Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013−2016

Publication history: Accepted - 27 June 2023; Published - 4 July 2023.Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted

Machine learning in marine ecology: an overview of techniques and applications

Publication history: Accepted - 26 May 2023; Published - 3 August 2023.Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.All authors acknowledge the support of ICES through the Working group on Machine Learning in Marine Science (WGMLEARN)

Optimising mechanical separation of anaerobic digestate for total solids and nutrient removal

Publication history: Accepted - 16 June 2023; Published - 28 June 2023.Mechanical separation of anaerobic digestate has been identified as a method to reduce pollution risk to waterways by partitioning phosphorus in the solid fraction and reducing its application to land. Separators have adjustable parameters which affect separation efficiency, and hence the degree of phosphorous partitioning, but information on how these parameters affect separation performance is limited in the literature. Two well known technologies were investigated, decanter centrifuge and screw press, to determine the most efficient method of separation. Counterweight load and the use of an oscillator were adjusted for the screw press, while bowl speed, auger differential speed, feed rate and polymer addition were modified for the decanter centrifuge. Separation efficiency was determined for total solids, phosphorus, nitrogen, potassium, and carbon, and the total solids content of resulting fractions was measured. The decanter centrifuge had higher separation efficiency for phosphorus in all cases, ranging from 51% to 71.5%, while the screw press had a phosphorus separation efficiency ranging from 8.5% to 10.9% for digestate of ~5% solids (slurry/grass silage mix). Separation by decanter centrifuge partitioned up to 56% of nitrogen in the solid fraction leaving a reduced nitrogen content in the liquid fraction available for land spreading; this nitrogen would most likely need to be replaced by chemical fertiliser which would add to the cost of the system. The decanter centrifuge is better suited to cases where phosphorus recovery is the most important factor, while the screw press could be advantageous in cases where cost is a limiting factor.This project was supported by The Bryden Centre. The Bryden Centre project is supported by the European Union’s INTERREG VA Programme, managed by the Special EU Programmes Body (SEUPB). The views and opinions expressed in this paper do not necessarily reflect those of the European Commission or the Special EU Programmes Body (SEUPB). The work was also supported by Queen’s University Belfast and the Agri-Food and Biosciences Institute in Northern Ireland

Overview of Virulence and Antibiotic Resistance in Campylobacter spp. Livestock Isolates

Publication history: Accepted - 10 February 2023; Published online - 17 February 2023Campylobacter remains the most prevalent foodborne pathogen bacterium responsible for causing gastroenteritis worldwide. Specifically, this pathogen colonises a ubiquitous range of environments, from poultry, companion pets and livestock animals to humans. The bacterium is uniquely adaptable to various niches, leading to complicated gastroenteritis and, in some cases, difficult to treat due to elevated resistance to certain antibiotics. This increased resistance is currently detected via genomic, clinical or epidemiological studies, with the results highlighting worrying multi-drug resistant (MDR) profiles in many food and clinical isolates. The Campylobacter genome encodes a rich inventory of virulence factors offering the bacterium the ability to influence host immune defences, survive antimicrobials, form biofilms and ultimately boost its infection-inducing potential. The virulence traits responsible for inducing clinical signs are not sufficiently defined because several populations have ample virulence genes with physiological functions that reflect their pathogenicity differences as well as a complement of antimicrobial resistance (AMR) systems. Therefore, exhaustive knowledge of the virulence factors associated with Campylobacter is crucial for collecting molecular insights into the infectivity processes, which could pave the way for new therapeutical targets to combat and control the infection and mitigate the spread of MDR bacteria. This review provides an overview of the spread and prevalence of genetic determinants associated with virulence and antibiotic resistance from studies performed on livestock animals. In addition, we have investigated the relevant coincidental associations between the prevalence of the genes responsible for pathogenic virulence, horizontal gene transfer (HGT) and transmissibility of highly pathogenic Campylobacter strain

Individual variation in field metabolic rates of wild living fish have phenotypic and ontogenetic underpinnings: insights from stable isotope compositions of otoliths

Publication history: Accepted - 17 May 2023; Published -13 June 2023.Introduction: Individual metabolism has been identified as a key variable for predicting responses of individuals and populations to climate change, particularly for aquatic ectotherms such as fishes. Predictions of organism standard metabolic rate (SMR), and the thermal sensitivity of metabolic rate are typically based on allometric scaling rules and respirometry-based measures of respiratory potential under laboratory conditions. The relevance of laboratory-based measurement and theoretical allometric rules to predict performance of free-ranging animals in complex natural settings has been questioned, but determining time averaged metabolic rate in wild aquatic animals is challenging. Methods: Here we draw on stable isotope compositions of aragonite in fish otoliths to estimate time averaged experienced temperature and expressed field metabolic rate (FMR) simultaneously and retrospectively at an individual level. We apply the otolith FMR proxy to a population of European plaice (Pleuronectes platessa) from the North Sea during a period of rapid warming between the 1980s to the mid-2000s, sampling otolith tissue grown in both juvenile and adult stages. Results: Among-individual variations in realized mass-specific FMR were large and independent of temperature and scaled positively with body size in adult life stages, contradicting simplistic assumptions that FMR follows scaling relationships inferred for standard metabolic rates (SMR). In the same individuals, FMR in the first summer of life co-varied positively with temperature. Discussion: We find strong evidence for the presence of consistent metabolic phenotypes within the sampled population, as FMR in the first year of life was the strongest single predictor for among individual variation in FMR at the point of sampling. Nonetheless, best fitting models explained only 20% of the observed variation, pointing to large among-individual variation in FMR that is unexplained by body mass, temperature or metabolic phenotype. Stable isotope-derived estimates of field metabolic rate have great potential to expand our understanding of ecophysiology in general and especially mechanisms underpinning the relationships between animal performance and changing environmental and ecological conditions.This work was funded from NERC Case award NE/P009700/1

