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Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion
Get PDFpeer-reviewedDirect application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment
Assessing stone walls habitat quality – Which factors affect bryophytes and macrolichens on farmland stone walls in Ireland?
Get PDFpeer-reviewedStone walls are ubiquitous field boundaries used to restrict livestock movement or to separate property. Bryophytes and lichens are often the dominant vegetation in dry stone walls and are strongly affected by local microhabitat characteristics. Bryophytes and lichens related metrics can be used to define habitat quality of stone walls.
The current study assessed how richness and cover of bryophytes and macrolichens in dry stone walls related to each other and how different environmental variables and farm management descriptors determined richness and cover of both groups in dry stone walls. Bryophytes and macrolichens were sampled in stone walls on sixteen farms across a management intensity gradient in Ireland.
Bryophyte cover correlated positively and significantly with bryophyte richness and macrolichen cover and richness, and can thus be used to assess stone walls quality. Farm management intensity emerged as the variable most strongly related with species richness of bryophytes and cover of both groups. Altitude also emerged as a strong predictor of both groups’ richness and cover. This study provides a novel perspective on stone wall habitat quality and results indicate that by promoting extensive farming it is possible to increase stone walls quality
X-ray computerized microtomography and confocal Raman microscopy as complementary techniques to conventional imaging tools for the microstructural characterization of Cheddar cheese
Get PDFpeer-reviewedThis study explored the use of X-ray computerized microtomography (micro-CT) and confocal Raman microscopy to provide complementary information to well-established techniques, such as confocal laser scanning microscopy (CLSM), for the microstructural characterization of cheese. To evaluate the potential of these techniques, 5 commercial Cheddar cheese samples, 3 with different ripening times and 2 with different fat contents, were analyzed. Confocal laser scanning microscopy was particularly useful to describe differences in fat and protein distribution, especially between the 2 samples with different fat contents. The quantitative data obtained through image analysis correlated well with the nutritional information provided in the product labels. Conversely, micro-CT was more advantageous for studying the size and spatial distribution of microcrystals present within the cheese matrix. Two types of microcrystals were identified that differed in size, shape, and X-ray attenuation. The smallest, with a diameter of approximately 10 to 20 μm, were more abundant in the samples and presented a more uniform roundish shape and higher X-ray attenuation. Larger and more heterogeneous crystals with diameters reaching 50 μm were also observed in scarcer numbers and showed lower X-ray attenuation. Confocal Raman microscopy was useful not only for identifying the distribution of all these components but also allowed comparing the presence of micronutrients such as carotenoids in the cheeses and provided compositional information on the crystals detected. Small and large crystals were identified as calcium phosphate and calcium lactate, respectively. Overall, using micro-CT, confocal Raman microscopy, and CLSM in combination generated novel and complementary information for the microstructural and nutritional characterization of Cheddar cheese. These techniques can be used to provide valuable knowledge when studying the effect of milk composition, processing, and maturation on the cheese quality attributes
Hoof lesions in partly housed pasture-based dairy cows
Get PDFpeer-reviewedLameness is a symptom of a painful disorder affecting the limbs, which impacts dairy cow welfare and productivity. Lameness is primarily caused by hoof lesions. The prevalence of different lesion types can differ depending on environmental conditions and farm management practices. The aims of this observational study were to establish the cow-level and herd-level lesion prevalence during both housing and grazing periods in a partly housed, pasture-based system, establish the prevalence of lesions always associated with pain (“alarm” lesion), identify the lesions associated with a higher lameness score, determine relationships between lesions, and identify risk factors for digital dermatitis. On 98 farms during the grazing period and on 74 of the same farms during the housing period, every cow was lameness scored (0–3 lameness scoring scale), and the hind hooves of lame cows (score 2 and 3) were examined (maximum 20 cows per visit) and the prevalence of each lesion type recorded. To gather data on potential predictors for the risk factor analysis, a questionnaire with the farmer was conducted on lameness management practices and infrastructure measurements were taken at each