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A research note: A short survey of key silage-making practices on Northern Ireland dairy farms and farmer's perceptions of the factors influencing silage quality
No full textNorthern Ireland dairy farmers (n = 174) were surveyed to identify key silage-making practices, and factors perceived to influence the quality of grass silage made on their farms. The majority of farmers (65%) harvested grass for silage three times/year: 62% normally used a contractor, while 47% routinely used a silage additive. Delays to mowing and delays to harvesting due to adverse weather or poor ground conditions were perceived to have a large or very large impact on silage quality (68% and 53% of farmers, respectively). Inadequate wilting, poor-quality swards on owned land, on rented land and “contamination” of first-cut grass with autumn or winter growth herbage were all perceived as having a large or very large impact on silage quality (32%, 27%, 40%, 30% of farmers, respectively). Over the previous decade, 11%, 41% and 37% of farmers claimed a small, moderate or large improvement in silage quality, mainly due to earlier cutting of grass and ensiling better quality swards.This work was co-funded by DAERA and AgriSearch. Thanks are owed to CAFRE Greenmount for permission to undertake the survey, to AFBI staff who undertook the survey and to the 174 participating farmer
Unifying approaches to Functional Marine Connectivity for improved marine resource management: the European SEA-UNICORN COST Action
Get PDFPublication history: Published online - 22 February 2022Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action within the European Union Horizon 2020 framework programme, is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policiesThis article is adapted from the MoU of the COST (European Cooperation in Science and Technology) Action CA19107 ‘Unifying Approaches to Marine Connectivity for improved Resource Management for the Seas” (SEA-UNICORN) - supported by the Horizon 2020 framework programme for research and innovation.
COST Action CA19107 ‘Unifying Approaches to Marine Connectivity for improved Resource Management for the Seas” (SEA-UNICORN) - https://www.cost.eu/actions/CA19107
Does Landscape Structure Affect the Presence of Woodland Specialist Pollinators in Farmland? Implications for Agri-Environment Scheme Design
Get PDFPublication history: Accepted - 19 October 2021; Published - 16 March 2022.natural or semi-natural habitats to nest and/or forage. Landscape structure has been shown to influence
pollinator communities and understanding how landscape structure affects farmland pollinators
can improve Agri-Environment Schemes (AES). This study explored how landscape metrics affect
the presence of pollinators associated with woody vegetation in farmland in the Republic of Ireland.
Two study regions were selected, and pollinators were collected using pan traps placed in farm linear
features. Hoverfly and bee species were selected based on their body size and association with woody
vegetation. Relevant landscape structure metrics were extracted from around each trap and used to
develop explanatory models for the abundance of pollinators. The total abundance of target species
was relatively low but correlated with three explanatory variables: the connectivity of the linear feature
to woodlands; the distance from the trap to the closest woodland; and edge density. Hoverfly and
bee abundance data, when analysed separately, showed significant differences within regions. Results
seem to indicate that incentivising the connectivity of farm linear features to surrounding woodland
patches and increasing optimal habitat availability in agricultural landscapes could benefit woodland
specialists. This information is helpful to improving AES design.This work was supported by the Irish Department of Agriculture, Food and the Marine (DAFM) (RSF15_S_619).
