Now showing items 21-40 of 2799

    • An in vitro study to assess bioaccessibility and bioavailability of calcium from blue whiting (Micromesistius poutassou) fish bone powder

      Busca, K.; Wu, S.; Miao, S.; Govindan, A.; Strain, C.R.; O’Donnell, S.T.; Whooley, J.; Gite, S.; Paul Ross, R.; Stanton, C.; et al. (Teagasc, 2021-12-21)
      The aim of this study was to determine how well calcium-rich mineral extracts derived from blue whiting fish bone powders compare with existing calcium sources (commercially available fish bone supplement, calcium carbonate and milk powder) in terms of physicochemical properties, in vitro bioaccessibility and bioavailability using simulated gastrointestinal tract treatment and a Caco-2 cell culture model. Blue whiting calcium-rich fish bone powders (A to E) were supplied by Bio-marine Ingredients Ireland (BII) and a commercial calcium-rich fish bone powder was used as the positive control F. The BII calcium-rich fish bone powders analysed through atomic emission spectrometry were shown to have similar levels of mineral content in comparison with powder F. Solubility and rheology tests were performed on the rehydrated powders. The pH of BII calcium-rich fish bone powders in water solution (10% w/v) ranged from 6.96 to 9.09 compared to control F (pH 7.33). Following simulated oral, gastric and duodenal in vitro digestion using the COST INFOGEST standardised static adult digestion method, the fish powders A, E and F showed higher values of soluble ionic calcium than rehydrated milk powder. We compared in vitro bioavailability of the powders using the Caco-2 cell line to test the effects of calcium on human colonic epithelial cells, which confirmed that calcium from blue whiting fish bone was more bioavailable than calcium from milk and calcium carbonate. These data indicate that calcium-rich blue whiting fish bone powder compares well with existing calcium sources, in terms of physicochemical properties, bioaccessibility and bioavailability.
    • Celebrating 60 years of the Irish Journal of Agricultural and Food Research

      O'Mara, Frank (Teagasc, 2022-12-23)
      This special issue consists of 12 papers, compiled in 2021 — the journal’s anniversary year, providing an overview of the wide range of research undertaken by Teagasc. These papers provide a great source of reference for those interested in Irish agricultural and food research. Topics include forestry, potato breeding and production, pig production, milk quality and processing, meat processing, ruminant nutrition, ruminant breeding, the Agricultural Catchments Programme, grassland, animal health and welfare, and the role of social science in agri food research.
    • Ruminant health research – progress to date and future prospects, with an emphasis on Irish research

      Mee, J.F.; Barrett, D.; Boloña, P. Silva; Conneely, M.; Earley, B.; Fagan, S.; Keane, O.M.; Lane, E.A. (Teagasc, 2022-05-20)
      This review addresses the progress that has been made in ruminant health research over the last 60 yr, with an emphasis on Irish research. The review focuses on the economically important infectious diseases of dairy and beef cattle and of sheep, calf diseases, regulated and non-regulated infectious diseases, lameness, mastitis and parasitoses. The progress to date, current knowledge and future challenges are all addressed. Paradigm shifts have occurred in many of these diseases, the most profound of which is the change from increasing antimicrobial usage (AMU) to the realisation of the challenge of antimicrobial resistance (AMR) and the current reduction in AMU. Another major change in thinking is the move away from focus on the pathogen exclusively towards a more holistic view of the roles of host immunity and adequacy of management. In the last 60 yr, many new diseases have emerged but in parallel many new technologies have rapidly evolved to monitor and control these threats to animal health. Irish research has contributed substantially to improved current ruminant health. The major future challenge is how to manage ruminant health in a OneHealth world where animal, human and environmental health and sustainability are intimately intertwined and interdependent.
    • ‘Come aboard’ the systems-based approach: the role of social science in agri-food research and innovation

