moles per cubic meter when the osmotic potential of cell isolation and CO(2) fixation media were optimal. The inhibition was reversible when stress was relieved. At 173 moles per cubic meter NaCl, photosynthesis was severely and irreversibly inhibited. This inhibition was attributed to toxic effects caused by high Cl(-) and Na(+) accumulation in the leaves. Uptake of sorbitol by intact cells was insignificant, and therefore not associated with cell volume changes. The light response curve of cells from low salinity grown plants was similar to the controls. Cells from plants grown at 173 moles per cubic meter NaCl were light saturated at a lower radiant flux density than were cells from lower salinity levels.

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Sixteen Holstein bull calves were fed a high-concentrate ratio supplemented with zinc, copper, and manganese, alone or in combination, for 10 wk. After 6 days of preliminary feeding of chromic oxide, fecal grab-samples were collected for 6 days. Calves were slaughtered, and samples of the contents of the reticulo-rumen, omasum, abomasum, small intestine, cecum, and large intestine were analyzed for chromic oxide, copper, and manganese. Absorption along the gastrointestinal tract, measured by comparison of one segment with the previous segment, indicated net secretion of copper in the abomasum but net absorption from the rest of the tract. The exception was that net secretion into the reticulo-rumen was associated with low dietary copper. Net secretion of manganese was mainly in the small intestine and cecum in all treatments. A higher proportion of copper apparently was absorbed when this mineral was supplemented in the ration. However, absorption of manganese was decreased slightly when manganese was supplemented in the ration. Reabsorption of manganese in the large intestine was probably greater than that of copper.

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The effects of supplemental zinc, copper, and manganese alone or in combination in a high-concentrate ration were studied in 16 Holstein bull calves during a 10-wk feeding trial. Metabolism was studied after the feeding trial. Apparent digestibility of dry matter, nitrogen, and gross energy, and nitrogen retention and urinary excretion of zinc, copper, and manganese were determined. The calves were slaughtered after the experiment, and liver, heart, and kidney were taken for analyses of trace minerals. Supplementation of the basal ration with the trace minerals did not affect body weight gains, which averaged 1.42 kg daily. The addition of trace minerals did not affect apparent digestibility co-efficients. A zinc-manganese interaction in digestion of nitrogen and gross energy was significant. Higher dietary manganese caused increased zinc concentrations in the liver, kidney, and heart. The copper concentration of liver was decreased by dietary zinc and increased by dietary copper and manganese. Supplemental manganese increased its net retention. There was no evidence of deficiency of any trace minerals in the unsupplemented treatments.

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