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Four fungi isolated from trunks and branches of European hazelnut (Corylus avellana L.) from commercial orchards in the Willamette Valley, Oregon were characterized and pathogenicity was tested on potted hazelnut trees. The acreage of hazelnuts in Oregon has expanded greatly in recent years in response to the availability of Eastern filbert blight resistant cultivars. Fungi were characterized using the BLASTn algorithm and the GenBank database with multiple partial gene sequence(s). If BLASTn and GenBank were not sufficient for species-level identification, then a multilocus sequence analysis (MLSA) was performed. The four pathogens were identified as Diplodia mutilla (Fr.) Mont., Dothiorella omnivora B.T. Linaldeddu, A. Deidda & B. Scanu, Valsa cf. eucalypti Cooke & Harkn., and Diaporthe eres Nitschke. All pathogens but D. omnivora have not been previously reported from European hazelnut in the literature. All four pathogens caused lesions on trunks bare root hazelnut trees cv. 'Jefferson' planted in pots in the greenhouse and fungi were re-isolated from inoculated trees. D. mutilla appeared particularly aggressive in repeated inoculation experiments. [ABSTRACT FROM AUTHOR]

Cross-border seasonal livestock movements in West Africa bring into close contact several cattle breeds. In the coastal countries hosting migrating herders from the Sahel, it often affects the genetic variability and geographical distribution of traditional cattle breeds, through their indiscriminate but also intended crossbreeding with larger-framed Sahelian cattle breeds. The need to secure and effectively manage this genetic variability, in order to respond to changing production and market conditions, is widely recognized by the scientific community, livestock herders and policy-makers. This however requires a comprehensive knowledge of the breeds’ characteristics. The indigenous criteria used by pastoralists to characterize and distinguish cattle breeds remain unclear and further validation is required. This study was therefore designed to document and validate herders' knowledge on cattle breeds. From June 2015 to June 2016, 803 cattle herders participated in a phenotypic breed description in seven pastoral communities across the country. Each cattle herder was asked to name and describe morphologically the different cattle breeds in his herd. Subsequently, fifteen body measurements taken on a total of 1401 adult cattle (964 cows and 439 bulls) were submitted to multivariate analyses. Participants distinguished ten different cattle breeds kept in traditional herds according to six primary morphological traits and clearly separated zebuine from taurine breeds. These results were consistent with those of the multivariate analyses of the measured traits. However, herders’ classification approach proved to be more accurate in distinguishing breeds within the zebuine subspecies. Hence, while metric measurements and molecular genetic analyses are promising approaches to fill the knowledge gap on the diversity of local farm animal genetic resources, they should integrate livestock herders’ traditional knowledge for more precision. [ABSTRACT FROM AUTHOR]

The presence of earthworm species in crop fields is as old as agriculture itself. The earthworms Pontoscolex corethrurus (invasive) and Balanteodrilus pearsei (native) are associated with the emergence of agriculture and sedentism in the region Amazon and Maya, respectively. Both species have shifted their preference from their natural habitat to the cropland niche. They contrast in terms of intensification of agricultural land use (anthropic impact to the symbiotic soil microbiome). P. corethrurus inhabits conventional agroecosystems, while B. pearsei thrives in traditional agroecosystems, i.e., P. corethrurus has not yet been recorded in soils where B. pearsei dwells. The demographic behavior of these two earthworm species was assessed in the laboratory over 100 days, according to their origin (OE; P. corethrurus and B. pearsei) food quality (FQ; soil only, maize stubble, Mucuna pruriens), and soil moisture (SM; 25, 33, 42%). The results showed that OE, FQ, SM, and the OE x FQ interaction were highly significant for the survival, growth, and reproduction of earthworms. P. corethrurus showed a lower survival rate (> mortality). P. corethrurus survivors fed a diet of low-to-intermediate nutritional quality (soil and stubble maize, respectively) showed a greater capacity to grow and reproduce; however, it was surpassed by the native earthworm when fed a high-quality diet (M. pruriens). Besides, P. corethrurus displayed a low cocoon hatching (emergence of juveniles). These results suggest that the presence of the invasive species was associated with a negative interaction with the soil microbiota where the native species dwells, and with the absence of natural mutualistic bacteria (gut, nephridia, and cocoons). These results are consistent with the absence of P. corethrurus in milpa and pasture-type agricultural niches managed by peasants (agroecologists) to grow food regularly through biological soil management. Results reported here suggest that P. corethrurus is an invasive species that is neither wild nor domesticated, that is, its eco-evolutionary phylogeny needs to be derived based on its symbionts. [ABSTRACT FROM AUTHOR]

Within the dairy industry, most antimicrobials are used for dry-cow therapy or mastitis treatment. To reduce antimicrobial usage in dairy cows, increasing awareness and behaviour change is necessary. As veterinarians are known to be influenced by their peers, peer study groups as a continuous education might contribute to this. Therefore, the objective of this study was to analyse written records of veterinary peer study group meetings to identify factors associated with antimicrobial prescribing decisions, and to analyse veterinarians’ attitude towards the benefits of this continuous education method. Twenty-three participating Swiss cattle practitioners were divided into three groups. Each group met every two to five months, together with a facilitator and an expert on the topic to be discussed. Written records from every meeting were taken and analysed qualitatively to identify factors influencing veterinarians’ decisions on antimicrobial prescribing and mastitis therapy. In addition, focus group discussions were conducted after the last meeting, to assess the veterinarians' learning achievements gained during the peer study group meetings. Extrinsic factors such as external pressure, competition, farmer, individual animal, farm and diagnostics as well as intrinsic factors such as own experience/attitude, knowledge and change of mindset during career could be shown to influence veterinarians’ decisions on antimicrobial prescribing. In the focus group discussions, the veterinarians stated that they gained new knowledge, received new stimuli, exchanged with their peers and felt supported in their relationship to their farmers. Since the identified factors are partly interrelated, it is not sufficient to change a single factor to achieve a change in the antimicrobial prescription behaviour of veterinarians. Veterinary peer study groups could contribute to the intention to change, because veterinarians experienced multiple benefits from this method of continuous education. In order to quantify this, the prescription data of the veterinarians are analysed in a next step. [ABSTRACT FROM AUTHOR]

Assessments of the global carbon (C) cycle typically rely on simplified models which consider large areas as homogeneous in terms of the response of soils to land use or consider very broad land classes. For example, “cropland” is typically modelled as an aggregation of distinct practices and individual crops over large regions. Here, we use the process-based Rothamsted soil Carbon Model (RothC model), which has a history of being successfully applied at a global scale, to calculate attainable SOC stocks and C mineralization rates for each of c. 17,000 regions (combination of soil type and texture, climate type, initial land use and country) in the World, under near-past climate conditions. We considered 28 individual crops and, for each, multiple production practices, plus 16 forest types and 1 grassland class (total of 80 classes). We find that conversion to cropland can result in SOC increases, particularly when the soil remains covered with crop residues (an average gain of 12 t C/ha) or using irrigation (4 t C/ha), which are mutually reinforcing effects. Attainable SOC stocks vary significantly depending on the land use class, particularly for cropland. Common aggregations in global modelling of a single agricultural class would be inaccurate representations of these results. Attainable SOC stocks obtained here were compared to long-term experiment data and are well aligned with the literature. Our results provide a regional and detailed understanding of C sequestration that will also enable better greenhouse gas reporting at national level as alternatives to IPCC tier 2 defaults. [ABSTRACT FROM AUTHOR]

This study evaluates the unique and combined effects of three complementary ICT-based extension methods ― interactive radio, mobile SMS messages and village-based video screenings ― on farmers’ knowledge and management of fall armyworm (FAW), an invasive pest of maize that is threatening food security in sub-Saharan Africa and Asia. Building on a survey of maize farmers in western Uganda and using various selection-on-observables estimators, we find consistent evidence that participation in the ICT-based extension campaigns significantly increases farmers’ knowledge about FAW and stimulates the adoption of agricultural technologies and practices for the management of the pest. We also show that exposure to multiple campaign channels yields significantly higher outcomes than exposure to a single channel, with some evidence of additive effects. These results are robust to alternative estimators and also to hidden bias. Results further suggest that among the three ICT channels, radio has greater reach, video exerts a stronger impact on the outcome measures, and greater gains are achieved when video is complemented by radio. Our findings imply that complementary ICT-based extension campaigns (particularly those that allow both verbal and visual communication) hold great potential to improve farmers’ knowledge and trigger behavioural changes in the identification, monitoring and sustainable management of a new invasive pest, such as FAW. [ABSTRACT FROM AUTHOR]