      Macken-Walsh, Á.; Henchion, M.M.; Regan, Á. (Teagasc, 2022-05-20)
      Increasingly, systems-based approaches are taken in agri-food research and innovation (R&I). Such approaches also align with changes in science governance and new policies related to research impact and responsible research and innovation. However, taking a holistic view of food systems to maximise impact from R&I in a societally acceptable manner poses theoretical and methodological challenges. How can diverse actors come to occupy roles in forming and pursuing common visions towards more sustainable food systems? This paper focuses on how social science can activate, mediate and add rigour to systems-based approaches. An overview is presented of the policy context in which greater attention is paid to systems-based approaches and we present a framework to theoretically and practically support systems-based approaches: transdisciplinarity and the “multi-actor approach” (MAA). These approaches explain practically how different scientific contributions and non-scientific actors can be engaged and unified in creatively addressing R&I challenges. Overall, because social science is used to inform and deliver R&I outcomes that take into account the whole system of actors, their different values and expectations and their interactions and knowledge exchange, it is a crucial source of knowledge for advancing and meeting the challenges of systems-based approaches. Illustrating this, we present a profile of projects where social science has been applied to enhance R&I within a systems-based approach. However, we also signal caveats, qualifications and provisos in applying such approaches. This paper will be of interest to researchers and practitioners planning to incorporate social science to systems-based R&I initiatives to avoid pitfalls and add rigour.
    • Effect of passive transfer status on response to a glycoprotein E (gE)-negative bovine herpesvirus type 1 (BoHV-1) and bovine respiratory syncytial virus (BRSV) vaccine and weaning stress in pre-weaned dairy calves

      Dunn, Amanda; Welsh, Michael; Gordon, Alan; Arguello, Anastasio; Morrison, Steven J.; Earley, Bernadette; Department of Agriculture, Food and the Marine; Department of Agriculture and Rural Development in Northern Ireland; AgriSearch (farmer levy (Informa UK Limited, 2018-01-09)
      The study objectives were to: 1) examine how calves of divergent immune status respond to BRSV vaccination at 3 weeks of age; 2) trace glycoprotein E negative BoHV-1 antibodies from vaccinated dams to calf sera and to investigate how passive transfer affects response to live BoHV-1 vaccine at 6 weeks of age; 3) explore the impact of passive transfer status on blood metabolites around weaning. Thirty seven Holstein cows and their calves were included in the study. All cows were immunised with a commercial marker vaccine against BoHV-1(gE-) administered intra-muscularly at 4 month prior to the start of calving. Calves were assigned to 1 of 2 colostrum treatment groups: 1) 5% of BW in colostrum fed at birth, or 2) 10% of BW in colostrum fed at birth. Calves were also immunised at 3 weeks of age with a respiratory commercial vaccine, and a booster administered 4 weeks later. Calves were also immunised against BoHV-1 at 6 weeks of age, using one dose of a live commercial vaccine. The results demonstrated that level of passive immunity had no effect on immune response to vaccination and the importance of feeding colostrum from vaccinated BoHV-1 gE- dams to provide calves with passive protection against IBRV.
    • Comparison of single radial immunodiffusion and ELISA for the quantification of immunoglobulin G in bovine colostrum, milk and calf sera

