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The spatial and temporal dynamics of sediment phosphorus attenuation and release in impacted stream catchments
No full textPublication history: Accepted - 22 September 2023; Published Online - 24 September 2023.Sediments can attenuate phosphorus (P) from overlying water and reduce trophic status in zero and first order ditches and streams. These features can be considered as intermediate mitigation features between P mobilised from land, and onward delivery to river systems, if the risk of chemical P release from sediments is minimal. However, risk assessments are rarely based on temporal scale dynamics and especially at fine scale in both sediment and water column environments. In this study, in eutrophic stream catchments, bed sediments were tested fortnightly and spatially over one year for EPC0 (to derive phosphate exchange potential—PEP) and for P across a spectrum from labile to recalcitrant fractions. At the same time stream discharge and P concentrations were measured synchronously at high frequency and resolved to 1-hour intervals and indicated high water quality pressures at all flow rates. PEP indicated spatial and temporal changes most likely caused by periods of source disconnection/reconnection and sediment mobilisation during storm events, moving from periods of high attenuation potential to near saturation. Despite these spatial and temporal changes, PEP did not indicate much potential for chemical P release from the sediments (distributing mostly below or close to zero). However, this may be a misleading risk assessment by itself as physical P release, especially of the labile bicarbonate-dithionite (B-D) P fraction of sediments, was a more dominant process mobilised during storm events reducing by up to 84 % during a succession of summer storm events. The total P and total reactive P loads monitored leaving the catchments were coincident with these changes. The specific downstream trophic effects of this episodic P release will need to be assessed in terms of its bioavailability, in combination with other more noted diffuse and point P source processes.This study was funded by the Special EU Programmes Body under EU INTERREG IIIa 20204 ‘BlackwaterTRACE’ and an Ulster University VCRS award
Unifying approaches to Functional Marine Connectivity for improved marine resource management: the European SEA-UNICORN COST Action
Get PDFPublication history: Received - 15 December 2022; Published - 22 December 2022.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.COST Action CA19107 ‘Unifying Approaches to Marine Connectivity for improved Resource Management for the Seas” (SEA-UNICORN) - https://www.cost.eu/actions/CA19107
Single Nucleotide Polymorphism Effects on Lamb Fecal Egg Count Estimated Breeding Values in Progeny-Tested Katahdin Sires
Get PDFPublication history: Accepted - 14 April 2022; Published - 3 May 2022.Estimated breeding values (EBV) for fecal egg counts (FEC) at 42–90 days of age (WFEC) and
91–150 days of age (PFEC) for 84 progeny-tested Katahdin sires were used to identify
associations of deregressed EBV with single-nucleotide polymorphisms (SNP) using 388,000
SNP with minor-allele frequencies ≥0.10 on an Illumina high-density ovine array. Associations
betweenmarkers and FEC EBVwere initially quantified by single-SNP linear regression. Effects
of linkage disequilibrium (LD) were minimized by assigning SNP to 2,535 consecutive 1-Mb
bins and focusing on the effect of the most significant SNP in each bin. Bonferroni correction
was used to define bin-based (BB) genome- and chromosome-wide significance. Six bins on
chromosome 5 achieved BB genome-wide significance for PFEC EBV, and three of those
SNP achieved chromosome-wide significance after Bonferroni correction based on the
14,530 total SNP on chromosome 5. These bins were nested within 12 consecutive bins
between 59 and 71 Mb on chromosome 5 that reached BB chromosome-wide significance.
The largest SNP effects were at 63, 67, and 70Mb, with LD among these SNP of r2 ≤ 0.2.
Regional heritability mapping (RHM) was then used to evaluate the ability of different genomic
regions to account for additive variance in FEC EBV. Chromosome-level RHM indicated that
one 500-SNP window between 65.9 and 69.9Mb accounted for significant variation in PFEC
EBV. Five additional 500-SNP windows between 59.3 and 71.6 Mb reached suggestive (p <
0.10) significance for PFEC EBV. Although previous studies rarely identified markers for
parasite resistance on chromosome 5, the IL12B gene at 68.5 Mbcodes for the p40 subunit of
both interleukins 12 and 23. Other immunoregulatory genes are also located in this region of
chromosome 5, providing opportunity for additive or associative effects.This research was funded by the USDA NIFA Organic
Agriculture Research and Extension Initiative grants no. 2016-
51300-25723 and 2010-51300-21641, and USDA Southern SARE
grant no. LS08-204
Blood and faecal biomarkers to assess dietary energy, protein and amino acid efficiency of utilization by growing and finishing pigs.
