Acidification of previously limed upland pastures - An overlooked flood risk factor?

In low-lying land, the impact of agriculture on flooding has focussed on soil compaction, whilst in the uplands there has been more interest in the influence of afforestation. The potential effect of acidification of previously limed upland grassland soils on this risk has been overlooked. The marginal economics of upland farms has led to inadequate lime application on these grasslands. In Wales, UK, agronomic improvement of upland acid grasslands with liming was widespread in the last century. The extent and topographical distribution of this land use in Wales was estimated and these characteristics were mapped in four catchments studied in more detail. Then 41 sites on improved pastures within the catchments were sampled, where lime had not been applied for periods of between two and 30 years; unimproved acid pastures adjacent to five of these sites were also sampled. Soil pH, organic matter, infiltration rates and earthworm populations were recorded. Grasslands at risk of acidification without maintenance liming were estimated to cover almost 20 % of upland Wales. The majority of these grasslands were located on steeper slopes (gradients >7o) where any reduction in infiltration would promote surface runoff and limit rainwater retention. The extent of these pastures varied markedly between the four study catchments. There was a 6-fold reduction in infiltration rates between high and low pH soils, and this trend was correlated with reductions in anecic earthworm abundance. The vertical burrows of these earthworms are important for infiltration and no such earthworms were present in the most acidic soils. Recently limed soils had infiltration rates similar to those of unimproved acid pastures. Soil acidification has the potential to exacerbate flood risk but further research is needed to assess the extent of any impact. Modelling of catchment specific flood risk should include the extent of upland soil acidification as an additional land use factor.

Associations between Gastrointestinal Nematode Infection Burden and Lying Behaviour as Measured by Accelerometers in Periparturient Ewes.

The application of precision livestock farming (PLF) technologies will underpin new strategies to support the control of livestock disease. However, PLF technology is underexploited within the sheep industry compared to other livestock sectors, and research is essential to identify opportunities for PLF applications. These opportunities include the control of endemic sheep disease such as parasitic gastroenteritis, caused by gastrointestinal nematode infections, which is estimated to cost the European sheep industry EUR 120 million annually. In this study, tri-axial accelerometers recorded the behaviour of 54 periparturient Welsh Mule ewes to discover if gastrointestinal nematode (GIN) infection burden, as measured by faecal egg count (FEC), was associated with behavioural variation. Linear mixed models identified that increasing FECs in periparturient ewes were significantly associated with a greater number of lying bouts per day and lower bout durations (p = 0.013 and p = 0.010, respectively). The results demonstrate that FECs of housed periparturient ewes are associated with detectable variations in ewe behaviour, and as such, with further investigation there is potential to develop future targeted selective treatment protocols against GIN in sheep based on behaviour as measured by PLF technologies.

Exploration of factors associated with spatial-temporal veterinary surveillance diagnoses of rumen fluke (Calicophoron daubneyi) infections in ruminants using zero-inflated mixed modelling.

Rumen fluke (Calicophoron daubneyi) has emerged as a prominent parasite of ruminants in Europe over the past decades. Epidemiological questions remain regarding this observed increase in prevalence as well as the prospect for future paramphistomosis risk. This study aimed to identify factors associated with the temporal−spatial prevalence of rumen fluke as measured by veterinary surveillance in a temperate region using zero-inflated negative binomial mixed modelling. Modelling revealed that summer rainfall, raindays and sunshine hours and mean winter temperature as significant positively associated climate variables for rumen fluke prevalence over space and time (P < 0.05). Rumen fluke prevalence was also higher in counties with higher cattle/sheep densities and was positively associated with rumen fluke case rates in the previous years (P < 0.05). Equivalent models for fasciolosis prevalence revealed no significant association with winter temperature and sunshine hours, (P > 0.05). These results confirm a strong association between rainfall and the prevalence of both fluke species in a temperate environment, likely due to the role of Galba truncatula as their intermediate snail host. It also highlights the potential added importance of winter temperature and sunshine hours in rumen fluke epidemiology when compared to liver fluke.

Temporal dynamics of trematode intermediate snail host environmental DNA in small water body habitats.