      Dunn, Amanda; Duffy, Catherine; Gordon, Alan; Morrison, Steven; Argűello, Anastasio; Welsh, Michael; Earley, Bernadette; Department of Agriculture and Rural Development in Northern Ireland; AgriSearch (farmer levy); Department of Agriculture, Food and Marine, Ireland; et al. (Informa UK Limited, 2017-11-02)
      The overall objective was to compare immunoglobulin G (IgG) concentrations measured by single radial immunodiffusion (sRID) and ELISA-based methods in samples of bovine colostrum and transition milk from contrasting breed types (Limousin × Friesian (n = 10) and Holstein (n = 10)). Jugular blood samples were collected at 48 h post-birth from beef (n = 10) and dairy (n = 10) calves and sera harvested subsequent to colostrum consumption. Absolute colostrum IgG values determined by ELISA showed poor agreement with mean (SD) IgG values measured using sRID, fixed bias (sRID – ELISA) was 31.89 (±9.84) mg/mL; having wide limits of agreement (12.61–51.17) and a low concordance coefficient (0.26). The agreement between ELISA and sRID when measuring serum IgG was greater than that of colostrum, fixed bias (sRID – ELISA) was 12.36 (±6.60) mg/mL; having narrower limits of agreement (−0.58 to 25.30) and serum IgG concentrations had a greater concordance coefficient (0.44) between samples. Calf sera IgG measured using the indirect zinc sulphate turbidity test showed a strong correlation with the sRID and ELISA methods (P < .001), R2 = 0.78 and R2 = 0.77 respectively. Overall, the ELISA and sRID methodologies had a strong positive association with almost a twofold (1.8) difference between values; therefore, they provide diverse absolute values of IgG concentration.
    • Isolation and characterization of an exopolysaccharide‐producing Leuconostoc citreum strain from artisanal cheese

      Domingos‐Lopes, M.F.P.; Lamosa, P.; Stanton, C.; Ross, R.P.; Silva, C.C.G.; FCT; FRCT; PTDC/AGR-ALI/104385/ 2008; M3.1.2/F/009/2011 (Wiley, 2018-10-18)
      High molar mass exopolysaccharides (EPS) produced from sucrose by lactic acid bacteria (LAB) are of great interest as natural additives to use in foods, medical and pharmaceutical industry. This study aimed to identify the EPS produced by Leuconostoc citreum L3C1E7 isolated from Pico cheese and characterize the strain for technological and probiotic potential. Purified EPS was isolated from the culture of L. citreum L3C1E7 by ethanol precipitation, with a yield of 520 mg ml−1. The EPS-producing strain had a mucoid phenotype and average molecular weight of 5·88 × 106 Da. The structural characterization of the purified EPS was determined by 1H, 13C and two-dimensional NMR spectroscopy. EPS was composed of alternating α-(1→6)-linked and α-(1→3)-linked D-glucopyranyl units, suggesting the existence of an alternan. The strain was slow acidifying, produced diacetyl and displayed high esterase/lipase and aminopeptidase activities, which promote the desirable flavours in dairy products. Moreover, L. citreum showed moderate resistance to the adverse conditions of the gastrointestinal (GI) tract and high adhesion to GI cells. This work provides a better understanding of EPS produced by L. citreum and the potential application of EPS-producing strain in food and/or as a probiotic culture.
    • Editorial, International Bull Fertility Conference – Theory to Practice, Westport, Ireland, 2018

      Diskin, MichaelG; Lonergan, Pat; Kenny, David A.; Fair, Sean (Elsevier, 2018)
      This supplement to Animal contains the papers associated with the keynote lectures delivered at the International Bull Fertility Conference – Theory to Practice held in Westport, Ireland from May 27th to 30th 2018. The conference was organised under the auspices of the British Society of Animal Science (BSAS) in close collaboration with Teagasc, University College Dublin, University of Limerick, the Cattle Association of Veterinary Ireland (CAVI), XL Vets, the British Cattle Veterinary Association (BCVA) and the Department of Agriculture Food and the Marine.
    • A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

      Cronin, Owen; Barton, Wiley; Skuse, Peter; Penney, Nicholas C.; Garcia-Perez, Isabel; Murphy, Eileen F.; Woods, Trevor; Nugent, Helena; Fanning, Aine; Melgar, Silvia; et al. (American Society for Microbiology, 2018-06-26)
      Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in the diversity, composition, and functional profiles of microbial populations in the gut have been described in cross-sectional studies of habitual athletes. However, this relationship is also affected by changes in diet, such as changes in dietary and supplementary protein consumption, that coincide with exercise. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomics- and metabolomics-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in the diversity of microbial populations in the gut. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement. IMPORTANCE The gut microbiota of humans is a critical component of functional development and subsequent health. It is important to understand the lifestyle and dietary factors that affect the gut microbiome and what impact these factors may have. Animal studies suggest that exercise can directly affect the gut microbiota, and elite athletes demonstrate unique beneficial and diverse gut microbiome characteristics. These characteristics are associated with levels of protein consumption and levels of physical activity. The results of this study show that increasing the fitness levels of physically inactive humans leads to modest but detectable changes in gut microbiota characteristics. For the first time, we show that regular whey protein intake leads to significant alterations to the composition of the gut virome.
    • Complete Genome Sequences of Sequence Type 71 (ST71) and ST97 Staphylococcus aureus Isolates from Bovine Milk

