Structural and functional response of the soil bacterial community to application of manure from difloxacin-treated pigs

Jechalke, Sven; Focks, Andreas; Rosendahl, Ingrid; Groeneweg, Joost; Siemens, Jan; Heuer, Holger; Smalla, Kornelia

doi:10.1111/1574-6941.12191

Cited by 69 publications

(47 citation statements)

References 41 publications

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“…It is also possible to monitor environmental selection of antibiotic resistance in bacterial communities by direct quantification of antibiotic resistance genes (ARGs) ( Table 3; Table S1; Jechalke et al, 2014). While there are no standardized assays for quantification of ARGs, non-standard methods employing direct extraction of metagenomic DNA followed by specific amplification of ARG fragments by quantitative real-time PCR are available (Pruden et al, 2006;Zhu et al, 2013).…”

Section: Assessing Impacts On Community Tolerancementioning

confidence: 99%

Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms

Brandt

Amézquita

Backhaus

et al. 2015

Environment International

227

102

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Section: Assessing Impacts On Community Tolerancementioning

confidence: 99%

Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms

Brandt

Amézquita

Backhaus

et al. 2015

Environment International

227

102

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“…Resident soil antibiotic-resistant bacteria were also found to significantly increase following application of manure from cows without antibiotic treatment history . Therefore, compared with the intensively investigated effects of manure from antibiotic-treated animals (Jechalke et al 2014a), the empirical evidence is scare regarding the fate of ARGs derived from antibiotic-free manure, potential co-selection of antibiotic resistance and the impact of manure application on soil resistome.…”

Section: Introductionmentioning

confidence: 99%

Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure

Han

Shi

et al. 2015

FEMS Microbiology Ecology

107

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One sentence summary: The study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Editor: Kornelia Smalla ABSTRACTThe emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.

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“…Along with its impact on the soil resistome, the application of manure can affect the composition and functional properties of soil microbial communities, as has been demonstrated by community fingerprinting (21,24). Recent advances in DNA-based analysis, such as metagenomics and quantitative PCR (qPCR), offer greater precision in such studies, enabling identification of affected community members (25) and their resistance genes (4).…”

mentioning

confidence: 99%

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

Udikovic-Kolic

Wichmann

Broderick

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

493

257

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The increasing prevalence of antibiotic-resistant bacteria is a global threat to public health. Agricultural use of antibiotics is believed to contribute to the spread of antibiotic resistance, but the mechanisms by which many agricultural practices influence resistance remain obscure. Although manure from dairy farms is a common soil amendment in crop production, its impact on the soil microbiome and resistome is not known. To gain insight into this impact, we cultured bacteria from soil before and at 10 time points after application of manure from cows that had not received antibiotic treatment. Soil treated with manure contained a higher abundance of β-lactam–resistant bacteria than soil treated with inorganic fertilizer. Functional metagenomics identified β-lactam–resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria in manure-amended soil was attributable to enrichment of resident soil bacteria that harbor β-lactamases. Quantitative PCR indicated that manure treatment enriched the blaCEP-04 gene, which is highly similar (96%) to a gene found previously in a Pseudomonas sp. Analysis of 16S rRNA genes indicated that the abundance of Pseudomonas spp. increased in manure-amended soil. Populations of other soil bacteria that commonly harbor β-lactamases, including Janthinobacterium sp. and Psychrobacter pulmonis, also increased in response to manure treatment. These results indicate that manure amendment induced a bloom of certain antibiotic-resistant bacteria in soil that was independent of antibiotic exposure of the cows from which the manure was derived. Our data illustrate the unintended consequences that can result from agricultural practices, and demonstrate the need for empirical analysis of the agroecosystem.

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Structural and functional response of the soil bacterial community to application of manure from difloxacin-treated pigs

Cited by 69 publications

References 41 publications

Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms

Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms

Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

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