Environmental DNA (eDNA) surveying has potential to become a powerful tool for sustainable parasite control. As trematode parasites require an intermediate snail host that is often aquatic or amphibious to fulfil their lifecycle, water-based eDNA analyses can be used to screen habitats for the presence of snail hosts and identify trematode infection risk areas. The aim of this study was to identify climatic and environmental factors associated with the detection of Galba truncatula eDNA. Fourteen potential G. truncatula habitats on two farms were surveyed over a 9-month period, with eDNA detected using a filter capture, extraction and PCR protocol with data analysed using a generalized estimation equation. The probability of detecting G. truncatula eDNA increased in habitats where snails were visually detected, as temperature increased, and as water pH decreased (P < 0.05). Rainfall was positively associated with eDNA detection in watercourse habitats on farm A, but negatively associated with eDNA detection in watercourse habitats on farm B (P < 0.001), which may be explained by differences in watercourse gradient. This study is the first to identify factors associated with trematode intermediate snail host eDNA detection. These factors should be considered in standardized protocols to evaluate the results of future eDNA surveys.

Evaluation of two Fasciola hepatica faecal egg counting protocols in sheep and cattle.

Fascioliasis causes significant economic losses and is a constant challenge to livestock farmers globally. Fluke faecal egg counts (flukeFECs) are a simple, non-invasive method used to detect the presence of patent liver fluke infection. Many flukeFEC techniques exist but they vary in complexity, precision and accuracy. The objective of this study was to evaluate the egg recovery capabilities of two simple flukeFEC methods at different egg concentrations in two ruminant species, using artificially spiked faecal samples. We added Fasciola hepatica eggs to sheep and cattle faeces at 2, 5 10 and 20 epg and utilised the Flukefinder® (FF) and a simple sedimentation method (referred to as the Becker method) to investigate the effects of methods, species and egg density on egg recovery. We calculated the proportion of fluke eggs recovered using each technique, and determined the lowest reliable egg detection threshold of each flukeFEC method. The performance of the flukeFEC methods were also compared using faecal samples collected from naturally infected animals. The egg-spiking study revealed that both FF and the Becker sedimentation method are significantly more likely to recover eggs from cattle faeces than sheep (P < 0.001). Overall, FF recovered more eggs than the Becker method (P < 0.001), and importantly has a reliable low egg detection threshold of 5 epg in sheep and cattle. The kappa coefficient indicated a substantial agreement between FF and the Becker method in naturally infected faecal samples collected from cattle (0.62, P < 0.05) and a moderate agreement in sheep (0.41, P < 0.05). This study demonstrated that FF has a low egg detection threshold and therefore has promising potential for the future of on-farm liver fluke diagnostics.

Gastrointestinal nematode control practices in ewes: Identification of factors associated with application of control methods known to influence anthelmintic resistance development.

Gastrointestinal nematodes (GIN) negatively impact productivity and welfare in sheep globally and are estimated to cost the European sheep industry €157-477 million annually. GIN are mainly controlled by anthelmintic treatment, however, as anthelmintic resistance becomes prominent, the routine treatment of ewes against GIN has been questioned. A questionnaire survey of 383 sheep farmers in Great Britain was conducted to identify strategies currently used to control GIN infections in ewes. Ordinal and binary regression analysis were used to identify factors associated with use of practices known to influence anthelmintic resistance development, including number and timing of ewe GIN anthelmintic treatment, targeted selective treatment (TST) of ewes, drench and move of ewes and long-acting moxidectin treatment of periparturient ewes. Participating farmers treated their ewes against GIN 1.68 times per year on average, with 42.3% and 32.1% of participating farmers worming their ewes once or twice a year on average, respectively. 17.2% of participating farmers wormed their ewes more than twice a year, and 8.4% never worm their ewes. Participating farmers who devised GIN control strategies based on SCOPS guidelines treated their ewes significantly less per year (P < 0.001), whilst those determining treatment timing based on ewe DAG scores or the time of year treated their ewes significantly more frequently (P < 0.001). Farmers who devised GIN control strategies in conjunction with their vet had greater odds of using TST (P < 0.001), as well as farmers who determined flock treatment timing based on ewe condition (P = 0.027). The use of narrow spectrum flukicides was significantly associated with reduced number of annual ewe GIN anthelmintic treatments (P < 0.001), TST of ewes against GIN (P < 0.001) and the avoidance of moving ewes to clean pastures following GIN treatment (P < 0.001). The presence of sheep scab on a farm or in the area was significantly associated with increased annual GIN treatments for ewes (P = 0.002), not using TST strategies to control GIN in ewes (P < 0.001) and moving ewes to clean pasture after anthelmintic treatment, whilst using macrocyclic lactones treatments to prevent sheep scab was significantly associated with the treatment of periparturient ewes with long-acting moxidectin (P = 0.001). This research suggests that by encouraging the application of evidence based targeted or targeted selective treatment strategies, further interaction between farmers and veterinarians/SCOPS guidance, and the uptake of best practices for controlling liver fluke and sheep scab on farms, sustainable GIN control strategies can become the common practice in ewes.