      Cormican, Paul; Keane, Orla M.; Department of Agriculture Food and the Marine; 14/S/802 (American Society for Microbiology, 2018-08-09)
      This is the announcement of draft genome sequences for Staphylococcus aureus strains belonging to sequence type 97 (ST97) and ST71. These sequence types are commonly associated with bovine mastitis, and the strains were isolated in Ireland in 2010 from the milk of cows with clinical mastitis.
    • Weed suppression greatly increased by plant diversity in intensively managed grasslands: A continental-scale experiment

      Connolly, John; Sebastià, Maria-Teresa; Kirwan, Laura; Finn, John Anthony; Llurba, Rosa; Suter, Matthias; Collins, Rosemary P.; Porqueddu, Claudio; Helgadóttir, Áslaug; Baadshaug, Ole H.; et al. (Wiley, 2017-09-27)
      Grassland diversity can support sustainable intensification of grassland production through increased yields, reduced inputs and limited weed invasion. We report the effects of diversity on weed suppression from 3 years of a 31-site continental-scale field experiment.At each site, 15 grassland communities comprising four monocultures and 11 four-species mixtures based on a wide range of species' proportions were sown at two densities and managed by cutting. Forage species were selected according to two crossed functional traits, "method of nitrogen acquisition" and "pattern of temporal development".Across sites, years and sown densities, annual weed biomass in mixtures and monocultures was 0.5 and 2.0 t DM ha-1 (7% and 33% of total biomass respectively). Over 95% of mixtures had weed biomass lower than the average of monocultures, and in two-thirds of cases, lower than in the most suppressive monoculture (transgressive suppression). Suppression was significantly transgressive for 58% of site-years. Transgressive suppression by mixtures was maintained across years, independent of site productivity.Based on models, average weed biomass in mixture over the whole experiment was 52% less (95% confidence interval: 30%-75%) than in the most suppressive monoculture. Transgressive suppression of weed biomass was significant at each year across all mixtures and for each mixture.Weed biomass was consistently low across all mixtures and years and was in some cases significantly but not largely different from that in the equiproportional mixture. The average variability (standard deviation) of annual weed biomass within a site was much lower for mixtures (0.42) than for monocultures (1.77). Synthesis and applications. Weed invasion can be diminished through a combination of forage species selected for complementarity and persistence traits in systems designed to reduce reliance on fertiliser nitrogen. In this study, effects of diversity on weed suppression were consistently strong across mixtures varying widely in species' proportions and over time. The level of weed biomass did not vary greatly across mixtures varying widely in proportions of sown species. These diversity benefits in intensively managed grasslands are relevant for the sustainable intensification of agriculture and, importantly, are achievable through practical farm-scale actions.
    • Optimized Use of Low-Depth Genotyping-by-Sequencing for Genomic Prediction Among Multi-Parental Family Pools and Single Plants in Perennial Ryegrass (Lolium perenne L.)