Open Access funding provided by IReL
An Inventory of Good Management Practices for Nutrients Reduction, Recycling and Recovery from Agricultural Runoff in Northern Periphery and Arctic (NPA) region
No full textPublication history: Accepted - 26 June 2022; Published online - 4 July 2022The excess loading of nutrients generated by agricultural activities is a leading cause of water quality impairment across the globe. Various management practices have been developed and widely implemented as conservation management strategies to combat water pollution originating from agricultural activities. In the last ten years, there has also been a widespread recognition of the need for nutrient harvesting from wastewaters and resource recovery. In Europe’s Northern Periphery and Arctic (NPA) areas, the expertise in water and runoff management is sporadic and needs to be improved. Therefore, the objective of this research was to perform a comprehensive review of the state of the art of Good Agricultural Practices (GAPs) for the NPA region. A set of questionnaires was distributed to project partners combined with a comprehensive literature review of GAPs focusing on those relevant and/or implemented in the NPA region. Twenty-four GAPs were included in the inventory. This review reveals that there is a large level of uncertainty, inconsistency, and a gap in the knowledge regarding the effectiveness of GAPs in nutrient reduction (NRE), their potential for nutrient recycling and recovery (NRR), and their operation and maintenance requirements (OMR) and costs. Although the contribution of GAPs to water quality improvement could not be quantified, this inventory provides a comprehensive and first-of-its-kind guide on available measures and practices to assist regional and local authorities and communities in the NAP region. A recommendation for incorporating and retrofitting phosphorus retaining media (PRMs) in some of the GAPs, and/or the implementation of passive filtration systems and trenches filled with PRMs to intercept surface and subsurface farm flows, would result in the enhancement of both NRE and NRRThis research was funded by the European Union European Research Development Fund Northern Periphery and Arctic Programme 2014–2020, grant number 304-2559-2016
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors.
Get PDFPublication history: Accepted - 11 September 2022; Published online - 31 October 2022Bacterial type VI secretion systems (T6SSs) are contractile nanomachines that deliver proteinic substrates into target prokaryotic or eukaryotic cells and the surrounding milieu. The genus Campylobacter encompasses 39 recognized species and 13 subspecies, with many belonging to a group known as ‘emerging Campylobacter pathogens’. Within Campylobacter, seven species have been identified to harbour a complete T6SS cluster but have yet to be comparatively assessed. In this study, using systematic bioinformatics approaches and the T6SS-positive Campylobacter jejuni 488 strain as a reference, we explored the genus-wide prevalence, similarity and make-up of the T6SS amongst 372 publicly available ‘complete’ Campylobacter genomes. Our analyses predict that approximately one-third of Campylobacter species possess a T6SS. We also putatively report the first identification of a T6SS in four species: Campylobacter cuniculorum, Campylobacter helveticus, Campylobacter armoricus and Campylobacter ornithocola. The Campylobacter T6SSs cluster into three distinct organizations (I–III), of which two break down into further variants. Thirty T6SS-containing genomes were found to harbour more than one vgrG gene, with Campylobacter lari strain NCTC 11845 possessing five. Analysis of the C. jejuni Pathogenicity Island-1 confirmed its conservation amongst T6SS-positive C. jejuni strains, as well as highlighting its diverse genetic composition, including additional putative effector–immunity pairs (e.g. PoNe and DUF1911 domains). Effector–immunity pairs were also observed neighbouring vgrGs in several other Campylobacter species, in addition to putative genes encoding nucleases, lysozymes, ATPases and a ferric ATP-binding cassette uptake system. These observations highlight the diverse genetic make-up of the T6SS within Campylobacter and provide further evidence of its role in pathogenesis
The impact of using novel equations to predict nitrogen excretion and associated emissions from pasture-based beef production systems.