The Mauritius fruit bat (Pteropus niger) has been the subject of repeated culling campaigns, apparently in response to pressure from the fruit-growing industry concerned over damage to commercially valuable orchard crops such as lychees. More than 31,000 fruit-bearing lychee trees also exist in private backyards, making this an issue pertinent to a wide cross-section of the Mauritian general public and not just those involved in commercial fruit production. The level of damage caused by bats to fruit crops is often debated and the low number of robust damage assessment studies hampers mitigation efforts. During the fruiting season of 2016/2017, we assessed the damage among backyard lychee trees attributable to fruit bats and other causes around Vacoas-Phoenix, Central Mauritius and evaluated the impact of using protective netting as a mitigation strategy. Fruit yield from panicles that were protected from depredation by nylon netting was approximately one third greater than that from unprotected panicles. We suspect that fruit bats were responsible for approximately 42% of the total damage but illustrate the difficulties in attributing damage to a single cause in such assessments. Although we demonstrate the value of protective netting, we recognize that barriers to implementation exist and that a more holistic approach that incorporates crop protection, forest restoration strategies and addresses negative public attitudes towards bats in general is required to ensure the persistence of this endemic species. [ABSTRACT FROM AUTHOR]

Understanding the challenges to increasing maize productivity in sub-Saharan Africa, especially agronomic factors that reduce on-farm crop yield, has important implications for policies to reduce national and global food insecurity. Previous research on the maize yield gap has tended to emphasize the size of the gap (theoretical vs. achievable yields), rather than what determines maize yield in specific contexts. As a result, there is insufficient evidence on the key agronomic and environmental factors that influence maize yield in a smallholder farm environment. In this study, we implemented a Bayesian analysis with plot-level longitudinal household survey data covering 1,197 plots and 320 farms in Central Malawi. Households were interviewed and monitored three times per year, in 2015 and 2016, to document farmer management practices and seasonal rainfall, and direct measurements were taken of plant and soil characteristics to quantify impact on plot-level maize yield stability. The results revealed a high positive association between a leaf chlorophyll indicator and maize yield, with significance levels exceeding 95% Bayesian credibility at all sites and a regression coefficient posterior mean from 28% to 42% on a relative scale. A parasitic weed, Striga asiatica, was the variable most consistently negatively associated with maize yield, exceeding 95% credibility in most cases, of high intensity, with regression means ranging from 23% to 38% on a relative scale. The influence of rainfall, either directly or indirectly, varied by site and season. We conclude that the factors preventing Striga infestation and enhancing nitrogen fertility will lead to higher maize yield in Malawi. To improve plant nitrogen status, fertilizer was effective at higher productivity sites, whereas soil carbon and organic inputs were important at marginal sites. Uniquely, a Bayesian approach allowed differentiation of response by site for a relatively modest sample size study (given the complexity of farm environments and management practices). Considering the biophysical constraints, our findings highlight management strategies for crop yields, and point towards area-specific recommendations for nitrogen management and crop yield. [ABSTRACT FROM AUTHOR]

The use of elasticities of substitution between inputs is a standard method for addressing the effect of a change in the mix of inputs used for production from a technical or cost standpoint. Most estimation methods use parametric production or cost functions or frontiers to estimate these elasticities. A potentially useful nonparametric alternative is data envelopment analysis (DEA). The purpose of this paper is to derive elasticities of input substitution for both technical and cost frontiers using DEA, extending the use of this approach in the field of economics and associated fields. The paper provides derivations for both Hicksian (production and cost frontier) and Morishima (cost frontier) elasticities of input substitution, as well as a parsimonious method for estimating them using DEA. The derivations are presented using an agricultural example form Kansas, USA. [ABSTRACT FROM AUTHOR]

We present a method for calculating the Acute Insecticide Toxicity Loading (AITL) on US agricultural lands and surrounding areas and an assessment of the changes in AITL from 1992 through 2014. The AITL method accounts for the total mass of insecticides used in the US, acute toxicity to insects using honey bee contact and oral LD50 as reference values for arthropod toxicity, and the environmental persistence of the pesticides. This screening analysis shows that the types of synthetic insecticides applied to agricultural lands have fundamentally shifted over the last two decades from predominantly organophosphorus and N-methyl carbamate pesticides to a mix dominated by neonicotinoids and pyrethroids. The neonicotinoids are generally applied to US agricultural land at lower application rates per acre; however, they are considerably more toxic to insects and generally persist longer in the environment. We found a 48- and 4-fold increase in AITL from 1992 to 2014 for oral and contact toxicity, respectively. Neonicotinoids are primarily responsible for this increase, representing between 61 to nearly 99 percent of the total toxicity loading in 2014. The crops most responsible for the increase in AITL are corn and soybeans, with particularly large increases in relative soybean contributions to AITL between 2010 and 2014. Oral exposures are of potentially greater concern because of the relatively higher toxicity (low LD50s) and greater likelihood of exposure from residues in pollen, nectar, guttation water, and other environmental media. Using AITL to assess oral toxicity by class of pesticide, the neonicotinoids accounted for nearly 92 percent of total AITL from 1992 to 2014. Chlorpyrifos, the fifth most widely used insecticide during this time contributed just 1.4 percent of total AITL based on oral LD50s. Although we use some simplifying assumptions, our screening analysis demonstrates an increase in pesticide toxicity loading over the past 26 years, which potentially threatens the health of honey bees and other pollinators and may contribute to declines in beneficial insect populations as well as insectivorous birds and other insect consumers. [ABSTRACT FROM AUTHOR]

Human-wildlife conflicts restrict conservation efforts, especially for wide-ranging animals whose home ranges overlap with human activities. We conducted a study to understand conflicts with, and factors influencing the perceived value of an expanding population of onagers (Equus hemionus onager) in local communities in southern Iran. We asked about locals’ perceptions of six potential management strategies intended to lessen human-onager conflict. We found that human-onager conflict was restricted to 45% of respondents within the Bahram-e-Goor Protected Area, all of whom were involved in farming or herding activities. Locals within the protected area were more knowledgeable about onagers and valued onagers more than those living outside the protected area. The perceived value of onagers increased with level of education, total annual income, and perceptions of onager population trends; the perceived value of onagers decreased with the magnitude of conflict between onagers and locals. To tolerate or avoid conflicts with onagers, locals were supportive of monetary compensation and changing from a traditional lifestyle to industrialized farming (for farmers) or livestock production (for herders) with the help of government; locals did not support selling land to the government. Our study is among the first in human-wildlife conflict and local attitudes towards an endangered species and its recovery in Iran. We conclude that current levels of human-onager conflict are relatively low and perceived value of onagers is still relatively high. Therefore, wildlife authorities should consider the development of mitigation strategies with local communities before conflicts intensify. [ABSTRACT FROM AUTHOR]

Criniviruses accumulate in the phloem tissue and damage crops by reducing chlorophyll which is essential for plant growth and development. Tomato chlorosis crinivirus (ToCV) is vectored by several whitefly species that damage tomato crops throughout the world. In South Africa, ToCV is a poorly studied pathogen of global economic importance. Therefore, a national survey was initiated to investigate the occurrence and distribution of criniviruses infecting tomato crops in South Africa. Whitefly infested tomato crops exhibiting interveinal leaf chlorosis and chlorotic flecking symptoms were assayed for crinivirus infections using a multiplex reverse transcription polymerase reaction (RT-PCR) approach to assess for the presence of crinivirus species that are known to infect solanaceous hosts. Next-generation sequencing (NGS) was used to generate the complete genome of ToCV from South Africa. Results from the survey indicated that ToCV is presently the only crinivirus species infecting tomatoes in South Africa. Blast analysis showed that the RNA-1 segment of ToCV from South Africa (ToCR1-186) matched 99% to Spanish isolates. On the other hand, the RNA-2 (ToCR2-186) segment matched 98% to a South Korean isolate and three Spanish isolates. Although recombination events were not detected, phylogenetic studies showed inconsistencies in the grouping of RNA-1 and RNA-2 segments for some of the ToCV isolates analyzed in this study. Therefore, we suggest the possibility of intraspecific reassortment. This is the first comprehensive study and full genome sequence of ToCV from South Africa. The information generated from this study is intended to raise awareness of ToCV infections on tomato crops in South Africa. [ABSTRACT FROM AUTHOR]

Bovine tuberculosis (bTB) caused by Mycobacterium bovis is an important re-emerging disease affecting livestock, wildlife and humans. Epidemiological studies are crucial to identifying the source of bTB infection, and its transmission dynamics and host preference, and thus to the implementation of effective strategies to contain it. In this study, we typed M. bovis isolates from livestock, and investigated their genetic diversity and distribution. A total of 204 M. bovis isolates were collected from cattle (n = 164) and Sicilian black pigs (n = 40) reared in a limited area of the province of Messina, northeastern Sicily, an area that had previously been identified as having the highest incidence of bTB in livestock on the island. All M. bovis isolates were typed by both spoligotyping and 12-loci MIRU-VNTR analysis. Results from both methods were then combined in order to improve the discriminatory power of M. bovis typing. We identified 73 combined genetic profiles. Thirty-five point six percent of the profiles were common to at least two animals, whereas 64.4% of profiles occurred in only one animal. A number of genetic profiles were predominant in either cattle or black pigs. We identified common genetic patterns in M. bovis isolates originating not only from neighboring districts, but also from non-neighboring districts. Our findings suggest that bTB is widespread in our setting, and is caused by a large number of genetically diverse M. bovis strains. The ecology and farming practices characteristic of the area may explain the substantial M. bovis heterogeneity observed, and could represent obstacles to bTB eradication. [ABSTRACT FROM AUTHOR]

