The AFBI Repository

The Agri-Food and Biosciences Institute Repository collects, preserves, and makes freely available research outputs and related documents created by AFBI researchers, including peer-reviewed articles and conference papers. Where material has already been published it is made available subject to the open-access policies of the original publishers. About AFBI



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Spatial and temporal environmental heterogeneity induced by internal tides influences faunal patterns on vertical walls within a submarine canyon
(Frontiers Media, 2023-03-29) Pearman, Tabitha R. R.; Robert, Katleen; Callaway, Alexander; Hall, Rob A.; Mienis, Furu; Huvenne, Veerle A. I.
Vertical walls of submarine canyons represent features of high conservation value that can provide natural areas of protection for vulnerable marine ecosystems under increasing anthropogenic pressure from deep-sea trawling. Wall assemblages are spatially heterogeneous, attributed to the high environmental heterogeneity over short spatial scales that is a typical feature of canyons. Effective management and conservation of these assemblages requires a deeper understanding of the processes that affect faunal distribution patterns. Canyons are recognised as sites of intensified hydrodynamic regimes, with focused internal tides enhancing near-bed currents, turbulent mixing and nepheloid layer production, which influence faunal distribution patterns. Faunal patterns also respond to broad-scale hydrodynamics and gradients in water mass properties (e.g. temperature, salinity, dissolved oxygen concentration). Oscillating internal tidal currents can advect such gradients, both vertically and horizontally along a canyon's walls. Here we take an interdisciplinary approach using biological, hydrodynamic and bathymetry-derived datasets to undertake a high-resolution analysis of a subset of wall assemblages within Whittard Canyon, North-East Atlantic. We investigate if, and to what extent, patterns in diversity and epibenthic assemblages on deep-sea canyon walls can be explained by spatial and temporal variability induced by internal tides. Vertical displacement of water mass properties by the internal tide was calculated from autonomous ocean glider and shipboard CTD observations. Spatial patterns in faunal assemblage structure were determined by cluster analysis and non-metric Multi-Dimensional Scaling plots. Canonical Redundancy Analysis and Generalised Linear Models were then used to explore relationships between faunal diversity and assemblage structure and a variety of environmental variables. Our results support the hypothesis that internal tides influence spatial heterogeneity in wall faunal diversity and assemblages by generating both spatial and temporal gradients in hydrodynamic properties and consequently likely food supply.
Initial ecological change in plant and arthropod community composition after wildfires in designated areas of upland peatlands
(Wiley, 2023-02-11) Kelly, Ruth; Montgomery, W. Ian; Reid, Neil
Wildfires are an increasing concern due to rising temperatures and incidence of droughts associated with changing climate, poor land management, and direct human interference. Most studies of the impact of fire on temperate heathland and bog examined the consequences of controlled or prescribed burning. Less is known about the impacts of uncontrolled wildfires on sites designated for their conservation value. We examined the initial impact and short-term trajectory (3.5 years) of cool temperate peatland plant and arthropod communities on designated upland sites in Northern Ireland following wildfires, that is, unplanned with respect to where and when they occur, severity, and duration. These near simultaneous wildfires were often due to a failure to control prescribed burns. Wildfires were associated with a loss of blanket bog and heath indicator species. Broad vegetation groups showed initial recovery characterized by a decrease in bare ground and increasing cover of shrub species and bryophytes. However, at a species level, Sphagnum spp and bryophyte communities, which are central to peatland ecosystem functioning, showed no sign of recovery to prefire composition. Rather, bryophyte communities became more divergent over the course of the study and were mainly characterized by increased abundance of the alien pioneer acrocarp Campylopus introflexus. Similarly, composition of arthropod communities (ground beetles and spiders) differed between burnt and unburnt areas and showed no evidence of a return to species composition in unburnt areas. The nationally rare beetle Carabus nitens was more common in the aftermath of wildfire. Synthesis. Whilst, long-term recovery was not investigated, these short-term changes suggest enduring detrimental impacts on the distinctive communities associated with peatlands, primarily through the loss of Sphagnum spp., affecting ecosystem services such as carbon sequestration and water and soil retention. It may not be possible to restore exact prefire species composition of plant and animal communities. We suggest a precautionary approach involving management of upland vegetation, public education, and vigilance, to prevent further wildfires and protect these key upland habitats.
