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A carrying capacity framework for soil phosphorus and hydrological sensitivity from farm to catchment scales
Get PDFPublication history: Accepted - 30 May 2019; Published online - 4 June 2019.Agricultural fieldswith above optimumsoil phosphorus (P) are considered to pose risks to water quality and especially
when those areas are coincident with hydrologically sensitive areas (HSAs) that focus surface runoff
pathways. This is a challenge tomanage in areas of agricultural intensity in surfacewater dominated catchments
where water quality targets have to be met. In this study, a soil P survey of 13 sub-catchments and 7693 fields
was undertaken in a 220 km2 catchment. HSAs were also determined as the top 25th percentile risk froma runoff
routingmodel that used a LiDAR digital elevation model and soil hydraulic conductivity properties. Distributions
of these spatial data were compared with river soluble reactive phosphorus (SRP) concentration measured fortnightly
over one year. The results showed that 41% of fields exceeded the agronomic optimumfor soil P across the
sub-catchments.When compared with the available water quality data, the results indicated that the high soil P
carrying capacity area of the sub-catchmentswas 15%. Combining high soil P and HSA, the carrying capacity area
of the sub-catchmentswas 1.5%. The opportunities to redistribute these riskswere analysed on fields with below
optimum soil P and where HSA risk was also minimal. These ranged from 0.4% to 13.8% of sub-catchment areas
and this limited potential, unlikely to fully reduce the P pressure to over-supplied fields, would need to be considered
alongside addressing this over-supply and also with targeted HSA interception measures.This work was undertaken as a component of the “EU EAA Soil Sampling
and Analysis Scheme”, funded by the Department of Agriculture,
Environment and Rural Affairs (DAERA), Northern Ireland, under the
European Union Exceptional Adjustment Aid Scheme.We thank catchment
farmers for land access and participation. We acknowledge the
contributions of AFBI scientific staffwhowere instrumental in the planning,
acquisition and processing of data, Colleen Ward (AFBI Project
Manager) and Peter Scott (DAERA lead). Finally we thank both anonymous
reviewers for insightful comments and suggestions on the
manuscript
Porcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed Intake
Get PDFPublication history: Accepted - 21 May 2019; Published online - 18 June 2019Optimal feed efficiency (FE) in pigs is important for economic and environmental reasons. Previous research identified FE-associated bacterial taxa within the intestinal microbiota of growing pigs. This study investigated whether FE-associated bacteria and selected FE-associated physiological traits were consistent across geographic locations (Republic of Ireland [ROI) [two batches of pigs, ROI1 and ROI2], Northern Ireland [NI], and Austria [AT]), where differences in genetic, dietary, and management factors were minimized. Pigs (n = 369) were ranked, within litter, on divergence in residual feed intake (RFI), and 100 extremes were selected (50 with high RFI and 50 with low RFI) across geographic locations for intestinal microbiota analysis using 165 rRNA amplicon sequencing and examination of FE-associated physiological parameters. Microbial diversity varied by geographic location and intestinal sampling site but not by RFI rank, except in ROI2, where more-feed-efficient pigs had greater ileal and cecal diversity. Although none of the 188 RFI-associated taxonomic differences found were common to all locations/batches, Lentisphaerae, Ruminococcaceae, RF16, Mucispirillum, Methanobrevibacter, and two uncultured genera were more abundant within the fecal or cecal microbiota of low-RFI pigs in two geographic locations and/or in both ROI batches. These are major contributors to carbohydrate metabolism, which was reflected in functional predictions. Fecal volatile fatty acids and salivary cortisol were the only physiological parameters that differed between RFI ranks. Despite controlling genetics, diet specification, dietary phases, and management practices in each rearing environment, the rearing environment, encompassing maternal influence, herd health status, as well as other factors, appears to impact intestinal microbiota more than FE.