100 essential questions for the future of agriculture

Publication history: Accepted - 8 March 2023; Published online - 11 April 2023.The world is at a crossroad when it comes to agriculture. The global population is growing, and the demand for food is increasing, putting a strain on our agricultural resources and practices. To address this challenge, innovative, sustainable, and inclusive approaches to agriculture are urgently required. In this paper, we launched a call for Essential Questions for the Future of Agriculture and identified a priority list of 100 questions. We focus on 10 primary themes: transforming agri-food systems, enhancing resilience of agriculture to climate change, mitigating climate change through agriculture, exploring resources and technologies for breeding, advancing cultivation methods, sustaining healthy agroecosystems, enabling smart and controlled-environment agriculture for food security, promoting health and nutrition-driven agriculture, exploring economic opportunities and addressing social challenges, and integrating one health and modern agriculture. We emphasise the critical importance of interdisciplinary and multidisciplinary research that integrates both basic and applied sciences and bridges the gaps among various stakeholders for achieving sustainable agriculture. Key points Growing demand and resource limitations pose a critical challenge for agriculture, necessitating innovative and sustainable approaches. The paper identifies 100 priority questions for the future of agriculture, indicating current and future research directions. Sustainable agriculture depends on interdisciplinary and multidisciplinary research that harmonises basic and applied sciences and fosters collaboration among different stakeholders

Planning and licensing for marine aquaculture

Publication history: Accepted - 22 December 2022; Published online - 11 January 2023.Marine aquaculture has the potential to increase its contribution to the global food system and provide valuable ecosystem services, but appropriate planning, licensing and regulation systems must be in place to enable sustainable development. At present, approaches vary considerably throughout the world, and several national and regional investigations have highlighted the need for reforms if marine aquaculture is to fulfil its potential. This article aims to map and evaluate the challenges of planning and licensing for growth of sustainable marine aquaculture. Despite the range of species, production systems and circumstances, this study found a number of common themes in the literature; complicated and fragmented approaches to planning and licensing, property rights and the licence to operate, competition for space and marine spatial planning, emerging species and diversifying marine aquaculture production (seaweed production, Integrated Multi-Trophic Aquaculture [IMTA], nutrient and carbon offsetting with aquaculture, offshore aquaculture and co-location and multiuse platforms), and the need to address knowledge gaps and use of decisionsupport tools. Planning and licensing can be highly complicated, so the UK is used as a case study to show more detailed examples that highlight the range of challenges and uncertainty that industry, regulators and policymakers face across interacting jurisdictions. There are many complexities, but this study shows that many countries have undergone, or are undergoing, similar challenges, suggesting that lessons can be learned by sharing knowledge and experiences, even across different species and production systems, rather than having a more insular focus.Biotechnology and Biological Sciences Research Council; European Commission; Horizon 2020 Framework Programme, Grant/Award Numbers: GA 774426, GA 818173; Natural Environment Research Council; Norges Forskningsråd, Grant/Award Number: 29479

Consumer assessment, in Ireland and the United Kingdom, of the impact of the method of suspension of carcasses from dairy-origin bulls and steers, on the sensory characteristics of the longissimus muscle

Publication history: Published online - 17 June 2023.The objective was to compare the assessment of beef produced in Ireland from a 19-month bull or a 24-month steer dairy beef production system by consumers in Ireland (Cork) and the United Kingdom (Belfast and Reading). Carcass sides were suspended by the Achilles tendon or by the pelvic bone and 21-d aged longissimus muscle assessed using Meat Standards Australia protocols. Carcass weight and classification were similar for bulls and steers. Consumers in Belfast and Cork rated aroma liking, tenderness, juiciness, overall liking and the composite meat quality score (MQ4) similarly, but lower (P < 0.05) than consumers in Reading. Consumers in Belfast and Cork rated flavour liking similarly as did consumers in Cork and Reading, but consumers in Reading rated flavour liking higher (P < 0.05) than consumers in Belfast. Muscle from steers had higher scores for aroma liking, flavour liking, overall liking and MQ4 scores than bulls (P < 0.05). On average, pelvic suspension increased (P < 0.05) the scores for aroma liking and flavour liking compared with conventional suspension but increased (P < 0.05) tenderness, juiciness, overall liking and MQ4 scores only in bulls. Consumers in Reading rated striploin from the traditional Achilles tendon-suspended steers similarly to striploin from pelvic-suspended bulls (MQ4 score of 71.8 and 68.2, respectively). Beef from the latter system could replace the traditional steer beef in this market, thereby benefiting the beef producer and the environment.The project was a part of the “Sensory Food Network Ireland” funded by the Irish Department of Agriculture, Food and the Marine Competitive research programmes (13/SN/401). The animal production portion was similarly funded (11/SF/322, BullBeef)

