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The introduction of Hymenoscyphus fraxineus to Northern Ireland and the subsequent development of ash dieback
Get PDFPublication history: Accepted - 12 December 2022; Published online - 11 January 2023.Ash dieback caused by Hymenoscyphus fraxineus was first recorded in Northern Ireland (NI) in November 2012. The disease was observed only on recently (<6 years) planted trees. An in-depth case study in 2015 of an ash plantation with severe symptoms indicated that many of the trees were infected at the time of planting. Apothecia were observed developing from pseudosclerotia beneath the epidermis of dead branches still attached to the tree, suggesting a possible mechanism whereby H. fraxineus could be disseminated without leaf or rachises infection. Apothecia also formed on roots, indicating that infections may also occur in the soil. Often young trees were killed by the formation of large basal lesions which did not arise from stem infections higher up. On first detecting the disease on the island of Ireland the Governments of NI and the Republic of Ireland published an “All-Ireland Chalara Control Strategy.” Part of that strategy was a ban on the importation of ash plants from regions where the disease was known to be present, to prevent the introduction of further inoculum, and the implementation of an ‘eradication and containment’ policy with the aim of preventing the establishment and spread of the disease. While these measures may have slowed disease establishment, they were ultimately unsuccessful and by 2018 ash dieback was widespread and established throughout the whole of NI in plantations and in the wider environment.Northern Ireland Department of Agriculture, Environment and Rural Affairs PhD Studentshi
Importance of tree diameter and species for explaining the temporal and spatial variations of xylem water δ18O and δ2H in a multi-species forest
Get PDFPublication history: Accepted - 17 March 2023; Published online - 23 May 2023.Identifying the vegetation and topographic variables influencing the isotopic variability of xylem water of forest vegetation remains crucial to interpret and predict ecohydrological processes in landscapes. In this study, we used temporally and spatially distributed xylem stable water isotopes measurements from two growing seasons to examine the temporal and spatial variations of xylem stable water isotopes and their relationships with vegetation and topographic variables in a Luxembourgish temperate mixed forest. Species-specific temporal variations of xylem stable water isotopes were observed during both growing seasons with a higher variability for beeches than oaks. Principal component regressions revealed that tree diameter at breast height explains up to 55% of the spatial variability of xylem stable water isotopes, while tree species explains up to 24% of the variability. Topographic variables had a marginal role in explaining the spatial variability of xylem stable water isotopes (up to 6% for elevation). During the drier growing season (2020), we detected a higher influence of vegetation variables on xylem stable water isotopes and a lower temporal variability of the xylem water isotopic signatures than during the wetter growing season (2019). Our results reveal the dominant influence of vegetation on xylem stable water isotopes across a forested area and suggest that their spatial patterns arise mainly from size- and species-specific as well as water availability-dependent water use strategies rather than from topographic heterogeneity. The identification of the key role of vegetation on xylem stable water isotopes has critical implications for the representativity of isotopes-based ecohydrological and catchments studies.This work was supported by the Luxembourg National Research Fund (FNR/CORE/C17/SR/11702136/EFFECT). The second author is supported by the Accelerator Programme (AP) 2022-24 and the Starter
Scheme by the University of the West of England, Bristol
Spatial and temporal environmental heterogeneity induced by internal tides influences faunal patterns on vertical walls within a submarine canyon
Get PDFPublication history: Accepted - 27 February 2023; Published - 29 March 2023.Vertical walls of submarine canyons represent features of high conservation value that can provide natural areas of protection for vulnerable marine ecosystems under increasing anthropogenic pressure from deep-sea trawling. Wall assemblages are spatially heterogeneous, attributed to the high environmental heterogeneity over short spatial scales that is a typical feature of canyons. Effective management and conservation of these assemblages requires a deeper understanding of the processes that affect faunal distribution patterns. Canyons are recognised as sites of intensified hydrodynamic regimes, with focused internal tides enhancing near-bed currents, turbulent mixing and nepheloid layer