Coffee berry borer (CBB, Hypothenemus hampei) (Coleoptera: Curculionidae: Scolytinae) is the most destructive pest of coffee worldwide. Information on CBB development times can be used to predict the initiation of new infestation cycles early in the coffee-growing season and thus inform the timing of insecticide applications. While laboratory estimates of CBB development under constant conditions exist, they have not been applied under the heterogeneous environmental conditions that characterize many coffee-growing regions. We measured CBB development times and abundance in commercial coffee farms across an elevational gradient on Hawai‘i Island and applied thermal accumulation models from previous laboratory studies to test their fit to field data. Artificial lures were used to infest coffee berries at five farms ranging in elevation from 279–792 m, and weather variables were monitored at macro (farm-level) and micro (branch-level) scales. CBB development was followed in the field from the time of initial berry infestation by the founding female through the development of F1 mature adults. Mean development time from egg to adult across all sites was 38.5 ± 3.46 days, while the mean time required for the completion of a full life cycle (from time of infestation to presence of mature F1 females) was 50.9 ± 3.35 days. Development time increased with increasing elevation and decreasing temperature. Using macro-scale temperature data and two different estimates for the lower temperature threshold (14.9°C and 13.9°C), we estimated a mean requirement of 332 ± 14 degree-days and 386 ± 16 degree-days, respectively, from the time of berry infestation to the initiation of a new reproductive cycle in mature coffee berries. Similar estimates were obtained using micro-scale temperature data, indicating that macro-scale temperature monitoring is sufficient for life-cycle prediction. We also present a model relating elevation to number of CBB generations per month. Our findings suggest that CBB development times from laboratory studies are generally applicable to field conditions on Hawai‘i Island and can be used as a decision support tool to improve IPM strategies for this worldwide pest of coffee. [ABSTRACT FROM AUTHOR]

Nowadays, consumers have become increasingly aware of their local food system as a result of concerning about health and nutrition, food safety and sustainability, and local economic development. This transitional shift from global to direct-to-consumer farm operations has increased the demand for locally produced foods. As an alternative, community supported agriculture (CSA), a direct and sustainable food channel, has gained tremendous popularity in the US. Despite the interest garnered by local agriculture and CSA, relatively few studies have empirically tested the determinants of why this marketing phenomenon has grown so rapidly. The purpose of this study is to explore the factors that drive producers to market their products through CSA by using a county-level data set from the US. Results using a Tobit model indicate that specific operator characteristics, such as young and female operators and those engaged in farming as primary occupation, play a strongly positive role in the likelihood of marketing through CSA; farms with small size, rented land, and engagement in growing vegetables, melons, fruits and tree nut crops are more interested in marketing via CSA; households with higher income and females significantly increase the share of farms marketing through CSA; presence of children and seniors and being married are negatively related to the demand for CSA foods. Moreover, counties with higher density of population, establishments-supermarket and other grocery stores, and legislation or active programs that encourage local food consumption tend to encourage more farms marketing through CSA. [ABSTRACT FROM AUTHOR]

Although rice has been a prominent cash crop in areas with access to lowland in Uganda, the adoption of rice and area expansion have stagnated despite the Government of Uganda’s 2009 National Rice Development Policy and its commitment to doubling rice production over 10 years. Using panel data collected in 2010 and 2017 as well as risk preference data elicited via lab-in-the-field experiments conducted in rural Uganda, we find that farmers with higher loss aversion are less likely to grow rice and expand their rice cultivation areas. This study affirms that risk preferences play a critical role in agricultural production decisions. [ABSTRACT FROM AUTHOR]

The aim of this study was to identify the main on-farm welfare issues likely to be encountered in extensive sheep farming systems. Thirty-two commercial sheep farms in Victoria, Australia were involved in this study. Of the 32 farms involved, 30 were visited twice (at mid-pregnancy and weaning), and 2 farms only once (both at weaning). In total, 62 visits were conducted and 6,200 ewes (aged 2–5 years) were examined using six animal-based indicators: body condition score (BCS), fleece condition, skin lesions, tail length, dag score and lameness. In addition, the number of ewes that needed further care (such as sick or injured sheep) was recorded and reported to the farmers. Generalised linear mixed models were conducted to investigate associations between welfare outcomes and visit, ewe breed and location, with all three, and their interactions, as fixed factors. In all instances, farm was set as a random factor to account for specific variation between farms. Overall, the welfare of the ewe flocks, based on the six indicators measured, was considered good. A total of 86.9% of the ewes were in adequate BCS (2.5–3.5), 91% had good fleece condition, 69.2% had no skin lesions, 97.1% had low dag scores, and overall lameness was 4.7%. An important and prevalent risk to welfare identified across farms was short tail length; with 85.7% of ewes having tails docked shorter than the third palpable joint. While the welfare of the flock was good, ewes in need of further care were identified at all farms. There were 185 (3.0%) cases needing further care, and the extent of welfare compromise of these animals was considered significant. Main reasons for further care were moderate/severe lameness or foot-related issues, BCS ≤ 2 and active dermatophilosis or broken wool. To our knowledge, this study constitutes the largest assessment of ewes conducted in Australia, and the findings provide valuable insight into the main welfare issues likely to be encountered in extensive sheep farming enterprises. Future studies should develop practical technologies that can assist in the detection of the welfare issues identified in this study. In addition, the thresholds identified here could be used for future comparison and sheep welfare benchmarking programs to assess farm performance and measure continuous improvements. [ABSTRACT FROM AUTHOR]

Mussel farming has been recognised as a low cost option for mitigating damage caused by eutrophication in the Baltic Sea. However, uncertain nutrient removal owing to weather and environmental conditions at the mussel farm site has not been previously considered. The purpose of this study was to estimate whether mussel farming has cost advantages even in conditions of uncertainty. To this end, the replacement cost method was used for the valuation of ecosystem services and a numerical cost minimisation model was constructed based on the safety-first approach to account for uncertainty in nutrient removal. This study showed that the value of mussel farming depends on the cost at the farm, and the impact on the mean and variability of nutrient removal in relation to other abatement measures. The study also pointed out the need of data on the decision makers’ risk attitudes and measurement of uncertainty. The application to the Baltic Sea showed that the total value of mussel farming increased from 0.34 billion Euro/year to 0.41 or 1.21 billion Euro when accounting for uncertainty depending on assumption of probability distribution. The increase was unevenly distributed between the Baltic Sea countries, with it found to be lower for countries equipped with highly productive mussel farms and long coastlines. [ABSTRACT FROM AUTHOR]

During the winter of 2016-2017, an epidemic of highly pathogenic avian influenza (HPAI) led to high mortality in poultry and put a serious burden on the poultry industry of the Republic of Korea. Effective control measures considering spatial heterogeneity to mitigate the HPAI epidemic is still a challenging issue. Here we develop a spatial-temporal compartmental model that incorporates the culling rate as a function of the reported farms and farm density in each town. The epidemiological and geographical data of two species, chickens and ducks, from the farms in the sixteen towns in Eumseong-gun and Jincheon-gun are used to find the best-fitted parameters of the metapopulation model. The best culling radius to maximize the final size of the susceptible farms and minimize the total number of culled farms is calculated from the model. The local reproductive number using the next generation method is calculated as an indicator of virus transmission in a given area. Simulation results indicate that this parameter is strongly influenced not only by epidemiological factors such as transmissibility and/or susceptibility of poultry species but also by geographical and demographical factors such as the distribution of poultry farms (or density) and connectivity (or distance) between farms. Based on this result, we suggest the best culling radius with respect to the local reproductive number in a targeted area. [ABSTRACT FROM AUTHOR]

