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Fusarium oxysporum f.sp. lactucae (Fol) causes a vascular disease in lettuce that results in significant yield losses. Race-specific and sensitive real-time PCR assays were developed for Fol races 1 and 4, which are prevalent in Europe. Using genotyping-by-sequencing, unique DNA loci specific to each race were identified and subsequently used for the design of primers and hydrolysis probes. Two assays per race were developed to ensure specificity. The two assays of each race could be run in duplex format, while still giving a sensitivity of 100 fg genomic DNA for all assays. Sample preparation methods were developed for plant tissue, soil, and surfaces, with an extra enrichment step when additional sensitivity was required. By controlling the incubation conditions during the enrichment step, the real-time PCR signal could be matched to the number of spore equivalents in the original sample. When enriching naturally infested soil, down to six conidiospore equivalents L-1 soil could be detected. As enrichment ensures sensitive detection and focuses on living Fol propagules, it facilitates the evaluation of control measures. The developed detection methods for soil and surfaces were applied to samples from commercial lettuce farms and confirmed the prevalence of Fol race 4 in Belgium. Monitoring of soil disinfestation events revealed that despite a dramatic decrease in quantity, the pathogen could still be detected either immediately after sheet steaming or after harvesting the first new crop. The detection method for plant tissue was successfully used to quantify Fol in lettuce inoculated with race 1, race 4 or a combination of both. Under the temperature conditions used, race 4 was more aggressive than race 1, as reflected in larger amounts of DNA of race 4 detected in the roots. These newly developed assays are a promising tool for epidemiological research as well as for the evaluation of control measures. [ABSTRACT FROM AUTHOR]

Bluetongue (BT) is a ruminant viral infectious disease transmitted by Culicoides spp. midges. In 2006, when bluetongue virus serotype 8 (BTV‐8) appeared for the first time in Northern Europe, it rapidly spread and infected a large proportion of animals. BThas a significant economic impact due to a direct effect on animal health and to an indirect effect in disrupting international trade of animals and animal products. In spring 2008, a compulsory subsidized vaccination programme in Europe resulted in a drastic decrease in the number of reported cases. However, due to the turn‐over of the population, without a continuous vaccination programme, the animal population was becoming progressively susceptible. Vaccination would enable Belgium to maintain its status of freedom from infection of BTV‐8 that could possibly be re‐introduced. Subsidizing it could be an incentive to convince more farmers to vaccinate. To finance this programme, both decision‐makers and stakeholders need to be persuaded by the effectiveness and the cost‐benefit of vaccination. The study evaluated the effectiveness of vaccination against BTV‐8 in Belgium. The change in serology which has shown the effectiveness of the vaccine to induce antibody production has been significantly associated with the time between the first injection and the sampling date and the number of injections of the primo‐vaccination. This study also clearly confirms the benefit of vaccination by reducing economic impact of treatment and production losses, especially in dairy cattle. Based on a participating epidemiological approach, a national voluntary and subsidized vaccination was accepted, and permitted Belgium to vaccinate more than 9,000 herds in 1 month. Because this mass vaccination occurred before the vector season, it probably helped Belgium remain free from BTV‐8. [ABSTRACT FROM AUTHOR]

