TY - JOUR
T1 - 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
AU - Riber, Leise
AU - Poulsen, Pernille Hasse Busk
AU - Abu Al-Soud, Waleed
AU - Hansen, Lea Benedicte Skov
AU - Bergmark, Lasse
AU - Brejnrod, Asker Daniel
AU - Norman, Anders
AU - Hansen, Lars H.
AU - Magid, Jakob
AU - Sørensen, Søren Johannes
N1 - This article is protected by copyright. All rights reserved.
PY - 2014/10/1
Y1 - 2014/10/1
N2 - 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.
AB - 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.
U2 - 10.1111/1574-6941.12403
DO - 10.1111/1574-6941.12403
M3 - Journal article
C2 - 25087596
SN - 0168-6496
VL - 90
SP - 206
EP - 224
JO - F E M S Microbiology Ecology
JF - F E M S Microbiology Ecology
IS - 1
ER -
