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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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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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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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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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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VHL University of Applied Sciences (VHL) is a sustainable University of AppliedSciences that trains students to be ambitious, innovative professionals andcarries out applied research to make a significant contribution to asustainable world. Together with partners from the field, they contribute to innovative and sustainable developments through research and knowledge valorisation. Their focus is on circular agriculture, water, healthy food & nutrition, soil and biodiversity – themes that are developed within research lines in the variousapplied research groups. These themes address the challenges that are part ofthe international sustainability agenda for 2030: the sustainable developmentgoals (SDGs). This booklet contains fascinating and representative examplesof projects – completed or ongoing, from home and abroad – that are linked tothe SDGs. The project results contribute not only to the SDGs but to their teaching as well.
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Plasmid-mediated dissemination of antibiotic resistance among fecal Enterobacteriaceae in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural Escherichia coli strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10–1) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (−3 logs for synthetic wastewater; −6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.
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Permanent grassland soils can act as a sink for carbon and may therefore positively contribute to climate change mitigation and adaptation. We compared young (5–15 years since latest grassland renewal) with old (>20 years since latest grassland renewal) permanent grassland soils in terms of carbon stock, carbon sequestration, drought tolerance and flood resistance. The research was carried out on marine clay soil at 10 dairy farms with young and old permanent grassland. As hypothesized, the carbon stock was larger in old grassland (62 Mg C ha−1) topsoil (0–10 cm) than in young grassland topsoil (51 Mg C ha−1). The carbon sequestration rate was greater in young (on average 3.0 Mg C ha−1 year−1) compared with old grassland (1.6 Mg C ha−1 year−1) and determined by initial carbon stock. Regarding potential drought tolerance, we found larger soil moisture and soil organic matter (SOM) contents in old compared with young grassland topsoils. As hypothesized, the old grassland soils were more resistant to heavy rainfall as measured by water infiltration rate and macroporosity (at 20 cm depth) in comparison with the young grassland soils. In contrast to our hypothesis we did not find a difference in rooting between young and old permanent grassland, probably due to large variability in root biomass and root tip density. We conclude that old grasslands at dairy farms on clay soil can contribute more to the ecosystem services climate change mitigation and climate change adaptation than young grasslands. This study shows that under real farm conditions on a clay topsoil, carbon stock increases with grassland age and even after 30 years carbon saturation has not been reached. Further study is warranted to determine by how much extending grassland age can contribute to climate change mitigation and adaptation.
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Renewing agricultural grasslands for improved yields and forage quality generally involves eliminating standing vegetation with herbicides, ploughing and reseeding. However, grassland renewal may negatively affect soil quality and related ecosystem services. On clay soil in the north of the Netherlands, we measured grass productivity and soil chemical parameters of ‘young’ (5–15 years since last grassland renewal) and ‘old’ (>20 years since last grassland renewal) permanent grasslands, located as pairs at 10 different dairy farms. We found no significant difference with old permanent grassland in herbage dry matter yield and fertilizer nitrogen (N) response, whereas herbage N yield was lower in young permanent grassland. Moreover, the young grassland soil contained less soil organic matter (SOM), soil organic carbon (C) and soil organic N compared to the old grassland soil. Grass productivity was positively correlated with SOM and related parameters such as soil organic C, soil organic N and potentially mineralizable N. We conclude that on clay soils with 70% desirable grasses (i.e., Lolium perenne and Phleum pratense) or more, the presumed yield benefit of grassland renewal is offset by a loss of soil quality (SOM and N-total). The current practice of renewing grassland after 10 years without considering the botanical composition, is counter-productive and not sustainable.
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Sustainable urban drainage systems (SuDS) such as swales are designed to collect, store and infiltrate a large amount of surface runoff water during heavy rainfall. Stormwater is known to transport pollutants, such as particle-bound heavy metals, which are known to often accumulate in the topsoil. In this study, a portable XRF instrument is used to provide in situ spatial characterization of soil pollutants. The method uses portable XRF measurements of heavy metals along profiles with set intervals (1 meter) to cover the swale with cross-sections, across the inlet, the deepest point and the outlet. Soil samples are collected, and the In-Situ measurements are verified by the results from laboratory analyses. Stormwater is here shown to be the transporting media for the pollutants, so it is of importance to investigate areas most prone to flooding and infiltration. This quick scan method is time and cost-efficient, easy to execute and the results are comparable to any known (inter)national threshold criteria for polluted soils. The results are of great importance for all stakeholders in cities that are involved in climate adaptation and implementing green infrastructure in urban areas. However, too little is still known about the long-term functioning of the soil-based SuDS facilities.
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