IMPORTANCE Interest in the role of intestinal microbiota in determining FE in pigs has increased in recent years. However, it is not known if the same FE-associated bacteria are found across different rearing environments. In this study, geographic location and intestinal sampling site had a greater influence on the pig gut microbiome than FE. This presents challenges when aiming to identify consistent reliable microbial biomarkers for FE. Nonetheless, seven FE-associated microbial taxa were common across two geographic locations and/or two batches within one location, and these indicated a potentially "healthier' and metabolically more capable microbiota in more-feed-efficient pigs. These taxa could potentially be employed as biomarkers for FE, although bacterial consortia, rather than individual taxa, may be more likely to predict FE. They may also merit consideration for use as probiotics or could be targeted by dietary means as a strategy for improving FE in pigs in the future.The research leading to these results received funding from the European Union’s
Seventh Framework Programme (ECO-FCE project number 311794) for research, technological
development, and demonstration independently of any commercial input,
financial or otherwise. U.M.M. was funded by the Teagasc Walsh Fellowship program.
Gwynneth Halley, who assisted with laboratory work, was funded by a Society for
Applied Microbiology Students into Work grant
Loss rates of honey bee colonies during winter 2017/18 in 36 countries participating in the COLOSS survey, including effects of forage sources
Get PDFPublication history: Accepted - 22 April 2019; Published online - 30 May 2019This short article presents loss rates of honey bee colonies over winter 2017/18 from 36 countries, including 33 in Europe, from data collected using the standardized COLOSS questionnaire. The 25,363 beekeepers supplying data passing consistency checks in total wintered 544,879 colonies, and reported 26,379 (4.8%, 95% CI 4.7–5.0%) colonies with unsolvable queen problems, 54,525 (10.0%, 95% CI 9.8–10.2%) dead colonies after winter and another 8,220 colonies (1.5%, 95% CI 1.4–1.6%) lost through natural disaster. This gave an overall loss rate of 16.4% (95% CI 16.1–16.6%) of honey bee colonies during winter 2017/18, but this varied greatly from 2.0 to 32.8% between countries. The included map shows relative risks of winter loss at regional level. The analysis using the total data-set confirmed findings from earlier surveys that smaller beekeeping operations with at most 50 colonies suffer significantly higher losses than larger operations (p < .001). Beekeepers migrating their colonies had significantly lower losses than those not migrating (p < .001), a different finding from previous research. Evaluation of six different forage sources as potential risk factors for colony loss indicated that intensive foraging on any of five of these plant sources (Orchards, Oilseed Rape, Maize, Heather and Autumn Forage Crops) was associated with significantly higher winter losses. This finding requires further study and explanation. A table is included giving detailed results of loss rates and the impact of the tested forage sources for each country and overall.he colony loss monitoring group which carried out this study is a core project of the COLOSS research association (prevention of honey bee colony losses), which supports regular workshops facilitating research discussions and collaboration between group members. The authors thank very much all the beekeepers who gave their time to complete the COLOSS questionnaire providing the data for this work, and the additional COLOSS partners who contributed to survey organisation, data collection and/or data processing. The authors are also grateful to various national funding sources for their support of some of the monitoring surveys [including, in the Republic of Serbia, MPNTR-RS, through Grant No. (III46002), Slovenian Research Program P1-0164, and “Zukunft Biene” (grant number: 100972) in Austria], and acknowledge the financial support by the University of Graz for open access
Feed Restriction Reveals Distinct Serum Metabolome Profiles in Chickens Divergent in Feed Efficiency Traits
Get PDFPublication history: Accepted - 20 February 2019; Published - 25 February 2019.Restrictive feeding influences systemic metabolism of nutrients; however, this impact
has not been evaluated in chickens of diverging feed efficiency. This study investigated the effect
of ad libitum versus restrictive feeding (85% of ad libitum) on the serum metabolome and white
blood cell composition in chickens of diverging residual feed intake (RFI; metric for feed efficiency).
