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Improving the predictive capability of benthic species distribution models by incorporating oceanographic data – Towards holistic ecological modelling of a submarine canyon
Get PDFPublication history: Accepted - 17 April 2020; Published online - 21 April 2020Submarine canyons are associated with increased biodiversity, including cold-water coral (CWC) colonies and reefs which are features of high conservation value that are under increasing anthropogenic pressure. Effective spatial management and conservation of these features requires accurate distribution maps and a deeper understanding of the processes that generate the observed distribution patterns. Predictive distribution modelling offers a powerful tool in the deep sea, where surveys are constrained by cost and technological capabilities. To date, predictive distribution modelling in canyons has focussed on integrating groundtruthed acoustically acquired datasets as proxies for environmental variables thought to influence faunal patterns. Physical oceanography is known to influence faunal patterns but has rarely been explicitly included in predictive distribution models of canyon fauna, thereby omitting key information required to adequately capture the species-environment relationships that form the basis of predictive distribution modelling. In this study, acoustic, oceanographic and biological datasets were integrated to undertake high-resolution predictions of benthic megafaunal diversity and CWC distribution within Whittard Canyon, North-East Atlantic. The main aim was to investigate which environmental variables best predict faunal patterns in canyons and to assess whether including oceanographic data improves predictive modelling. General additive models, random forests and boosted regression trees were used to build predictive maps for CWC occurrence, megafaunal abundance, species richness and biodiversity. To provide more robust predictions, ensemble techniques that summarise the variation in predictions and uncertainties between modelling approaches were applied to build final maps. Model performance improved with the inclusion of oceanographic data. Ensemble maps identified areas of elevated current speed that coincided with steep ridges and escarpment walls as the areas most likely to harbour CWCs and increased biodiversity, probably linked to local hydrodynamics interacting with topography to concentrate food resources. This study shows how incorporating oceanographic data into canyon models can broaden our understanding of processes generating faunal patterns and improve the mapping of features of conservation, supporting effective procedures for spatial ecosystem management.This work was funded by the NERC MAREMAP programme, the ERC CODEMAP project (Grant no 258482), the EC FP7 IP HERMIONE, DEFRA and the NERC CLASS programme (Grant No NE/R015953/1). Tabitha Pearman is a PhD student in the NERC-funded SPITFIRE Doctoral Training Programme (Grant number NE/L002531/1). Veerle Huvenne currently receives funding from the NERC CLASS programme and from the European Union’s Horizon2020 research and innovation programme iAtlantic project (grant agreement No 818123)
Approaches to herbicide (MCPA) pollution mitigation in drinking water source catchments using enhanced space and time monitoring
Get PDFPublication history: Accepted - 30 September 2020; Published online - 8 October 2020Freshwater occurrences of the selective acid herbicide 2-methyl-4-chloro-phenoxyacetic acid (MCPA) are an ongoing regulatory and financial issue for water utility industries as the number and magnitude of detections increase, particularly in surface water catchments. Assessments for mitigating pesticide pollution in catchments used as drinking water sources require a combination of catchment-based and water treatment solutions, but approaches are limited by a lack of empirical data. In this study, an enhanced spatial (11 locations) and temporal (7-hourly to daily sampling) monitoring approach was employed to address these issues in an exemplar surface water source catchment (384 km2). The spatial sampling revealed that MCPA was widespread, with occurrences above the 0.1 μg L−1 threshold for a single pesticide being highly positively correlated to sub-catchments with higher proportions of ‘Improved Grassland’ land use (r = 0.84). These data provide a strong foundation for targeting catchment-based mitigation solutions and also add to the debate on the ecosystems services provided by such catchments. Additionally, of the 999 temporal samples taken over 12 months from the catchment outlet, 25% were above the drinking water threshold of 0.1 μg L−1. This prevalence of high concentrations presents costly problems for source water treatment. Using these data, abstraction shutdowns were simulated for five scenarios using hydrometeorological data to explore the potential to avoid intake of high MCPA concentrations. The scenarios stopped abstraction for 4.2–9.3% of the April–October period and reduced intake of water containing over 0.1 μg L−1 of MCPA by 16–31%. This represents an important development for real-time proxy assessments for water abstraction in the absence of more direct pesticide monitoring data.This work was funded by the Source to Tap project (project reference IVA5018 – www.sourcetotap.eu). The Source to Tap project is supported by the European Union's INTERREG VA Programme, managed by the Special EU Programmes Body (SEUPB)
Challenges and Opportunities for Management of Crop and Tree Diseases in Northern Ireland
Get PDFPublication history: Accepted - 22 October 2020; Published online - 24 October 2020.Phytopathogens have beleaguered the island of Ireland since the 19th century great famine caused by the potato blight