In developing countries, the cost of vaccination limits the use of prophylactic rabies vaccination, especially in cattle. Intradermal vaccination delivers antigen directly to an area with higher number of antigen-presenting cells. Therefore, it could produce equivalent or higher antibody titres than conventional intramuscular vaccination even when a lower dose is given. This study aimed to compare the antibody response in cattle vaccinated intramuscularly with 1mL of inactivated rabies vaccine (Raksharab, Indian Immunologicals) against intradermally vaccinated cattle with 0.2mL of the same vaccine. The study was conducted in Haa province of Bhutan where rabies is not endemic. One hundred cattle from 27 farms were selected for the study. Virus neutralising antibody (VNA) response was measured using the fluorescent antibody virus neutralisation test on the day of vaccination (day 0) and 14, 30, 60 and 90 days later. Overall, 71% of intradermally vaccinated cattle and 89% of the intramuscularly vaccinated cattle produced an adequate response (≥0.5IU/mL). On days 14 and 30 post vaccination fewer cattle (P<0.02) in the intradermal group had adequate titres with 36% and 58%, respectively, having titres ≥0.5 IU/mL compared to the equivalent figures of 78% and 77% in the intramuscular group. The mean VNA titres were lower for the intradermal group than intramuscular group (p<0.001) with the mean difference being > 0.6 IU/mL. Although low dose intradermal vaccination did produce a detectable antibody response, it was inferior to intramuscular vaccination. Thus, although intradermal vaccination has the potential to reduce the cost of vaccination by reducing the dose required, this study showed that a single dose of 0.2 mL intradermally was inferior to an intramuscular dose of 1 mL. Further research evaluating dose and dose regimen is needed before intradermal vaccination using the Raksharab rabies vaccine can be recommended in cattle. [ABSTRACT FROM AUTHOR]

While there is a general belief that reforesting marginal, often unprofitable, croplands can result in water quality benefits, to date there have been very few studies that have attempted to quantify the magnitude of the reductions in nutrient (N and P) and sediment export. In order to determine the magnitude of a credit for water quality trading, there is a need to develop quantitative approaches to estimate the benefits from forest planting in terms of load reductions. Here we first evaluate the availability of marginal croplands (i.e. those with low infiltration capacity and high slopes) within a large section of the Ohio River Basin (ORB) to assess the magnitude of the land that could be reforested. Next, we employ the Nutrient Tracking Tool (NTT) to study the reduction in N, P and sediment losses from converting corn or corn/soy rotations to forested lands, first in a case study and then for a large region within the ORB. We find that after reforestation, N losses can decrease by 40 to 80 kg/ha-yr (95–97% reduction), while P losses decrease by 1 to 4 kg/ha-yr (96–99% reduction). There is a significant influence of local conditions (soils, previous crop management practices, meteorology), which can be considered with NTT and must be taken into consideration for specific projects. There is also considerable interannual and monthly variability, which highlights the need to take the longer view into account in nutrient credit considerations for water quality trading, as well as in monitoring programs. Overall, there is the potential for avoiding 60 million kg N and 2 million kg P from reaching the streams and rivers of the northern ORB as a result of conversion of marginal farmland to tree planting, which is on the order of 12% decrease for TN and 5% for TP, for the entire basin. Accounting for attenuation, this represents a significant fraction of the goal of the USEPA Gulf of Mexico Hypoxia Task Force to reduce TN and TP reaching the dead zone in the Gulf of Mexico, the second largest dead zone in the world. More broadly, the potential for targeted forest planting to reduce nutrient loading demonstrated in this study suggests further consideration of this approach for managing water quality in waterways throughout the world. The study was conducted using computational models and there is a need to evaluate the results with empirical observations. [ABSTRACT FROM AUTHOR]

The need to consider the role of social factors in the efficacy of farm management and, consequently, in the onset and persistence of diseases typical to animal farms is increasingly being realized increasingly worldwide. Many risk analysis studies have been conducted to assess the role of various factors in the development of animal diseases; however, very few have accounted for the role of social factors. The aim of this work was to bridge this gap, with the main hypothesis that different socio-economic factors could be valid indicators for the occurrence of different animal diseases. A socio-economic analysis was performed using demographic characteristics of the farmers and data from 44 social indicators released by the Italian Statistician National Institute of Statistics (ISTAT) database. African swine fever (ASF) in wild boars (WB) and domestic pigs and other endemic animal diseases and zoonoses in Sardinia were considered, such as cistic echinococcosis (CE), contagious agalactia (CA), trichinellosis, West Nile disease (WND), and bluetongue (BT). Seven different negative binomial regression models were fitted using the number of cases between 2011–2017. Three indicators—cultural demand, employment rate, and legality—showed a statistically significant association with risk for all the diseases considered, but with varying effects. Some indicators, such as the age and sex of the farmer, material deprivation index, number of farms and animals, micro-criminality index, and rate of reported thefts were common to ASF, CA, trichinellosis, and CE cases. Others such as the forest surface and the energy produced from renewable sources were common to BT, WND, and ASF in WB. Tourism in seasons other than summer was a valid predictor of ASF and trichinellosis, while out-of-region hospital use had a statistically significant role in CE risk identification. These results may help understand the social context in which these diseases may occur and thus guide the design and implementation of additional risk management measures that go beyond well-known veterinary measures. [ABSTRACT FROM AUTHOR]

Coffee farms have been adopting the microterraces system, a technique that reduces the effect of the slope by moving the soil between the crop lines. In this way, all the mechanized operations can be carried out normally, except for harvesting, due to the work limitation of the harvesters, who work in areas with a maximum slope of 20%. One option is to use unilateral harvesters, which crop one side at a time; however, there has been no research on these microterrace machines to evaluate their performance and to compare it with those of the other harvesting methods in those regions. This study aimed to compare the mechanized harvest performance in the microterraces with the manual and semimechanized harvesting methods. The study was carried out in an agricultural area of the municipality of Ouro Fino / MG, Brazil, in a crop production site where the microterraces were built six years before the experiment. The treatments were assigned to a split-block design with seven repetitions and consisted of mechanized harvest—unilateral harvester with bag storage; manual harvest—regionally experienced workers; and semimechanized harvest—with portable breakers. Through an analysis of the times and movements, the operational efficiency and operational and effective field capabilities were measured. The adoption of microterraces allows the efficient mechanization of areas previously impossible to mechanize. The unilateral harvester is a potential tool for the partial replacement of manual labor in the harvest, performing a service equivalent to that of 23.68 manual workers and 10.55 manual workers in the semimechanized system. [ABSTRACT FROM AUTHOR]

Sustainable agriculture is an important global issue. The use of organic fertilizers can enhance crop yield and soil properties while restraining pests and diseases. The objective of this study was to assess the effects of long-term use of chemical and organic fertilizers on tea and rhizosphere soil properties in tea orchards. Inductively coupled plasma mass spectrometry (ICP-MS) and high-throughput sequencing technology analyses were used to investigate heavy metals content and bacterial composition in rhizosphere soils. Our results indicated that organic fertilizer treatment significantly decreased Cu, Pb and Cd contents in rhizosphere soil sample. The results also showed that treatment with organic fertilizer significantly decreased the contents of Cd, Pb and As in tea leaves. Furthermore, organic fertilizer significantly increased the amino acids content of tea and the pH of the soil. The use of organic fertilizer significantly increased in the relative abundance of Burkholderiales, Myxococcales, Streptomycetales, Nitrospirales, Ktedonobacterales, Acidobacteriales, Gemmatimonadales, and Solibacterales, and decreased the abundance of Pseudonocardiales, Frankiales, Rhizobiales, and Xanthomonadales. In conclusion, organic fertilizer can help to shape the microbial composition and recruit beneficial bacteria into the rhizosphere of tea, leading to improved tea quality and reduced heavy metals content in rhizosphere soil and tea leaves. [ABSTRACT FROM AUTHOR]

The use of agricultural resources or environments by wildlife may result in opportunities for transmission of infections amongst wild animals, livestock and humans. Targeted use of biosecurity measures may therefore reduce disease risks, although this requires practical knowledge of where such measures would be most effective, and effective means of communicating risks so that stakeholders can make informed decisions about such investment. In parts of Europe, the European badger Meles meles may act as a wildlife reservoir for Mycobacterium bovis, the causative agent of bovine tuberculosis, and badger visits to farmyards may provide potential opportunities for transmission of M. bovis to cattle. Biosecurity measures are effective in reducing badger activity in farmyards, although it is unclear which farms should be targeted with such measures. We used cameras to monitor badger activity in 155 farmyards in south west England and Wales, and related variations in the presence and frequency of badger visits to farm characteristics. Badgers were recorded on camera in 40% of farmyards monitored. However, the frequency of visits was highly variable, with badgers recorded on >50% of nights in only 10% of farms. The presence of badgers in farmyards was positively associated with the density of badger setts, the number of feed stores and the number of cattle sheds, and negatively associated with the distance to the nearest active badger sett, the presence of a house/dwelling and the number of cattle housed on the farm. The frequency of visits was negatively associated with the distance to the nearest active badger sett and the number of cattle housed. Models predicted the presence/absence of badgers in farmyards with 73% accuracy (62% sensitivity, 81% specificity, using a cut off value of 0.265). Models could not distinguish between farms with low/high frequency of visits, although farms predicted as having badgers present typically had a higher frequency of visits than those that were not. We developed and present an interactive web based application: the Badger Farm Assessment Tool (BFAT), to allow users to enter the characteristics of a farm and generate a relative risk score describing the likelihood of badger visits. [ABSTRACT FROM AUTHOR]