Blood samples were collected between days 33 and 37 post-hatch. While serum glucose was
similar, serum uric acid and cholesterol were indicative of the nutritional status and chicken’s
RFI, respectively. Feed restriction and RFI rank caused distinct serum metabolome profiles, whereby
restrictive feeding also increased the blood lymphocyte proportion. Most importantly, 10 amino
acids were associated with RFI rank in birds, whereas restrictive feeding affected almost all detected
lysophosphatidylcholines, with 3 being higher and 6 being lower in restrictively compared to ad
libitum fed chickens. As indicated by relevance networking, isoleucine, lysine, valine, histidine, and
ornithine were the most discriminant for high RFI, whereas 3 biogenic amines (carnosine, putrescine,
and spermidine) and 3 diacyl-glycerophospholipids (38:4, 38:5, and 40:5) positively correlated with
feed intake and body weight gain, respectively. Only for taurine, feed intake mostly explained
the RFI-associated variation, whereas for most metabolites, other host physiological factors played
a greater role for the RFI-associated differences, and was potentially related to insulin-signaling,
phospholipase A2, and arachidonic acid metabolism. Alterations in the hepatic synthesis of long-chain
fatty acids and the need for precursors for gluconeogenesis due to varying energy demand may
explain the marked differences in serum metabolite profiles in ad libitum and restrictively fed birds.This project (ECO-FCE) has received funding from the European Union’s Seventh Framework
Programme for research, technological development, and demonstration under grant agreement no. 311794
Antimicrobial resistance (AMR): significance to food quality and safety
Get PDFPublication history: Accepted - 28 February 2019; Published online - 9 April 2020.Antibiotic resistance presents a significant challenge to clinical, veterinary, and plant health and is
now recognized by the World Health Organization (WHO) as a major emerging problem of global
significance. As yet, there have been no successful discoveries of classes of novel antibiotics since
1987. There is an antibiotic discovery void, and it is now widely acknowledged that there is an
urgent need for the development of novel antimicrobial agents. For economic reasons, many of the
largest pharmaceutical companies have abandoned the antibiotic field, and research conducted by
academia was scaled back due to funding cuts following the economic crisis. A post-antibiotic era—
in which common infections and minor injuries can kill—far from being an apocalyptic fantasy, is
indeed a very real possibility for the 21st century.DWN thanks Professors James Dooley and Ibrahim Banat at Ulster University
for critical comments. The Department of Agriculture, Environment and Rural
Affairs (DAERA) is gratefully acknowledged for facilitating this literature
review process through an Evidence and Innovation project 16/3/11 (activity
48125)
How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal
Get PDFPublication history: Accepted - 23 August 2019, Published Online - 30 August 2019, Published - 3 January 2020There is growing international interest in better managing soils to increase soil organic carbon (SOC) content to contribute to climate change mitigation, to enhance resilience to climate change and to underpin food security, through initiatives such as international ‘4p1000’ initiative and the FAO's Global assessment of SOC sequestration potential (GSOCseq) programme. Since SOC content of soils cannot be easily measured, a key barrier to implementing programmes to increase SOC at large scale, is the need for credible and reliable measurement/monitoring, reporting and verification (MRV) platforms, both for national reporting and for emissions trading. Without such platforms, investments could be considered risky. In this paper, we review methods and challenges of measuring SOC change directly in soils, before examining some recent novel developments that show promise for quantifying SOC. We describe how repeat soil surveys are used to estimate changes in SOC over time, and how long‐term experiments and space‐for‐time substitution sites can serve as sources of knowledge and can be used to test models, and as potential benchmark sites in global frameworks to estimate SOC change. We briefly consider models that can be used to simulate and project change in SOC and examine the MRV platforms for SOC change already in use in various countries/regions. In the final section, we bring together the various components described in this review, to describe a new vision for a global framework for MRV of SOC change, to support national and international initiatives seeking to effect change in the way we manage our soils.AGRISOST‐CM,Grant/AwardNumber:S2018/BAA‐4330;MinisteriodeEconomiayCompetitividad,Grant/AwardNumber:AGL2017‐84529‐C3‐1‐R;NUEVA;GlobalResearchAllianceonAgriculturalGreenhouseGases;REMEDIA;DanishMinistryofClimate,EnergyandUtilities,Grant/AwardNumber:SINKS2;NewZealandAgriculturalGreenhouseGasResearchCentre;EuropeanUnion,Grant/AwardNumber:774378;DEVIL,Grant/AwardNumber:NE/M021327/1;Soils‐R‐GRREAT,Grant/AwardNumber:NE/P019455/1;CGIARTrustFund;UKER