production, which influence faunal distribution patterns. Faunal patterns also respond to broad-scale hydrodynamics and gradients in water mass properties (e.g. temperature, salinity, dissolved oxygen concentration). Oscillating internal tidal currents can advect such gradients, both vertically and horizontally along a canyon's walls. Here we take an interdisciplinary approach using biological, hydrodynamic and bathymetry-derived datasets to undertake a high-resolution analysis of a subset of wall assemblages within Whittard Canyon, North-East Atlantic. We investigate if, and to what extent, patterns in diversity and epibenthic assemblages on deep-sea canyon walls can be explained by spatial and temporal variability induced by internal tides. Vertical displacement of water mass properties by the internal tide was calculated from autonomous ocean glider and shipboard CTD observations. Spatial patterns in faunal assemblage structure were determined by cluster analysis and non-metric Multi-Dimensional Scaling plots. Canonical Redundancy Analysis and Generalised Linear Models were then used to explore relationships between faunal diversity and assemblage structure and a variety of environmental variables. Our results support the hypothesis that internal tides influence spatial heterogeneity in wall faunal diversity and assemblages by generating both spatial and temporal gradients in hydrodynamic properties and consequently likely food supply.This work was based on data collected from various expeditions. JC125 was funded by the ERC CODEMAP project (Starting Grant no 258482) and the NERC MAREMAP programme, the JC035_JC036 expedition was funded by the NERC core programme OCEANS2025, the EU FP7 IP HERMIONE; the 64PE421, 64PE453 and 64PE437 expeditions were funded by the NICO initiative by NWO and NIOZ and the NWO-VIDI, grant agreement 016.161.360 and MESH Joint copyright© 2007 Defra, JNCC, Marine Institute, BGS, UoP data were recorded during a collaborative survey (MESH Cruise 01-07-01) involving the Joint Nature Conservation Committee, the Marine Institute, the British Geological Survey and the University of Plymouth. The Department of the Environment, Fisheries and Rural Affairs (Defra) Natural Environmental Group Science Division (CRO361) made a significant financial contribution to this work. The MESH work contributed to the MESH project (www.searchmesh.net) that received European Regional Development Funding through the INTERREG III B Community Initiative (www.nweurope.org). TP was a PhD student in the NERC-funded SPITFIRE Doctoral Training Programme (Grant number NE/L002531/1) and received further funding from the National Oceanography Centre and the CASE partner CEFAS. VH was funded by the ERC Starting Grant project CODEMAP (Grant No 258482), by the NERC National Capability programme CLASS (Grant No NE/R015953/1), and the EU H2020 research and innovation programme project iAtlantic (grant agreement No 818123). During the final preparation stages of this manuscript she enjoyed a Fellowship from the Hanse-Wissenschaftskolleg Institute for Advanced Study. FM is supported by the innovational research scheme NWO-VIDI, grant agreement 016.161.36
Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle
Get PDFPublication history: Accepted - 8 August 2023; Published - 11 August 2023.Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.No external funding
High-resolution assessment of riverbank erosion and stabilization techniques with associated water quality implications
No full textPublication history: Accepted - 13 May 2023; Published online - 26 May 2023.Agriculture is a key contributor to poor water quality, but the sources of sediment and nutrient losses from agricultural catchments – including from riverbank erosion – are highly variable. Riverbank erosion is particularly difficult to quantify and control. Here, we developed a quick assessment approach to quantify riverbank erosion rates and associated sediment and nutrient loading rates into waterways using airborne LiDAR combined with field-collected data. We applied this approach and explored its relationships to water quality at four sites within the Blackwater catchment in Northern Ireland for two analysis periods. GIS LiDAR image differencing revealed that volume changes in riverbank elevation equated to average erosion rates which indicated spatial and temporal variability in erosion rates. Combining the erosion rates with in-situ riverbank bulk density and total extractable phosphorus content provided sediment and phosphorus loading rates. The relative differences between estimated erosion at the different sites corresponded well with in-stream suspended sediment variations, but patterns for total phosphorus concentrations were more complex. We conclude that the use of LiDAR combined with field data is an innovative means for riverbank erosion quantification. Furthermore, by using LiDAR-to-LiDAR analyses, the reductions in erosion, sediment, and phosphorus loading rates following riverbank stabilization techniques can be determined.This research was funded by the NERC QUADRAT DTP [grant number 2280708]. The riverbank stabilization work at Site 3 was funded by the CatchmentCARE project (project reference IVA5058—www.catchmentcare.eu). The CatchmentCARE project is supported by the European Union's INTERREG VA Programme, managed by the Special EU Programmes Body (SEUPB)