Fresh produce outbreaks due to Shiga toxin-producing Escherichia coli (STEC) continue to occur in the United States (US). Manure-amended soils can pose a public health risk when used for growing raw agricultural commodities. Knowing the prevalence and concentration of STEC in untreated biological soil amendments of animal origin (BSAAO) is important to help guide the most appropriate pre-harvest interval(s) following application to limit risks from these soil amendments. Bovine manure samples were collected from 12 farms in Florida, including samples from piles, lagoons, barns, and screened solids. Two methods were used to detect stx1/2 and rfbE genes in samples. A prevalence rate of 9% for stx1 and/or stx2 and 19% for rfbE was observed from the 518 bovine manure samples evaluated. A most probable number (MPN) assay was performed on stx+ samples when applicable. The geometric mean for stx+ samples (n = 20) was 3.37 MPN g-1 (0.53 log MPN g-1) with a maximum value of 6,800 MPN g-1 (3.83 log MPN g-1). This research was part of a larger nationwide geographical study on the prevalence and concentration of STEC in bovine manure to help guide regulations on feasible pre-harvest intervals for the application of untreated BSAAO. [ABSTRACT FROM AUTHOR]

Leptospirosis, an emerging infectious disease caused by bacteria of the genus Leptospira, is thought to be the most widespread zoonotic disease in the world. A first step in preventing the spread of Leptospira is delineating the animal reservoirs that maintain and disperse the bacteria. Quantitative PCR (qPCR) methods targeting the LipL32 gene were used to analyze kidney samples from 124 House mice (Mus musculus), 94 Black rats (Rattus rattus), 5 Norway rats (R. norvegicus), and 89 small Indian mongooses (Herpestes auropunctatus) from five cattle farms in Puerto Rico. Renal carriage of Leptospira was found in 38% of the sampled individuals, with 59% of the sampled mice, 34% of Black rats, 20% of Norway rats, and 13% of the mongooses. A heterogeneous distribution of prevalence was also found among sites, with the highest prevalence of Leptospira-positive samples at 52% and the lowest at 30%. Comparative sequence analysis of the LipL32 gene from positive samples revealed the presence of two species of Leptospira, L. borgpetersenii and L. interrogans in mice, detected in similar percentages in samples from four farms, while samples from the fifth farm almost exclusively harbored L. interrogans. In rats, both Leptospira species were found, while mongooses only harbored L. interrogans. Numbers tested for both animals, however, were too small (n = 7 each) to relate prevalence of Leptospira species to location. Significant associations of Leptospira prevalence with anthropogenic landscape features were observed at farms in Naguabo and Sabana Grande, where infected individuals were closer to human dwellings, milking barns, and ponds than were uninfected individuals. These results show that rural areas of Puerto Rico are in need of management and longitudinal surveillance of Leptospira in order to prevent continued infection of focal susceptible species (i.e. humans and cattle). [ABSTRACT FROM AUTHOR]

Agriculture is a primary driver of biodiversity loss worldwide, and several expensive schemes have been designed to make modern farming landscapes more hospitable for wildlife. One such market-based mechanisms is the agri-environment-climate schemes (AES) in the European Union (EU). AES compensate farmers for reducing land-use intensity and maintaining or introducing biodiversity-rich habitats. Despite their high costs, impacts of AES vary by measure, region and taxonomic group considered, and have rarely been studied over large areas covering an entire country. Here we assess the country-wide impact of several AES measures on bird abundance using citizen science data on birds and detailed information on AES take up from across Finland. We report a positive impact of organic animal farming on abundance of all farmland associated birds. This effect was particularly strong for insectivorous species, species that are associated to farmyards and long-distance species. None of the other AES measures considered for study did show any relationship with bird abundance. Overall, these findings highlight the potential positive impact that some compensatory measures, such as organic animal farming, may have on wildlife. Traditional animal husbandry is based on grazing of animals and restriction on external inputs, similarly to what is stipulated under organic production contract. As such, traditional animal husbandry may represent an effective landscape management tool for restoring or maintaining threatened species and ecosystems in rural areas of the EU. Ultimately, the apparent lack of a measurable effect of the other AES considered here supports the current move towards evidence-based regional targeting of compensatory measures, so as to concentrate scarce resources to where they can yield the highest ecological benefits. [ABSTRACT FROM AUTHOR]

Diversification of shrimp farming with marine finfish in a farmer participatory research model was attempted. The study is intended to find an economically viable finfish culture during the fallow period of shrimp farms. The Silver pompano, Trachinotus blochi iintercropped with Pacific white shrimp, Litopenaeus vannamei culture in coastal shrimp ponds was assessed for growth, survival, and economic viability. During the grow-out period of 100 days, fishes grew from 40.23 ± 1.40 g to 256.56 ± 1.08 g in weight and 12.83 ± 0.19 cm to 25.11 ± 0.09 cm in length. The daily weight gain (DWG) and daily length gain (DLG) were 2.16 g/day and 0.12 cm/day, respectively. Relative growth rate (RGR) and specific growth rate (SGR) recorded for weight was 537.80% in 100 days and 1.85% per day, respectively. Pompano has exhibited its sturdiness and adaptability to the land-based culture system as evidenced by an overall survival percentage of 89.8% including nursery and grow-out phases. The realized feed conversion ratio was 1.94. The culture period of 100 days is found to be enough to attain a desirable harvest size of 250 g. The projected production potential of the experimental demonstration farm of 4500 m2 water spread area for culture was 16.2 tonnes/cycle with a benefit-cost ratio (BCR) of 1.34 over operational cost. The present participatory trial empirically proved the viability of Silver pompano as an intercrop in coastal shrimp ponds. Thus, the introduction of Pompano in shrimp ponds is recommended and can be promoted for sustainable intercropping with shrimp farming along the Indian coast for improving people’s livelihoods. [ABSTRACT FROM AUTHOR]

Fusarium graminearum is responsible for production of the mycotoxin deoxynivalenol (DON) on maize and wheat in Ontario, Canada. It has been understood since the early 1980s that in most parts of Canada, the predominant chemotype of F. graminearum is 15ADON, and not the 3ADON chemotype mainly found in Europe and Asia. The discovery of F. graminearum strains that did not produce DON but the structurally related 7-α hydroxy, 15-deacetylcalonectrin (3ANX) and its hydrolysis product 7-α hydroxy, 3,15-dideacetylcalonectrin to (NX) demonstrated that we still have a lot to learn about this well studied but complicated fungus. We conducted a survey of maize and wheat samples from Ontario farms. In the 2015 crop year, we isolated 86 strains and tested a representative subset of 20 using the published genetic probes for assessing genotype. We also developed a targeted LC-MS/MS method for the identification and quantitation of known toxins from this species to determine chemotype. The results showed that 80% of our strains produced some 3ANX in addition to 15ADON and one strain produced 3ANX and no 15ADON. Comparison of chemical data with genotyping revealed that in more than 50% of the cases there was no clear agreement. These data demonstrate the importance of chemical analysis for understanding the toxigenic potential of strains, especially using a LC-MS method that is capable of differentiating 3ADON and 15ADON. For this collection, genotyping of isolates did not produce reliable information on the chemotype. This is the first report of 3ANX toxin production concurrently with 15ADON and suggests that the 3ANX producers in North America likely originated from the 15ADON background. [ABSTRACT FROM AUTHOR]

Movement of insect pests between spatially subdivided populations can allow them to recolonize areas where local extinction has occurred, increasing pest persistence. Populations of woolly apple aphid (Eriosoma lanigerum [Hausmann]; Hemiptera: Aphididae), a worldwide pest of apple (Malus domestica [Borkhausen]), occur both below- and aboveground. These spatially subdivided subpopulations encounter different abiotic conditions, natural enemies, and control tactics. Restricting movement between them might be an effective management tactic to decrease woolly apple aphid persistence and abundance. We examined this possibility in the field, using sticky barriers to restrict upward woolly apple aphid movement to tree canopies, and in the greenhouse, using mulches and sand amendments to restrict downward movement to roots. In the field, blocking aphid movement up tree trunks did not decrease the number of colonies in tree canopies. Instead, sticky-banded apple trees had higher aphid colony counts late in the study. Earwigs, which are woolly apple aphid predators, were excluded from tree canopies by sticky bands. In the greenhouse, fewer root galls (indicative of aphid feeding) occurred on trees in sandy potting media and on those with mulch (wood chips or paper slurry). Our results suggest that upward movement is less important than other factors that affect aboveground aerial woolly apple aphid population dynamics. In addition, apple orchards planted in sandier soils or with mulches may be partially protected from woolly apple aphid root feeding. [ABSTRACT FROM AUTHOR]

