Real-time PCR for Quantification of Toxigenic Fusarium Species in Barley and Malt

A real-time PCR technique was applied for the quantification of trichothecene-producing Fusarium species (TMTRI assay) as well as the highly toxigenic Fusarium graminearum (TMFg12 assay) present in barley grain and malt. PCR results were compared to the amounts of trichothecenes detected in the samples to find out if the PCR assays can be used for trichothecene screening instead of expensive and laborious chemical analyses. DNA was extracted from ground kernels using a commercial DNA extraction kit and analysed in a LightCycler® system using specific primers and fluorogenic TaqMan probes. Both naturally and artificially contaminated grains were analysed. The TMTRI assay and the TMFg12 assay enabled the quantification of trichothecene-producing Fusarium DNA and F. graminearum DNA present in barley grain and malt samples, respectively. Both TaqMan assays were considered to be sensitive and reproducible. Linearity of the assays was 4–5 log units when pure Fusarium DNAs were tested. The amount of Fusarium DNA analysed with the TMTRI-trichothecene assay could be used for estimation of the deoxynivalenol (DON) content in barley grain. Furthermore, the TMFg12 assay for F. graminearum gave a good estimation of the DON content in north American barley and malt samples, whilst the correlation was poor among Finnish samples. DON content and the level of F. graminearum DNA were found to be naturally low in Finnish barleys.     

Development of Strain-specific Primers for a Strain of Gliocladium catenulatum Used in Biological Control

The randomly amplified polymorphic DNA (RAPD) technique was used to develop strain-specific primers for Gliocladium catenulatum strain J1446, which is promising in biological control. One of the primer pairs developed proved to be strain-specific; strain J1446 was differentiated from 16 G. catenulatum strains and six other strains of two Gliocladium species, as well as from Trichoderma virens, and isolates of Nectria spp. and Fusarium spp. Specific primers were also tested with DNA isolated from cucumber leaves, treated or untreated with a solution made from Gliocladium powder. The expected amplification product was produced only from treated leaves. DNA isolated from Gliocladium-treated potato tubers and fungi grown in peat was also used in amplification reactions. Strain-specific primers detected strain J1446 when the amount of DNA was 5pg or more. Some variation between the Gliocladium strains was found by the random amplified microsatellites method (RAMS) and the universally primed polymerase chain reaction method (UP-PCR), but no clear fragments specific to strain J1446 were produced. Cross-blot hybridisation of UP-PCR products differentiated strain J1446 from T. virens, but not from the Gliocladium isolates. The 28S rDNA sequences and -tubulin sequences were identical or very similar in all Gliocladium strains. Thus, it is possible that the Gliocladium strains of the present study are conspecific, which means that a revision in the taxonomy of Gliocladium species may be necessary.     

Agro-morphological traits of <Emphasis Type="Italic">Cicer reticulatum</Emphasis> Ladizinsky in comparison to <Emphasis Type="Italic">C. echinospermum</Emphasis> P.H. Davis in terms of potential to improve cultivated chickpea (<Emphasis Type="Italic">C. arietinum</Emphasis> L.)

Germplasm collections of C. reticulatum and C. echinospermum are limited, while both species face threats from over-grazing and habitat change in their natural environments. Recently many new accessions of C. reticulatum and C. echinospermum were collected in east and south-east Anatolia (Turkey) but they have not yet been evaluated for agro-morphological traits. Therefore, the current study investigated agro-morphological traits of new germplasm sources of C. reticulatum and C. echinospermum and evaluated resistance to biotic and abiotic stresses for chickpea improvement. The most attractive agro-morphological traits were canopy width, number of stems and pods per plant and biological yield. The most productive accessions of C. reticulatum and C. echinospermum had 712 and 625 pods per plant, respectively. Two distinct seed, flower and leaf shapes were found in accessions of C. echinospermum. Path analyses indicated that biological yield and harvest index had the most direct influence on seed yield in both species. Factor analyses showed that high seed yield in C. reticulatum depended on high biological yield and number of pods per plant, whereas high seed yield in C. echinospermum depended on harvest index. It was concluded that most accessions of C. reticulatum and C. echinospermum were not only resistant to some biotic and abiotic stresses but also had hidden alleles that could produce transgressive segregation in crosses to cultivated material.     

