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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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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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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Climate change is increasing the challenges for water management worldwide. Extreme weather conditions, such as droughts and heavy rainfall, are increasingly limiting the availability of water, especially for agriculture. Nature-Based Solutions (NBS) offer potential solutions. They help to collect and infiltrate rainwater and thus play an important role in climate adaptation.Green infrastructure, such as rain gardens (sunken plant beds) and wadis (sunken grass fields for temporary storage of rainwater), help to restore the urban water balance. They reduce rainwater runoff, stabilize groundwater levels and solve problems with soil moisture and temperature. Despite these advantages, there is still much ignorance in practice about the possibilities of NBS. To remedy this, freely accessible knowledge modules are being developed that can help governments and future employees to better understand the application of these solutions. This research, called GINA (Green Infrastructure in Urban Areas), aims to create more sustainable and climate-resilient cities by developing and sharing knowledge about NBS, and supports local governments and students in effectively deploying these green infrastructures.
This project has received funding from the Bio-based Industries Joint Undertaking under the European Union's Horizon 2020 research and innovation programme under grant agreement No 720726LIBBIO is a European research project on Andes Lupin (Lupinus mutabilis, tarwi) cropping in marginal lands for enhanced bio economy. Lupin has the ability to fix nitrogen, mobilise soil phosphate and has low nutritional requirements for cultivation. Varieties will be chosen that give high yield of green silage or high yield of seeds which contain more than 20% oil, more than 40% protein and the remaining materials are carbohydrates, mainly oligosaccharides characterized as “prebiotics”. Andes lupin will be grown as a summer crop in N-central Europe and as winter crop in Mediterranean conditions. Pre-industrial processing is developed and optimized for the lupin, properties of the different fractions analysed, their advantage for different industrial use evaluated, and a few products developed as an example. Social and environmental impact will be evaluated as well as techno-economic viability and effect on farm and biorefinery income.This project has received funding from the Bio-based Industries Joint Undertaking under the European Union's Horizon 2020 research and innovation programme under grant agreement No 720726
The project virtually breaks down a large timber structure into pieces and simultaneously simulates and tests each piece in a different laboratory or facility. In this way, unique aspects of each facility can be used at the same time. The experiments take place in a synchronized way, which is a difficult task considering 4 countries (UK, Canada, Greece and the Netherlands) will work at the same time for testing one hypothetical timber structure. Geographically distributed hybrid testing blue sky research, timber structure testing including soil-structure-interactionHYSTERESIS project aims to use geographically distributed hybrid testing for providing experimental evidence for energy dissipation and SSI response of buildings composed of mass timber and CLT panels. The project outcomes will give a boost to the efforts of building multi-story timber structures in areas with wind and/or earthquake loading conditions. The particularities of the problem in hand and the need for testing in large scale while taking into account the SSI, dictate using a novel hybrid testing approach.
