Effects of veterinary medicines in manure on the abundance and transfer of bacterial antibiotic resistance genes in soil: importance of the rhizosphere and of prepeated manure applications

• Applicant: Professorin Dr. Kornelia Smalla
• Subject Area: Microbial Ecology and Applied Microbiology ; Soil Sciences
• Term: from 2005 to 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 5471428

• Final Report Year: 2014

Final Report Abstract

Large amounts of antibiotics are applied in veterinary medicine and reach agricultural fields by manure fertilization. In soil, the fate of these substances and their effects on the structure and function of bacterial communities and the development and spread of antibiotic resistance genes and mobile genetic elements were largely unknown. However, the respective knowledge is crucial for an assessment of risks associated with the application of antibiotics with manure to agricultural soils and potential effects on human health. In this project we aimed at the assessment of effects of the veterinary medicines amoxicillin (AMX), difloxacin (DIF) and sulfadiazine (SDZ) amended via manure to soils on the abundance, diversity, and mobility of bacterial antibiotic resistance genes in soil bacteria, with special focus on the importance of the rhizosphere, the impact of repeated manure applications and the effects of varying soil moisture conditions. Therefore, manure spiked with antibiotics or collected from treated animals was once or repeatedly applied to agricultural soil in microcosm-, mesocosm- and field experiments and these treatments were compared to soil amended with manure free of antibiotics. The dissipation of the antibiotics in manure, bulk soil and rhizosphere was followed in cooperation with another research group and correlated to the abundance and transferability of resistance genes and mobile genetic elements, measured by quantitative real time PCR, Southern blot hybridization and exogenous plasmid isolation. We could demonstrate that manure itself is a reservoir of transferable antibiotic resistance plasmids of different incompatibility groups. In contrast to the diversity of plasmids and gene cassettes, a similar bacterial community structure and consistently high abundance of sulfonamide resistance genes was observed in field scale manures. The application of manure and antibiotics synergistically increased the abundance of antibiotic resistance genes in soil and their transferability. The repeated application of manure containing antibiotics even caused an accumulation of resistance genes, antibiotics and bacterial responders in bulk soil under controlled microcosm conditions. In the field, this accumulation was neither observed in bulk soil nor in the rhizosphere, which might be due to different reasons such as the lower concentrations of sulfadiazine but also organic matter in the manure from treated pigs, and an accelerated dissipation of SDZ in the rhizosphere. Varying soil moisture conditions were also tested as a possible reason for this discrepancy but seemed to have only a minor influence on the fate and effects of veterinary medicines applied with manure to soil. Mobile genetic elements, which likely play a major role in horizontal spread of resistance genes between manure and soil bacteria, were identified as IncP-1 Epsilon plasmids as well as the in this project firstly described LowGC-type plasmids. These plasmids showed a remarkable diversity of antibiotic resistance genes, the ability to efficiently transfer under soil conditions, and a correlation to antibiotic selective pressure, which strongly suggest that these plasmids are important vectors for the spread of antibiotic resistance in the agro-ecosystem. Competition experiments in soil microcosms comparing the persistence of "Acinetobacter baylyi" BD413 with or without plasmid pHHV216 in soil revealed a fitness advantage of the plasmid carrying strain when the soil was treated with SDZ spiked manure. The results obtained in this project provide significant progress in the understanding of the fate and effects of antibiotics applied with manure to soil and the associated risks for human health.

Publications

• 2007. Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environmental Microbiology, Vol. 9. 2007, Issue 3, pp. 657–666.
  Heuer H., Smalla K.
  
• 2007. Short-term effects of amoxicillin on bacterial communities in manured soil. FEMS Microbiology Ecology, Vol. 62.2007, Issue 3, Pp. 290 - 302.
  Binh C.T.T., Heuer H., Gomes N.C.M., Kotzerke A., Fulle M., Wilke B.M., Schloter M., Smalla K.
  
• 2008. Fate of sulfadiazine administered to pigs and its quantitative effect on the dynamics of bacterial resistance genes in manure and manured soil. Soil Biology and Biochemistry, Vol. 40. 2008, Issue 7, pp. 1892–1900.
  Heuer H., Focks A., Lamshöft M., Smalla K., Matthies M., Spiteller M.
  
