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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.
MULTIFILE
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.
MULTIFILE
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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De ambitie is het ontwikkelen van een toegespitste homogeniserende egalisatiemachine inclusief een in de grond flexibel in te bouwen sensorisch meetsysteem voor het implementeren van een innovatieve meetopstelling in het Aeres Innovation Centre (Bodem Band Bassin). In het Bodem Band Bassin wordt in kaart gebracht welke bodemdruk ontstaat door banden- of trackkeus en band/track afstelling bij inzet van machines en werktuigen. Essentie bij onderzoek in het BBB is het preventief zoeken naar de mogelijkheden om de ondergrondverdichting te minimaliseren. Dit stimuleert duurzaam bodembeheer in de landbouw en maakt ondernemers bewust van hoe de afstelling tussen bandformaat, bandafstelling, gewicht werktuig en bodemgesteldheid op elkaar afgestemd kunnen worden. In dit project wordt een, eerder zelf ontwikkelt, sensorisch meetsysteem doorontwikkeld en toepasbaar gemaakt voor vertalingen naar praktijksituaties. Na één test is de bodem in het bassin verstoord en daarom moet na elke meting de voorgaande bodemsituatie hersteld worden. Daarvoor wordt in dit project via een morfologische analyse een werktuigbouwkundig constructieplan ontwikkeld zodat na afronding van dit project een dergelijke homogeniserende egalisatiemachine gebouwd kan worden. De essentie van de onderzoeksvraag van dit project ligt in het uitwerken van de zelf ontwikkelde meetopstelling en daarbij gebruik maken van bestaande kennis rondom band- en sensortechniek en bodemkunde. Door de meetopstelling en het egalisatiewerktuig op de tekentafel samen met de telers en mechanisatiebedrijven door te ontwikkelen in een praktijksetting vergroten we het inzicht in de (on)mogelijkheden van deze toepassing en kunnen we een innovatie ontwikkelen die nauw aansluit op de wens van telers zo min mogelijk bodemdruk te veroorzaken. Het ultieme doel is om ondergrondverdichting in de landbouw een halt toe te roepen. Op basis van dit project wordt een groter onderzoeksvoorstel geschreven waar de lectoraten Precisielandbouw (Aeres), Duurzaam Bodembeheer (Aeres) en Mechatronica (Saxion) samen het initiatief in nemen.
Plastic products are currently been critically reviewed due to the growing awareness on the related problems, such as the “plastic soup”. EU has introduced a ban for a number of single-use consumer products and fossil-based polymers coming in force in 2021. The list of banned products are expected to be extended, for example for single-use, non-compostable plastics in horticulture and agriculture. Therefore, it is crucial to develop sustainable, biodegradable alternatives. A significant amount of research has been performed on biobased polymers. However, plastics are made from a polymer mixed with other materials, additives, which are essential for the plastics production and performance. Development of biodegradable solutions for these additives is lacking, but is urgently needed. Biocarbon (Biochar), is a high-carbon, fine-grained residue that is produced through pyrolysis processes. This natural product is currently used to produce energy, but the recent research indicate that it has a great potential in enhancing biopolymer properties. The biocarbon-biopolymer composite could provide a much needed fully biodegradable solution. This would be especially interesting in agricultural and horticultural applications, since biocarbon has been found to be effective at retaining water and water-soluble nutrients and to increase micro-organism activity in soil. Biocarbon-biocomposite may also be used for other markets, where biodegradability is essential, including packaging and disposable consumer articles. The BioADD consortium consists of 9 industrial partners, a branch organization and 3 research partners. The partner companies form a complementary team, including biomass providers, pyrolysis technology manufacturers and companies producing products to the relevant markets of horticulture, agriculture and packaging. For each of the companies the successful result from the project will lead to concrete business opportunities. The support of Avans, University of Groningen and Eindhoven University of Technology is essential in developing the know-how and the first product development making the innovation possible.
Circular BIOmass CAScade to 100% North Sea Region (NSR) economic activity and growth are mostly found in urban areas. Rural NSR regions experience population decline and negative economic growth. The BIOCAS project expects revitalizing and greening of rural areas go hand in hand. BIOCAS will develop rural areas of the NSR into smart specialized regions for integrated and local valorization of biomass. 13 Commercial running Bio-Cascade-Alliances (BCA’s) will be piloted, evaluated and actively shared in the involved regions. These proven concepts will accelerate adoption of high to low value bio-cascading technologies and businesses in rural regions. The project connects 18 regional initiatives around technologies, processes, businesses for the conversion of biomass streams. The initiatives collaborate in a thematic approach: Through engineering, value chain assessments, BCA’s building, partners tackle challenges that are shared by rural areas. I.e. unsustainable biomass use, a mineral surplus and soil degradation, deprivation of potentially valuable resources, and limited involvement of regional businesses and SMEs in existing bio-economy developments. The 18 partners are strongly embedded in regional settings, connected to many local partners. They will align stakeholders in BCA’s that would not have cooperated without BIOCAS interventions. Triple helix, science, business and governmental input will realize inclusive lasting bio cascade businesses, transforming costly waste to resources and viable business.Interreg IVB North Sea Region Programme: €378,520.00, fEC % 50.00%1/07/17 → 30/06/21