Agricultural lands are the widest Human-modified ecosystems, making crop production the most extensive form of land use on Earth. However, in conventional agricultural land management, soil erosion may be boosted up to 1–2 orders of magnitude higher than the natural rates of soil production, making unproductive about the 30% of the world’s arable. Nowadays in Europe, vineyards represent the most erosion-prone agricultural lands, especially in Mediterranean countries, showing the highest erosion rates in comparison to other type of land uses. Prosecco wine is produced in NE Italy by a rate of 400 M bottles per year, with the fastest growing demand in the global market at present. A production of 90 M bottles year-1 is currently running in the historical Prosecco DOCG (215 km2), in a steep hilly landscape of Veneto Region (Conegliano-Valdobbiadene). To sustain wine production, agricultural intensification is at present increasing, by re-setting of hillslopes and land use changes towards new vineyard plantations. The aim of this study is to estimate and to map potential soil erosion rate, calculating a sort of “soil footprint” for wine production in different agricultural land-management scenarios. RUSLE model was adopted to estimate potential soil erosion in Mg ha−1 year−1, by using high resolution topographic data (LiDAR), 10 years rainfall data analysis, detailed land use and local soil characteristics. For a conventional land-management scenario the estimated that total potential soil erosion in the Prosecco DOCG area is 411,266 Mg year-1, with an erosion rate of 19.5 Mg ha year-1. Modelled soil erosion is mainly clustered on steep slopes, with rates higher than 40 Mg ha-1 year-1. In Prosecco vineyards potential soil erosion could reach 300,180 Mg year-1, by a mean rate of 43.7 Mg ha-1 year-1, which is 31 times higher than the upper limit of tolerable soil erosion threshold defined for Europe. In contrast, simulation of different nature-based scenarios (hedgerows, buffer strips, and grass cover) showed soil erosion could be effectively reduced: a 100% inter-row grass cover showed a reduction of almost 3 times in vineyards (from 43.7 to 14.6 Mg ha-1 year-1), saving about 50% of soil in the whole Prosecco DOCG. The soil footprint modelled for a conventional land-management scenario is about 3.3 kg every bottle produced; in contrast it would be reduced to 1.1 kg/bottle in the completely green land-management scenario. This study, as the first estimation of potential soil erosion at Prosecco DOCG scale, suggests that an integrated and public soil erosion monitoring system is strongly needed in viticultural area, by implementing direct/indirect field measures with spatial analyses at agricultural landscape scale. [ABSTRACT FROM AUTHOR]

A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal’s health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AR) is a worldwide concern. Up to a 160% increase in antibiotic usage in food animals is expected in Latin American countries. The poultry industry is an increasingly important segment of food production and contributor to AR. The objective of this study was to evaluate the prevalence, AR patterns and the characterization of relevant resistance genes in Extended Spectrum β-lactamases (ESBL) and AmpC-producing E. coli from large poultry farms in Ecuador. Sampling was performed from June 2013 to July 2014 in 6 slaughterhouses that slaughter broilers from 115 farms totaling 384 flocks. Each sample of collected caeca was streaked onto TBX agar supplemented with cefotaxime (3 mg/l). In total, 176 isolates were analyzed for AR patterns by the disk diffusion method and for blaCTX-M, blaTEM, blaCMY, blaSHV, blaKPC, and mcr-1 by PCR and sequencing. ESBL and AmpC E. coli were found in 362 flocks (94.3%) from 112 farms (97.4%). We found that 98.3% of the cefotaxime-resistant isolates were multi-resistant to antibiotics. Low resistance was observed for ertapenem and nitrofurantoin. The most prevalent ESBL genes were the ones belonging to the blaCTX-M group (90.9%), specifically the blaCTX-M-65, blaCTX-M-55 and blaCTX-M-3 alleles. Most of the AmpC strains presented the blaCMY-2 gene. Three isolates showed the mcr-1 gene. Poultry production systems represent a hotspot for AR in Ecuador, possibly mediated by the extensive use of antibiotics. Monitoring this sector in national and regional plans of AR surveillance should therefore be considered. [ABSTRACT FROM AUTHOR]

Increased global regulation and restrictions on the non-therapeutic use of antibiotics in the poultry industry means that there is a need to identify alternatives that prevent infection while still conveying the growth and performance benefits afforded by their use. Biochars are produced by the incomplete pyrolysis of organic materials, with reports of use as a feed supplement and activity against pathogenic bacteria. In the current study the dose-dependent effects of biochar dietary inclusion in layer diets at 1%, 2% and 4% w/w were investigated to determine a) the efficacy of biochar as an anti-pathogenic additive on the intestinal microbiota and b) the optimal inclusion level. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Poultry pathogens such as Gallibacterium anatis and campylobacters, including Campylobacter hepaticus, were found to be significantly lower in biochar fed birds. A shift in microbiota was also associated with the incorporation of 2% w/w biochar in the feed in two large scale trials on two commercial layer farms. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Differential effects of the timing of biochar administration (supplementation beginning at hatch or at point of lay) were also evident, with greater impact on community microbial structure at 48 weeks of age when birds were fed from hatch rather than supplemented at point of lay. [ABSTRACT FROM AUTHOR]

Banana production landscapes in the African Great Lakes Region (AGLR) have been under immense pressure from Xanthomonas wilt (XW) disease over the past two decades. XW, first reported on banana in central Uganda and eastern DR Congo in 2001, has since spread to the entire AGLR. XW is currently spreading westwards from hot spots in eastern DR Congo highlands, putting the plantain (Musa AAB genome) belt of central and west Africa at risk. In-depth understanding of the key variables responsible for disease spread, current hotspots, and vulnerable landscapes is crucial for disease early warning and management. We mapped aggregated disease distribution and hotspots in the AGLR and identified vulnerable landscapes across African banana production zones. Available data on disease prevalence collected over 11 years was regressed against environmental and expert developed covariates to develop the AGLR XW hotspots map. For the Africa-wide risk map, precipitation, distance to hotspots, degree of trade in fresh banana products, production zone interconnectedness and banana genotype composition were used as covariates. In the AGLR, XW was mainly correlated to precipitation and disease/banana management. Altitude and temperature had unexpectedly low effects, possibly due to an overriding impact of tool-mediated spread which is part of the management covariate. In the AGLR, the eastern part of DR Congo was a large hotspot with highest vulnerability. Apart from endemic zones in the AGLR and Ethiopia, northern Mozambique was perceived as a moderate risk zone mainly due to the predominance of ‘Bluggoe’ (Musa ABB type) which is highly susceptible to insect-vectored transmission. Presence of XW hotspots (e.g. eastern DR Congo) and vulnerable areas with low (e.g. north-western Tanzania) or no disease (e.g. Congo basin, western DR Congo and northern Mozambique) pressure suggest key areas where proactive measures e.g. quarantines and information sharing on XW diagnosis, epidemiology, and control could be beneficial. [ABSTRACT FROM AUTHOR]

Escherichia coli is a normal inhabitant of the intestinal microbiota of chickens, a small proportion of which may be avian pathogenic E. coli (APEC) or potential extraintestinal pathogenic E. coli (ExPEC), capable of causing disease in humans. These E. coli may also be resistant to antimicrobials of critical importance in human or veterinary health. This study aims to 1) determine the prevalence of antimicrobial resistance (AMR) and resistance genes, multidrug resistance (MDR), chromosomal mechanisms of quinolone-resistance and virulence profiles of E. coli isolated from healthy chicken farms in the region of Dakar, Senegal, 2) investigate the spread of third-generation cephalosporins (3GC) resistance in E. coli isolated from healthy chicken farms with respect to virulence and resistance genes, serogroups, Pulsed-Field Gel Electrophoresis (PFGE), phylogenetic groups, plasmid types and transferability and 3) determine whether nonsusceptibility against 3GC on farms could be linked to risk factors. More than 68% of isolates from environmental faecal and drinking water samples, carcasses and carcass washes collected on 32 healthy chicken farms were multidrug resistant (MDR), resistance to antimicrobials critical in human health (3GC or ciprofloxacin) being found in all types of samples. Ciprofloxacin resistance was due to mutations in the gyrA and parC genes, 95% of tested farms harboring isolates carrying three mutations, in gyrA (Ser83Ile and Asp87Asn) and parC (Ser80Ile). Nine of the 32 farms (28.1%) demonstrated the presence of one or more 3GC-nonsusceptible indicator isolates but none of the potential risk factors were significantly associated with this presence on farms. Following ceftriaxone enrichment, presumptive extended-spectrum beta-lactamase/AmpC-beta-lactamase (ESBL/AmpC)-producer isolates were found in 17 of the 32 farms. 3GC resistance was mediated by blaCMY-2 or blaCTX-M genes, blaCTX-M being of genotypes blaCTX-M-1, blaCTX-M-8 and for the first time in chickens in Senegal, the genotype blaCTX-M-15 . Clonally related ESBL/AmpC-producer isolates were found on different farms. In addition, blaCTX-M genes were identified on replicon plasmids I1 and K/B and blaCMY-2 on K/B, I1 and B/O. These plasmids were found in isolates of different clusters. In addition, 18 isolates, some of which were ESBL/AmpC-producers, were defined as potential human ExPEC. In conclusion, E. coli isolates potentially pathogenic for humans and demonstrating MDR, with resistance expressed against antimicrobials of critical importance in human health were found in healthy chickens in Senegal. Our results suggest that both clonal spreading and horizontal gene transfer play a role in the spread of 3GC-resistance and that chickens in Senegal could be a reservoir for AMR and ExPEC for humans. These results highlight the importance of raising awareness about compliance with biosecurity measures and prudent use of antimicrobials. [ABSTRACT FROM AUTHOR]