Methodological fallacies and perceptions of rural disparity: How rural proofing addresses real versus abstract needs
Get PDFPublication history: Accepted - 11 December 2018; Published online - 20 December 2018; Published - 1 May 2019.In 2016, the EU committed to 'rural proofing' its policies. Rural proofing has now become a priority across Europe. Prior to this, rural proofing or mainstreaming, the reviewing of universal policies to ensure comparable treatment of rural areas, was relatively unique to England and Northern Ireland. The first case of legislating rural proofing has occurred with The Rural Needs Act (Northern Ireland) 2016. Qualitative data was collected from civil and public servants with experience of pre-legislative 'rural proofing', as well as those facing new responsibilities under the Act. Additional data was obtained from key informants active in agricultural, environmental, and rural organisations. Several key findings emerge, all underpinned by a central issue: that the approach entirely stands on an assumption of rural disadvantage, the nature of which is never articulated. We argue that this is not driven by a lack of evidence, but by a more fundamental problem: the pervasiveness of viewing rural issues through a lens tinted by methodological fallacies. Failure to correct for these weaknesses by means of a dynamic theory of rural leads to flawed policy, because it is designed to treat disparity rather than accommodate diversity. In other words, it is premised on a binary of urban/rural. The findings of this research will inform the development of rural proofing policies going forward.This paper is based on research funded by the Northern Ireland Department of Agricultural and Rural Development Department of Agriculture, Environment and Rural Affairs (Evidence and Innovation Project Number 15/2/02)
Forensic microbiology reveals that Neisseria animaloris infections in harbour porpoises follow traumatic injuries by grey seals
Get PDFPublication history: Accepted – 20 September 2019; Published online – 11 October 2019Neisseria animaloris is considered to be a commensal of the canine and feline oral cavities. It is able to cause systemic infections in animals as well as humans, usually after a biting trauma has occurred. We recovered N. animaloris from chronically inflamed bite wounds on pectoral fins and tailstocks, from lungs and other internal organs of eight harbour porpoises. Gross and histopathological evidence suggest that fatal disseminated N. animaloris infections had occurred due to traumatic injury from grey seals. We therefore conclude that these porpoises survived a grey seal predatory attack, with the bite lesions representing the subsequent portal of entry for bacteria to infect the animals causing abscesses in multiple tissues, and eventually death. We demonstrate that forensic microbiology provides a useful tool for linking a perpetrator to its victim. Moreover, N. animaloris should be added to the list of potential zoonotic bacteria following interactions with seals, as the finding of systemic transfer to the lungs and other tissues of the harbour porpoises may suggest a potential to do likewise in humans.The Scottish Marine Animal Stranding Scheme receives financial support from the Scottish Government
Marine Directorate and the UK Department of Environment, Farming and Rural Afairs (Defra). Bacterial
characterisation work at APHA performed in this study was funded by the UK Department of Environment,
Farming and Rural Afairs (Defra) under programme CR2001A. Necropsies conducted on English stranded
porpoises in this study were carried out under the aegis of the Cetacean Strandings Investigation Programme,
which is co-funded by Defra and the Devolved Governments of Scotland and Wales. Moredun Research Institute
receives funding via Rural and Environment Science and Analytical Services (RESAS) division of the Scottish
Government. Post mortem research on harbour porpoises in the Netherlands is commissioned by the Dutch
Ministry of Agriculture, Nature and Food Quality (2008–2015 under project reference number 140000353; 2016
and 2017 under project reference number WOT-04-009-045). We are grateful for the help of Paulien Bunskoek,
Tierry Jauniaux, Marco Snijders and Stiching SOS Dolfjn in the stranding events of the two cases examined at
Utrecht University; for Sjoukje Hiemstra for her assistance at the necropsy of case UT692 and for Robert Reid for
his help with the necropsy on one of the Scottish cases
Variation in Mycobacterium bovis genetic richness suggests that inwards cattle movements are a more important source of infection in beef herds than in dairy herds
Get PDFPublication history: Accepted - 25 June 2019; Published online - July 2019Background
We used genetic Multi-Locus VNTR Analysis (MLVA) data gathered from surveillance efforts to better understand the ongoing bovine tuberculosis (bTB) epidemic in Northern Irish cattle herds. We modelled the factors associated with Mycobacterium bovis MLVA genotype richness at three analytical scales; breakdown level, herd level, and patch level, and compared the results between dairy and non-dairy production types.
