Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect of the microbiota composition on the breeding value of an animal is the conditional expectation of its breeding value, given the vector with microbiota frequencies, that is The breeding value of an animal can therefore be decomposed into a heritable contribution that arises from an altered microbiota composition and a heritable contribution that arises from altered metabolic pathways within the animal, so Instead of selecting for breeding value , an index comprising the two components and with appropriate weights, that is , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.     

Short‐term degradation of semiarid grasslands—results from a controlled‐grazing experiment in Northern China

The assessment of grassland degradation due to overgrazing is a global challenge in semiarid environments. In particular, investigations of beginning steppe degradation after a change or intensification of the land use are needed in order to detect and adjust detrimental land‐use management rapidly and thus prevent severe damages in these sensitive ecosystems. A controlled‐grazing experiment was established in Inner Mongolia (China) in 2005 that included ungrazed (UG) and heavily grazed plots with grazing intensities of 4.5 (HG4.5) and 7.5 (HG7.5) sheep per hectare. Several soil and vegetation parameters were investigated at all sites before the start of the experiment. Topsoil samples were analyzed for soil organic C (SOC), total N (N_tot), total S (S_tot), and bulk density (BD). As vegetation parameters, aboveground net primary productivity (ANPP), tiller density (TD), and leaf‐area index (LAI) were determined. After 3 y of the grazing experiment, BD increased and SOC, N_tot, S_tot, ANPP, and LAI significantly decreased with increasing grazing intensity. These sensitive parameters can be regarded as early‐warning indicators for degradation of semiarid grasslands. Vegetation parameters were, however, more sensitive not only to grazing but also to temporal variation of precipitation between 2006 and 2008. Contrary, soil parameters were primarily affected by grazing and resistant against climatic variations. The assessment of starting conditions in the study area and the application of defined grazing intensities is essential for the investigation of short‐term degradation in semiarid environments.     

Microbial activity affected by lime in a long-term no-till soil

Under conventional farming practices, lime is usually applied on the soil surface and then incorporated into the soil to correct soil acidity. In no-till (NT) systems, where lime is surface applied or only incorporated into the soil to very shallow depth, lime will likely not move to where it is required within reasonable time. Consequently, lime may have to be incorporated into the soil by mechanical means. The objective of this laboratory study was to characterize the effect of lime, incorporated to different depths, on chemical and biological soil properties in a long-term NT soil. Soil samples taken from the 0–5, 0–10, and 0–20 cm depths were analyzed in incubation studies for soil pH, nitrate, CO₂ respiration, and microbial biomass-C (MBC). Lime (CaCO₃) was applied at rates equivalent to 0, 4.4, 8.8, and 17.6 Mg ha⁻¹. Application of lime to both 0–10 and 0–20 cm depths increased soil pH from about 4.9 by 1, 1.7, and 2.8 units for the low, medium, and high liming rates, respectively. Soil nitrate increased over time and in proportion to liming rate, suggesting that conditions were favorable for N-mineralization and nitrification. Greater respiration rates and greater MBC found in lime-treated than in non-limed soils were attributed to higher soil pH. Faster turnover rates and increased mineralization of organic matter were found in lime-treated than in non-limed soils. These studies show that below-surface lime placement is effective for correcting soil acidity under NT and that microbial activity and nitrification can be enhanced.     

Respiration pattern and microbial use of field-grown transgenic Bt-maize residues

A 49-day incubation experiment was carried out with the addition of field-grown maize stem and leaf residues to soil at three different temperatures (5, 15, and 25 °C). The aim was to study the effects of two transgenic Bt-maize varieties in comparison to their two parental non-Bt varieties on the mineralization of the residues, on their incorporation into the microbial biomass and on changes in the microbial community structure. The stem and leaf residues of Novelis-Bt contained 3.9 μg g⁻¹ dry weight of the Bt toxin Cry1Ab and those of Valmont-Bt only 0.8 μg g⁻¹. The residues of the two parental non-Bt varieties Nobilis and Prelude contained higher concentrations of ergosterol (+220%) and glucosamine (+190%) and had a larger fungal C-to-bacterial C ratio (+240%) than the two Bt varieties. After adding the Bt residues, an initial peak in respiration of an extra 700 μg CO₂-C g⁻¹ soil or 4% of the added amount was observed in comparison to the two non-Bt varieties at all three temperatures. On average of the four varieties, 19-38% of the maize C added was mineralized during the 49-day incubation at the three different temperatures. The overall mean increase in total maize-derived CO₂ evolution corresponded to a Q₁₀ value of 1.4 for both temperature steps, i.e. from 5 to 15 °C and from 15 to 25 °C. The addition of maize residues led to a strong increase in all microbial properties analyzed. The highest contents were always measured at 5 °C and the lowest at 25 °C. The variety-specific contents of microbial biomass C, biomass N, ATP and adenylates increased in the order Novelis-Bt ? Prelude<Valmont-Bt ? Nobilis. The mineralization of Novelis-Bt residues with the highest Bt concentration and lowest N concentration and their incorporation into the microbial biomass was significantly reduced compared to the parental non-Bt variety Nobilis. These negative effects increased considerably from 5 to 25 °C. The transgenic Bt variety Valmont did not show further significant effects except for the initial peak in respiration at any temperature.     