Human-carnivore conflict can threaten human life and livelihoods, leading to retaliation that negatively affects carnivore conservation. The endangered African wild dog Lycaon pictus is prone to human-carnivore conflict. Therefore, it is imperative to understand which landscape features are associated with African wild dog occurrence since selection or avoidance of these features could predict the levels of conflict. We investigated resource selection in the African wild dog in relation to four anthropogenic landscape features (livestock density, agriculture, roads and human land use) within the landscape that may pose a mortality risk, as well as one natural feature (nature reserves). We compared spatio-temporal space use patterns of four African wild dog packs in north-eastern South Africa. Data were collected from one collared individual per pack. These packs constituted approximately 10% of the total remaining African wild dog population in South Africa. Two packs occurred outside of the Kruger National Park and had access to multiple areas with farmland and other anthropogenic features, whereas the remaining two packs mainly occurred within the boundaries of the Kruger National Park but made occasional forays outside of park boundaries. Utilising Resource Selection Functions and GIS analyses, we found that agricultural landscape features, roads and nature reserves were important predictors of African wild dog occurrence for all four packs. In addition to potential conflict with farmers, high odds of occurrence on roads with fast-moving traffic and road mortality was highlighted as a concern for three of the packs. While farms and areas that house livestock were readily available, pack presence occurred in areas with few farms and low livestock densities, pointing to avoidance of areas where human-carnivore conflict and resulting mortality could occur. Our study highlights potential threats to the persistence of the African wild dog, which can be used to inform future conservation efforts of the species. [ABSTRACT FROM AUTHOR]

'HoneySweet', a transgenic plum (Prunus domestica) resistant to plum pox virus through RNAi, was deregulated in the U.S. in 2011. The compositional study of 'HoneySweet' fruit was expanded to include locations outside of the US as well as utilizing a wide variety of comparators and different collection years to see the variability possible. The results revealed that plums have a wide variation in composition and that variation among locations was greater than variation among cultivars. This was also the case for different years at one location. The results supported the supposition that the transgene and insertion event had no significant effect on the composition of 'HoneySweet' fruit even under virus pressure, and that it fell in the normal range of composition of commercially grown plums. It also suggested that the effect of environment is as great as that of genetics on the fruit composition of plums. [ABSTRACT FROM AUTHOR]

Little information exists on the microbiomes of livestock workers. A cross-sectional, epidemiological study was conducted enrolling 59 participants (26 of which had livestock contact) in Iowa. Participants were enrolled in one of four ways: from an existing prospective cohort study (n = 38), from the Iowa Department of Natural Resources Animal Feeding Operations database (n = 17), through Iowa county fairs (n = 3), and through snowball sampling (n = 1). We collected swabs from the nares and oropharynx of each participant to assess the microbiome via 16s rRNA sequencing. We observed livestock workers to have greater diversity in their microbiomes compared to those with no livestock contact. In the nares, there were 27 operational taxonomic units found to be different between livestock workers and non-livestock workers with the greatest difference seen with Streptococcus and Proteobacteria. In the oropharynx, livestock workers with swine exposure were more likely to carry several pathogenic organisms. The results of this study are the first to characterize the livestock worker nasal and oropharyngeal microbiomes. [ABSTRACT FROM AUTHOR]

Male Annihilation Technique (MAT) is a key tool to suppress or eradicate pestiferous tephritid fruit flies for which there exist powerful male lures. In the case of Bactrocera dorsalis (Hendel), a highly invasive and destructive species, current implementations of MAT utilize a combination of the male attractant methyl eugenol (ME) and a toxicant such as spinosad (“SPLAT-MAT-ME”) applied at a high density with the goal of attracting and killing an extremely high proportion of males. We conducted direct comparisons of trap captures of marked B. dorsalis males released under three experimental SPLAT-MAT-ME site densities (110, 220, and 440 per km2) near Hilo, Hawaii using both fresh and aged traps to evaluate the effectiveness of varying densities and how weathering of the SPLAT-MAT-ME formulation influenced any density effects observed. Counterintuitively, we observed decreasing effectiveness (percent kill) with increasing application density. We also estimated slightly higher average kill for any given density for weathered grids compared with fresh. Spatial analysis of the recapture patterns of the first trap service per replicate x treatment reveals similar positional effects for all grid densities despite differences in overall percent kill. This study suggests that benefits for control and eradication programs would result from reducing the application density of MAT against B. dorsalis through reduced material use, labor costs, and higher effectiveness. Additional research in areas where MAT programs are currently undertaken would be helpful to corroborate this study’s findings. [ABSTRACT FROM AUTHOR]

An unusual decline and collapse of young established trees known as “rapid apple decline” (RAD) has become a major concern for apple growers, particularly in the northeastern United States. This decline is characterized by stunted growth, pale yellow to reddish leaves, and tree collapse within weeks after onset of symptoms. We studied declining apple trees to identify potential involvement of abiotic and biotic stresses. We used 16S and ITS to profile bacterial and fungal communities in the soil, rhizosphere, roots, and shoots and tested for the presence of six viruses in scions and rootstocks of symptomatic and asymptomatic trees. The viruses detected were not associated with RAD symptoms. Bacterial and fungal populations were highly variable in plant tissue, soil and rhizosphere samples, with bacteroidetes, firmicutes, proteobacteria, acidobacteria, and actinobacteria the predominant bacterial classes in various samples. ‘Alphaproteobacteria-rickettsiales’, a bacterial class usually reduced in water-limiting soils, had significantly low abundance in root samples of symptomatic trees. Basidiomycota and Ascomycota fungal classes were the most common fungal classes observed, but neither showed differential enrichment between symptomatic and asymptomatic trees. Analyzing weather data showed an extremely cold winter followed by drought in 2015–2016, which likely weakened the trees to make them more susceptible to varied stresses. In addition, similar physical and nutritional soil composition from symptomatic and asymptomatic trees rules out the role of nutritional stress in RAD. Necrotic lesions and wood decay symptoms dispersing from bark or vascular cambium towards the heartwood were observed primarily below the graft union of declining apple trees, suggesting that the rootstock is the originating point of RAD. We speculate that differences in abiotic factors such as moisture levels in declining roots in combination with extreme weather profiles might cause RAD but cannot clearly rule out the involvement of other factors. [ABSTRACT FROM AUTHOR]

The porcine epidemic diarrhea virus (PEDV) that emerged and spread throughout Taiwan in 2014 triggered significant concern in the country’s swine industry. Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government’s open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. Genetic sequences, locations, and dates of identified PEDV-positive cases were used to assess spatial, temporal, clustering, GIS, and phylogeographic factors affecting PEDV dissemination. Our conclusion is that S gene sequences from 2014 PEDV-positive clinical samples collected in Taiwan were part of the same Genogroup 2 identified in the US in 2013. According to phylogenetic and phylogeographic data, viral strains collected in different areas were generally independent of each other, with certain clusters identified across different communities. Data from GIS and multiple potential infection factors were used to pinpoint cluster dissemination in areas with large numbers of swine farms in southern Taiwan. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area. [ABSTRACT FROM AUTHOR]

Earthworms are primary candidates for national soil health monitoring as they are ecosystem engineers that benefit both food production and ecosystem services associated with soil security. Supporting farmers to monitor soil health could help to achieve the policy aspiration of sustainable soils by 2030 in England; however, little is known about how to overcome participation barriers, appropriate methodologies (practical, cost-effective, usefulness) or training needs. This paper presents the results from a pilot #60minworms study which mobilised farmers to assess over >1300 ha farmland soils in spring 2018. The results interpretation framework is based on the presence of earthworms from each of the three ecological groups at each observation (20 x 20 cm x 20 cm pit) and spatially across a field (10 soil pits). Results showed that most fields have basic earthworm presence and abundance, but 42% fields may be over-worked as indicated by absence/rarity of epigeic and/or anecic earthworms. Tillage had a negative impact (p < 0.05) on earthworm populations and organic matter management did not mitigate tillage impacts. In terms of farmer participation, Twitter and Farmers Weekly magazine were highly effective channels for recruitment. Direct feedback from participants included excellent scores in trust, value and satisfaction of the protocol (e.g. 100% would do the test again) and 57% would use their worm survey results to change their soil management practices. A key training need in terms of earthworm identification skills was reported. The trade-off between data quality, participation rates and fieldwork costs suggests there is potential to streamline the protocol further to #30minworms (5 pits), incurring farmer fieldwork costs of approximately £1.48 ha-1. At national scales, £14 million pounds across 4.7 M ha-1 in fieldwork costs per survey could be saved by farmer participation. [ABSTRACT FROM AUTHOR]