visit. Cow-level data were also collected (e.g., parity, breed, milk yield, and so on). Noninfectious lesions were found to be more prevalent than infectious lesions in this system type. The most prevalent lesion types during both grazing and housing periods were white line separation, sole hemorrhages and overgrown claws; all remaining lesions had a cow-level prevalence of less than 15%. The cow-level prevalence of alarm lesions was 19% during the grazing period and 25% during the housing period; the most prevalent alarm lesion was sole ulcers during both periods. We found significantly more foreign bodies within the hoof sole (grazing = 14%, housing = 7%) and overgrown claws (grazing = 71%, housing = 55%) during the grazing period compared with the housing period. Cows with foul of the foot, sole ulcer, white line abscess, toe necrosis or an amputated claw had higher odds of being more severely lame, compared with mildly lame. The strongest correlation between lesions were between toe necrosis and digital dermatitis (r = 0.40), overgrown claws and corkscrew claws (r = 0.33), and interdigital hyperplasia and digital dermatitis (r = 0.31) at herd level. At the cow level, the strongest correlation was between overgrown claws and corkscrew claws (r = 0.27), and digital dermatitis and heel erosion (r = 0.22). The farmers' perception of the presence of digital dermatitis (and lameness) was significantly correlated with the actual presence of digital dermatitis recorded. Additional risk factors for the presence of digital dermatitis were cow track and verge width near the collecting yard, and stone presence on the cow tracks. Results from this study help further our understanding of the causes of lameness in partly housed, pasture-based dairy cows, and can be used to guide prevention and treatment protocols
Shared and non-shared sIgA-coated and uncoated bacteria in intestine of mother-infant pairs
Get PDFpeer-reviewedThe infant gut microbiota is critical for promoting and maintaining early-life health. The study aimed to analyze the composition of sIgA-coated and sIgA-uncoated bacterial communities at genus level and lactobacilli and bifidobacterial communities at species level in human breast milk (HBM) and infant and maternal feces. Eleven pregnant women were recruited successfully. HBM; infant feces during colostrum, transition, and mature stages; and maternal feces within the mature stage were collected. sIgA-coated and sIgA-uncoated bacteria were separated with magnetic-activated cell sorting. Then, 16S rRNA sequencing, bifidobacterial groEL gene sequencing, and lactobacilli groEL gene sequencing were performed to analyze the bacterial community. PCoA revealed that the compositions of sIgA-coated and sIgA-uncoated bacteria were different among HBM and infant and maternal feces. Higher relative abundance of sIgA-uncoated Bifidobacterium was found in the three lactation stages in infant feces compared to the corresponding HBM, and a higher relative abundance of sIgA-uncoated Faecalibacterium was found in maternal feces compared to HBM and infant feces. For bifidobacterial community, sIgA-coated and sIgA-uncoated B. longum subsp. infantis and B. pseudocatenulatum was dominant in infant feces and maternal feces, respectively. The relative abundance of sIgA-uncoated B. longum subsp. infantis was significantly higher in infant feces compared to that in maternal feces. For the Lactobacillus community, L. paragasseri and L. mucosae were dominant in infant and maternal feces, respectively. HBM and infant and maternal feces showed distinct diversity and composition of both sIgA-coated and sIgA-uncoated bacteria at genus level. Infant and maternal feces showed similar composition of Bifidobacterium at species level. The same Bifidobacterium species could be detected both in sIgA-coated and -uncoated form. This article provided deeper understanding on the microbiota profile in HBM and infant and maternal feces
Skeletal muscle miRNA profiling in Charolais steers divergent for feed efficiency potential
No full textEfficient utilisation of feed resources in beef production systems is a major determinant of overall financial and
environmental sustainability. Thus, identifying genes implicated in feed efficiency may allow for the identification and
subsequent breeding of feed efficient cattle, benefiting sustainability. Moreover, it is crucial that genes contributing to
feed efficiency are robust across varying management settings including for example dietary source. RNAseq analysis
was employed to profile the skeletal muscle tissue miRNAome of Charolais steers divergent for residual feed intake
(RFI) over consecutive contrasting dietary phases. During phase 1, steers were offered zero-grazed grass, followed
by a high-concentrate diet for dietary phase 2. Muscle biopsies were collected at the end of each dietary phase from
cattle most divergent for RFI. RNAseq was subsequently undertaken on muscle biopsies followed by bioinformatic
analysis to determine differentially expressed (DE) miRNA between steers divergent for RFI across each dietary phase.
