Multilocus identification and thiophanate-methyl sensitivity of Colletotrichum gloeosporioides species complex associated with fruit with symptoms and symptomless leaves of mango

Colletotrichum spp. are known causal agents of anthracnose in a broad host range, causing severe losses. Currently, the most effective way to reduce disease is by fungicide application, which could give rise to resistant populations. This study aimed to determine the Colletotrichum species present in conventional and organic mango orchards and to evaluate their pathogenicity and sensitivity to the benzimidazole fungicide thiophanate-methyl. Seventy-one isolates from fruit with symptoms and symptomless leaves were obtained. From these, 20 representative morphotypes were analysed based on glyceraldehyde-3-phosphate dehydrogenase partial gene sequencing. A subset of 10 isolates based on different species, isolation source, and fungicide sensitivity was used for morphological and multilocus phylogenetic analysis. Colletotrichum queenslandicum was only identified in conventional production systems, C. chrysophilum only in organic systems, and C. asianum and C. siamense in both. Pathogenicity tests showed all species were pathogenic, and only C. asianum caused symptoms via both unwounded and wounded inoculation methods. Overall, 25.3% of isolates (n = 18) that belong to C. siamense, isolated from a conventional orchard, grew on thiophanate-methyl amended media at 1,000 µg/ml, suggesting high resistance. Resistance was not correlated with any common point mutations at positions 198 and 200 of the β-tubulin 2 protein, as commonly found in other fungal pathogens resistant to benzimidazole. The 74.7% remaining isolates (n = 53) belonging to the other species were sensitive, reaching 100% inhibition at <10 µg/ml. Even with benzimidazole application, anthracnose symptoms persist due to the emergence of pathogenic Colletotrichum subpopulations that are resistant to thiophanate-methyl.     

A multiplex real-time PCR assay enables simultaneous rapid detection and quantification of bacteria associated with acute oak decline

Acute oak decline (AOD) is a syndrome affecting mature oak trees and is characterized by stem bleeds from vertical fissures on trunks, and inner bark necrosis caused by a polybacterial consortium, in which Gibbsiella quercinecans and Brenneria goodwinii, and to a lesser extent Rahnella victoriana and Lonsdalea britannica, play key roles. Here we report a novel multiplex real-time PCR assay that enables simultaneous and rapid detection and quantification of these four bacterial species from stem bleed swabs. Experiments with axenic cultures were performed to determine specificity and sensitivity of the multiplex quantitative PCR (qPCR). Whilst the primer/probe set for B. goodwinii was species-specific, primer/probe sets for the other three species were able to identify other members of their respective genera. There was no cross detection of genera within the multiplex qPCR, and non-target bacteria were not detected. The multiplex AOD assay had differential sensitivity for each bacterial species. The assay was evaluated on swab samples collected from stem bleeds of declining oak trees at a site in south-east England and was able to detect all four bacterial species. Absolute quantification of the bacteria from swab samples was possible through the inclusion of a standard curve prepared from dilutions of gene copy standards. This diagnostic tool will facilitate rapid detection of AOD-associated bacteria from samples that can easily be taken by non-specialists without specific training, and will also find application in other experimental work such as pathogenicity and control trials.     

Genotyping-by-sequencing of waxy and glossy near-isogenic broccoli lines

Wild-type Brassica oleracea L. have matte blue-green leaves caused by an interaction between leaf pigmentation and a waxy bloom coating the surface. Glossy mutants have reduced and/or altered epicuticular wax giving the leaves a shiny green appearance and have been identified in most B. oleracea crop varieties, including cauliflower, kale, broccoli, Brussels sprouts, cabbage, and collard. The genetic basis of glossy mutants has not been studied in B. oleracea. Glossiness can confer resistance to multiple herbivores mediated by modification of herbivore feeding behavior and foraging efficiency of their predators. The USDA-ARS-U.S. Vegetable Laboratory released two pairs of near-isogenic broccoli lines (NILs) that visibly differ only for glossiness, providing ideal germplasm for the genetic study of epicuticular wax in B. oleracea. Genotyping-by-sequencing resulted in hundreds of polymorphisms between each pair of NILs. Polymorphisms were identified in or near three different wax synthesis genes suggesting the two glossy mutants were caused by alteration of different steps of the pathway.     