Gaping behaviour of Blue mussels (Mytilus edulis) in relation to freshwater runoff risks
No full textPublication history: Accepted - 3 September 2023; Published - 21 September 2023.Shellfish grown for food are vulnerable to environmental contamination, potentially rendering them unsafe for human consumption. Non-invasive gape (valve openness) sensing allows in-situ monitoring of bivalve shellfish behaviours, such as feeding, that can result in exposure to contaminated waters. Sensors were attached to Blue mussels and deployed for 10 days on natural mussel beds in Dundrum Bay, Northern Ireland. Data showed a tidally synchronous behaviour pattern of high openness at high water and vice versa. It is likely that this is, at least in part, due to extreme salinity variation (1.8–33.6) resulting from near total water exchange with each tide in the bay. This behaviour is likely to infer a degree of protection from contaminants during periods of low water, a time at which runoff-derived pollutants are most concentrated.This work was supported by the Natural Environment Research Council (BB/S004203/), the ARIES Doctoral Training Partnership (grant number NE/S007334/1) and the Agri-Food and Biosciences Institute, Northern Ireland
Predicting Chemical Composition and Apparent Total Tract Digestibility on Freeze-Dried Not Ground Faeces Using Near-Infrared Spectroscopy in Pigs
Get PDFPublication history: Accepted - 19 June 2023; Published - 24 June 2023.The present study aimed to compare NIRS results using freeze-dried ground or not ground (FDG or FDNG) faeces to predict faecal chemical composition and apparent total tract digestibility (ATTD) coefficients. Two different batches of pigs were used (n = 20 mixed sex pens/batch; 11 pigs/pen; Duroc × (Large White × Landrace)). The first batch of pigs (B1; 50.1 ± 3.44 kg body weight (BW)) was used at 13 wks of age and the second batch (B2; 87.0 ± 4.10 kg BW) was used at 18 wks of age. For both B1 and B2, pens were assigned to five diets formulated to obtain a control [10.03 MJ of net energy (NE), 160.0 g of crude protein (CP), and 9.5 g of standardized ileal digestive (SID) lysine (Lys) per kg of feed], low protein (132.0 g CP and 7.5 g SID Lys), high protein (188.0 g CP and 11.5 g SID Lys), low energy (9.61 MJ NE/kg), and high energy (10.45 MJ NE/kg) diets. After a 10-day adaptation period, one faecal sample was collected daily from each pen floor during 6 days in both B1 and B2 (n = 120/batch). Faecal samples were freeze-dried and analysed via NIRS as FDNG and FDG faeces. Dry matter (DM), organic matter (OM), CP, gross energy (GE), fat, and ATTD coefficients were analysed/calculated. The NIRS calibrations were evaluated by cross-validation, splitting the data in four random groups, or using the leave-one-out method. For both FDNG and FDG faeces, coefficients of determination for calibration (R2cv) and residual predictive deviation (RPD) values were: close to 0.9 and 3 for DM and CP, 0.7–0.8 and ≥2 for OM and GE, 0.6 and <2 for fat, and 0.54–0.75 and ≤2 for ATTD coefficients, respectively. CP was better predicted using FDG faeces (p < 0.05), while DM and OM ATTD were better predicted using FDNG faeces (p < 0.05). In conclusion, NIRS successfully predicts faeces’ chemical components and ATTD coefficients of nutrients using FDNG or FDG faeces.Jordi Camp Montoro was supported by the TeagascWalsh Scholarship Scheme grant-in-aid project Introducing new feeding programs and facilities for Irish finishing pigs ref 0415. David Solà-Oriol is supported by the UAB-Banco de Santander Talent Programme. Ramon Muns is supported by the Department of Agriculture, Environment, and Rural Affairs of Northern Ireland, under the Evidence
and Innovation project Towards precision feeding: a precise and cost-effective feeding system (ref.: 18 1 08)
Investigating the Genetic Diversity of H5 Avian Influenza Viruses in the United Kingdom from 2020–2022
Get PDFPublication history: Accepted - 27 April 2023; Published - 26 June 2023.Since 2020, the United Kingdom and Europe have experienced annual
epizootics of high-pathogenicity avian influenza virus (HPAIV). The first epizootic, during the autumn/winter of 2020–2021, involved six H5Nx subtypes, although H5N8 HPAIV dominated in the United Kingdom. While genetic assessments of the H5N8 HPAIVs within the United Kingdom demonstrated relative homogeneity, there was a background of other
genotypes circulating at a lower degree with different neuraminidase and internal genes.
