Manure application can spread antimicrobial resistance (AMR) from manure to soil and surface water. This study evaluated the role of the soil texture on the dynamics of antimicrobial resistance genes (ARGs) in soils and surrounding surface waters. Six dairy farms with distinct soil textures (clay, sand, and peat) were sampled at different time points after the application of manure, and three representative ARGs sul1, erm(B), and tet(W) were quantified with qPCR. Manuring initially increased levels of erm(B) by 1.5 ± 0.5 log copies/kg of soil and tet(W) by 0.8 ± 0.4 log copies/kg across soil textures, after which levels gradually declined. In surface waters from clay environments, regardless of the ARG, the gene levels initially increased by 2.6 ± 1.6 log copies/L, after which levels gradually declined. The gene decay in soils was strongly dependent on the type of ARG (erm(B) < tet(W) < sul1; half-lives of 7, 11, and 75 days, respectively), while in water, the decay was primarily dependent on the soil texture adjacent to the sampled surface water (clay < peat < sand; half-lives of 2, 6, and 10 days, respectively). Finally, recovery of ARG levels was predicted after 29–42 days. The results thus showed that there was not a complete restoration of ARGs in soils between rounds of manure application. In conclusion, this study demonstrates that rather than showing similar dynamics of decay, factors such as the type of ARG and soil texture drive the ARG persistence in the environment.
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Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.
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Soil organic carbon (SOC) prediction from remote sensing is often hindered by disturbing factors at the soil surface, such as photosynthetic active and non–photosynthetic active vegetation, variation in soil moisture or surface roughness. With the increasing amount of freely available satellite data, recent studies have focused on stabilizing the soil reflectance by building reflectance composites using time series of images. Although composite imagery has demonstrated its potential in SOC prediction, it is still not well established if the resulting composite spectra mirror the reflectance fingerprint of the optimal conditions to predict topsoil properties (i.e. a smooth, dry and bare soil).
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Soil compaction and soil bulk density are key soil properties affecting soil health and soil ecosystem services like crop production, water retention and purification and carbon sequestration. The standard method for soil bulk density measurements using Kopecky rings is very labour intensive, time consuming and leaves notable damage to the field. This study tested a portable gamma ray sensor (RhoC) for in situ bulk density measurements up to 1 m depth. Measurements were made in two agricultural fields in the Netherlands (a sandy clay loam and a sandy soil), with large variation in sub-soil compaction. Keywords: gamma-ray attenuation, in situ measurement, mineral soil, novel sensor technique, RhoC-sensor, soil compaction, soil monitoring, soil organic carbon stocks, soil threat analysis
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The quantification and identification of new plasmid-acquiring bacteria in representative mating conditions is critical to characterize the risk of horizontal gene transfer in the environment. This study aimed to quantify conjugation events resulting from manure application to soils and identify the transconjugants resulting from these events. Conjugation was quantified at multiple time points by plating and flow cytometry, and the transconjugants were recovered by fluorescence-activated cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants were only observed within the first 4 days after manure application and at values close to the detection limits of this experimental system (1.00–2.49 log CFU/g of manured soil, ranging between 10–5 and 10–4 transconjugants-to-donor ratios). In the pool of recovered transconjugants, we found amplicon sequence variants (ASVs) of genera whose origin was traced to soils (Bacillus and Nocardioides) and manure (Comamonas and Rahnella). This work showed that gene transfer from fecal to soil bacteria occurred despite the less-than-optimal conditions faced by manure bacteria when transferred to soils, but these events were rare, mainly happened shortly after manure application, and the plasmid did not colonize the soil community. This study provides important information to determine the risks of AMR spread via manure application.
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Soil quality is directly linked to food quality and quantity. However the globalisation and the pressure to increase the agricultural production results to deterioration of the environment, climate change and a serious threat to human and animal health. Soil contamination effected by the environmental pollution is one of the most pressing issues in the political and expertise debate on food safety within the related EU policies as Common agricultural policy, EU agri-environmental, EU food policy and EU health policy. Numerous studies have shown that heavy metals can accumulate in tissues, subsequently affect organ functions, and disrupt the reproductive, nervous or endocrine system. Therefore, the health status in relation to xenobiotics should be monitored and explored. The international scientific conference „Quality Soil as a Pathway to Healthy Food in the EU- Challenges to 2030“ aimed to highlight challenges of the food and feed management on the EU until 2030, including identification of risk factors for food and feed production, food chain, and sustainable agriculture. At the conference experts from 9 EU countires presented their latest research results related to soil and food quality and their visions and proposals how to decrease the negative effects of contamination of soil and food.
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Precast concrete structures are preferred for facilities with large open areas due to easiness in construction. Such structures are typically composed of individual columns and long-span beams, and are quite flexible and of limited redundancy. In this paper, nonlinear dynamic analyses of a typical such structure are conducted using as excitation 54 ground motions recorded on top of a variety of soils (hard, soft, and liquefied soil sites). The results show that liquefaction-affected level-ground motions systematically impose a greater threat to precast-concrete structures in terms of seismic demand, even when low values of elastic spectral acceleration prevail, as opposed to soft-soil records and even more to hard-soil ones. Thus, elastic spectral acceleration appears to be an insufficient engineering demand parameter for design. Soil effects, the “signature” of which is born on ground motions, are first uncovered using wavelet analysis to detect the evolution of the energy and frequency content of the ground motion in the time domain. From this, the changes in effective (“dominant”) excitation period are noted, persuasively attributed to the nature of the soil, and finally correlated with the observed structural behavior.
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Sustainable urban drainage systems (SuDS) or nature-based solutions (NBSs) are widely implemented to collect, store and infiltrate stormwater. The buildup of pollutants is expected in NBSs, and Dutch guidelines advise monitoring the topsoil of bio-swales every 5 years. In the Netherlands, almost every municipality has implemented bio-swales. Some municipalities have over 300 bio-swales, and monitoring all their NBSs is challenging due to cost and capacity. In this study, 20 locations where bio-swales with ages ranging between 10 and 20 years old were selected for a field investigation to answer the following question: is the soil quality of bio-swales after 10 years still acceptable? Portable XRF instruments were used to detect potential toxic elements (PTEs) for in situ measurements. The results showed that for copper (Cu), zinc (Zn) and lead (Pb), 30%, 40% and 25% of the locations show values above the threshold and 5%, 20% and 0% above the intervention threshold, meaning immediate action should be taken. The results are of importance for stakeholders in (inter)national cities that implement, maintain, and monitor NBS. Knowledge of stormwater and soil quality related to long-term health risks from NBS enables urban planners to implement the mostappropriate stormwater management strategies. With these research results, the Dutch guidelines for design, construction, and maintenance can be updated, and stakeholders are reminded that the monitoring of green infrastructure should be planned and executed every 5 years.
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There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil‐borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below‐ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root‐associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil‐borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species‐specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density‐dependent effects of root‐associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity‐ecosystem functioning relationships.
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