This paper presents a novel technique for the determination of the material damping ratio in shallow soil layers. It is based on the spectral analysis of surface waves (SASW) test. The technique is an alternative to existing methods, where the damping ratio is determined from the spatial decay of the Rayleigh wave. These methods rely on the knowledge of the geometric damping, and may lead to incorrect results if the geometric damping is calculated based on an inaccurate shear wave velocity profile. The existing methods may also lead to incorrect results when higher modes contribute to the wavefield in the soil. In the proposed technique, the wavefield is transformed to the frequency–wavenumber domain. The resulting frequency–wavenumber spectrum exhibits a peak that corresponds to the fundamental Rayleigh wave. The dispersion curve is derived from the peak's position, whereas the attenuation curve is derived from its width, using the half-power bandwidth method. Due to the use of the appropriate wavenumber transformation, this method does not require the calculation of the geometric damping. In addition, the occurrence of higher Rayleigh modes does not affect the attenuation curve associated with the fundamental Rayleigh wave, as higher modes appear as separate peaks in the frequency–wavenumber spectrum that do not interfere with the peak corresponding to the fundamental Rayleigh wave (except at the osculation points). Three benchmark problems are considered to validate the outlined technique; the results are compared with those obtained using existing methods. All methods perform well when applied to a regular soil profile, where the stiffness of the soil increases with depth. For soil profiles with a soft layer trapped between two stiffer layers, or where the soil properties vary smoothly with depth, the proposed technique yields more accurate results than the existing methods. The practical applicability of the new method is finally illustrated using experimental data collected from a test site in Belgium. [ABSTRACT FROM AUTHOR]

Biosecurity seems to be the most promising tool for Campylobacter control on poultry farms. A longitudinal molecular epidemiological study was performed during two production cycles, in which the broilers, the poultry house, and the environment of 10 (mixed) broiler farms were monitored weekly. Cecal droppings from the second production cycle were also used for 16S metabarcoding to study the differences in the microbiota of colonized and uncolonized flocks. Results showed that 3 out of 10 farms were positive for Campylobacter in the first production cycle, and 4 out of 10 were positive in the second. Broilers became colonized at the earliest when they were four weeks old. The majority of the flocks (57%) became colonized after partial depopulation. Before colonization of the flocks, Campylobacter was rarely detected in the environment, but it was frequently isolated from cattle and swine. Although these animals appeared to be consistent carriers of Campylobacter, molecular typing revealed that they were not the source of flock colonization. In accordance with previous reports, this study suggests that partial depopulation appears to be an important risk factor for Campylobacter introduction into the broiler house. Metabarcoding indicated that two Campylobacter-free flocks carried high relative abundances of Megamonas in their ceca, suggesting potential competition with Campylobacter. [ABSTRACT FROM AUTHOR]

The objective of this study was to analyze if maternal supply of rumen-protected protein during the dry period can affect the IgG concentration and microbial composition of colostrum and the IgG absorption and fecal microbial composition in the calf. Seventy-four multiparous Holstein Friesian (HF) dairy cows were stratified per parity and randomly assigned to one of 2 different dry period diets, a diet with a low crude protein (CP) level (LP) and a diet with a high CP level (HP) by addition of rumen-undegraded protein (RUP; formaldehyde-treated soybean meal, Mervobest, Nuscience, Drongen, Belgium). Colostrum was collected within 1 h after calving and IgG concentration was quantified by radial immunodiffusion analysis. Forty-nine calves (23 female and 26 male) were enrolled in the trial with a 2 × 2 factorial design, with prenatal and postnatal treatment as the 2 independent variables. This led to 4 experimental groups: LPLP, LPHP, HPLP, and HPHP, in which the first 2 letters refer to the prenatal treatment (diet of the dam) and the last 2 refer to the postnatal treatment (diet of the colostrum-producing cow). Calves received 3× 2 L of colostrum within 2, 6, and 24 h after birth. Meconium and feces were collected solely from female calves (n = 18) by digital palpation of the rectum, immediately after birth and before colostrum administration and at d 3 of age. Microbial DNA was extracted from meconium (n = 9), feces (n = 15), and colostrum (n = 49). Amplicon sequencing of the bacterial V3-V4 region of the 16S rRNA gene was performed for characterization of the bacterial communities. Colostrum IgG concentration was higher in cows that were supplemented with RUP, especially in cows entering their second lactation (LSM ± SEM 61.3 ± 2.3 vs. 55.2 ± 2.8 g of IgG/L). Calves born out of LP cows that received colostrum from HP cows (LPHP) had a lower serum IgG level compared with HPHP and LPLP calves (LSM ± SEM 14.2 ± 1.3 vs. 18.8 ± 1.2 and 20.9 ± 1.3 g of IgG/L in HPHP and LPLP, respectively). The most abundant phyla in colostrum were Proteobacteria (48.2%), Firmicutes (24.8%), Bacteroidetes (9.5%), and Actinobacteria (5.0%). The most abundant phyla in calf meconium and feces were Firmicutes (42.5 and 47.5%), Proteobacteria (21.7% and 33.7%), Bacteroidetes (16.8% and 15.7%), and Actinobacteria (2.9% and 3.1%). There was no difference in the overall microbial communities between colostrum from HP and LP cows. However, 2 genera (both members of the family Lachnospiraceae) were more abundant in colostrum from HP cows compared with LP cows. The microbial composition of meconium, feces and colostrum differed from each other. Fecal samples were more similar to each other and are characterized by a lower intersample diversity compared with colostrum and meconium samples. To conclude, increasing the CP level by addition of RUP in the dry period diet affected the colostrum IgG concentration and the transfer of passive immunity, but did not change the overall microbial composition of colostrum nor of meconium and feces in the calf. [ABSTRACT FROM AUTHOR]