Prevalence and risk-factor analysis of Shiga toxigenic Escherichia coli in faecal samples of organically and conventionally farmed dairy cattle

Cattle are a natural reservoir for Shiga toxigenic Escherichia coli (STEC), however, no data are available on the prevalence and their possible association with organic or conventional farming practices. We have therefore studied the prevalence of STEC and specifically O157:H7 in Swiss dairy cattle by collecting faeces from approximately 500 cows from 60 farms with organic production (OP) and 60 farms with integrated (conventional) production (IP). IP farms were matched to OP farms and were comparable in terms of community, agricultural zone, and number of cows per farm. E. coli were grown overnight in an enrichment medium, followed by DNA isolation and PCR analysis using specific TaqMan assays. STEC were detected in all farms and O157:H7 were present in 25% of OP farms and 17% of IP farms. STEC were detected in 58% and O157:H7 were evidenced in 4.6% of individual faeces. Multivariate statistical analyses of over 250 parameters revealed several risk-factors for the presence of STEC and O157:H7. Risk-factors were mainly related to the potential of cross-contamination of feeds and cross-infection of cows, and age of the animals. In general, no significant differences between the two farm types concerning prevalence or risk for carrying STEC or O157:H7 were observed. Because the incidence of human disease caused by STEC in Switzerland is low, the risk that people to get infected appears to be small despite a relatively high prevalence in cattle. Nevertheless, control and prevention practices are indicated to avoid contamination of animal products.     

Evaluation of immunoglobulin G concentration in colostrum of mares by ELISA, refractometry and colostrometry

In 360 samples of colostrum and 36 samples of blood of warmblood mares, the concentration of immunoglobulin G (IgG) was evaluated in the post partal period with an ELISA and the results were compared to values obtained with 2 field methods--refractometry and colostrometry. A significant correlation (p < 0.0001) was determined between ELISA and colostrometry (r = +0.88) and between ELISA and refractometry (r = +0.93). So both field-methods seem suitable for evaluation of the colostral IgG-concentration in mares. Further the kinetic of the IgG concentration in colostrum, the volume of colostrum and the total amount of IgG was measured in the 12 hours post partum (p.p.) in each half udder of 36 mares of different parity. Immediately p.p. primiparous mares have a greater mean concentration of IgG (68 mg/ml) than multiparous mares (51 mg/ml). However, multiparous mares have a mean colostral volume of 1020 ml whereas, in primiparous mares, a mean volume of 527 ml was determined within the first three hours p.p. As a result of this the total amount of IgG was lower in primiparous (31.5 g) than in multiparous mares (48.5 g). A significant decrease of IgG concentration was measured in multiparous mares in the 1.5 hours following partum versus 3 hours in primiparous mares. The mean IgG concentration in the blood serum of the 36 mares immediately p.p. was 13.4 +/- 3.6 mg/ml. No significant correlation was observed between values of IgG concentration in the blood and in the colostrum of the mares.     

Drought damage in the park forests of the city of Helsinki

During spring and summer 2003 severe drought-caused damage was observed in the park forests of the city of Helsinki; especially in barren site pine and spruce stands. The objectives of this study were to map and document the extent of the damage through the use of existing geographical information, digital aerial photography and field surveys and to examine the feasibility of assessing drought damage by visual interpretation of digital aerial photography. Our aim was also to assess the reasons for drought damage in Helsinki city park forests using geographic information system (GIS) analyses of existing interpretative and geographical data, i.e. digital aerial photographs, rainfall statistics and the compartmentwise GIS database of the park forest site and soil types.The total amount of area falling into serious damage classes represented approximately 25 ha (the total forested area in Helsinki is about 3700 ha). A majority of these areas were located on rocky sites having low stem volumes. The total proportion of damaged stock volume was estimated as 17 300 m³, which is 3.3% of the total stock volume in the study area. An accuracy assessment showed that visual interpretation of digital aerial photos is an excellent tool for assessing drought damage. The mean estimation error was 0.7 classes, and errors comprising 2 classes were found in all test grids. The overall correct percentage of photointerpretation was 46%, and estimation was unbiased (kappa 0.264). The forest site and soil type together with the tree species on site showed the greatest correlation with drought damage. The drier and more barren the site, the more likely that damage will occur. Roadside forests were in better condition than areas located further off the roads. Hills clearly impacted the condition of the trees through soil type and flow.     

Botrytis cinerea Infection of Grape Flowers: Light and Electron Microscopical Studies of Infection Sites

ABSTRACT Specific floral organs including the calyptra, stigma, and receptacle area of glasshouse-grown grapevines (Vitis vinifera cv. Cabernet Sauvignon) were inoculated with aqueous suspensions of Botrytis cinerea conidia, and the initial steps involved in colonization and infection of the host tissues were studied for several days postinoculation using light microscopy as well as scanning and transmission electron microscopy. Conidia germinated on all floral organs examined and became attached to the host surface within 48 h after inoculation. However, in all cases the vast majority of conidia accumulated in a channel-like gap between the ovary and the calyx that extended in a narrowing fashion into the flower interior where the ovary joined the receptacle. Very few conidial germ tubes were detected in the style following inoculation of the stigma, and no evidence for their growth toward the ovaries could be found. In contrast, hyphae were more abundant in the receptacle area, regardless of the site of inoculation. Tips of the calyx became necrotic and mycelium formed in the gap between ovary and calyx within 72 h following inoculation, providing a major point of colonization and infection. B. cinerea colonized dehiscent calyptras within 72 h of inoculation, providing a potential source of inoculum from calyptras that remained stuck in the cluster. The results suggest that the grape flower's receptacle area is the predominant site of infection for B. cinerea, although a minor portion of infections may also occur through the stigma and style.