We investigated immediate and long-term effects on bacterial populations of soil amended with cat... more 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.
We investigated immediate and long-term effects on bacterial populations of soil amended with cat... more 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.
ABSTRACT The impact of different fertilizer treatments on prokaryotic diversity in a Danish urban... more ABSTRACT The impact of different fertilizer treatments on prokaryotic diversity in a Danish urban waste field trial was investigated using tag-encoded amplicon pyrosequencing. The field trial was established in 2003 to investigate the application of urban organic waste as fertilizer in agriculture and to identify the effects on soil quality. The fertilizers (e.g. composted organic household waste, sewage sludge and human urine) contain a large amount of nutrients but possibly also undesirable toxic compounds that may influence the bacterial flora in the soil. A 561 bp fragment of the 16S rRNA gene flanking the V4, V5 and V6 regions, was amplified from each soil sample, tagged and sequenced using pyrosequencing. The major classified bacterial phyla and proteobacterial classes for all treatments were Actinobacteria, Acidobacteria and Betaproteobacteria, while the Crenarchaeota was the most frequent phylum of Archaea. No major changes in the community composition due to different fertilizer treatments were found, demonstrating a high robustness of the soil microbiota. However, some differences were observed e.g. Cyanobacteria were most frequent in the unfertilized soil, in comparison to the soils treated with nitrogen containing fertilizers and Firmicutes had higher occurrence in the soil with the composted household waste compared to all other treatments. Additionally, we used quantitative PCR (qPCR) to quantify specific bacterial groups, and used these numbers to convert the relative abundances of all bacteria obtained by pyrosequencing, to the actual numbers present in one gram of soil. All treatments resulted in a total number of bacteria between 1.99 × 109 and 4.11 × 109 gram−1 soil.
We investigated immediate and long-term effects on bacterial populations of soil amended with cat... more 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.
We investigated immediate and long-term effects on bacterial populations of soil amended with cat... more 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.
ABSTRACT The impact of different fertilizer treatments on prokaryotic diversity in a Danish urban... more ABSTRACT The impact of different fertilizer treatments on prokaryotic diversity in a Danish urban waste field trial was investigated using tag-encoded amplicon pyrosequencing. The field trial was established in 2003 to investigate the application of urban organic waste as fertilizer in agriculture and to identify the effects on soil quality. The fertilizers (e.g. composted organic household waste, sewage sludge and human urine) contain a large amount of nutrients but possibly also undesirable toxic compounds that may influence the bacterial flora in the soil. A 561 bp fragment of the 16S rRNA gene flanking the V4, V5 and V6 regions, was amplified from each soil sample, tagged and sequenced using pyrosequencing. The major classified bacterial phyla and proteobacterial classes for all treatments were Actinobacteria, Acidobacteria and Betaproteobacteria, while the Crenarchaeota was the most frequent phylum of Archaea. No major changes in the community composition due to different fertilizer treatments were found, demonstrating a high robustness of the soil microbiota. However, some differences were observed e.g. Cyanobacteria were most frequent in the unfertilized soil, in comparison to the soils treated with nitrogen containing fertilizers and Firmicutes had higher occurrence in the soil with the composted household waste compared to all other treatments. Additionally, we used quantitative PCR (qPCR) to quantify specific bacterial groups, and used these numbers to convert the relative abundances of all bacteria obtained by pyrosequencing, to the actual numbers present in one gram of soil. All treatments resulted in a total number of bacteria between 1.99 × 109 and 4.11 × 109 gram−1 soil.
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Papers by Lasse Bergmark