Rapid prediction of gross energy and utilizable energy in cereal food products using near-infrared reflectance spectroscopy

Near-infrared (NIR) spectroscopy has been used in foods for the rapid assessment of several macronutrients; however, little is known about its potential for the evaluation of the utilizable energy of foods. Using NIR reflectance spectra (1104-2494 nm) of ground cereal products (n = 127) and values for energy measured by bomb calorimetry, chemometric models were developed for the prediction of gross energy and available energy of diverse cereal food products. Standard errors of cross-validation for NIR prediction of gross energy (range = 4.05-5.49 kcal/g), energy of samples after adjustment for unutilized protein (range = 3.99-5.38 kcal/g), and energy of samples after adjustment for unutilized protein and insoluble dietary fiber (range = 2.42-5.35 kcal/g) were 0.053, 0.053, and 0.088 kcal/g, respectively, with multiple coefficients of determination of 0.96. Use of the models on independent validation samples (n = 58) gave energy values within the accuracy required for U.S. nutrition labeling legislation. NIR spectroscopy, thus, provides a rapid and accurate method for predicting the energy of diverse cereal foods.     

Indian land use in the Raposa–Serra do Sol Reserve,Roraima, Amazonia,Brazil: Physical and chemical attributes of a soil catena developed from mafic rocks under shifting cultivation

Native Indians (Macuxi, Ingarikó and Uapishana) in the Raposa–Serra do Sol Indian Reserve have been cultivating forest soils since the early XIX century, especially those derived from dolerite sills, scattered within the quartzitic dominated landscape. Representative soils developed from mafic rocks under Indian shifting cultivation in northeastern Roraima, were submitted to physical, chemical and mineralogical analyses to characterize their pedogenetic characteristics and infer on their status under native Indian shifting cultivation. The soil profiles were classified as: Orthic Ebanic Chernosol (USDA Mollisol), vertic Orthic Ebanic Chernosol (USDA Mollisol), Eutrophic Haplic Cambisol (USDA mollic Inceptisol) and Eutrophic Red Nitosol (USDA Red Alfisol), which occupy, respectively, lower slopes and less dissected terrains (Mollisols) and steeper slopes (Alfisols). The first two are eutrophic, and not typical of the Amazon region. Their mineralogies range from kaolinite/goethite rich upland, deeply weathered Nitosol, to 2:1 clay rich downslope Chernosols. The latter has primary minerals in the silt fraction and high CEC resulting in high fertility. The Nitosols reveal a process of severe topsoil loss, due to widespread sheet erosion from deforestation and shifting cultivation. Chemical analyses showed varied soil fertility, ranging from high levels in the Chernosols to a low level in the non-cultivated Nitosol. Phosphorus levels are limited in all soils, despite the high fertility. The Chernosols located in lowland, flat areas close to the valley floor are more suitable environments for the slash-and-burn native farming system. In the Chernosols and Cambisols, the clay activity below the value limit for this class indicates a current natural process of increasing leaching. The more weathered and eroded Nitosol showed low Fe-oxalate and Si-oxalate levels. Micronutrients such as total zinc and copper, decreased with depth and weathering. The Nitosols showed the highest phosphate adsorption levels (1.574 mg g^− 1 of soil) which can be attributed to its clayey texture. Chernosols showed overall lower P adsorption values, increasing with depth. All soils under native Indian cultivation display signs of physical and chemical degradation due to shortened fallow under intense land use pressure in the Raposa–Serra do Sol Reserve.     