Get PDFPublication history: Accepted - 6 June 2022; Published online - 14 June 2022The excretion of nitrogen (N) in faeces and urine from beef cattle contributes to atmospheric pollution through greenhouse gas and ammonia emissions and eutrophication of land and aquatic habitats through excessive N deposition and nitrate leaching to groundwater. As N excretion by beef cattle is rarely measured directly, it is important to accurately predict losses by utilising a combined knowledge of diet and production parameters so that the effect of dietary changes on the potential environmental impact of beef production systems can be estimated. This study aimed to identify differences between IPCC and more detailed country-specific models in the prediction of N excretion and N losses at a system level and determine how the choice of model influences the interpretation of differences in diet at the system scale. The data used in this study were derived from a farm-scale experimental system consisting of three individual grazing farms, each with a different sward type: a permanent pasture, a high sugar ryegrass monoculture, and a high sugar ryegrass with white clover (~30% groundcover). Data were analysed using a mixed linear model (residual maximum likelihood analysis). The IPCC methods demonstrated significantly lower estimates of N excretion than country-specific models for the first housing period and significantly greater losses for the grazing and second housing periods. The country-specific models enabled prediction of N partitioning to urine and faeces, which is important for estimation of subsequent N losses through the production system, although the models differed in their estimates. Overall, predicted N losses were greater using the IPCC approaches compared to using more detailed country-specific approaches. The outcomes of the present study have highlighted that different models can have a substantial impact on the predicted N outputs and subsequent losses to the environment for pasture-based beef finishing systems, and the importance, therefore, of using appropriate models and parametersThe authors would like to acknowledge funding support from the University of Reading, Rothamsted Research, and UK Biotechnology and Biological Sciences Research Council (BBS/E/C/000I0320). The
NWFP is a UK National Capability, also supported by the Biotechnology and Biological Sciences
Research Council (BBS/E/C/000J0100)
Animal-vehicle collisions during the COVID-19 lockdown in early 2020 in the Krakow metropolitan region, Poland
Get PDFPublication history: Accepted - 11 April 2022; Published online - 9 May 2022The interrelations between human activity and animal populations are of increasing interest due to the emergence of the novel COVID-19 and the consequent pandemic across the world. Anthropogenic impacts of the pandemic on animals in urban-suburban environments are largely unknown. In this study, the temporal and spatial patterns of urban animal response to the COVID-19 lockdown were assessed using animal-vehicle collisions (AVC) data. We collected AVC data over two 6-month periods in 2019 and 2020 (January to June) from the largest metropolis in southern Poland, which included lockdown months. Furthermore, we used traffic data to understand the impact of lockdown on AVC in the urban area. Our analysis of 1063 AVC incidents revealed that COVID-19 related lockdown decreased AVC rates in suburban areas. However, in the urban area, even though traffic volume had significantly reduced, AVC did not decrease significantly, suggesting that lockdown did not influence the collision rates in the urban area. Our results suggest that there is a need to focus on understanding the effects of changes in traffic volume on both human behaviour and wildlife space use on the resulting impacts on AVC in the urban area.S.M.B is supported by the project ATUT PhD Programme in Biology. The project is co-financed by the European Union under the European Social Fund – Operational Programme Knowledge Education Development Axis III Higher Education for Economy and Development, Action 3.2 PhD Programme
Reducing MCPA herbicide pollution at catchment scale using an agri-environmental scheme
Get PDFPublication history: Accepted - 16 May 2022; Published online - 20 May 2022.In river catchments used as drinking water sources, high pesticide concentrations in abstracted waters require an expensive
treatment step prior to supply. The acid herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) is particularly
problematic as it is highly mobile in the soil-water environment following application. Here, an agri-environmental
scheme (AES) was introduced to a large-scale catchment (384 km2) to potentially reduce the burden of pesticides in
the water treatment process. The main measure offered was contractor application of glyphosate by weed wiping as
a substitute for boom spraying of MCPA, supported by educational and advisory activities. A combined innovation applied
in the assessment was, i) a full before-after-control-impact (BACI) framework over four peak application seasons
(April to October 2018 to 2021) where a neighbouring catchment (386 km2) did not have an AES and, ii) an enhanced
monitoring approach where river discharge and MCPA concentrations were measured synchronously in each catchment.
During peak application periods the sample resolution was every 7 h, and daily during quiescent winter periods.
This sampling approach enabled flow- and time-weighted concentrations to be established, and a detailed record of
export loads. These loads were up to 0.242 kg km−2 yr−1, and over an order of magnitude higher than previously reported
in the literature. Despite this, and accounting for inter-annual and seasonal variations in river discharges, the
AES catchment indicated a reduction in both flow- and time-weighted MCPA concentration of up to 21% and 24%, respectively,
compared to the control catchment. No pollution swapping was detected. Nevertheless, the percentage of
MCPA occurrences above a 0.1 μg L−1 threshold did not reduce and so the need for treatment was not fully resolved.