The experiments were conducted in a fully-productive olive orchard (cv. Frantoio) at the experimental farm of University of Pisa at Venturina (Italy) in 2015 to assess the ability of an unmanned aerial vehicle (UAV) equipped with RGB-NIR cameras to estimate leaf area index (LAI), tree height, canopy diameter and canopy volume of olive trees that were either irrigated or rainfed. Irrigated trees received water 4–5 days a week (1348 m3 ha-1), whereas the rainfed ones received a single irrigation of 19 m3 ha-1 to relieve the extreme stress. The flight altitude was 70 m above ground level (AGL), except for one flight (50 m AGL). The Normalized Difference Vegetation Index (NDVI) was calculated by means of the map algebra technique. Canopy volume, canopy height and diameter were obtained from the digital surface model (DSM) obtained through automatic aerial triangulation, bundle block adjustment and camera calibration methods. The NDVI estimated on the day of the year (DOY) 130 was linearly correlated with both LAI and leaf chlorophyll measured on the same date (R2 = 0.78 and 0.80, respectively). The correlation between the on ground measured canopy volumes and the ones by the UAV-RGB camera techniques yielded an R2 of 0.71–0.86. The monthly canopy volume increment estimated from UAV surveys between (DOY) 130 and 244 was highly correlated with the daily water stress integral of rainfed trees (R2 = 0.99). The effect of water stress on the seasonal pattern of canopy growth was detected by these techniques in correspondence of the maximum level of stress experienced by the rainfed trees. The highest level of accuracy (RMSE = 0.16 m) in canopy height estimation was obtained when the flight altitude was 50 m AGL, yielding an R2 value of 0.87 and an almost 1:1 ratio of measured versus estimated canopy height. [ABSTRACT FROM AUTHOR]

With increasing affluence in many developing countries, the demand for livestock products is rising and the increasing feed requirement contributes to pressure on land resources for food and energy production. However, there is currently a knowledge gap in our ability to assess the extent and intensity of the utilization of land by livestock, which is the single largest land use in the world. We developed a spatial model that combines fine-scale livestock numbers with their associated energy requirements to distribute livestock grazing demand onto a map of energy supply, with the aim of estimating where and to what degree pasture is being utilized. We applied our model to Kazakhstan, which contains large grassland areas that historically have been used for extensive livestock production but for which the current extent, and thus the potential for increasing livestock production, is unknown. We measured the grazing demand of Kazakh livestock in 2015 at 286 Petajoules, which was 25% of the estimated maximum sustainable energy supply that is available to livestock for grazing. The model resulted in a grazed area of 1.22 million km2, or 48% of the area theoretically available for grazing in Kazakhstan, with most utilized land grazed at low intensities (average off-take rate was 13% of total biomass energy production). Under a conservative scenario, our estimations showed a production potential of 0.13 million tons of beef additional to 2015 production (31% increase), and much more with utilization of distant pastures. This model is an important step forward in evaluating pasture use and available land resources, and can be adapted at any spatial scale for any region in the world. [ABSTRACT FROM AUTHOR]

Cocoa agroforestry systems have the potential to conserve biodiversity and provide environmental or ecological benefits at various nested scales ranging from the plot to ecoregion. While integrating organic practices into cocoa agroforestry may further enhance these potentials, empirical and robust data to support this claim is lacking, and mechanisms for biodiversity conservation and the provision of environmental and ecological benefits are poorly understood. A field study was conducted in the Eastern Region of Ghana to evaluate the potential of organic cocoa agroforests to conserve native floristic diversity in comparison with conventional cocoa agroforests. Shade tree species richness, Shannon, Simpson’s reciprocal and Margalef diversity indices were estimated from 84 organic and conventional cocoa agroforestry plots. Species importance value index, a measure of how dominant a species is in a given ecosystem, and conservation status were used to evaluate the conservation potential of shade trees on studied cocoa farms. Organic farms recorded higher mean shade tree species richness (5.10 ± 0.38) compared to conventional farms (3.48 ± 0.39). Similarly, mean Shannon diversity index, Simpson’s reciprocal diversity index and Margalef diversity index were significantly higher on organic farms compared to conventional farms. According to the importance value index, fruit and native shade tree species were the most important on both organic and conventional farms for all the cocoa age groups but more so on organic farms. Organic farms maintained 14 native tree species facing a conservation issue compared to 10 on conventional cocoa farms. The results suggest that diversified organic cocoa farms can serve as reservoirs of native tree species, including those currently facing conservation concerns thereby providing support and contributing to the conservation of tree species in the landscape. [ABSTRACT FROM AUTHOR]

Little is known about how Drosophila adults behave in the wild, including mating, allocation of food and space, and escape from predators. This lack of information has negative implications for our ability to understand the capabilities of the nervous system to integrate sensory cues necessary for the adaptation of organisms in natural conditions. We characterized a set of behavioral routines of D. melanogaster and D. simulans adults in three ecologically different orchards: grape, apple and prickly pear. We also investigated how the flies identify conspecifics and aliens in the wild to better understand relationships between group formation and adaptation of Drosophila to breeding sites. We characterized the locations by recording in each orchard humidity, temperature, illumination conditions, pH of fruits, the presence/absence of other Drosophila species and the predator ant Linepithema humile. Our findings suggest that the home range of these species of Drosophila includes decaying fruits and, principally, a variety of microhabitats that surround the fruits. The ecological heterogeneity of the orchards and odors emitted by adult D. melanogaster and D. simulans influence perch preferences, cluster formation, court and mating, egg-laying site selection, and use of space. This is one of the first large examinations of the association between changing, complex environments and a set of adult behaviors of Drosophila. Therefore, our results have implications for understanding the genetic differentiation and evolution of populations of species in the genus Drosophila. [ABSTRACT FROM AUTHOR]

The availability of accurate techniques to discriminate between marked laboratory-reared flies and unmarked wild flies captured in monitoring traps is essential for programs that integrate the Sterile Insect Technique (SIT) to manage fruit flies. In this study, the feasibility of using a stable isotope marking technique for the South American fruit fly, Anastrepha fraterculus (Wiedemann), was assessed. Wild flies were collected from apple orchards, which are a target of a SIT project in southern Brazil. To verify if adult flies could be labelled by the stable isotopes from larval diets, larvae were reared on two different C4-based diets and fruits in laboratory. To evaluate the influence of the two most common attractants applied to capture A. fraterculus (grape juice and CeraTrapTM) and the most common preservation method in fruit fly collections (ethanol), laboratory-reared flies were immersed in McPhail traps containing the respective treatments for two periods of time. Samples were analyzed in an elemental analyzer coupled to a Continuous Flow Isotope Ratio Mass Spectrometer (CF-IRMS) at CENA/USP. The δ13C signatures of flies reared on artificial diets differed significantly from the δ13C of flies whose larvae were reared on fruits and from wild flies. In contrast, the δ15N values were less conclusive and the technique could not rely solely on them. In all cases considered, the δ13C and δ15N signatures from males did not differ from females. Despite the alterations caused by the attractants tested and ethanol, laboratory-flies could be distinguished from the wild ones based on δ13C signatures. This is the first comprehensive study to demonstrate that it is possible to distinguish wild A. fraterculus from flies reared on larval diets containing C4 sugar. The first experimentally derived trophic discrimination factors were also obtained for this species. Thus, intrinsic isotope labelling can serve as a backup to conventional dye marking. [ABSTRACT FROM AUTHOR]

This paper develops an empirical agent-based model to assess the impacts of Brexit on Scottish cattle farms. We first identify several trends and processes among Scottish cattle farms that were ongoing before Brexit: the lack of succession, the rise of leisure farming, the trend to diversify and industrialise, and, finally, the phenomenon of the “disappearing middle”, characterised by the decline of medium-sized farms and the polarization of farm sizes. We then study the potential impact of Brexit amid the local context and those ongoing social processes. We find that the impact of Brexit is indeed subject to pre-Brexit conditions. For example, whether industrialization is present locally can significantly alter the impact of Brexit. The impact of Brexit also varies by location: we find a clear divide between constituencies in the north (highland and islands), the middle (the central belt) and the south. Finally, we argue that policy analysis of Brexit should consider the heterogeneous social context and the complex social processes under which Brexit occurs. Rather than fitting the world into simple system models and ignoring the evidence when it does not fit, we need to develop policy analysis frameworks that can incorporate real world complexities, so that we can assess the impacts of major events and policy changes in a more meaningful way. [ABSTRACT FROM AUTHOR]