Implications of Organic Dairy Management on Herd Performance and Milk Fatty Acid Profiles and Interactions with Season

Publication history: Accepted - 30 March 2023; Published - 8 April 2023.Interest in organic cows’ milk has increased due to the perceived superior nutritional quality and improved sustainability and animal welfare. However, there is a lack of simultaneous assessments on the influence of organic dairy practices and dietary and breed drivers on productivity, feed efficiency, health parameters, and nutritional milk quality at the herd level. This work aimed to assess the impact of organic vs. conventional management and month on milk yield and basic composition, herd feed efficiency, health parameters, and milk fatty acid (FA) composition. Milk samples (n = 800) were collected monthly from the bulk tanks of 67 dairy farms (26 organic and 41 conventional) between January and December 2019. Data on breed and feeding practices were gathered via farm questionnaires. The samples were analyzed for their basic composition and FA profile using Fourier transform infrared spectroscopy (FTIR) and gas chromatography (GC), respectively. The data were analyzed using a linear mixed model, repeated measures design and multivariate redundancy analysis (RDA). The conventional farms had higher yields (kg/cow per day) of milk (+7.3 kg), fat (+0.27 kg), and protein (+0.25 kg) and higher contents (g/kg milk) of protein, casein, lactose, and urea. The conventional farms produced more milk (+0.22 kg), fat (+8.6 g), and protein (+8.1 g) per kg offered dry matter (DM). The organic farms produced more milk per kg of offered non-grazing and concentrate DM offered, respectively (+0.5 kg and +1.23 kg), and fat (+20.1 g and +51 g) and protein (+17 g and +42 g). The organic milk had a higher concentration of saturated fatty acid (SFA; +14 g/kg total FA), polyunsaturated fatty acid (PUFA; +2.4 g/kg total FA), and nutritionally beneficial FA alpha linolenic acid (ALNA; +14 g/kg total FA), rumenic acid (RA; +14 g/kg total FA), and eicosapentaenoic acid (EPA; +14 g/kg total FA); the conventional milk had higher concentrations of monounsaturated FA (MUFA; +16 g/kg total FA). Although the conventional farms were more efficient in converting the overall diet into milk, fat, and protein, the organic farms showed better efficiency in converting conserved forages and concentrates into milk, fat, and protein as a result of reduced concentrate feeding. Considering the relatively small differences in the FA profiles between the systems, increased pasture intake can benefit farm sustainability without negatively impacting consumer nutrition and health.Financial support for this work has been provided by (i) EIT Food, the innovation community on Food of the European Institute of Innovation and Technology (EIT), a body of the EU, under the Horizon 2020, the EU Framework Program for Research and Innovation; via the NMR MIRACLE (NMR-based metabolomics for organic milk authentication; No 19118 and 19118-20), and (ii) the Biotechnology and Biological Sciences Research Council (BBSRC) [grant number BB/T008776/1] as part of the Doctoral Training Partnership FoodBioSystems: biological processes across the Agri-Food system from pre-farm to post-fork. Gergely Faludi was in receipt of a fellowship via EIT Food’s Regional Innovation Scheme Talents

The Impact on Cow Performance and Feed Efficiency When Individual Cow Milk Composition and Energy Intake Are Accounted for When Allocating Concentrates

Publication history: Accepted - 27 June 2023; Published - 3 July 2023.The objective of this three-treatment, 12-week study (involving 69 dairy cows) was to test three methods of concentrate allocation on milk production efficiency. All treatments were offered a basal mixed ration of grass silage and concentrates, with additional concentrates offered to individual cows based on either milk yield alone (Control), milk energy output (Precision 1) or energy intake and milk energy output (Precision 2). Concentrate requirements were calculated and adjusted weekly. Control cows had lower concentrate dry matter intake (DMI; p = 0.040) and milk protein content (p = 0.003) but yield of milk and energy-corrected milk (ECM), energy balance, bodyweight and condition score were unaffected by treatment. Efficiency measures such as ECM/DMI and ECM/metabolizable energy intake were also unaffected by treatment. Less concentrates were used per kg ECM yield in the Control compared to the Precision treatments (p < 0.001). In conclusion, accounting for individual cow milk composition or milk composition combined with individual cow energy intake did not improve production efficiency compared to an approach based on individual cow milk yield only.This research was funded by Department of Agriculture, Environment and Rural Affairs and AgriSearch through the Research Challenge Fund, grant number 16-1-10