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.     

Influence of nursery soil amendments on water relations,root architectural development,and field performance of Douglas-fir transplants

This experiment evaluated the influence of manure, peat, and vermiculite incorporated at low and high rates (0.0118 and 0.0236 m³/m²) and under two soil moisture regimes on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedling (1+0 for 1+1) xylem water potential (_xylem), whole-plant growth, root architectural development, and subsequent field performance under fertilized and non-fertilized conditions. Trends in soil moisture retention were observed (high manure > high peat > control) but there were no differences in _xylem. Root length in the wetter soil moisture experiment was initially (three months) greatest for seedlings in high vermiculite and least in high manure but there were no differences among treatments at lifting (eight months). Mean height was greatest for seedlings grown in vermiculite and peat (wetter nursery experiment) after two field seasons. Field fertilization (35 g/seedling) with controlled-release fertilizer in the planting hole stimulated height growth initially, but decreased height and diameter growth during the second growing season. Dramatic improvements associated with the use of nursery soil amendments were not realized, but the failure to identify negative effects, a potential reduction in disease incidence, and improvement of nursery soil physical and chemical properties may justify their use.     

Trunk inoculations of Phytophthora cinnamomi in red oaks

Trunks of northern red oaks were inoculated with Phytophthora cinnamomi. To study lesion growth in bark tissues over several years, lesion assessment methods were perfected and tested. Koch's postulates were demonstrated. Development and longevity of lesions were studied. Intra-specific variability of red oak susceptibility was investigated.     

Seasonal effect on infection and development of lesions caused by Cryphonectria parasitica in Castanea sativa

Seasonal variation in the development of chestnut blight, caused by Cryphonectria parasitica, was investigated by inoculating in situ chestnut trees and in vitro excised chestnut segments, at either monthly or 3‐monthly intervals throughout 30 months. Inoculations were made with conidia and mycelium of a virulent isolate and with mycelium of a hypovirulent isolate. Conidial inoculations of living sprouts or excised segments between May and July resulted in the greatest incidence of infection whereas inoculations in autumn and winter, in vitro as well as in situ, did not reveal any visible disease. However, from these symptomless inoculated stems, C. parasitica was isolated 3 months after inoculation. Inoculations with the mycelium of the virulent isolate always resulted in lesions, except in January 1999, and the greatest rate of lesion development occurred for inoculations made in the spring and summer. There was a significant seasonal effect on lesion development. Lesions caused by the hypovirulent isolate, smaller than those caused by the virulent isolate, followed a similar seasonal pattern. The same seasonal variations were observed for inoculations in vitro of excised segments. Relative water content (RWC) of chestnut bark significantly varied with bark sampling date. The rate of lesion development in sprouts significantly correlated with average minimum (ATn) and maximum (ATx) temperatures and the sum of rainfall during inoculation period, with the rate of lesion development measured in excised segments 10 days after inoculation (R10d) and with RWC measured on the day of inoculation. In multiple regression models, variables ATx and R10d best explained variation in lesion development.     

Impact of agroforestry intervention on farm income under the subsistence farming system of the middle hills, Nepal

Practices that minimize the rate of soil degradation, increase crop yields and raise farm income are key to sustaining agricultural productivity in the hills of Nepal. The use of farmland is undergoing rapid changes in response to increasing population pressure, deforestation and subsistence needs. Against this background, this study examined the impact of an agroforestry intervention project on farm income based on a sample of subsistence farm households in Dhadhing district. The project was implemented by Nepal Agroforestry Foundation in 1993/94 to increase fodder production through the promotion of agroforestry. A total of 223 households (82 with project and 141 without project) were interviewed during May–October 1998 to collect information on production and agroforestrys' impact on farm income. The benefit-cost analysis showed that the agricultural system including agroforestry was more profitable than the conventional one. The results also showed that the introduction of mulberry trees for sericulture could further enhance the profitability of an agroforestry-based system. Thus, agroforestry has great potential for enhancing food production and farmers' economic conditions in a sustainable manner through its positive contributions to household income.This revised version was published online in November 2005 with corrections to the Cover Date.     