oomycete, Phytophthora infestans and in recent times by cohorts of serious bacterial wilt diseases such as Erwinia,
Dickeya, Ralstonia, and fungal wilt diseases predominantly caused by saprophyte fungi (e.g. Fusarium oxysporum, Pythium,
Rhizoctonia) have all shown their growing resistance to various conventional chemical control agents, and create
enormous impact on sustainable agriculture, further exacerbated by global climate change pressures. The plant health
outlook in Northern Ireland has further been tested by emergent Europe wide agro-forestry related diseases including
the recent broad host insect vector-borne Xanthamonas bacterial phytopathogen Xylella fastidiosa that can affect a wide
array of ornamental, arable crops and tree species alike. This mini-review focuses on potential alternative plant extracts
and microbial sources as agents broadly known as biostimulants for not only their growth promotion via plant and soil
nutrient management but also controlling phytopathogens in Northern Ireland. The multi-actor approach comprising
stake holders, plant health policy makers, farmers, plant health advisors, researchers, knowledge transfer centres will be
the key drivers for an effective data input and sustainable plant health. Integration of precision farming with latest information
and communications technology (ICT), advanced automation for need based/site-specific use of biostimulants to
combat biotic and abiotic stress, on-field plant pathogen remote sensors and their extended new tool applications for
soil and phytosanitory inspections at port of entry points are some of the overarching comprehensive strategies planned
for the future.The authors gratefully acknowledge the Department of
Agriculture, Environment and Rural Affairs (DAERA), Northern
Ireland for facilitating this literature review process through
an Evidence and Innovation project 16/3/11, (activity 48125) and the European Commission funding via EU FP7-BIOFECTOR
Grant (Agreement No. 312117), administered at Agri-Food &
Biosciences Institute (AFBI), (www.afbini.gov.uk) to support
plant health research
Methods and approaches to advance soil macroecology
Get PDFPublication history: Accepted - 17 June 2020; Published online - 2 August 2020Motivation and aim
Soil biodiversity is central to ecosystem function and services. It represents most of terrestrial biodiversity and at least a quarter of all biodiversity on Earth. Yet, research into broad, generalizable spatial and temporal patterns of soil biota has been limited compared to aboveground systems due to complexities of the soil system. We review the literature and identify key considerations necessary to expand soil macroecology beyond the recent surge of global maps of soil taxa, so that we can gain greater insight into the mechanisms and processes shaping soil biodiversity. We focus primarily on three groups of soil taxa (earthworms, mycorrhizal fungi and soil bacteria) that represent a range of body sizes and ecologies, and, therefore, interact with their environment at different spatial scales.
Results
The complexities of soil, including fine‐scale heterogeneity, 3‐D habitat structure, difficulties with taxonomic delimitation, and the wide‐ranging ecologies of its inhabitants, require the classical macroecological toolbox to be expanded to consider novel sampling, molecular identification, functional approaches, environmental variables, and modelling techniques.
Main conclusions
Soil provides a complex system within which to apply macroecological research, yet, it is this property that itself makes soil macroecology a field ripe for innovative methodologies and approaches. To achieve this, soil‐specific data, spatio‐temporal, biotic, and abiotic considerations are necessary at all stages of research, from sampling design to statistical analyses. Insights into whole ecosystems and new approaches to link genes, functions and diversity across spatial and temporal scales, alongside methodologies already applied in aboveground macroecology, invasion ecology and aquatic ecology, will facilitate the investigation of macroecological processes in soil biota, which is key to understanding the link between biodiversity and ecosystem functioning in terrestrial ecosystems.Funding Information
British Ecological Society Macroecology Special Interest Group
H2020 Marie Skłodowska‐Curie Actions. Grant Number: MSCA‐IF‐2014‐GF‐660378
FP7 People: Marie‐Curie Actions. Grant Number: EC FP7 ‐ 631399 ‐ SENSE1100
Royal Entomological Society
Department for the Economy, Northern Ireland
Suomen Akatemia. Grant Number: 285882
Natural Environment Research Council. Grant Number: NE/M017036/1
British Ecological Society. Grant Number: 285882
Academy of Finland
FP7. Grant Numbers: M017036, 15, 2881
Science Foundation Ireland. Grant Number: 15/IA/288
Co-infection status of novel parvovirus’s (PPV2 to 4) with porcine circovirus 2 in porcine respiratory disease complex and porcine circovirus-associated disease from 1997 to 2012
Get PDFPublication history: Accepted - 12 September 2020; Published online - 18 October 2020.As global pig health diseases, porcine respiratory disease complex (PRDC) and porcine
circovirus-associated disease (PCVAD) generate substantial economic losses despite
pigs been vaccinated against the primary causative virus, highlighting the importance
of understanding virome interactions and specifically co-factor infections. Established
primary endemic pathogens for PRDC include porcine circovirus 2 (PCV2), porcine
reproductive and respiratory syndrome virus (PRRSv) and swine influenza virus (SIV),
and PCV2 aetiology in interaction with other co-infecting viruses can result in PCVAD.
