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The Plankton Lifeform Extraction Tool: a digital tool to increase the discoverability and usability of plankton time-series data
Get PDFPublication history: Accepted - 25 October 2021; Published online - 6 December 2021.Plankton form the base of the marine food web and are sensitive indicators of environmental change. Plankton time series are therefore an essential part of monitoring progress towards global biodiversity goals, such as the Convention on Biological Diversity Aichi Targets, and for informing ecosystem-based policy, such as the EU Marine Strategy Framework Directive. Multiple plankton monitoring programmes exist in Europe, but differences in sampling and analysis methods prevent the integration of their data, constraining their utility over large spatio-temporal scales. The Plankton Lifeform Extraction Tool brings together disparate European plankton datasets into a central database from which it extracts abundance time series of plankton functional groups, called “lifeforms”, according to shared biological traits. This tool has been designed to make complex plankton datasets accessible and meaningful for policy, public interest, and scientific discovery. It allows examination of large-scale shifts in lifeform abundance or distribution (for example, holoplankton being partially replaced by meroplankton), providing clues to how the marine environment is changing. The lifeform method enables datasets with different plankton sampling and taxonomic analysis methodologies to be used together to provide insights into the response to multiple stressors and robust policy evidence for decision making. Lifeform time series generated with the Plankton Lifeform Extraction Tool currently inform plankton and food web indicators for the UK's Marine Strategy, the EU's Marine Strategy Framework Directive, and for the Convention for the Protection of the Marine Environment of the North-East Atlantic (OSPAR) biodiversity assessments. The Plankton Lifeform Extraction Tool currently integrates 155 000 samples, containing over 44 million plankton records, from nine different plankton datasets within UK and European seas, collected between 1924 and 2017. Additional datasets can be added, and time series can be updated. The Plankton Lifeform Extraction Tool is hosted by The Archive for Marine Species and Habitats Data (DASSH) at https://www.dassh.ac.uk/lifeforms/ (last access: 22 November 2021, Ostle et al., 2021). The lifeform outputs are linked to specific, DOI-ed, versions of the Plankton Lifeform Traits Master List and each underlying dataset.Funding that supports this work and the data collected has come from the European Commission, European Union (EU) grant no. 11.0661/2015/712630/SUB/ENVC.2 OSPAR; UK Natural Environment Research Council (grant nos. NE/R002738/1 and NE/M007855/1); EMFF, Climate Linked Atlantic Sector Science (grant no. NE/R015953/1), Department for Environment, Food and Rural Affairs, UK Government (grant nos. ME-5308 and ME-414135), NSF USA OCE-1657887, DFO CA F5955150026/001/HAL, Natural Environment Research Council UK (grant no. NC-R8/H12/100); Horizon 2020 (MISSION ATLANTIC (grant no. 862428)); iCPR (grant no. SBFF-2019-36526), IMR Norway; DTU Aqua Denmark; and the French Ministry of Environment, Energy, and the Sea (MEEM). Recent funding for the development of PLET and the Pelagic Habitats Indicator has been provided by HBDSEG/Defra and MMO/EMFF. The MSS Scottish Coastal Observatory data and analyses are funded and maintained by the Scottish Government Schedules of Service (grant nos. ST05a and ST02H), MSS Stonehaven Samplers, North Atlantic Fisheries College, Shetland, Orkney Islands Harbour Council, and Isle Ewe Shellfish
Multi-Actor Platforms in theWater–Agriculture Nexus: Synergies and Long-Term Meaningful Engagement
Get PDFPublication history: Accepted - 3 November 2021; Published - 12 November 2021.Solutions to current complex environmental challenges demand the consultation and
involvement of various groups in society. In light of the WFD’s requirements of public participation,
this paper presents an analysis of the establishment and development of nine different multi-actor
platforms (MAPs) across Europe set up as arenas for long-term engagements to solve water quality
challenges in relation to agriculture. The MAPs represent different histories and legacies of engagement;
some are recent initiatives and some are affiliated with previous government-initiated
projects, while other MAPs are long-term engagement platforms. A case study approach drawing on