• Biomass of oligotrophic indicator species dropped above 11.5 mg P Olsen kg−1. • The experimental P Olsen threshold is comparable to the threshold in remnant fields. • Oligotrophic indicator species' relative biomass was high if total biomass was low. • Oligotrophic indicator species persisted in phosphorus-poor mesocosms. The restoration of Nardus grasslands is often hampered by high bioavailability of soil phosphorus and disturbed soil communities. In order to better understand these bottlenecks, we studied Nardus grassland species grown together in communities with fast-growing species in 50-liter pots along a gradient of bioavailable phosphorus with or without inoculated soil biota. These mesocosms allowed the plants to freely interact, including competition for light and nutrients. We investigated changes in the plant community composition along the phosphorus gradient using Threshold Indicator Taxa Analysis (TITAN). We found a negative threshold of 11.5 mg P Olsen kg−1 with six significant indicator plant species. Above the threshold, a small increase in phosphorus resulted in a disproportionally large drop in biomass for the indicator species, including four typical Nardus grassland species. The decline in these 'oligotrophic indicator species' was also linked to increasing plant community biomass, so we suggest the oligotrophic indicator species to be outcompeted for light by fast-growing plant species. We did not find an effect of the soil biota treatment on the biomass of the oligotrophic indicator species, but did observe a positive effect of inoculation with soil biota on the total biomass of the plant community. Interestingly, the threshold for the plant communities in the mesocosm experiment was comparable to the upper bioavailable phosphorus concentrations in remnant Nardus grasslands in northern Belgium. For the restoration of Nardus grasslands, such phosphorus-poor soil conditions appear to be essential, because the plant species that typically occur in these grasslands are able to handle nutrient limitation, but not light limitation. [ABSTRACT FROM AUTHOR]