Porcine parvovirus (PPV) 1 is a well-characterized virus with an available vaccine preventing
reproductive failure in sows. However, whilst novel PPV 2 to 7 viruses have been
identified since 2001, their viral pathogenic potential in clinical and subclinical disease
remains to be determined. Therefore, this study has sought to develop a better understanding
of their potential role as associated co-infections in PRDC and PCVAD by examining
archival samples for the presence of PCV2 and the novel parvoviruses PPV2-4
from clinically diseased pigs across production age stages. Epidemiologically, the novel
PPV2 was found to be the most prevalent within the fattener age group with PPV2-4
statistically associated with pig respiratory disease and enteric ulcers. Additionally, statistical
modelling by latent class analysis (LCA) on veterinary pathology scored pigs found
a clustering co-factor association between PPV2 and PCV2, suggesting the novel PPV
may be involved in PRDC and PCVAD. Phylogenetic analysis of novel PPVs revealed the
PPV2 capsid evolution to be diverged from the original strains with a low nucleotide homology
of 88%–96% between two distinct clades. These findings determine that novel
PPV 2–4 viruses are statistically associated as co-infectors in a diseased pig population,
and significantly detected PPV2 clustering co-infection frequency with PCV2 in PRDC
and PCVAD diseased pigs through LCA analysis
The Expression of Terpenoid Indole Alkaloid (TIAs) Pathway Genes in Catharanthus roseus in Response to Salicylic Acid treatment
Get PDFPublication history: Accepted - 28th August 2020; Published online - 4th September.Vinblastine and vincristine are two important anti-cancer drugs that are synthesized by the Terpenoid Indole Alkaloids (TIAs) pathway in periwinkle (Catharanthus roseus). The major challenge in the pharmaceutical industry is the low production rate of these alkaloids. TIA pathway is affected by elicitors, such as salicylic acid (SA). This study aimed to investigate the expression pattern of some key genes in TIAs pathway under SA treatment. Foliar application of SA (0.01 and 0.1 mM) was used and leaves samples were taken at 0, 12, 18, 24 and 48 hours after the treatment. qRT-PCR was used to investigate the expression pattern of Chorismate mutase (Cm), Tryptophan decarboxylase (Tdc), Geraniol-10-hydroxylase (G10h), Secologanin synthase (Sls), Strictosidine synthase (Str), Desacetoxyvindoline-4-hydroxylase (D4h) and Deacetylvindoline-4-O-acetyltransferase (Dat) genes, following the SA treatment. The results of this experiment showed that transcript levels of Tdc, G10h, Sls, Str, D4h and Dat genes were significantly up-regulated in both SA concentration treatments. Furthermore, the highest transcript levels of Dat was observed after 48 hours of the SA treatments. qRT-PCR results suggests that SA induces transcription of major genes involved in alkaloids biosynthesis in Catharanthus roseus. It can be concluded that up-regulation of Tdc, G10h, Sls, Str, D4h and Dat genes can result in a higher production rate of vinblastine and vincristine alkaloids
Unraveling the impact of variable external input use on the cost efficiency of dairy farms in Europe
Get PDFPublication history: Accepted - 11 October 2020; Published online - 12 October 2020There has been a global shift towards intensification in the dairy sector in recent years which may have considerable impact on the cost efficiency and economic returns of farms. Considering this, the goal of this study is to offer an empirical analysis of the effect of variable external input use on dairy farms. Employing a novel Activity Analysis Model (AAM), the study analysis was conducted in two distinct but complementary steps. In the first step, we discriminated two technologies (low and high inputs) which allow us to classify a sample of dairy farms according to their level of intensification, while in the second step, we evaluated two cost efficient frontiers instead of assessing individual farm inefficiency scores. With this approach, we explore different technologies within a sample of EU dairy farms. Our results, on average, shows that agricultural practices using low inputs dominates the high input ones for farms operating on a large scale while a slight dominance of high input over low inputs exist for small scale farmers. While we reckon that low input can be cost competitive with their high input counterparts, we also note that regional differences do exist. Thus, showing that the significant gap between the two discriminating frontiers depends not only on farm size but also on farm region. We found that increased cost efficiency can reduce the negative environmental impact of EU-dairy farms while simultaneously reducing farmers’ production costs. The results of the study can therefore provide a direction to policymakers and dairy farmers alike as regards the efficient use of external inputs which may consequently reduce environmental burdens associated with dairy farms.This work was supported by the European Commission project Sustainable Organic and LI Dairying (SOLID) funded Framework 7 Contract no. 266367
Evidence and perception of phosphorus loss risk factors in farmyards