Rapid detection of Galba truncatula in water sources on pasture-land using loop-mediated isothermal amplification for control of trematode infections.

BACKGROUND: Fascioliasis caused by the trematodes Fasciola hepatica and F. gigantica, is a global neglected zoonotic disease estimated to cost the livestock industry over €2.5 billion annually. Farm management measures and sustainable use of anthelmintics can, in principle, effectively control trematode infection in livestock and reduce the rate of developing anthelmintic resistance. Previously, we designed an environmental DNA (eDNA) assay to identify a common trematode intermediate host, the freshwater snail Galba truncatula, in water sources to measure specific trematode infection risk areas on pasture-land. To improve this procedure, we now report a loop-mediated isothermal amplification (LAMP) assay to identify G. truncatula eDNA. METHODS: A LAMP assay was designed and optimised (e.g. temperature, time duration and primer concentration) to identify G. truncatula DNA. The ability of the LAMP assay to target G. truncatula DNA was identified, and LAMP assay limit of detection was investigated in comparison to conventional PCR. In the field, 48 water samples were collected from stream, ditch and water pool habitats in four locations at two Aberystwyth University farms over a seven week period to investigate the applicability of the LAMP assay for use on eDNA samples, in comparison to conventional PCR. RESULTS: The LAMP assay delivered detectable results in 30 min at 63 °C. The assay discriminated between G. truncatula DNA and non-target DNA, presenting a level of DNA detection comparable to conventional PCR. No significant difference was found between the ability of the LAMP and PCR assay to identify G. truncatula eDNA in water samples. Kappa coefficient analysis revealed a moderate level of agreement between LAMP and PCR assays. CONCLUSIONS: This study demonstrated that the LAMP assay can detect G. truncatula eDNA in a simple and rapid manner. The LAMP assay may become a valuable tool to determine optimum pasture management for trematode parasite control.

Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations.

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the "Precipitation in the Driest Quarter" on the central subpopulation and "Temperature of the Coldest Month" on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.

Detection of Galba truncatula, Fasciola hepatica and Calicophoron daubneyi environmental DNA within water sources on pasture land, a future tool for fluke control?

BACKGROUND: Increasing trematode prevalence and disease occurrence in livestock is a major concern. With the global spread of anthelmintic resistant trematodes, future control strategies must incorporate approaches focusing on avoidance of infection. The reliance of trematodes on intermediate snail hosts to successfully complete their life-cycle means livestock infections are linked to the availability of respective snail populations. By identifying intermediate snail host habitats, infection risk models may be strengthened whilst farmers may confidently apply pasture management strategies to disrupt the trematode life-cycle. However, accurately identifying and mapping these risk areas is challenging. METHODS: In this study, environmental DNA (eDNA) assays were designed to reveal Galba truncatula, Fasciola hepatica and Calicophoron daubneyi presence within water sources on pasture land. eDNA was captured using a filter-based protocol, with DNA extracted using the DNeasy® PowerSoil® kit and amplified via PCR. In total, 19 potential G. truncatula habitats were analysed on four farms grazed by livestock infected with both F. hepatica and C. daubneyi. RESULTS: Galba truncatula eDNA was identified in 10/10 habitats where the snail was detected by eye. Galba truncatula eDNA was also identified in four further habitats where the snail was not physically detected. Fasciola hepatica and C. daubneyi eDNA was also identified in 5/19 and 8/19 habitats, respectively. CONCLUSIONS: This study demonstrated that eDNA assays have the capabilities of detecting G. truncatula, F. hepatica and C. daubneyi DNA in the environment. Further assay development will be required for a field test capable of identifying and quantifying F. hepatica and C. daubneyi infection risk areas, to support future control strategies. An eDNA test would also be a powerful new tool for epidemiological investigations of parasite infections on farms.

