The Irish Programme to Eradicate Bovine Viral Diarrhoea Virus-Organization, Challenges, and Progress.

A mandatory national Irish bovine viral diarrhoea (BVD) eradication programme, coordinated by Animal Health Ireland, commenced in 2013. Key decisions and programme review are undertaken by a cross-industry Implementation Group (BVDIG) supported by a Technical Working Group. Ear notch tissue is collected from all new-born calves using modified official identity tags, supplemented by additional blood sampling, including for confirmatory testing of calves with initial positive results and testing of their dams.

A large-scale epidemiological model of BoHV-1 spread in the Irish cattle population to support decision-making in conformity with the European Animal Health Law.

We present a new modelling framework to address the evaluation of national control/surveillance programs planned in line with the European Animal Health Law (AHL) for livestock diseases. Our modelling framework is applied to the cattle sector in Ireland where there is need for policy support to design an optimal programme to achieve bovine herpesvirus type 1 (BoHV-1) free status under the AHL. In this contribution, we show how our framework establishes a regional model that is able to mechanistically reproduce the demography, management practices and transport patterns of an entire cattle population without being dependent on continuous livestock registry data.

An improved method for the segmentation of roots from X-ray computed tomography 3D images: Rootine v.2.

Background: X-ray computed tomography is acknowledged as a powerful tool for the study of root system architecture of plants growing in soil. In this paper, we improved the original root segmentation algorithm "Rootine" and present its succeeding version "Rootine v.2".

Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life.

Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life.

Unravelling the chemical exposome in cohort studies: routes explored and steps to become comprehensive.

Environmental factors contribute to the risk for adverse health outcomes against a background of genetic predisposition. Among these factors, chemical exposures may substantially contribute to disease risk and adverse outcomes. In fact, epidemiological cohort studies have established associations between exposure against individual chemicals and adverse health effects.

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.

Background: Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments.

Combining expert knowledge and machine-learning to classify herd types in livestock systems.

A detailed understanding of herd types is needed for animal disease control and surveillance activities, to inform epidemiological study design and interpretation, and to guide effective policy decision-making. In this paper, we present a new approach to classify herd types in livestock systems by combining expert knowledge and a machine-learning algorithm called self-organising-maps (SOMs). This approach is applied to the cattle sector in Ireland, where a detailed understanding of herd types can assist with on-going discussions on control and surveillance for endemic cattle diseases.

Bio-imaging with the helium-ion microscope: A review.

Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology.

Abiotic Transformation of Lamotrigine by Redox-Active Mineral and Phenolic Compounds.

The anticonvulsant drug lamotrigine is a recalcitrant environmental pollutant. It was detected in drinking water, surface water, reclaimed wastewater, arable soils, and even in edible crops. In this work, we studied the mechanisms of lamotrigine transformation by a common redox soil mineral, birnessite, in a single-solute system and in bisolute systems with vanillic acid or -methoxyphenol.

Redox Potential Heterogeneity in Fixed-Bed Electrodes Leads to Microbial Stratification and Inhomogeneous Performance.

Bed electrodes provide high electrode area-to-volume ratios represent a promising configuration for transferring bioelectrochemical systems close to industrial applications. Nevertheless, the intrinsic electrical resistance leads to poor polarization behavior. Therefore, the distribution of Geobacter spp.

Electro-bioremediation of nitrate and arsenite polluted groundwater.

The coexistence of different pollutants in groundwater is a common threat. Sustainable and resilient technologies are required for their treatment. The present study aims to evaluate microbial electrochemical technologies (METs) for treating groundwater contaminated with nitrate (NO) while containing arsenic (in form of arsenite (As(III)) as a co-contaminant.

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.

Background: Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities.

Phytoremediation potential of twelve wild plant species for toxic elements in a contaminated soil.

Green remediation of soils highly contaminated with potentially toxic elements (PTEs) can be achieved using suitable plants. Such phytoremediation procedure often takes into consideration PTE concentrations in plants only, but not produced biomass. Phytoremediation potential of certain species of wild plants for PTEs in contaminated floodplain soils has not been assessed yet.

Seasonal Patterns of Dominant Microbes Involved in Central Nutrient Cycles in the Subsurface.

Microbial communities play a key role for central biogeochemical cycles in the subsurface. Little is known about whether short-term seasonal drought and rewetting events influence the dominant microbes involved in C- and N-cycles. Here, we applied metaproteomics at different subsurface sites in winter, summer and autumn from surface litter layer, seepage water at increasing subsoil depths and remote located groundwater from two wells within the Hainich Critical Zone Exploratory, Germany.

Application of the World Café method to discuss the efficiency of African swine fever control strategies in European wild boar (Sus scrofa) populations.

In the current epidemic of African swine fever (ASF) in Europe, the maintenance and spread of the disease among wild boar populations remains the most important epidemiological challenge. Affected and at-risk countries have addressed this situation using a diversity of wild boar management methods with varying levels of success. The methods applied range from conventional animal disease intervention measures (zoning, stakeholder awareness campaigns, increased surveillance and biosecurity measures) to measures aimed at reducing wild boar population movements (fencing and baiting/feeding) or population numbers (intensive hunting).

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals.

Uptake of α-HCH by wheat from the gas phase and translocation to soil analyzed by a stable carbon isotope labeling experiment.

Hexachlorocyclohexane isomers (HCH) are persistent organic pollutants which cause serious environmental pollution. Phytoextraction is one of the strategies of phytoremediation, which was considered as a promising method for the clean-up of HCH contaminated field sites. To understand the uptake and translocation mechanisms of HCH in soil-plant system, the uptake of HCH from the gas phase was investigated in a tracer experiment with C-labeled α-HCH.

Epidemiology of age-dependent prevalence of Bovine Herpes Virus Type 1 (BoHV-1) in dairy herds with and without vaccination.

Many studies report age as a risk factor for BoHV-1 infection or seropositivity. However, it is unclear whether this pattern reflects true epidemiological causation or is a consequence of study design and other issues. Here, we seek to understand the age-related dynamics of BoHV-1 seroprevalence in seasonal calving Irish dairy herds and provide decision support for the design and implementation of effective BoHV-1 testing strategies.

Dynamics of localised nitrogen supply and relevance for root growth of Vicia faba ('Fuego') and Hordeum vulgare ('Marthe') in soil.

Root growth responds to local differences in N-form and concentration. This is known for artificial systems and assumed to be valid in soil. The purpose of this study is to challenge this assumption for soil mesocosms locally supplied with urea with and without nitrification inhibitor.

Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx.

Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS.

Altered energy partitioning across terrestrial ecosystems in the European drought year 2018.

Drought and heat events, such as the 2018 European drought, interact with the exchange of energy between the land surface and the atmosphere, potentially affecting albedo, sensible and latent heat fluxes, as well as CO exchange. Each of these quantities may aggravate or mitigate the drought, heat, their side effects on productivity, water scarcity and global warming. We used measurements of 56 eddy covariance sites across Europe to examine the response of fluxes to extreme drought prevailing most of the year 2018 and how the response differed across various ecosystem types (forests, grasslands, croplands and peatlands).

The archives are half-empty: an assessment of the availability of microbial community sequencing data.

As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g.