Modeling a farm population to estimate on-farm compliance costs and environmental effects of a grassland extensification scheme at the regional scale

We used a farm-level modeling approach to estimate on-farm compliance costs and environmental effects of a grassland extensification scheme in the district of Ostprignitz-Ruppin, Germany. The behavior of the regional farm population (n = 585) consisting of different farm types with different production orientations and grassland types was modeled under the presence and absence of the grassland extensification scheme using the bio-economic model MODAM. Farms were based on available accountancy data and surveyed production data, while information on farm location within the district was derived from a spatial allocation procedure. The reduction in total gross margin per unit area was used to measure on-farm compliance costs. A dimensionless environmental index was used to assess the suitability of the scheme to reduce the risk of nitrate-leaching.Calculated on-farm compliance costs and environmental effects were heterogeneous in space and farm types as a result of different agricultural production and site characteristics. On-farm costs ranged from zero up to almost 1500 Euro/ha. Such high costs occurred only in a very small part of the regional area, whereas the majority of the grassland had low on-farm costs below 50 Euro/ha. Environmental effects were moderate and greater on high-yield than on low-yield grassland. The low effectiveness combined with low on-farm costs in large parts of the region indicates that the scheme is not well targeted. The soft scheme design results from an attempt to achieve environmental and rural development objectives with only one scheme. Improving the efficiency of the scheme would require designing separate instruments for the two distinct objectives. This is in line with the Tinbergen rule, which states that consistent economic policy requires that the number of instruments equals the number of targets.     

Effects of feeding lubabegron on gas emissions,growth performance,and carcass characteristics of beef cattle housed in small-pen environmentally monitored enclosures during the last 3 mo of the finishing period

The development of technologies that promote environmental stewardship while maintaining or improving the efficiency of food animal production is essential to the sustainability of producing a food supply to meet the demands of a growing population. As such, Elanco (Greenfield, IN) pursued an environmental indication for a selective β-modulator (lubabegron; LUB). LUB was recently approved by the United States Food and Drug Administration (FDA) to be fed to feedlot cattle during the last 14 to 91 d of the feeding period for reductions in gas emissions/kg of unshrunk final BW and HCW. A 4 × 2 factorial arrangement of treatments was used with the factors of dose (0.0, 1.38, 5.5, or 22.0 mg·kg⁻¹ DM basis) and sex (steers or heifers). Three 91-d cycles were conducted (112 cattle/cycle) with each dose × sex combination being represented by a single cattle pen enclosure (CPE; 14 cattle/CPE) resulting in a total of 168 steers and 168 heifers (n = 6 replicates/dose). There were no interactions observed between dose and sex for any variable measured in the study (P ≥ 0.063). Five gases were evaluated for all pens based on CPE concentrations relative to ambient air: NH₃, CH₄, N₂O, H₂S, and CO₂. Cumulative NH₃ gas emissions were reduced by feeding cattle 5.5 and 22.0 mg·kg⁻¹ LUB (P ≤ 0.023) and tended (P = 0.076) to be lower for the cattle fed 1.38 mg·kg⁻¹ LUB compared with the negative controls (CON). The cumulative NH₃ gas emission reductions of 960 to 1032 g, coupled with HCW increases (P ≤ 0.019) of 15 to 16 kg for all LUB doses vs. CON, led to reductions in NH₃ gas emissions/kg HCW for all three LUB treatments (P ≤ 0.004). Similar to HCW, reductions in NH₃ gas emissions/kg of unshrunk final BW were observed for all LUB doses (P ≤ 0.009) and were attributable to both decreases in NH₃ gas emissions and numerical increases in BW. Dose had no effect on cumulative emissions or emissions standardized by BW or HCW for the other four gases (P ≥ 0.268). LUB is a novel tool to reduce emissions of NH₃ gas per kilogram of unshrunk live BW and hot carcass weight.     

Phylogenetic and morphological identification of Colletotrichum godetiae,a novel pathogen causing anthracnose on loquat fruits (Eriobotrya japonica)

Journal of Plant Diseases and Protection - Loquat (Eriobotrya japonica) has potential to be produced in the central part of Mexico. During summer 2017, anthracnose symptoms were observed in Tetela,...