The prevalence and development of digenean parasites within their intermediate snail host, Galba truncatula, in a geographic area where the presence of Calicophoron daubneyi has recently been confirmed.

During the past decade, rumen fluke (Calicophoron daubneyi) has established as a prominent parasite of livestock within numerous European countries. Its development and spread is enabled by the presence of its intermediate snail host G. truncatula. However, the dynamics of this stage of the C. daubneyi lifecycle is yet to be recorded in numerous northern European countries including the UK. Here, the prevalence of C. daubneyi along with F. hepatica, H. cylindracea and other parasites infecting G. truncatula snails on 10 Welsh farms was recorded using morphological and PCR techniques. A total of 892 G. truncatula snails were collected between May and October 2016. The prevalence of C. daubneyi in sampled G. truncatula snails (4%) was lower compared to F. hepatica (5.6%). No association in prevalence between these species was recorded. Haplometra cylindracea was found infecting 8.2% of G. truncatula snails, with its prevalence within G. truncatula populations negatively associated with F. hepatica cercariae prevalence (P=0.004). Generalized estimation equation (GEE) linear regression models identified the levels of respective fluke eggs shed onto pasture as the main significant association between prevalence levels of both C. daubneyi and F. hepatica within G. truncatula populations (P<0.001). However, equivalent prevalence levels of C. daubneyi and F. hepatica within G. truncatula populations were associated with higher C. daubneyi egg outputs and lower F. hepatica egg outputs from livestock grazing the G. truncatula habitats. Only one of 36C. daubneyi infected G. truncatula snails was found harbouring its cercarial stages, a significantly lower proportion compared to the 29 of 50 F. hepatica infected G. truncatula harbouring its respective cercariae (P<0.05). These results signify that C. daubneyi may be less adept at infecting and developing in the UK's native G. truncatula populations in comparison with F. hepatica. However, C. daubneyi has previously demonstrated its ability to progressively adapt to an intermediate host in a new environment. If C. daubneyi were to adapt to infect and develop more efficiently in UK G. truncatula populations, paramphistomosis risk would significantly increase leading to increased livestock losses. Questions are also raised regarding potential interaction between digenean species at intermediate snail host level, which could impact subsequent livestock trematodosis risk.

Rumen fluke (Calicophoron daubneyi) on Welsh farms: prevalence, risk factors and observations on co-infection with Fasciola hepatica.

Reports of Calicophoron daubneyi infecting livestock in Europe have increased substantially over the past decade; however, there has not been an estimate of its farm level prevalence and associated risk factors in the UK. Here, the prevalence of C. daubneyi across 100 participating Welsh farms was recorded, with climate, environmental and management factors attained for each farm and used to create logistic regression models explaining its prevalence. Sixty-one per cent of farms studied were positive for C. daubneyi, with herd-level prevalence for cattle (59%) significantly higher compared with flock-level prevalence for sheep (42%, P = 0·029). Co-infection between C. daubneyi and Fasciola hepatica was observed on 46% of farms; however, a significant negative correlation was recorded in the intensity of infection between each parasite within cattle herds (rho = -0·358, P = 0·007). Final models showed sunshine hours, herd size, treatment regularity against F. hepatica, the presence of streams and bog habitats, and Ollerenshaw index values as significant positive predictors for C. daubneyi (P < 0·05). The results raise intriguing questions regarding C. daubneyi epidemiology, potential competition with F. hepatica and the role of climate change in C. daubneyi establishment and its future within the UK.

Challenges and priorities for modelling livestock health and pathogens in the context of climate change.