Interlaboratory Evaluation of Multiple LC–MS/MS Methods and a Commercial ELISA Method for Determination of Tetrodotoxin in Oysters and Mussels
(Oxford Univerity Press, 2023-01-06) Turner, Andrew D.; Dean, Karl J.; Dhanji-Rapkova, Monika; Dall’Ara, Sonia; Pino, Florella; McVey, Claire; Haughey, Simon; Logan, Natasha; Elliott, Christopher; Gago-Martinez, Ana; Leao, Jose Manuel; Giraldez, Jorge; Gibbs, Ryan; Thomas, Krista; Perez-Calderon, Ruth; Faulkner, Dermot; McEneny, Hugh; Savar, Veronique; Reveillon, Damien; Hess, Philipp; Arevalo, Fabiola; Lamas, J. Pablo; Cagide, Eva; Alvarez, Mercedes; Antelo, Alvaro; Klijnstra, Mirjam D.; Oplatowska-Stachowiak, Michalina; Kleintjens, Tim; Sajic, Nermin; Boundy, Michael J.; Maskrey, Benjamin H.; Harwood, D. Tim; Gonzalez Jartın, Jesus M.; Alfonso, Amparo; Botana, Luis
Background Given the recent detection of tetrodotoxin (TTX) in bivalve molluscs but the absence of a full collaborative validation study for TTX determination in a large number of shellfish samples, interlaboratory assessment of method performance was required to better understand current capabilities for accurate and reproducible TTX quantitation using chemical and immunoassay methods. Objective The aim was to conduct an interlaboratory study with multiple laboratories, using results to assess method performance and acceptability of different TTX testing methods. Methods Homogenous and stable mussel and oyster materials were assessed by participants using a range of published and in-house detection methods to determine mean TTX concentrations. Data were used to calculate recoveries, repeatability, and reproducibility, together with participant acceptability z-scores. Results Method performance characteristics were good, showing excellent sensitivity, recovery, and repeatability. Acceptable reproducibility was evidenced by HorRat values for all LC–MS/MS and ELISA methods being less than the 2.0 limit of acceptability. Method differences between the LC–MS/MS participants did not result in statistically different results. Method performance characteristics compared well with previously published single-laboratory validated methods and no statistical difference was found in results returned by ELISA in comparison with LC–MS/MS. Conclusion The results from this study demonstrate that current LC–MS/MS methods and ELISA are on the whole capable of sensitive, accurate, and reproducible TTX quantitation in shellfish. Further work is recommended to expand the number of laboratories testing ELISA and to standardize an LC–MS/MS protocol to further improve interlaboratory precision. Highlights Multiple mass spectrometric methods and a commercial ELISA have been successfully assessed through an interlaboratory study, demonstrating excellent performance.
Biological and synthetic surfactant exposure increases antimicrobial gene occurrence in a freshwater mixed microbial biofilm environment
(2023-03-17) Gill, Stephanie P.; Snelling, William J.; Dooley, James S. G.; Ternan, Nigel G.; Banat, Ibrahim M.; Arnscheidt, Joerg; Hunter, Billy
Aquatic habitats are particularly susceptible to chemical pollution, such as antimicrobials, from domestic, agricultural, and industrial sources. This has led to the rapid increase of antimicrobial resistance (AMR) gene prevalence. Alternate approaches to counteract pathogenic bacteria are in development including synthetic and biological surfactants such as sodium dodecyl sulfate (SDS) and rhamnolipids. In the aquatic environment, these surfactants may be present as pollutants with the potential to affect biofilm formation and AMR gene occurrence. We tested the effects of rhamnolipid and SDS on aquatic biofilms in a freshwater stream in Northern Ireland. We grew biofilms on contaminant exposure substrates deployed within the stream over 4 weeks. We then extracted DNA and carried out shotgun sequencing using a MinION portable sequencer to determine microbial community composition, with 16S rRNA analyses (64,678 classifiable reads identified), and AMR gene occurrence (81 instances of AMR genes over 9 AMR gene classes) through a metagenomic analysis. There were no significant changes in community composition within all systems; however, biofilm exposed to rhamnolipid had a greater number of unique taxa as compared to SDS treatments and controls. AMR gene prevalence was higher in surfactant-treated biofilms, although not significant, with biofilm exposed to rhamnolipids having the highest presence of AMR genes and classes compared to the control or SDS treatments. Our results suggest that the presence of rhamnolipid encourages an increase in the prevalence of AMR genes in biofilms produced in mixed-use water bodies.
Unifying approaches to Functional Marine Connectivity for improved marine resource management: the European SEA-UNICORN COST Action
(Pensoft Publishers, 2022-12-22) Darnaude, Audrey M.; Arnaud-Haond, Sophie; Hunter, Ewan; Gaggiotti, Oscar; Sturrock, Anna; Beger, Maria; Volckaert, Filip A. M.; Pérez-Ruzafa, Angel; López-López, Lucía; Tanner, Susanne E.; Turan, Cemal; Ahmet Doğdu, Servet; Katsanevakis, Stelios; Costantini, Federica
Truly 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 supported by COST (European Cooperation in Science and Technology), 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 policies.