The Warrumbungle Post‐Fire Recovery Project—raising the profile of soils

The impacts of a wildfire and subsequent rainfall event in 2013 in the Warrumbungle National Park in New South Wales, Australia were examined in a project designed to provide information on post‐fire recovery expectations and options to land managers. A coherent suite of sub‐projects was implemented, including soil mapping, and studies on soil organic carbon (SOC) and nitrogen (N), erosion rates, groundcover recovery and stream responses. It was found that the loss of SOC and N increased with fire severity, with the greatest losses from severely burnt sandstone ridges. Approximately 2.4 million t of SOC and ~74,000 t of N were lost from soil to a depth of 10 cm across the 56,290 ha affected. Soil loss from slopes during the subsequent rainfall event was modelled up to 25 t ha^?1, compared to a long‐term mean annual soil loss of 1.06 t ha^?1 year^?1. Groundcover averages generally increased after the fire until spring 2015, by which time rates of soil loss returned to near pre‐fire levels. Streams were filled with sand to bank full levels after the fire and rainfall. Rainfall events in 2015–2016 shifted creek systems into a major erosive phase, with incision through the post‐fire sandy bedload deposits, an erosive phase likely related to loss of topsoils over much of the catchment. The effectiveness of the research was secured by a close engagement with park managers in issue identification and a communications programme. Management outcomes flowing from the research included installation of erosion control works, redesign of access and monitoring of key mass movement hazard areas.     

Using knowledge of behaviour and optic physiology to improve fish passage through culverts

Culverts reduce connectivity for aquatic animals by being both a hydraulic and physical barrier. However, altered light intensity may also be a behavioural barrier to fish movement, especially for diurnal species that have adapted to moving when it is light. We propose that knowledge of optical physiology and fish behaviour, two important mechanisms underpinning movement, can inform efforts to improve fish movement through culverts. We firstly review the sensory systems of fish with reference to visual sense and explore how this affects fish movement. We then highlight theoretical knowledge that can help us understand fish behaviour and the potential mismatch between the conditions under which fish have evolved and altered conditions within culverts. We describe potential knowledge gaps and directions for future research to improve our understanding of how culverts may affect fish movement. Finally, we explore the potential costs and ecological benefits of different mitigation options to identify those with the most promise for managing the light environment in culverts to facilitate movement. For researchers and managers exploring this subject, we suggest an approach that: (a) identifies light requirements for movement by different species, (b) tests movement under different light conditions and (c) considers an integrative assessment method for testing fish behaviour around culverts. Understanding how optical physiology, fish behaviour and culvert design influence fish movement can improve connectivity for a range of species.     

Assessing the sublethal impacts of anthropogenic stressors on fish: An energy‐budget approach

Fish are increasingly exposed to anthropogenic stressors from human developments and activities such as agriculture, urbanization, pollution and fishing. Lethal impacts of these stressors have been studied but the potential sublethal impacts, such as behavioural changes or reduced growth and reproduction, have often been overlooked. Unlike mortality, sublethal impacts are broad and difficult to quantify experimentally. As a result, sublethal impacts are often ignored in regulatory frameworks and management decisions. Building on established fish bioenergetic models, we present a general method for using the population consequences of disturbance framework to investigate how stressors influence ecologically relevant life processes of fish. We partition impact into the initial energetic cost of attempts to escape from the stressor, followed by the energetic impacts of any injury or behavioural change, and their consequent effects on life processes. As a case study, we assess the sublethal effects of catch and release angling for the European sea bass (Dicentrachus labrax, Moronidae), a popular target species for recreational fishers. The energy budget model described is not intended to replace existing experimental approaches but does provide a simple way to account for sublethal impacts in assessment of the impact of recreational fisheries and aid development of robust management approaches. There is potential to apply our energy budget approach to investigate a broad range of stressors and cumulative impacts for many fish species while also using individual‐based models to estimate population‐level impacts.     

Assessment of molecular detection of Fusarium circinatum in insects and passive spore traps in Pinus radiata plantations

Fusarium circinatum is the causal agent of pitch canker, a destructive disease that threatens natural and planted pine forests around the world. Although pitch canker has caused problems in Spain and Portugal, concerning Europe as a whole, the fungus is not established across the pine distribution area. Its dispersion by wind and/or insect vectors could nevertheless play a role in the colonization of currently uninfected stands. It is therefore crucial to develop monitoring tools for its detection. To this end, we assessed the molecular detection of the pathogen in environmental samples of bark beetles and passive spore traps, collected in two infected Pinus radiata plantations in Basque country, Spain. The spread pattern of F. circinatum was assessed by an experimental design that included insect and spore traps installed at the centre, at the edge and outside the plots. Our results showed that F. circinatum was detected in both types of samples, at almost all collection dates. In both type of samples, positive detections were mainly found at the centre of the plots, a lower proportion at the edge, and very few outside. This suggests that long‐distance dispersion of Fusarium circinatum does not rely on wind spore dispersal neither on insect flight. Our study also shows that molecular methods are a powerful tool to monitor the pathogen in environmental samples.