Get PDFPublication history: Accepted - 20 June 2022; Published online - 4 July 2022Background: Diet evaluation and optimization is a slow and expensive process and it is not possible to do it at a
farm level. This study aimed to use the blood serum metabolite (BSM) and faecal volatile fatty acid (VFA) profles as
potential biomarkers to identify changes in protein, amino acid and energy dietary content in growing and fnishing
pig diets at farm level.
Results: Two studies were conducted. The frst study (S1) included 20 pens of 11 pigs (87.0±4.10 kg; 18 weeks old)
assigned to 5 diets: control (C1), high or low crude protein (HP1 and LP1, respectively), and high or low net energy
(HE1 and LE1, respectively). The second study (S2) included 28 pens of 11 pigs (41.3±2.60 kg; 12 weeks old) assigned
to 7 diets: control (C2), high or low crude protein (HP2 and LP2, respectively), high or low amino acid (HA2 and LA2,
respectively), and high or low net energy (HE2 and LE2, respectively). Pigs were followed for 10 (S1) and 20 (S2) days,
and blood and faecal samples were collected at 20 (S1) and 14 (S2) weeks of age. Data were analysed using gen‑
eral linear models and receiver operating characteristic curve analysis. Urea nitrogen showed the best results as a
biomarker. Urea nitrogen was higher in pigs fed high protein diets, HP1 (13.6±0.95 mg/dL) and HP2 (11.6±0.61),
compared to those fed low protein diets, LP1 (6.0±0.95) and LP2 (5.2±0.61; P<0.001), showing good discrimination
ability (Area under the curve (AUC)=98.4 and 100%, respectively). These diferences were not observed between
diets LA2 (6.5±0.61) and HA2 (8.7±0.61; P>0.05; AUC=71.9%), which were formulated based on the ideal protein
profle but with no excess of protein. Creatinine, triglycerides, branched-chain fatty acids, albumin, propionic acid, and
cholesterol showed diferences between at least 2 diets but only in one of the studies.
Conclusions: Urea nitrogen showed high accuracy to detect excess of crude protein in growing and fnishing pig
diets. Other biomarkers like BCFA showed promising results and need to be further studied.Jordi Camp Montoro was supported by the Teagasc Walsh Scholarship Scheme grant-in-aid project Introducing new feeding programs and facilities for Irish finishing pigs ref 0415. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript
Effects of the Lipid Profile, Type 2 Diabetes and Medication on the Metabolic Syndrome—Associated Gut Microbiome
Get PDFPublication history: Accepted - 4 July 2022; Published online - 6 July 2022Metabolic syndrome (MetSyn) is a major health problem affecting approximately 25% of the worldwide population. Since the gut microbiota is highly connected to the host metabolism, several recent studies have emerged to characterize the role of the microbiome in MetSyn development and progression. To this end, our study aimed to identify the microbiome patterns which distinguish MetSyn from type 2 diabetes mellitus (T2DM). We performed 16S rRNA amplicon sequencing on a cohort of 70 individuals among which 40 were MetSyn patients. The microbiome of MetSyn patients was characterised by reduced diversity, loss of butyrate producers (Subdoligranulum, Butyricicoccus, Faecalibacterium prausnitzii) and enrichment in the relative abundance of fungal populations. We also show a link between the gut microbiome and lipid metabolism in MetSyn. Specifically, low-density lipoproteins (LDL) and high-density lipoproteins (HDL) display a positive effect on gut microbial diversity. When interrogating the signature of gut microbiota in a subgroup of patients harbouring both MetSyn and T2DM conditions, we observed a significant increase in taxa such as Bacteroides, Clostridiales, and Erysipelotrichaceae. This preliminary study shows for the first time that T2DM brings unique signatures of gut microbiota in MetSyn patients. We also highlight the impact of metformin treatment on the gut microbiota. Metformin administration was linked to changes in Prevotellaceae, Rickenellaceae, and Clostridiales. Further research focusing on the microbiome-metabolome patterns is needed to clarify the exact association of various gut microbial communities with the progression of T2DM and the occurrence of various complications in MetSyn patientsThis research was funded by UEFISCDI, project ID PN-III-P1-1.1-36PD-2019-0499, Grant number 224/2021 and C1.2.PFE-CDI.2021-587
Perspectives on water quality monitoring approaches for behavioural change research
