Recently, several EU countries, including the Republic of Ireland, have struggled to meet legally binding commitments to reduce ammonia emissions. Some farmers readily embrace abatement measures, whereas others reject them and it could be argued that farmers’ technology rejection decisions have been studied in less detail within the literature. However, understanding why some farmers reject recommended farming practices holds critical information that helps to inform policy, tailor government support schemes, and reduce pro-innovation biases. This study builds on the Grounded Theory method, data collected from focus group discussions with dairy and beef cattle farmers across eight key farming regions, and inductive thematic analysis. Three main themes, six subthemes and 26 codes were defined. The adoption of recommended bovine farming methods was hindered by affordability, compatibility, usability, availability, and information-related barriers. Participants also expressed frustration with unfair pressure to reduce agricultural emissions along with insufficient recognition of the environmental benefits provided by well-managed grasslands, the contributions cattle production makes to global food production, and the sustainability progress they have already achieved. We recommend that future reforms of the EU Common Agricultural Policy adopt a coordinated policy approach. It should simultaneously target all the nitrogen-related farm environmental issues and fully consider the local farmers perspectives in policy design and implementation. The reforms should include accessible support schemes for small-scale farm owners and more effective efforts to raise awareness about the causes and consequences of farm ammonia3 emissions, available abatement methods, and the correction of misinformation.
ABSTRACT Plasmid-encoded mobile colistin resistance ( mcr ) genes have raised concern due to dissemination potential. While mcr variants are reported across One Health compartments, they remain unreported in grass. This study characterises a novel mcr variant ( mcr-13.1 ), detected in Escherichia coli isolated from the grass phylosphere within an agricultural grassland. The two mcr -positive isolates were clonal copies isolated at timepoints eight weeks apart. They belonged to the serotype O17:H18 and were of the sequence type ST394. The E. coli were phenotypically susceptible to β-lactams, aminoglycosides, quinolones, sulphonamides, phenicols, tetracyclines, diaminopyrimidine and colistin (Minimum Inhibitory Concentration (MIC) = 0.5 µg/mL). The mcr-13.1 gene was encoded on an IncFIB plasmid. This plasmid was transferable by conjugation but the colistin MIC of the E. coli J53 transconjugant did not change (0.5 µg/mL). Further, cloned pUC19:: mcr-13.1 did not alter the colistin MIC for E. coli DH5α (0.25 µg/mL). The translated amino acid sequence showed highest homology (82 %) to MCR-10.2 and MCR-10.4. Our findings identify grass as a previously unrecognised reservoir for E. coli carrying mobile mcr genes, reports the identification of the novel mcr-13.1 variant from this niche and demonstrates the importance of genomic screening in identifying mcr genes that would otherwise remain undetected.
Background Metagenomic next-generation sequencing (mNGS) is an untargeted approach that enables detection of pathogens directly from samples without prior knowledge of their genetic sequences. In the context of pandemic preparedness and One Health surveillance, there is a pressing need for validated viral mNGS workflows that perform reliably across diverse hosts sample types and pre-analytical conditions. Results The study designed and evaluated two mNGS workflows, one for swabs and one for complex tissue matrices, using a reference repository of clinical and post-mortem samples. The panel comprised swabs and tissue samples positive for 19 DNA and RNA viruses (including 12 species) from nine host species and nine anatomical sites, encompassing a range of transport media, storage temperatures and processing timelines. Quality control metrics were embedded throughout nucleic acid extraction, library preparation and sequencing to monitor performance and support interpretation. Overall, 89.5% of 19 known DNA and RNA viruses were detected, including from samples with low nucleic acid concentrations (< 1 ng/µl) and variable integrity and purity. The workflows identified viral co-infections that had not been detected by prior targeted testing, as well as Phocid herpesvirus 7 (PHV7) for which no complete reference genome was initially available. Conclusions These results demonstrate that the validated swab and tissue mNGS workflows are sufficiently robust and sensitive for deployment in investigations of suspected viral disease of unknown aetiology and for early detection of emerging viral threats at the animal–human interface.
Common scab, caused by Streptomyces spp., is worldwide an important skin disease of potato, capable of significant reductions in marketable value. Resistant varieties developed through phenotypic selection have been the most effective strategy thus far. Previous studies on the genetics of resistance have identified only minor-effect QTLs. In the current study, we explored the value of historical data for genetic analysis, derived from 52 sources. Based on partial replication of the 3500+ varieties, generalized (entry-mean) heritability was estimated at 0.66. For a subset of 292 varieties with genome-wide markers, the genomic (narrow-sense) heritability was only 0.10. The historical data was combined with a contemporary US dataset spanning 6 environments and 416 varieties. Genome-wide association studies identified four QTLs, which together explained 7.3
Milk and water kefir are fermented beverages prepared by inoculating milk or sugar-rich solutions with kefir grains - containing complex microbial consortia of bacteria and yeast. The increasing global popularity of kefir has driven interest in their microbiomes. Beyond their culinary significance, kefir serves as a model system for studying microbial community assembly, ecological filtering, and evolutionary dynamics. Kefir’s suitability as a model is enhanced by its simplicity (including short fermentation times), adaptability to experimental manipulation, and scalability for both controlled laboratory studies and citizen science initiatives. In this study, we employed genome-resolved metagenomics to investigate milk and water kefir microbiomes, produced over 21 weeks from an initial common source milk or water kefir grain by citizen scientists, using diverse substrates and conditions. Early fermentation (weeks 1–9) was marked by rapid compositional, functional and volatile shifts, leading to reproducible transitions between community states, with values not changing considerably thereafter. At the strain level, we identified multiple coexisting strains within dominant species, with initial fluctuations. While rare environmental species occasionally appeared, they were selectively filtered and did not persist. The sustained coexistence of key species and strains, alongside the emergence of reproducible community types, highlights the resilience and stability of kefir microbiomes across both short- and long-term timeframes. Our findings reinforce kefir’s value as a model for investigating microbial interactions, environmental microbial acquisition, and strain-level dynamics. The co-occurrence patterns observed among specific strains and species provide insight into microbial assembly and persistence, with broader relevance to complex ecosystems such as the gut microbiome. By elucidating patterns of compositional and functional change and assessing how selective pressures shape microbial communities, this study underscores kefir’s utility in microbial ecology and evolution.