Over each dietary phase, growth rates were not different (P>0.05) between RFI groups, however High-RFI (feed
inefficient) steers consumed more feed (P<0.05). In total, 8 miRNA were identified as DE (P-value<0.05) between
steers divergent in RFI, 6 were DE following the zero-grazed grass diet and 2 DE following the high-concentrate
dietary phase. Of particular interest were miR-2419-5p and miR-2415-3p, both of which were up-regulated in the
Low-RFI (feed efficient) steers compared to their High-RFI contemporaries across each dietary phase. The predicted
target mRNA genes of miR-2419-5p and miR-2415-3p revealed an involvement in processes related to growth and
metabolism. These results provide insight into the skeletal muscle miRNAome of beef cattle and their potential
molecular regulatory mechanisms relating to feed efficiency. This research was funded by the Irish Department
of Agriculture, Food and the Marine (RSF13/S/519) and by the Research Leaders 2025 programme, co-funded by
Teagasc and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie grant agreement number 754380
ScabEomics: Effector-based breeding for resistance to Spongospora subterranea (powdery scab) in potato
No full textPowdery scab caused by Spongospora subterranea sp. subterranea (Sss) can cause significant yield
losses in potato. Lesions on potato skin affect marketability and provide entry points for other
pathogens. Moreover, Sss can spread Potato MopTop Virus (PMTV). Efforts to breed for Sss-resistant
varieties are impaired by troublesome phenotyping methods.
Plants possessing a specific resistance (R) gene are resistant towards a pathogen that produces the
corresponding avirulence (Avr) gene product, also known as effector. Highly expressed effectors that do
not trigger hypersensitive response (HR) in susceptible plants, are considered candidate AVRs. Effectors
triggering HR are most prominent among the diverse part of the secretome (Van de Vossenberg et al.,
2019). Therefore, candidate AVRs can be identified using comparative genomics, and transcriptomics of
the secretome.
In order to identify genetic diversity and potential Avr genes, we sequenced the genomes of over 20
different Sss isolates from 15 different countries in 5 continents. We mined the secretomes and selected
candidate Avrs based on their diversity across different isolates and expression analysis with RNAseq
data. These candidate Avr genes will be used to screen a germplasm collection and accessions in which
hypersensitive responses are triggered will be selected. The plant components involved in the HR will be
genetically identified, and may provide novel R gene sources which can be easily selected in breeding
programs
‘Come aboard’ the systems-based approach: the role of social science in agri-food research and innovation
Get PDFpeer-reviewedIncreasingly, 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
Ruminant health research – progress to date and future prospects, with an emphasis on Irish research
Get PDFpeer-reviewedThis 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
Quantifying MCPA load pathways at catchment scale using high temporal resolution data
Get PDFpeer-reviewedDetection of the agricultural acid herbicide MCPA (2-methyl-4-chlorophenoxyacetic acid) in drinking water source catchments is of growing concern, with economic and environmental implications for water utilities and wider ecosystem services. MCPA is poorly adsorbed to soil and highly mobile in water, but hydrological pathway processes are relatively unknown at the catchment scale and limited by coarse resolution data. This understanding is required to target mitigation measures and to provide a framework to monitor their effectiveness. To address this knowledge gap, this study reports findings from river discharge and synchronous MCPA concentration datasets (continuous 7 hour and with additional hourly sampling during storm events) collected over a 7 month herbicide spraying season. The study was undertaken in a surface (source) water catchment (384 km2—of which 154 km2 is agricultural land use) in the cross-border area of Ireland. Combined into loads, and using two pathway separation techniques, the MCPA data were apportioned into event and baseload components and the former was further separated to quantify a quickflow (QF) and other event pathways. Based on the 7 hourly dataset, 85.2 kg (0.22 kg km−2 by catchment area, or 0.55 kg km−2 by agricultural area) of MCPA was exported from the catchment in 7 months. Of this load, 87.7 % was transported via event flow pathways with 72.0 % transported via surface dominated (QF) pathways. Approximately 12 % of the MCPA load was transported via deep baseflows, indicating a persistence in this delayed pathway, and this was the primary pathway condition monitored in a weekly regulatory sampling programme. However, overall, the data indicated a dominant acute, storm dependent process of incidental MCPA loss during the spraying season. Reducing use and/or implementing extensive surface pathway disconnection measures are the mitigation options with greatest potential, the success of which can only be assessed using high temporal resolution monitoring techniques