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

Leise Riber; Pernille Hasse Busk Poulsen; Waleed Abu Al-Soud; Lea Benedicte Skov Hansen; Lasse Bergmark; Asker Daniel Brejnrod; Anders Norman; Lars H. Hansen; Jakob Magid; Søren Johannes Sørensen

doi:10.1111/1574-6941.12403

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

Leise Riber, Pernille Hasse Busk Poulsen, Waleed Abu Al-Soud, Lea Benedicte Skov Hansen, Lasse Bergmark, Asker Daniel Brejnrod, Anders Norman, Lars H. Hansen, Jakob Magid, Søren Johannes Sørensen

42 Citations (Scopus)

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.

Original language	English
Journal	F E M S Microbiology Ecology
Volume	90
Issue number	1
Pages (from-to)	206-224
Number of pages	19
ISSN	0168-6496
DOIs	https://doi.org/10.1111/1574-6941.12403
Publication status	Published - 1 Oct 2014

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Riber, L., Poulsen, P. H. B., Abu Al-Soud, W., Hansen, L. B. S., Bergmark, L., Brejnrod, A. D., Norman, A., Hansen, L. H., Magid, J., & Sørensen, S. J. (2014). 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. F E M S Microbiology Ecology, 90(1), 206-224. https://doi.org/10.1111/1574-6941.12403

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. / Riber, Leise; Poulsen, Pernille Hasse Busk; Abu Al-Soud, Waleed et al.

In: F E M S Microbiology Ecology, Vol. 90, No. 1, 01.10.2014, p. 206-224.

Research output: Contribution to journal › Journal article › Research › peer-review

Riber, L, Poulsen, PHB, Abu Al-Soud, W, Hansen, LBS, Bergmark, L, Brejnrod, AD, Norman, A, Hansen, LH , Magid, J & Sørensen, SJ 2014, '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', F E M S Microbiology Ecology, vol. 90, no. 1, pp. 206-224. https://doi.org/10.1111/1574-6941.12403

Riber L, Poulsen PHB, Abu Al-Soud W, Hansen LBS, Bergmark L, Brejnrod AD et al. 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. F E M S Microbiology Ecology. 2014 Oct 1;90(1):206-224. doi: 10.1111/1574-6941.12403

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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.",

author = "Leise Riber and Poulsen, {Pernille Hasse Busk} and {Abu Al-Soud}, Waleed and Hansen, {Lea Benedicte Skov} and Lasse Bergmark and Brejnrod, {Asker Daniel} and Anders Norman and Hansen, {Lars H.} and Jakob Magid and S{\o}rensen, {S{\o}ren Johannes}",

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