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

• Published in: FEMS microbiology ecology Vol. 90; no. 1; pp. 206 - 224
• Main Authors: Riber, Leise, Poulsen, Pernille H.B., Al-Soud, Waleed A., Skov Hansen, Lea B., Bergmark, Lasse, Brejnrod, Asker, Norman, Anders, Hansen, Lars H., Magid, Jakob, Sørensen, Søren J.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.10.2014; Oxford University Press
• Subjects: Agricultural land; Animal wastes; Animals; Antibiotic resistance; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; bacterial diversity; Biodiversity; Cattle; Cattle manure; Community structure; compost; Composts; Drug Resistance, Microbial - genetics; Ecology; Fertilizer application; Fertilizers; Gene Transfer, Horizontal; horizontal gene transfer; Manure; Mercury; Microbiology; Municipal solid waste; Organic wastes; Pseudomonas - drug effects; Pseudomonas - genetics; Pseudomonas - isolation & purification; Recycling; Sequence Analysis, DNA; Sewage; Sewage sludge; sludge; Soil amendment; Soil Microbiology; Soil profiles; bacterial diversity; sludge; manure; antibiotic resistance; horizontal gene transfer; compost
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/1574-6941.12403

Abstract 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 ongoing 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. Amplicon sequencing indicates that 16S rRNA gene agricultural soil bacterial communities are highly resilient towards amendment with animal and urban organic waste fertilizers. Amplicon sequencing indicates that 16S rRNA gene agricultural soil bacterial communities are highly resilient towards amendment with animal and urban organic waste fertilizers.