insights from the nine engagement processes is used to discuss conditions for enabling long-term
multi-actor engagement. The perceived pressure for change and preferred prioritization in complying
with mitigating water quality problems vary within and among the MAPs. The results show that
governmental and local actors’ concern for water quality improvements and focusing on pressure for
change are important for establishing meaningful multi-actor engagement when concerns translate
into a clear mandate of the MAP. Furthermore, the degree to which the MAPs have been able to
establish relationships and networks with other institutions such as water companies, agricultural
and environmental authorities, farmers, and civil society organizations influences possibilities for
long-term meaningful engagement.This project received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 727984
A Review of the Emerging White Chick Hatchery Disease
Get PDFPublication history: Accepted - 30 November 2021; Published online - 4 December 2021.White chick hatchery disease is an emerging disease of broiler chicks with which the virus, chicken astrovirus, has been associated. Adult birds typically show no obvious clinical signs of infection, although some broiler breeder flocks have experienced slight egg drops. Substantial decreases in hatching are experienced over a two-week period, with an increase in mid-to-late embryo deaths, chicks too weak to hatch and pale, runted chicks with high mortality. Chicken astrovirus is an enteric virus, and strains are typically transmitted horizontally within flocks via the faecal–oral route; however, dead-in-shell embryos and weak, pale hatchlings indicate vertical transmission of the strains associated with white chick hatchery disease. Hatch levels are typically restored after two weeks when seroconversion of the hens to chicken astrovirus has occurred. Currently, there are no commercial vaccines available for the virus; therefore, the only means of protection is by good levels of biosecurity. This review aims to outline the current understanding regarding white chick hatchery disease in broiler chick flocks suffering from severe early mortality and increased embryo death in countries worldwideThis work was supported by the Department of Agriculture, Environment and Rural Affairs (NI) under Grant 18/1/14 and the author was in receipt of Houghton Trust (Avian Pathology) small project award
Selenium dietary supplement affects rumen bacterial population dynamics and fermentation parameters in Tibetan sheep (Ovis aries) in alpine meadow
Get PDFPublication history: Accepted - 31 May 2021; Published online - 2 July 2021.Selenium (Se) deficiency is a widespread and seasonally chronic phenomenon observed in Tibetan sheep (Ovis aries) traditionally grazed on the Qinghai–Tibet Plateau (QTP). Effects of the dietary addition of Se-enriched yeast (SeY) on the bacterial community in sheep rumen and rumen fermentation were evaluated with the aim of gaining a better understanding of the rumen prokaryotic community. Twenty-four yearling Tibetan rams [initial average body weight (BW) of 31.0 ± 0.64 kg] were randomly divided into four treatment groups, namely, control (CK), low Se (L), medium Se (M), and high Se (H). Each group comprised six rams and was fed a basic diet of fresh forage cut from the alpine meadow, to which SeY was added at prescribed dose rates. This feed trial was conducted for over 35 days. On the final day, rumen fluid was collected using a transesophageal sampler for analyzing rumen pH, NH3-N content, volatile fatty acid (VFA) level, and the rumen microbial community. Our analyses showed that NH3-N, total VFA, and propionate concentrations in the M group were significantly higher than in the other groups (P < 0.05). Both the principal coordinates analysis (PCoA) and the analysis of similarities revealed that the bacterial population structure of rumen differed among the four groups. The predominant rumen bacterial phyla were found to be Bacteroidetes and Firmicutes, and the three dominant genera in all the samples across all treatments were Christensenellaceae R7 group, Rikenellaceae RC9 gut group, and Prevotella 1. The relative abundances of Prevotella 1, Rikenellaceae RC9 gut group, Ruminococcus 2, Lachnospiraceae XPB1014 group, Carnobacterium, and Hafnia-Obesumbacterium were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Tax4fun metagenome estimation revealed that gene functions and metabolic pathways associated with carbohydrate and other amino acids were overexpressed in the rumen microbiota of SeY-supplemented sheep. To conclude, SeY significantly affects the abundance of rumen bacteria and ultimately affects the rumen microbial fermentation.This research was funded by the Second Tibetan Plateau Scientific Expedition and Research: Grassland Ecosystem and Ecological Animal Husbandry (2019QZKK0302), the Program for Strategic Priority Research Program of the Chinese Academy of Sciences (XDA20100102), the National Natural Science Foundation of China (No. 31672472 and No. 31201821), and Innovative Research Team of Ministry of Education (IRT_17R50)