Although the work highlights the advantages of catchment management approaches for pollution reduction in source
water catchments, it also indicates that maximising participation will be essential for future AES.This work was carried out as part of Source to Tap (IVA5018), a project supported by the European Union's INTERREG VA Programme, managed by the Special EU Programmes Body (SEUPB)
Evaluation of Chemcatcher® passive samplers for pesticide monitoring using high-frequency catchment scale data
Get PDFPublication history: Accepted - 13 September 2022; Published online - 30 September 2022Passive samplers (PS) have been proposed as an enhanced water quality monitoring solution in rivers, but their performance against high-frequency data over the longer term has not been widely explored. This study compared the performance of Chemcatcher® passive sampling (PS) devices with high-frequency sampling (HFS: 7-hourly to daily) in two dynamic rivers over 16 months. The evaluation was based on the acid herbicides MCPA (2-methyl-4-chlorophenoxyacetic acid), mecoprop-P, fluroxypyr and triclopyr. The impact of river discharge parameters on Chemcatcher® device performance was also explored. Mixed effects modelling showed that time-weighted mean concentration (TWMC) and flow-weighted mean concentration (FWMC) values obtained by the HFS approach were both significantly higher (p 0.05). There was little indication that river flow parameters altered PS performance—some minor effects were not significant or consistent. Despite this, the PS recovery of very low concentrations indicated that Chemcatcher® devices may be used to evaluate the presence/absence and magnitude of acid herbicides in hydrologically dynamic rivers in synoptic type surveys where space and time coverage is required. However, a period of calibration of the devices in each river would be necessary if they were intended to provide a quantitative review of pesticide concentration as compared with HFS approaches.This work was funded in part by the Source to Tap project (project
reference IVA5018 – http://www.sourcetotap.eu), supported by the
European Union’s INTERREG VA Programme which is managed by the
Special EU Programmes Body (SEUPB). The work was also part-funded
by the FAIRWAY project (project reference 727984 - http://www.fair
way-project.eu/). supported by the European Union’s HORIZON 2020
Programme
In silico Methods for Modeling of Genomic Regions for Immunological and Metabolic Gene Modulating to Stress Response in Chicken: Where We Are?
Get PDFPublication history: Accepted - 30 April 2022; Published online - 1 September 2022Traditionally, commercial broilers are not well adapted and currently subjected to a variety of environmental challenges. In recent years, researchers have shown an increased interest in stress as one of the
greatest environmental challenges to the profitability of sustainable intensive poultry production. In this
scenario, understanding the complexity of the molecular basis and genomics of the stress response is critical
to successful breeding programs for climate-adapted chickens. Recently, numerous popular studies have
attempted to identify candidate genes that control stress responses in chickens. However, a number of questions regarding the choice of stress response remain unanswered or inadequately answered regarding the
number of lead candidate genes that control components of the non-infectious and infectious stress response. With this motivation, 89 journal articles were collected for the primary investigation and those with
low validity were excluded from further analysis. In short, we used three types of information sources,
namely: text-based systematic review, in silico modeling, and both network and pathway approaches, to
introduce more effective and bio-indicators of gene-controlling stress responses in chickens through older
literature. Gene ontology (GO) and pathway networking of candidate gene associated with stress was
loaded into Cytoscape for analysis. The result provides additional evidence and highlights, including nearly
9 candidate genes. According to published studies, CRYAB, HSP90AA1, IL6, HSPA2, HSF2, HSPB1, HSF3,
PLK1, BAG3 are mostly associated with non-infectious and infectious stressors and may deserve further
attention. String database analysis illustrated role of highlighted gene in multiple cellular task and functionally such as ATPase activity, cellular processes, including protection of the proteome from stress, folding
and transport of newly synthesized polypeptides, activation of proteolysis of misfold proteins and the formation and dissociation of protein complexes. Obtained information from Animal QTL database indicated
important role of chromosomes numbers 2, 3, 4, 5, 12, 14 and 24 associated with stress resistance and susceptibility. On this basis, this report attempts to find out whi