      Cericola, Fabio; Lenk, Ingo; Fè, Dario; Byrne, Stephen; Jensen, Christian S.; Pedersen, Morten G.; Asp, Torben; Jensen, Just; Janss, Luc; Danish Ministry of Food, Agriculture and Fisheries; et al. (Frontiers Media SA, 2018-03-21)
      Ryegrass single plants, bi-parental family pools, and multi-parental family pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS) assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage depth leads to a higher proportion of missing data, and leads to a reduction in accuracy when identifying the allele-frequency at each locus. As a consequence of the latter, genomic relationship matrices (GRMs) will be biased. This bias in GRMs affects variance estimates and the accuracy of GBLUP for genomic prediction (GBLUP-GP). We derived equations that describe the bias from low-coverage sequencing as an effect of binomial sampling of sequence reads, and allowed for any ploidy level of the sample considered. This allowed us to combine individual and pool genotypes in one GRM, treating pool-genotypes as a polyploid genotype, equal to the total ploidy-level of the parents of the pool. Using simulated data, we verified the magnitude of the GRM bias at different coverage depths for three different kinds of ryegrass breeding material: individual genotypes from single plants, pool-genotypes from F2 families, and pool-genotypes from synthetic varieties. To better handle missing data, we also tested imputation procedures, which are suited for analyzing allele-frequency genomic data. The relative advantages of the bias-correction and the imputation of missing data were evaluated using real data. We examined a large dataset, including single plants, F2 families, and synthetic varieties genotyped in three GBS assays, each with a different coverage depth, and evaluated them for heading date, crown rust resistance, and seed yield. Cross validations were used to test the accuracy using GBLUP approaches, demonstrating the feasibility of predicting among different breeding material. Bias-corrected GRMs proved to increase predictive accuracies when compared with standard approaches to construct GRMs. Among the imputation methods we tested, the random forest method yielded the highest predictive accuracy. The combinations of these two methods resulted in a meaningful increase of predictive ability (up to 0.09). The possibility of predicting across individuals and pools provides new opportunities for improving ryegrass breeding schemes.
    • Use of clinic refractometer at farm as a tool to estimate the IgG content in goat colostrum

      Castro, Noemí; Gómez-González, Lenny Andrea; Earley, Bernadette; Argüello, Anastasio (Informa UK Limited, 2018-11-22)
      Refractometry has been proposed as a farm technique to estimate the IgG concentration in colostrum. In order to validate the method in goat colostrum using a clinical refractometer, 216 colostrum and milk samples were obtained from 54 dairy goats. Samples were evaluated for protein concentration using a clinical refractometer and IgG concentration was measured using a commercial ELISA. The r2 for the linear regression between refractometry value and IgG concentration measured by ELISA was 0.79, and the area under the receiver operating characteristics curve was 0.99. The proposed cut-off value using the clinical refractometer was 10 mg/mL. At this point, the sensitivity, specificity, negative predictive value, positive predictive value, Youden’s index and accuracy were 100%, 95.19%, 100%, 76.32%, 0.95% and 95.83%, respectively.
    • RNA Phage Biology in a Metagenomic Era

      Callanan, Julie; Stockdale, Stephen; Shkoporov, Andrey; Draper, Lorraine; Ross, R.; Hill, Colin; Science Foundation Ireland (SFI); SFI/12/RC/2273 (Multidisciplinary Digital Publishing Institute, 2018-07-21)
      The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.
    • The Potential of Combined Emulsification and Spray Drying Techniques for Encapsulation of Polyphenols from Rosemary ( Rosmarinus officinalis L.) Leaves