Applying the nutrient transfer continuum framework to phosphorus and nitrogen losses from livestock farmyards to watercourses
Get PDFPublication history: Accepted - 25 August 2021; Published online - 5 October 2021.Farmyards are commonly conceptualized as point sources of nutrient pollution nested within the wider agricultural landscape. However, within farmyards there are individual sources and delivery pathways, each of which is affected by a range of management practices and infrastructure. Rainfall mobilizes these nutrients, which may then be delivered to a receptor or to the wider drainage network. As such, the nutrient transfer continuum (NTC), which has been established as a framework to understand and mitigate nutrient loss at a landscape scale, can be similarly applied to disentangle the stages of nutrient transfer from farmyards. The NTC differentiates nutrient transfer into source, mobilization, delivery, and impact stages. This differentiation allows targeting of mitigation measures and evaluation of costs and benefits. This review paper applies the NTC template to farmyard nitrogen and phosphorus transport to conceptualize causative factors and to identify mitigation options.This work 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). The views and opinions expressed in this document do not necessarily reflect those of the European Commission or the SEUPB. The authors thank Russell McCune for providing the graphical abstract illustration
Grass silage composition and nutritive value on Northern Ireland farms between 1998 and 2017
No full textPublication history: Accepted - 28 February 2021; Published online - 25 May 2021.Grass silage is the predominant conserved forage offered to ruminant livestock within Northern Ireland (NI) when housed. This study involved the analysis of a dataset (n = 76,452 samples) comprising silage samples from commercial farms, analysed by the Agri-Food and Biosciences Institute (AFBI) between 1998 and 2017. The effects of harvest number (1, 2 or 3) and year were examined. Most of the differences between harvests 1–3 were significant although these differences were of little biological significance. Silage crude protein (CP) increased from harvests 1 to 3, while ammonia N concentration was higher in 3rd harvests. Acid detergent fibre (ADF) and neutral detergent fibre (NDF) concentrations decreased from harvest 1 to 3, while dry-matter (DM) digestibility and D-value (% DM) were higher in 1st compared to 2nd harvest. Across the twenty year period, silage DM and water soluble carbohydrate concentrations increased, while ADF and NDF concentrations decreased. Crude protein concentration did not change over time. There was no significant improvement in silage digestibility. While silage intake potential for dairy cows increased by approximately 8% (from 88.8 to 96.1 g kg W0.75, meant across all harvests), silage intake potential for beef cattle increased only within harvest 1. Despite overall increases in silage DM concentration, silage digestibility parameters did not show any significant improvement over the 20-year period, highlighting the need for a renewed focus on improving silage nutritive value.This study was funded by the Department of Agriculture, Environment, and Rural Affairs (DAERA) in Northern Ireland, and by AgriSearc
The Role of Proximal Sensors to Improve Land Management, Meet Environmental Targets and Increase Nutrient Use Efficiency on Farms
