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

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We investigated immediate and long-term effects on bacterial populations of soil amended with cattle manure, sewage sludge or municipal solid waste-compost in an on-going agricultural field trial. Soils were sampled in weeks 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil-bacterial community structure was investigated using 16S-rRNA amplicon pyrosequencing. Bacterial community structure at phylum-level remained mostly unaffected. Actinobacteria, Proteobacteria and Chloroflexi were the most prevalent phyla significantly responding to sampling time. Seasonal changes seemed to prevail with decreasing bacterial richness in 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 in week 0, indicating a temporary increase in prevalence of transferable antibiotic resistance genes. This article is protected by copyright. All rights reserved.

Original languageEnglish
JournalF E M S Microbiology Ecology
Issue number1
Pages (from-to)206-224
Number of pages19
Publication statusPublished - 2014

ID: 120837755