Get PDFPublication history: Accepted - 18 September 2020; Published online - 14 October 2020.Farmyards present potential point sources of phosphorus loss to watercourses, affecting their 16 ecological quality and attainment of environmental goals. Unlike many relatively simple point sources, 17 farmyards are complex sub-systems within the wider agricultural setting, including individual runoff, 18 management and infrastructure factors which influence the risk (likelihood and magnitude) of 19 phosphorus loss. Comparison across these factors is confounded by heterogeneity in farmyard design 20 and management, however, weighting of individual factors will support estimation of the relative 21 riskiness of farmyards. This will allow identification of appropriate mitigation measures and evaluation 22 of cost-benefit ratios. The aim of this study is to evaluate the riskiness of runoff, management, and 23 infrastructure factors on phosphorus loss from farmyards to water, using expert opinion and to 24 evaluate whether those estimates are supported by the literature. A survey of research, advisory and 25 policy stakeholders was conducted (147 respondents) in which individuals rated the importance of 26 individual factors from 0 (having no impact) to 10 (having critical impact) on phosphorus loss from 27 farmyards. The most highly ranked factors were within the infrastructure category, followed by runoff 28 and finally management factors. Factors relating to silage effluent and slurry storage were assigned 29 the greatest risk (≥8.4). Runoff factors were also high risk but may be difficult to mitigate compared 30 to infrastructure. Management factors were rated lower by all stakeholder groups but may offer low 31 cost options to offset more intransigent risks. High consensus was observed between stakeholder 32 groups, with significant differences in risk ratings for only 8 out of 29 individual factors.This research was funded by the Interreg VA 386 CatchmentCARE project
Farm Diversification: Drivers, Barriers and Future Growth Potential
Get PDFPublication history: Accepted - 24 October 2020; Published online - 21 December 2020Family farm businesses throughout Europe are facing new economic, environmental and social challenges. In order to deliver a more resilient primary agriculture sector national and regional governments are identifying mechanisms to support farm businesses to adapt to these changing demands. This qualitative study, explored the drivers of and barriers to farm diversification and its potential as a strategy to make farms more sustainable. Although there are a range of farm diversification strategies being pursued regionally, farm diversification is under exploited as an opportunity to achieve additional household income. Areas considered to have the potential for growth included, agri-tourism, care services (including social farming), professional services and developing artisan food products. Beyond the need to generate new income sources, creating employment for other family members was considered an important motivation. Those factors identified as constraints to diversification included internet access, planning, business rates, support around skills development, networks and a farmer’s own fear of failure. For smaller scale, family farm businesses located in more marginal areas, there is a need to identify a range of policy levers which support local farming systems and capture the multifaceted nature of the products and services that these farm businesses could provide and may be asked to deliver in the future
Honey bee colony winter loss rates for 35 countries participating in the COLOSS survey for winter 2018–2019, and the effects of a new queen on the risk of colony winter loss.
Get PDFPublication history: Accepted - 14 July 2020; Published Online - 11 August 2020This article presents managed honey bee colony loss rates over winter 2018/19 resulting from using the standardised
COLOSS questionnaire in 35 countries (31 in Europe). In total, 28,629 beekeepers supplying valid loss data wintered
738,233 colonies, and reported 29,912 (4.1%, 95% confidence interval (CI) 4.0–4.1%) colonies with unsolvable queen
problems, 79,146 (10.7%, 95% CI 10.5–10.9%) dead colonies after winter and 13,895 colonies (1.9%, 95% CI 1.8–2.0%)
lost through natural disaster. This gave an overall colony winter loss rate of 16.7% (95% CI 16.4–16.9%), varying greatly
between countries, from 5.8% to 32.0%. We modelled the risk of loss as a dead/empty colony or from unresolvable
queen problems, and found that, overall, larger beekeeping operations with more than 150 colonies experienced significantly lower losses (p < 0.001), consistent with earlier studies. Additionally, beekeepers included in this survey who did
not migrate their colonies at least once in 2018 had significantly lower losses than those migrating (p < 0.001). The percentage of new queens from 2018 in wintered colonies was also examined as a potential risk factor. The percentage of
colonies going into winter with a new queen was estimated as 55.0% over all countries. Higher percentages of young
queens corresponded to lower overall losses (excluding losses from natural disaster), but also lower losses from unresolvable queen problems, and lower losses from winter mortality (p < 0.001). Detailed results for each country and
overall are given in a table, and a map shows relative risks of winter loss at regional level