      Bušić, Arijana; Komes, Draženka; Belščak-Cvitanović, Ana; Vojvodić Cebin, Aleksandra; Špoljarić, Igor; Mršić, Gordan; Miao, Song; National Natural Science Foundation of China; European Union; 31628016; et al. (PubMed, 2018-12)
      The present study evaluates the potential of encapsulation of polyphenolic antioxidants from rosemary (Rosmarinus officinalis L.) leaves by combining emulsification and spray drying techniques. To stabilize the emulsions and prepare samples suitable for use in dry products, double emulsions encapsulating rosemary polyphenolic extract and containing polyglycerol polyricinoleate (4%), whey protein isolates (2 and 4%) as emulsifiers, and maltodextrins (MDE 10 and 21) as enhancing coatings were subjected to spray drying. The obtained results show insignificant (p>0.05) effect of used maltodextrin type and protein content on mean particle size of double emulsions containing rosemary polyphenols. Morphology analyses showed that double emulsions were successfully prepared, spherical microcapsules were obtained after spray drying of double emulsions and double emulsion form was still preserved after rehydration of spray-dried microcapsules. Regardless of used maltodextrins, significantly (p>0.05) higher encapsulation efficiencies (EE) of total polyphenols (39.57 and 42.83%) in rehydrated samples were achieved when higher protein content (4% whey protein isolate) was used, indicating the major impact of protein content on EE of rosemary polyphenols. Also, using HPLC analysis, rosmarinic and caffeic acids, apigenin and luteolin derivatives were detected among specific polyphenols, where rosmarinic acid had notable encapsulation efficiency ranging from 62.15 to 67.43%. In this way, the obtained microcapsules encapsulating rosemary polyphenols could be easily blended with various dry mixtures, and serve for delivery in different functional products.
    • C7 vertebra homeotic transformation in domestic dogs – are Pug dogs breaking mammalian evolutionary constraints?

      Brocal, J.; De Decker, S.; José‐López, R.; Garcia Manzanilla, Edgar; Penderis, J.; Stalin, C.; Bertram, S.; Schoenebeck, J. J.; Rusbridge, C.; Fitzpatrick, N.; et al. (Wiley, 2018-05-14)
      The number of cervical vertebrae in mammals is almost constant at seven, regardless of their neck length, implying that there is selection against variation in this number. Homebox (Hox) genes are involved in this evolutionary mammalian conservation, and homeotic transformation of cervical into thoracic vertebrae (cervical ribs) is a common phenotypic abnormality when Hox gene expression is altered. This relatively benign phenotypic change can be associated with fatal traits in humans. Mutations in genes upstream of Hox, inbreeding and stressors during organogenesis can also cause cervical ribs. The aim of this study was to describe the prevalence of cervical ribs in a large group of domestic dogs of different breeds, and explore a possible relation with other congenital vertebral malformations (CVMs) in the breed with the highest prevalence of cervical ribs. By phenotyping we hoped to give clues as to the underlying genetic causes. Twenty computed tomography studies from at least two breeds belonging to each of the nine groups recognized by the Federation Cynologique Internationale, including all the brachycephalic 'screw-tailed' breeds that are known to be overrepresented for CVMs, were reviewed. The Pug dog was more affected by cervical ribs than any other breed (46%; P < 0.001), and was selected for further analysis. No association was found between the presence of cervical ribs and vertebral body formation defect, bifid spinous process, caudal articular process hypoplasia/aplasia and an abnormal sacrum, which may infer they have a different aetiopathogenesis. However, Pug dogs with cervical ribs were more likely to have a transitional thoraco-lumbar vertebra (P = 0.041) and a pre-sacral vertebral count of 26 (P < 0.001). Higher C7/T1 dorsal spinous processes ratios were associated with the presence of cervical ribs (P < 0.001), supporting this is a true homeotic transformation. Relaxation of the stabilizing selection has likely occurred, and the Pug dog appears to be a good naturally occurring model to further investigate the aetiology of cervical ribs, other congenital vertebral anomalies and numerical alterations.
    • Distinct responses of soil respiration to experimental litter manipulation in temperate woodland and tropical forest