Get PDFPublication history: Accepted - 7 June 2022; Published online - 1 July 2022This review considers enhanced approaches to river water quality monitoring in
north-western Europe following a series of study visits (11 sites in 7 countries). Based
on the evidence gathered, options were identified and evaluated for their suitability
to deliver specific water quality monitoring objectives and with a focus on effecting
behavioral change. Monitoring programs were diverse, ranging from enhanced grab
sampling and laboratory analysis to sub-hourly sampling of multiple parameters and
nutrients in autonomous high-specification, bank-side or mobile laboratories. Only one
program out of all the cases evaluated could readily identify influences that had produced
behavioral change among stakeholders. This was principally because the other programs
were focused on top-down policy change or surveillance rather than specifically focused
on influencing behavior. Nevertheless, program researchers were clear that stakeholder
engagement potential was very high and that the sites acted as important focus points
for discussion on water quality issues, and so part of a suite of tools that might ultimately
change behavior. This identifies a space where water quality monitoring solutions could
be adapted for behavioral change research.This study was funded by the Department for Agriculture Environment and Rural Affairs, Belfast (Project 17/4/07)
Case Report of Puffinosis in a Manx Shearwater (Puffinus puffinus) Suggesting Environmental Aetiology
Get PDFPublication history: Accepted - 1 December 2022; Published online - 7 December 2022Puffinosis is a disease of a range of seabirds characterised by dorsal and ventral blistering of their webbed feet, conjunctivitis, dry necrosis, leg spasticity, head shaking, loss of balance, tremors, and death. It is associated with Manx shearwaters (Puffinus puffinus), frequently affecting chicks within their underground nesting burrows. The aetiology of the disease is unclear but has been attributed to a type-2 coronavirus associated with Neotombicula mites as a potential vector. However, there is some uncertainty given potential laboratory contamination with mouse hepatitis virus and failure to fulfil Koch’s postulates, with birds injected with isolates remaining healthy. We describe a detailed case report of puffinosis in a Manx Shearwater covering necropsy, histology, bacteriology, and metagenomics including viral sequencing. We found no evidence of viral infection or parasites. Our results are consistent with an entirely environmental aetiology, with caustic faecal ammonia in damp nesting burrows causing conjunctivitis and foot dermatitis breaking the skin, allowing common soil bacteria (i.e., Flavobacterium, Staphylococcus and Serratia spp., Clostridia perfringens and Enterococcus faecalis) to cause opportunistic infection, debilitating the bird and leading to death. A similar condition (foot pad dermatitis or FPD) has been reported in broiler chickens, attributed to caustic faeces, high humidity, and poor environmental conditions during indoor rearing, preventable by adequate ventilation and husbandry. This is consistent with puffinosis being observed in Shearwater nesting burrows situated in tall, dense, vegetation (e.g., bracken Pteridium aquilinum) but rarely reported in burrows situated in well-ventilated, short coastal grasslands. This proposed environmental aetiology accounts for the disease’s non-epizootic prevalence, spatial variation within colonies, and higher frequency in chicks that are restricted to nesting burrows.Niamh Esmonde was supported by a UKRI QUADRAT Doctoral Training Programme (DTP) studentship, grant number NE/S007377/1 funded by the Natural Environment Research Council (NERC). The Agri-Food and Biosciences Institute (AFBI) funded the costs of necropsy, histology, bacteriology, parasitology, and metagenomics as part of the Queen’s–AFBI Alliance. Jignasha Patel, who conducted the metagenomics, was funded by the Research Leaders 2025 Programme cofounded by Teagasc and the European Union Horizon 2020 Research and Innovation Programme under a Marie Skłodowska-Curie grant (grant 754380). Paris Jaggers was supported by a UKRI NERC scholarship (grant NE/S007474/1)
Rabbit Haemorrhagic Disease Virus 2 (RHDV2; GI.2) in Ireland Focusing on Wild Irish Hares (Lepus timidus hibernicus): An Overview of the First Outbreaks and Contextual Review.