Horizon scans have emerged as a valuable tool to anticipate the incoming invasive alien species (IAS) by judging species on their potential impacts. However, little research has been conducted on quantifying actual impacts and assessing causes of species-specific vulnerabilities to particular IAS due to persistent methodological challenges. The underlying interspecific mechanisms driving species-specific vulnerabilities therefore remain poorly understood, even though they can substantially improve the accuracy of risk assessments. Given that interspecific interactions underlying ecological impacts of IAS are often shaped by phenological synchrony, we tested the hypothesis that temporal mismatches in breeding phenology between native species and IAS can mitigate their ecological impacts. Focusing on the invasive American bullfrog (Lithobates catesbeianus), we combined an environmental DNA (eDNA) quantitative barcoding and metabarcoding survey in Belgium with a global meta-analysis, and integrated citizen-science data on breeding phenology. We examined whether the presence of native amphibian species was negatively related to the presence or abundance of invasive bullfrogs and whether this relationship was affected by their phenological mismatches. The field study revealed a significant negative effect of increasing bullfrog eDNA concentrations on native amphibian species richness and community structure. These observations were shaped by species-specific vulnerabilities to invasive bullfrogs, with late spring- and summer-breeding species being strongly affected, while winter-breeding species remained unaffected. This trend was confirmed by the global meta-analysis. A significant negative relationship was observed between phenological mismatch and the impact of bullfrogs. Specifically, native amphibian species with breeding phenology differing by 6 weeks or less from invasive bullfrogs were more likely to be absent in the presence of bullfrogs than species whose phenology differed by more than 6 weeks with that of bullfrogs. Taken together, we present a novel method based on the combination of aqueous eDNA quantitative barcoding and metabarcoding to quantify the ecological impacts of biological invaders at the community level. We show that phenological mismatches between native and invasive species can be a strong predictor of invasion impact regardless of ecological or methodological context. Therefore, we advocate for the integration of temporal alignment between native and IAS's phenologies into invasion impact frameworks., (© 2024 The Ecological Society of America.)

For centuries, multicellular organisms have lived in symbiosis with microorganisms. The interaction with microorganisms has been shown to be very beneficial for humans and animals. During a natural birth, the initial inoculation with bacteria occurs when the neonate passes through the birth canal. Colostrum and milk intake are associated with the acquisition of a healthy gut flora. However, little is known about the microbial composition of bovine colostrum and the possible beneficial effects for the neonatal calf. In this prospective cohort study, the microbial composition of first-milking colostrum was analyzed in 62 Holstein Friesian (HF) and 46 Belgian Blue (BB) cows by performing amplicon sequencing of the bacterial V3-V4 region of the 16S rRNA gene. Calves received, 3 times, 2 L of their dam's colostrum within 24 h after birth. Associations between colostral microbial composition and its IgG concentration, as well as each calf's serum IgG levels, were analyzed. Colostrum samples were dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. The 10 most abundant genera in the complete data set were Acinetobacter (16.2%), Pseudomonas (15.1%), a genus belonging to the Enterobacteriaceae family (4.9%), Lactococcus (4.0%), Chryseobacterium (3.9%), Staphylococcus (3.6%), Proteus (1.9%), Streptococcus (1.8%), Enterococcus (1.7%), and Enhydrobacter (1.5%). The remaining genera (other than these top 10) accounted for 36.5% of the counts, and another 8.7% were unidentified. Bacterial diversity differed significantly between HF and BB samples. Within each breed, several genera were found to be differentially abundant between colostrum of different quality. Moreover, in HF, the bacterial composition of colostrum leading to low serum IgG levels in the calf differed from that of colostrum leading to high serum IgG levels. Results of the present study indicate that the microbes present in colostrum are associated with transfer of passive immunity in neonatal calves., (© 2022, The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

The introduction, transmission, and persistence of Listeria monocytogenes in Belgian beef slaughterhouses was investigated using genetic characterization. During slaughter, samples were taken of the hide, carcass, and environment to detect the pathogen. Remarkably, L. monocytogenes was massively present on the hide of incoming animals (93%; 112/120), regardless of their visual cleanliness, which implies high contamination pressure levels entering the slaughterhouses. Pathogen transfer via cross-contamination was conclusively confirmed in this study, with the same pulsotypes isolated from the hide, carcass, and environmental samples. Despite the important bacterial presence on the hide of incoming animals, most slaughterhouses succeeded in limiting the transfer as cause of carcass contamination. Persistence along the slaughter line seemed to be a more significant problem, as it was clearly linked to most of the L. monocytogenes positive carcasses. In one slaughterhouse, whole genome sequencing (WGS) revealed that the carcass splitter had been contaminating carcasses with the same strain belonging to CC9 for more than one year., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)