      Bréchet, Laëtitia M.; Lopez-Sangil, Luis; George, Charles; Birkett, Ali J.; Baxendale, Catherine; Castro Trujillo, Biancolini; Sayer, Emma J.; European Research Council; ERC/307888 (Wiley, 2018-03-13)
      Global change is affecting primary productivity in forests worldwide, and this, in turn, will alter long-term carbon (C) sequestration in wooded ecosystems. On one hand, increased primary productivity, for example, in response to elevated atmospheric carbon dioxide (CO2), can result in greater inputs of organic matter to the soil, which could increase C sequestration belowground. On other hand, many of the interactions between plants and microorganisms that determine soil C dynamics are poorly characterized, and additional inputs of plant material, such as leaf litter, can result in the mineralization of soil organic matter, and the release of soil C as CO2 during so-called “priming effects”. Until now, very few studies made direct comparison of changes in soil C dynamics in response to altered plant inputs in different wooded ecosystems. We addressed this with a cross-continental study with litter removal and addition treatments in a temperate woodland (Wytham Woods) and lowland tropical forest (Gigante forest) to compare the consequences of increased litterfall on soil respiration in two distinct wooded ecosystems. Mean soil respiration was almost twice as high at Gigante (5.0 μmol CO2 m−2 s−1) than at Wytham (2.7 μmol CO2 m−2 s−1) but surprisingly, litter manipulation treatments had a greater and more immediate effect on soil respiration at Wytham. We measured a 30% increase in soil respiration in response to litter addition treatments at Wytham, compared to a 10% increase at Gigante. Importantly, despite higher soil respiration rates at Gigante, priming effects were stronger and more consistent at Wytham. Our results suggest that in situ priming effects in wooded ecosystems track seasonality in litterfall and soil respiration but the amount of soil C released by priming is not proportional to rates of soil respiration. Instead, priming effects may be promoted by larger inputs of organic matter combined with slower turnover rates.
    • Challenges of Reducing Phosphorus Based Water Eutrophication in the Agricultural Landscapes of Northwest Europe

      Bol, Roland; Gruau, Gerard; Mellander, Per-Erik; Dupas, Rémi; Bechmann, Marianne; Skarbøvik, Eva; Bieroza, Magdalena; Djodjic, Faruk; Glendell, Miriam; Jordan, Philip; et al. (Frontiers Media SA, 2018-08-23)
      In this paper, we outline several recent insights for the priorities and challenges for future research for reducing phosphorus (P) based water eutrophication in the agricultural landscapes of Northwest Europe. We highlight that new research efforts best be focused on headwater catchments as they are a key influence on the initial chemistry of the larger river catchments, and here many management interventions are most effectively made. We emphasize the lack of understanding on how climate change will impact on P losses from agricultural landscapes. Particularly, the capability to disentangle current and future trends in P fluxes, due to climate change itself, from climate driven changes in agricultural management practices and P inputs. Knowing that, future climatic change trajectories for Western Europe will accelerate the release of the most bioavailable soil P. We stress the ambiguities created by the large varieties of sources and storage/transfer processes involved in P emissions in landscapes and the need to develop specific data treatment methods or tracers able to circumvent them, thereby helping catchment managers to identify the ultimate P sources that most contribute to diffuse P emissions. We point out that soil and aqueous P exist not only in various chemical forms, but also in range of less considered physical forms e.g., dissolved, nanoparticulate, colloidal and other particulates, all affected differently by climate as well as other environmental factors, and require bespoke mitigation measures. We support increased high resolution monitoring of headwater catchments, to not only help verify the effectiveness of catchments mitigation strategies, but also add data to further develop new water quality models (e.g., those include Fe-P interactions) which can deal with climate and land use change effects within an uncertainty framework. We finally conclude that there is a crucial need for more integrative research efforts to deal with our incomplete understanding of the mechanisms and processes associated with the identification of critical source areas, P mobilization, delivery and biogeochemical processing, as otherwise even high-intensity and high-resolution research efforts will only reveal an incomplete picture of the full global impact of the terrestrial derived P on downstream aquatic and marine ecosystems.
    • Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese

      Bertuzzi, A. S.; Walsh, A. M.; Sheehan, J. J.; Cotter, P. D.; Crispie, F.; McSweeney, P. L. H.; Kilcawley, K. N.; Rea, M. C.; Science Foundation Ireland; APC Microbiome Institute; et al. (American Society for Microbiology, 2018-02-27)
      In this study, a young Cheddar curd was used to produce two types of surface-ripened cheese, using two commercial smear-culture mixes of yeasts and bacteria. Whole-metagenome shotgun sequencing was used to screen the microbial population within the smear-culture mixes and on the cheese surface, with comparisons of microorganisms at both the species and the strain level. The use of two smear mixes resulted in the development of distinct microbiotas on the surfaces of the two test cheeses. In one case, most of the species inoculated on the cheese established themselves successfully on the surface during ripening, while in the other, some of the species inoculated were not detected during ripening and the most dominant bacterial species, Glutamicibacter arilaitensis, was not a constituent of the culture mix. Generally, yeast species, such as Debaryomyces hansenii and Geotrichum candidum, were dominant during the first stage of ripening but were overtaken by bacterial species, such as Brevibacterium linens and G. arilaitensis, in the later stages. Using correlation analysis, it was possible to associate individual microorganisms with volatile compounds detected by gas chromatography-mass spectrometry in the cheese surface. Specifically, D. hansenii correlated with the production of alcohols and carboxylic acids, G. arilaitensis with alcohols, carboxylic acids and ketones, and B. linens and G. candidum with sulfur compounds. In addition, metagenomic sequencing was used to analyze the metabolic potential of the microbial populations on the surfaces of the test cheeses, revealing a high relative abundance of metagenomic clusters associated with the modification of color, variation of pH, and flavor development. IMPORTANCE Fermented foods, in particular, surface-ripened cheese, represent a model to explain the metabolic interactions which regulate microbial succession in complex environments. This study explains the role of individual species in a heterogeneous microbial environment, i.e., the exterior of surface-ripened cheese. Through whole-metagenome shotgun sequencing, it was possible to investigate the metabolic potential of the resident microorganisms and show how variations in the microbial populations influence important aspects of cheese ripening, especially flavor development. Overall, in addition to providing fundamental insights, this research has considerable industrial relevance relating to the production of fermented food with specific qualities.
    • Surveillance Data Highlights Feed Form, Biosecurity, and Disease Control as Significant Factors Associated with Salmonella Infection on Farrow-to-Finish Pig Farms

      Argüello, Hector; Garcia Manzanilla, Edgar; Lynch, Helen; Walia, Kavita; Leonard, Finola C.; Egan, John; Duffy, Geraldine; Gardiner, Gillian E.; Lawlor, Peadar G.; Department of Agriculture Food and the Marine; et al. (Frontiers Media SA, 2018-02-15)
      Among the zoonotic pathogens affecting pigs, Salmonella stands out due to the high number of human cases linked to pork consumption. In the last two decades many countries have put considerable effort into the control of the infection by surveillance and control strategies on farm. Despite this effort, many herds still have a high Salmonella prevalence and they require guidance to address this problem. The present study, using the serological surveillance data of finishing pigs from the Irish National pig Salmonella Control Programme, aimed to highlight factors associated with increased risk or that might mitigate Salmonella occurrence on farm. A questionnaire with 33 questions regarding herd characteristics, management, feeding, biosecurity, and health was completed for 61 individual herds. After the multivariate analysis by linear regression, nine variables were retained in the final model and linked to herd seroprevalence. Home produced-feed linked to the use of meal showed an eight points reduction in Salmonella prevalence compared to purchased feed (p = 0.042). Different biosecurity measures were associated to lower seroprevalence. Changing of footwear from outside to inside the farm decreased seroprevalence nearly 20 units (p = 0.014) and policies not permitting access to the farmyard to feed trucks (p = 0.048) or avoiding the presence of cats on the farm (p = 0.05) were estimated in 10 units less of seroprevalence. In contrast, the lack of perimeter fence increased the chance to have higher seroprevalence in five units (p = 0.05). Finally, intestinal diseases such as swine dysentery (p = 0.044) and E. coli diarrhea (p = 0.1) were estimated to increase Salmonella prevalence in ∼20 and 10 units, respectively, demonstrating the importance of controlling other enteric pathogens in an on-farm Salmonella control programme. These results show the usefulness of surveillance data to improve on-farm control and confirm that Salmonella infection in pigs is multi-factorial and the approach to its control should be multifaceted.