Climate change has the potential to impair livestock health, with consequences for animal welfare, productivity, greenhouse gas emissions, and human livelihoods and health. Modelling has an important role in assessing the impacts of climate change on livestock systems and the efficacy of potential adaptation strategies, to support decision making for more efficient, resilient and sustainable production. However, a coherent set of challenges and research priorities for modelling livestock health and pathogens under climate change has not previously been available. To identify such challenges and priorities, researchers from across Europe were engaged in a horizon-scanning study, involving workshop and questionnaire based exercises and focussed literature reviews. Eighteen key challenges were identified and grouped into six categories based on subject-specific and capacity building requirements. Across a number of challenges, the need for inventories relating model types to different applications (e.g. the pathogen species, region, scale of focus and purpose to which they can be applied) was identified, in order to identify gaps in capability in relation to the impacts of climate change on animal health. The need for collaboration and learning across disciplines was highlighted in several challenges, e.g. to better understand and model complex ecological interactions between pathogens, vectors, wildlife hosts and livestock in the context of climate change. Collaboration between socio-economic and biophysical disciplines was seen as important for better engagement with stakeholders and for improved modelling of the costs and benefits of poor livestock health. The need for more comprehensive validation of empirical relationships, for harmonising terminology and measurements, and for building capacity for under-researched nations, systems and health problems indicated the importance of joined up approaches across nations. The challenges and priorities identified can help focus the development of modelling capacity and future research structures in this vital field. Well-funded networks capable of managing the long-term development of shared resources are required in order to create a cohesive modelling community equipped to tackle the complex challenges of climate change.

Confirmation of Galba truncatula as an intermediate host snail for Calicophoron daubneyi in Great Britain, with evidence of alternative snail species hosting Fasciola hepatica.

BACKGROUND: Fasciola hepatica is a highly prevalent parasite infecting livestock in Great Britain, while Calicophoron daubneyi is an emerging parasite within the GB livestock industry. Both F. hepatica and C. daubneyi require an intermediate host snail to complete their life-cycles and infect ruminants; however, there has been no confirmation of the intermediate host of C. daubneyi in GB, while there are questions regarding alternative host snails to Galba truncatula for F. hepatica. In this study, PCR was used to identify C. daubneyi hosting snail species on Welsh pastures and to identify any alternative snail species hosting F. hepatica. FINDINGS: Two hundred and sixty four snails were collected between May-September 2015 from six farms in mid-Wales known to have livestock infected with C. daubneyi and F. hepatica. Fifteen out of 134 G. truncatula were found positive for C. daubneyi, one of which was also positive for F. hepatica. Three snail species were found positive for F. hepatica [18/134 G. truncatula, 13/52 Radix balthica, and 3/78 Potamopyrgus antipodarum (New Zealand mud snail)], but no evidence of C. daubneyi infection in the latter two species was found. CONCLUSION: This study indicates that G. truncatula is a host for C. daubneyi in GB. Galba truncatula is also an established host of F. hepatica, and interactions between both species at intermediate host level could potentially occur. Radix balthica and P. antipodarum were found positive for F. hepatica but not C. daubneyi. This could indicate a role for alternative snail species other than G. truncatula in infecting pastures with F. hepatica in GB.

Climate suitability for European ticks: assessing species distribution models against null models and projection under AR5 climate.

BACKGROUND: There is increasing evidence that the geographic distribution of tick species is changing. Whilst correlative Species Distribution Models (SDMs) have been used to predict areas that are potentially suitable for ticks, models have often been assessed without due consideration for spatial patterns in the data that may inflate the influence of predictor variables on species distributions. This study used null models to rigorously evaluate the role of climate and the potential for climate change to affect future climate suitability for eight European tick species, including several important disease vectors. METHODS: We undertook a comparative assessment of the performance of Maxent and Mahalanobis Distance SDMs based on observed data against those of null models based on null species distributions or null climate data. This enabled the identification of species whose distributions demonstrate a significant association with climate variables. Latest generation (AR5) climate projections were subsequently used to project future climate suitability under four Representative Concentration Pathways (RCPs). RESULTS: Seven out of eight tick species exhibited strong climatic signals within their observed distributions. Future projections intimate varying degrees of northward shift in climate suitability for these tick species, with the greatest shifts forecasted under the most extreme RCPs. Despite the high performance measure obtained for the observed model of Hyalomma lusitanicum, it did not perform significantly better than null models; this may result from the effects of non-climatic factors on its distribution. CONCLUSIONS: By comparing observed SDMs with null models, our results allow confidence that we have identified climate signals in tick distributions that are not simply a consequence of spatial patterns in the data. Observed climate-driven SDMs for seven out of eight species performed significantly better than null models, demonstrating the vulnerability of these tick species to the effects of climate change in the future.