Estimation of light interception properties of conifer shoots by an improved photographic method and a 3D model of shoot structure

The spherical mean of the shoot silhouette-to-total leaf area ratio (STAR) and the shoot transmission coefficient (c) are two key structural parameters in radiative transfer models for calculating canopy photosynthesis and leaf area index. The standard optical method for estimating these parameters might introduce errors in the estimates for species with flexible shoots and needles by changing shoot inclination relative to its inclination in situ. We devised and tested two methods to address this problem. First, we modified the standard optical method by designing an apparatus that allows shoots to be photographed in their original orientation. Second, we developed a faster, model-based approach to replace photography and tested the results against the established approach. We used shoots of three pine species, Pinus echinata Mill. (needle length ~50 mm), P. taeda L. (~150 mm) and P. palustris Mill. (~300 mm). Values of the parameters simulated by the model were similar to those measured from the photographs. In our data, STAR varied about twofold among the pine species and was ~40% higher in shade shoots than in sun shoots of P. taeda. The transmission coefficient for P. taeda shade shoots was also ~40% higher than that of sun shoots of all three species. We tested the versatility of the model by employing it on shoots of two other pine species (P. strobus L. and P. thumbergiana Parl.) as well as on shoots of Tsuga canadensis L. Carr. and Picea pungens Engelm. Regardless of shoot characteristics, the model generated values of shoot structural parameters similar to those estimated with the optical method. Although species-specific and vertical gradients in parameter values are best for modeling radiative transfer in conifer canopies, our results suggest that, in the absence of adequate data, STAR can be approximated as 0.16 for a wide range of shoot structures. For applications requiring angle-dependent parameterization, our new model facilitates rapid generation of these radiative transfer parameters.     

Whole‐community facilitation by beaver: ecosystem engineer increases waterbird diversity

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Surface drainage nitrate loading estimate from agriculture fields and its relationship with landscape metrics in Tajan watershed

Pasture, forest, and farmland are the dominant land covers in the Tajan River watershed and this landscape status has a direct connection with nitrate pollution. Understanding the correlations between landscape variables and nitrate pollutant is a priority in order to assess pollutants loading and predicting the impact on surface water quality. The soil and water assessment tool was used to simulate nitrate loads in different land cover types in different years. The landscape pattern was calculated by FRAGSTATS. The contributing share of each land use/land cover shows nitrate pollutant produced by grassland (5.7%) and forest (29%) are less than those produced by agricultural land (64.2%). Agricultural land was identified as the main source of nitrate pollution. Paddy fields and orchards had the most intensive soluble nitrate loss especially in spring and summer. Statistical analysis indicated that nitrate was positively associated with patch density, edge density, patch number, total edge, effective mesh size, largest patch index, and landscape shape index (p ≤ 0.01). We then analyzed how nitrate was related to landscape attributes in six different sites. Also the regression analysis results suggested that landscape metrics could account for more than 94% of the variance of nitrate in the whole catchment. The regression models confirmed the great importance of the agriculture metrics and forest metric in predicting nitrate in watershed. Defining the generation and extent of pollution in this particular watershed which discharges into the Caspian Sea can constitute an important step toward protecting this ecosystem.     

Breaking Seed Dormancy of Laurel (Laurus nobilis L.)

Laurel (Laurus nobilis L.) seeds were collected from the west part of Turkey in the fall of 2002. Seeds with pericarp (+) or without pericarp (−) were treated with 1000 mg/l, 2000 mg/l and 3000 mg/l GA₃ concentrations, cold stratified at +4 ± 1°C for 25 and 50 days, punctured and seed coat removed to overcome and assess the mechanism of laurel seed dormancy. A period of 50 days cold stratification and removing seed coat significantly increased germination rate to 55% ± 1.91 (Mean ± SE) and 85% ± 3.00, respectively. None of the seeds with pericarp germinated regardless of treatment they underwent. Results suggested that seed dormancy was mainly due to pericarp and perhaps inhibitors linked to seed coat.     

Growth, allocation and tissue chemistry of Picea abies seedlings affected by nutrient supply during the second growing season

One-year-old Norway spruce (Picea abies (L.) Karst.) seedlings were grown hydroponically in a growth chamber to investigate the effects of low and high nutrient availability (LN; 0.25 mM N and HN; 2.50 mM N) on growth, biomass allocation and chemical composition of needles, stem and roots during the second growing season. Climatic conditions in the growth chamber simulated the mean growing season from May to early October in Flakaliden, northern Sweden. In the latter half of the growing season, biomass allocation changed in response to nutrient availability: increased root growth and decreased shoot growth led to higher root/shoot ratios in LN seedlings than in HN seedlings. At high nutrient availability, total biomass, especially stem biomass, increased, as did total nonstructural carbohydrate and nitrogen contents per seedling. Responses of stem chemistry to nutrient addition differed from those of adult trees of the same provenance. In HN seedlings, concentrations of alpha-cellulose, hemicellulose and lignin decreased in the secondary xylem. Our results illustrate the significance of retranslocation of stored nutrients to support new growth early in the season when root growth and nutrient uptake are still low. We conclude that nutrient availability alters allocation patterns, thereby influencing the success of 2-year-old Norway spruce seedlings at forest planting sites.