Following a small number of detections of H5N1 in wild birds over the summer of 2021, the autumn/winter of 2021–2022 saw another European H5 HPAIV epizootic that dwarfed the prior epizootic. This second epizootic was dominated almost exclusively by H5N1 HPAIV, although six distinct genotypes were defined. We have used genetic analysis to evaluate the emergence of different genotypes and proposed reassortment events that have been observed. The existing data suggest that the H5N1 viruses circulating in Europe during late 2020 continued to circulate in wild birds throughout 2021, with minimal adaptation, but then went on to reassort with AIVs in the wild bird population.
We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the United Kingdom over two winter seasons and demonstrate the utility of in-depth genetic analyses in defining the diversity of H5 HPAIVs circulating in avian species, the potential for zoonotic risk, and whether incidents of lateral spread can be defined over independent incursions of infections from wild birds. This provides key supporting data for mitigation activities.This work was funded by the Department for Environment, Food, and Rural Affairs
(Defra) (United Kingdom) and the Devolved Administrations of Scotland and Wales through
the following programs of work: SV3400, SV3032, SV3006, and SE2213. Funding for
diagnostic testing in Northern Ireland was provided by the Department for Agriculture,
Environment, and Rural Affairs (DAERA). The writing and data analysis for the manuscript
were also supported in part by the DELTA-FLU project funded by the European Union’s
Horizon 2020 research and innovation program under grant agreement no. 727922. A.C.B.,
J.J., and I.H.B. were also partly funded by the BBSRC/Defra-funded research initiative FluMAP
(BB/X006204/1)
Vitality in Newborn Farm Animals: Adverse Factors, Physiological Responses, Pharmacological Therapies, and Physical Methods to Increase Neonate Vigor
Get PDFPublication history: Accepted - 29 April 2023; Published - 4 may 2023.Vitality is the vigor newborn animals exhibit during the first hours of life. It can be assessed by a numerical score, in which variables, such as heart rate, respiratory rate, mucous membranes’ coloration, time the offspring took to stand up, and meconium staining, are monitored. Vitality can be affected by several factors, and therapies are used to increase it. This manuscript aims to review and analyze pharmacological and physical therapies used to increase vitality in newborn farm animals, as well as to understand the factors affecting this vitality, such as hypoxia, depletion of glycogen, birth weight, dystocia, neurodevelopment, hypothermia, and finally, the physiological mechanism to achieve thermostability. It has been concluded that assessing vitality immediately after birth is essential to determine the newborn’s health and identify those that need medical intervention to minimize the deleterious effect of intrapartum asphyxia. Vitality assessment should be conducted by trained personnel and adequate equipment. Evaluating vitality could reduce long-term neonatal morbidity and mortality in domestic animals, even if it is sometimes difficult with the current organization of some farms. This review highlights the importance of increasing the number of stock people during the expected days of parturitions to reduce long-term neonatal morbidity and mortality, and thus, improve the farm’s performance.This research received no external funding
Evaluating Groundwater Nitrate Status across the River Ythan Catchment (Scotland) following Two Decades of Nitrate Vulnerable Zone Designation
Get PDFPublication history: Accepted - 14 April 2023; Published - 18 April 2023.Diffuse agricultural pollution is one of the greatest challenges to achieving good chemical and ecological status of Scotland’s water bodies. The River Ythan in Aberdeenshire was designated a Nitrate Vulnerable Zone (NVZ) in the year 2000, due to the eutrophication of the Ythan Estuary and rising nitrate trends in Private Water Supply (PWS) groundwater abstractions. The third River Basin Management Plan (RBMP) for Scotland reported the Ellon groundwater body of the River Ythan catchment to be of poor chemical status as of 2021 with respect to nitrate, and forecasted groundwater recovery beyond 2027. Following two decades of NVZ designation, we investigated the drivers of groundwater nitrate across the River Ythan catchment through an analysis of long-term (2009–2018) groundwater quality monitoring data collected by the Scottish Environmental Protection Agency (SEPA) and a recent synoptic groundwater nitrate sampling survey of PWSs. Groundwater nitrate was found to remain elevated across the catchment area, and appeared to be highly sensitive to agricultural practices and meteorological forcing, indicating a high sensitivity of groundwater quality to environmental change. Further hydrogeological characterisation is recommended to better understand the effects of agricultural practices on groundwater quality, and to facilitate achievement of future RBMP goals under a changing climate.This research was supported by the Natural Environment Research Council and the QUADRAT Doctoral Training Partnership [NE/S007377/1]