Exploring the immediate –and long-term impact on microbial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for bacterial transfer of antibiotic resistance.. Soil fertilizers and prevalence of antibiotic resistance

We investigated the immediate –and long-term effects on microbial populations of soil amended with cattle manure, sewage sludge and municipal solid waste compost in an on-going agricultural field trial. Soils were sampled at week 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil-microbial community structure was investigated using 16S-rRNA amplicon pyrosequencing. Community structure at phylum-level remained unaffected. Significant increase in Actinobacteria at the expense of Acidobacteria was seen over time. Seasonal changes seemed to prevail with decreasing microbial richness at week 9 followed by a significant increase in week 29 (springtime). The Pseudomonas population richness seemed temporarily affected by fertilizer treatments, especially in sludge- and compost-amended soils. To explain these changes, prevalence of antibiotic –and mercury resistant pseudomonads was investigated. Fertilizer amendment had a transient impact on the resistance profile of the soil community; abundance of resistant isolates decreased with time after fertilizer application, but persistent strains appeared multiresistant, also in unfertilized soil. Finally, the ability of a P. putida strain to take up resistance genes from indigenous soil bacteria by horizontal gene transfer was present only for week 0, indicating a temporary increase in prevalence of resistance encoding mobile genetic elements.