Get PDFIncreasing nutrient use efficiency on farms; improving land management; changing land use to capture more carbon, along with boosting renewable energy and the wider bio economy are practices that have been identified as key mechanisms by which the ambitious goal of achieving carbon net zero by 2050 can be achieved [1,2]. In order to increase nutrient use efficiency on farms, it requires knowledge and data collection to manage inputs, outputs, emissions and productivity. Soil and crop sensors can play an important role in improving the precision of agricultural practices while minimising harmful emissions to the environment. Rapid advances in technology mean that today there are many soil and crop sensors which provide a fast, powerful, non-destructive means of measuring a large number of chemical and physical properties. However, disentangling the data provided by soil and crop sensors can often be a challenge, particularly as some sensors and proximal sensor systems can be good proxies for more than one soil property. While it is possible to create very accurate and detailed soil maps using proximal sensors, there is nearly always a requirement to calibrate with local samples, as multiple factors can affect sensor measurements [3]. Good processing and calibration are key, and the best results will be achieved when there is a wide variation of in-field properties [4]. This mini review identifies two important case examples where proximal sensors can improve land management and farm nutrient use efficiency, which are both important concepts towards carbon net zero
The perception and use of cover crops within the island of Ireland
Get PDFPublication history: Accepted - 14 December 2020; Published - 26 January 2021.The integration of cover crops within arable rotations is becoming increasingly popular
due to their widely acknowledged benefits. Subsidisation of cover cropping is available
to eligible farmers in the Republic of Ireland (ROI) but not to Northern Ireland (NI)
farmers. There has been little research focus on ROI and NI growers' perceptions about
the husbandry associated with cover crops and the benefits of growing them. Surveys
to gauge farmer use and perception of cover crops were conducted at two arable conferences,
with 55 respondents in NI and 77 in ROI (132 respondents in total). Growers
used cover crops mainly to improve and maintain soil structure in an overall bid to
enhance soil health in ROI, whereas in NI it was predominantly for forage. The impact
of subsidies provided by Ireland and its stipulated policy influences species choice, and
farmers were more likely to plant cover crops after later harvested commercial crops,
for example, September. Compared to growers in NI, they were found predominantly
to plant after crops harvested in August. In ROI, 63% of respondents receiving subsidies
would continue to use cover crops if this monetary incentive ceased
Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland
Get PDFPublication history: Accepted - 29 July 2021; Published online - 6 August 2021.Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.This research was funded by Norwegian Seafood Research Fund (FHF) grant 90079
Mixtures of natural antimicrobials can reduce Campylobacter jejuni, Salmonella enterica and Clostridium perfringens infections and cellular inflammatory response in MDCK cells
Get PDFPublication history: Accepted - 1 June 2021; Published online - 7 June 2021Background: The classification of natural antimicrobials as potential antibiotic replacements is still hampered by the
absence of clear biological mechanisms behind their mode of action. This study investigated the mechanisms underlying
the anti-bacterial effect of a mixture of natural antimicrobials (maltodextrin, citric acid, sodium citrate, malic
acid, citrus extract and olive extract) against Campylobacter jejuni RC039, Salmonella enterica SE 10/72 and Clostridium
perfringens ATCC® 13124 invasion of Madin–Darby Canine Kidney cells (MDCK).
Results: Minimum sub-inhibitory concentrations were determined for Campylobacter jejuni (0.25%), Salmonella
enterica (0.50%) and Clostridium perfringens (0.50%) required for the in vitro infection assays with MDCK cells. The
antimicrobial mixture significantly reduced the virulence of all three pathogens towards MDCK cells and restored the
integrity of cellular tight junctions through increased transepithelial resistance (TEER) and higher expression levels
of ZO-1 (zonula occludens 1) and occludin. This study also identified the ERK (external regulated kinase) signalling
pathway as a key mechanism in blocking the pro-inflammatory cytokine production (IL-1β, IL-6, IL-8, TNF-α) in infected
cells. The reduction in hydrogen peroxide (
H2O2) production and release by infected MDCK cells, in the presence of
the antimicrobial mixture, was also associated with less tetrathionate formed by oxidation of thiosulphate (p < 0.0001).
Conclusion: The present study describes for the first time that mixtures of natural antimicrobials can prevent the formation
of substrates used by bacterial pathogens to grow and survive in anaerobic environments (e.g. tetrathionate).This study was supported by a grant awarded to NC by Environtech, Dublin, Ireland