Get PDFPublication history: Accepted - 22 February 2022; Published online - 24 February 2022Rabbit haemorrhagic disease virus 2 (RHDV2; GI.2) is a pathogenic lagovirus that emerged in 2010, and which now has a global distribution. Outbreaks have been associated with local population declines in several lagomorph species, due to rabbit haemorrhagic disease (RHD)-associated mortality raising concerns for its potential negative impact on threatened or vulnerable wild populations. The Irish hare (Lepus timidus hibernicus) is endemic to Ireland, and is of conservation interest. The first cases of RHDV2 in Ireland were reported in domestic rabbits (Oryctolagus cuniculus) in 2016, soon followed by the first known case in a wild rabbit also in 2016, from a population reported to be experiencing high fatalities. During summer 2019, outbreaks in wild rabbits were confirmed in several locations throughout Ireland. Six cases of RHDV2 in wild hares were confirmed between July and November 2019, at four locations. Overall, 27 cases in wildlife were confirmed in 2019 on the island of Ireland, with a predominantly southern distribution. Passive surveillance suggests that the Irish hare is susceptible to lethal RHDV2 infection, and that spillover infection to hares is geographically widespread in eastern areas of Ireland at least, but there is a paucity of data on epidemiology and population impacts. A literature review on RHD impact in closely related Lepus species suggests that intraspecific transmission, spillover transmission, and variable mortality occur in hares, but there is variability in reported resistance to severe disease and mortality amongst species. Several key questions on the impact of the pathogen in Irish hares remain. Surveillance activities throughout the island of Ireland will be important in understanding the spread of infection in this novel hostThis research received no external fundin
Are stakeholders ready to transform phosphorus use in food systems? A transdisciplinary study in a livestock intensive system.
Get PDFPublication history: Accepted - 18 January 2022; Published online - 12 February 2022.Food systems worldwide are vulnerable to Phosphorus (P) supply disruptions and price fluctuations. Current P use is also highly inefficient, generating large surpluses and pollution. Global food security and aquatic ecosystems are in jeopardy if transformative action is not taken. This paper pivots from earlier (predominantly conceptual) work to develop and analyse a P transdisciplinary scenario process, assessing stakeholders potential for transformative thinking in P use in the food system. Northern Ireland, a highly livestock-intensive system, was used as case study for illustrating such process. The stakeholder engagement takes a normative stance in that it sets the explicit premise that the food system needs to be transformed and asks stakeholders to engage in a dialogue on how that transformation can be achieved. A Substance Flow Analysis of P flows and stocks was employed to construct visions for alternative futures and stimulate stakeholder discussions on system responses. These were analysed for their transformative potential using a triple-loop social learning framework. For the most part, stakeholder responses remained transitional or incremental, rather than being fundamentally transformative. The process did unveil some deeper levers that could be acted upon to move the system further along the spectrum of transformational change (e.g. changes in food markets, creation of new P markets, destocking, new types of land production and radical land use changes), providing clues of what an aspirational system could look like. Replicated and adapted elsewhere, this process can serve as diagnostics of current stakeholders thinking and potential, as well as for the identification of those deeper levers, opening up avenues to work upon for global scale transformation.This research forms part of the RephoKUs project (The role of Phosphorus in the Resilience and Sustainability of the UK food system), funded by the Global Food Security’s ‘Resilience of the UK Food System' Programme with funding from the UK’s Biotechnology and Biological Science Research Council (BBSRC), the Economic and Social Research Council (ESRC), the Natural Environment Research Council (NERC) and the Scottish Government (Grant No. BB/R005842/1
Behavioural traits of rainbow trout and brown trout may help explain their differing invasion success and impacts
Get PDFPublication history: Accepted - 11 Jaunary 2022; Published - 2 February 2022.Animal behaviour is increasingly recognised as critical to the prediction of non-native species success and impacts. Rainbow trout and brown trout have been introduced globally, but there appear to be differences in their patterns of invasiveness and ecological impact. Here, we investigated whether diploid rainbow trout and diploid and triploid brown trout differ among several key behavioural measures linked to invasiveness and impact. We assessed activity, boldness, aggression, and feeding, using open field, novel object, shelter, mirror, feeding, and functional response experiments. We also tested within each fish type for behavioural syndromes comprising correlations among activity, boldness and aggression. Rainbow trout were more active and aggressive but less bold than diploid and triploid brown trout. In small groups, however, rainbow trout were bolder than both types of brown trout. Diploid brown trout were more active and bolder than triploids when tested individually, and had a higher functional response than both rainbow trout and triploid brown trout. In terms of behavioural syndromes, there was no association between activity and boldness in rainbow trout, however, there was in both brown trout types. The increased activity and aggression of rainbow trout may reflect an increased stress response to novel situations, with this response reduced in a group. These results suggest that rainbow trout do not manage their energy budgets effectively, and may explain why they have limited survival as invaders. In addition, the lower functional response of rainbow trout may explain why they are implicated in fewer ecological impacts, and the triploidy treatment also appears to lower the potential impact of brown trout. Comparative analyses of multiple behaviours of invasive species and genetic variants may thus be key to understanding and predicting invader success and ecological impacts.Department of Agriculture, Environment and Rural Affairs.
Thanks also to the Natural Environment Research Council (NERC)
and Biotechnology and Biological Sciences Research Council (BBSRC)