Results
In 83% of breakdowns and in 63% of herds, a single MLVA genotype was isolated. Five or more MLVA genotypes were found in less than 3 % of herds. Herd size and the total number of reactors were important explanatory variables, suggesting that increasing MLVA genotype richness was positively related to increases in the number of host animals. Despite their smaller relative size, however, the highest MLVA genotype richness values were observed in non-dairy herds. Increasing inwards cattle movements were important positive predictors of MLVA genotype richness, but mainly in non-dairy settings.
Conclusions
The principal finding is that low MLVA genotype richness indicates that small-scale epidemics, e.g. wildlife, contiguous farms, and within-herd recrudescence, are important routes of M. bovis infection in cattle herds. We hypothesise that these mechanisms will maintain, but may not explicitly increase, MLVA genotype richness. The presence of elevated MLVA richness is relatively rare and likely indicates beef fattening enterprises, which purchase cattle from over long distances. Cattle movements were furthermore an important predictor of MLVA genotype richness in non-dairy herds, but not in dairy herds; this may represent reduced cattle purchasing levels in dairy enterprises, compared to beef. These observations allude to the relative contribution of different routes of bTB infection between production types; we posit that infection associated with local factors may be more evident in dairy herds than beef herds, however in beef herds, inwards movements offer additional opportunities for introducing M. bovis into the herd
Spotting the pests of tomorrow—Sampling designs for detection of species associations with woody plants
Get PDFPublication history: Accepted - 1 July 2019, Published - 4 August 2019.Aim
Early warning against potentially harmful organisms of woody plant species can be achieved by sampling sentinel plants in exporting countries. However, it is unclear where sentinel plants can best be located, and how many samples are required and when and how often sampling optimally should take place for the adequate assessment of the biodiversity associated with the target plant species. We aimed to review spatial and temporal factors affecting associate biodiversity of single woody plant species and to develop guidance for the design of global biodiversity sampling studies.
Location
Worldwide.
Taxon
Insects and Fungi.
Methods
Literature about factors affecting the diversity of insects and fungi in association with single plant species on global, regional, local and different temporal scales was reviewed. Case studies of insect and fungal diversity, primarily collected on single plant species, and the cost of collecting and analysing samples from locations around the world were analysed.
Results
The review of the literature illustrated various factors affecting diversity, and the case studies allowed quantification of the relative impact of some spatial, temporal and financial aspects on captured biodiversity and, thus, illustrate the need to consider all possible factors that may affect the result of the sampling when deciding on a sampling design.
Main conclusions
Our study illustrates the factors that should be considered when deciding on the location and timing of sampling for sentinel plants, which is important because of the trade‐off between the number of samples and sampling locations needed to detect many of the species which may be potential pests, and the cost of (repeated) sampling in many locations. Decisions about the sampling design must be based on the objective of the sampling, but our recommendations apply irrespective of the targeted plant species or country.EuropeanCooperationinScienceandTechnology,Grant/AwardNumber:FP1401;SwissStateSecretariatforScience,EducationandResearchc,Grant/AwardNumber:C15.008