• 2008. Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids. FEMS Microbiology Ecology, Vol. 66.2008, Issue 1, Pp. 25 - 37.
  Binh C.T.T., Heuer H., Kaupenjohann M., Smalla K.
  
• 2009. Diverse aadA gene cassettes on class 1 integrons introduced into soil via spread manure. Research in Microbiology, Vol. 160. 2009, Issue 6, pp. 427–433.
  Binh C.T.T., Heuer H., Kaupenjohann M., Smalla K.
  
• 2009. Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content. Environmental Microbiology, Vol. 11. 2009, Issue 4, pp. 937–949.
  Heuer H., Kopmann C., Binh C.T.T., Top E.M., Smalla K.
  
• 2010. Effect of sulfadiazine on abundance and diversity of denitrifying bacteria by determining nirK and nirS genes in two arable sols. Microbial Ecology, Vol. 60. 2010, Issue 4, pp. 703–707.
  Kleineidam K., Sharma S., Kotzerke A., Heuer H., Thiele-Bruhn S., Smalla K., Wilke B.M., Schloter M.
  
• 2011. Accumulation of sulfonamide resistance genes in arable soils due to repeated application of manure containing sulfadiazine. Applied and Environmental Microbiology, Vol. 77. 2011, no. 7, pp. 2527-2530.
  Heuer H., Solehati Q., Zimmerling U., Kleineidam K., Schloter M., Müller T., Focks A., Thiele-Bruhn S., Smalla K.
  
• 2011. Antibiotic resistance gene spread due to manure application on agricultural fields. Current Opinion in Microbiology, Vol. 14. 2011, Issue 3, Pp. 236–243.
  Heuer H., Schmitt H., Smalla K.
  
• 2012. IncP-1ε plasmids are important vectors of antibiotic resistance genes in agricultural systems: diversification driven by class 1 integron gene cassettes. Frontiers in Microbiology, Vol. 3. 2012, Article 2.
  Heuer H., Binh C.T.T., Jechalke S., Kopmann C., Zimmerling U., Krögerrecklenfort E., Ledger T., González B., Top E., Smalla K.
  
• 2013. Abundance and transferability of antibiotic resistance as related to the fate of sulfadiazine in maize rhizosphere and bulk soil. FEMS Microbiology Ecology, Vol. 83. 2013, Issue 1, Pp. 125 - 134.
  Kopmann C., Jechalke S., Rosendahl I., Groeneweg J., Krögerrecklenfort E., Zimmerling U., Weichelt V., Siemens J., Amelung W., Heuer H., Smalla, K.
  
• 2013. Increased abundance and transferability of resistance genes after field application of manure from sulfadiazine-treated pigs. Applied and Environmental Microbiology, vol. 79. 2013, no. 5, pp. 1704-1711.
  Jechalke S, Kopmann C, Rosendahl I, Groeneweg J, Weichelt V, Krögerrecklenfort E, Brandes N, Nordwig M, Ding GC, Siemens J, Heuer H, Smalla K
  
• 2013. Plasmid-mediated fitness advantage of Acinetobacter baylyi in sulfadiazine-polluted soil. FEMS Microbiology Letters 348, 127–132. FEMS Microbiology Letters, Vol. 348. 2013, Issue 2, Pp. 127 - 132.
  Jechalke S., Kopmann C., Richter M., Moenickes S., Heuer H., Smalla K.
  
• 2013. Quantification of IncP-1 plasmid prevalence in environmental samples. Applied and Environmental Microbiology, Vol. 79. 2013, no. 4, pp. 1410-1413.
  Jechalke S., Dealtry S., Smalla K., Heuer H.
  
• 2014. Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine. PLoS One, Vol. 9. 2014, Issue 3: e92958.
  Ding G.C., Radl V., Hai B., Jechalke S., Heuer H., Smalla K., Schloter M.
  
• 2014. Fate and effects of veterinary antibiotics in soil. Trends in Microbiology, Vol. 22. 2014, Issue 9, pp. 536–545.
  Jechalke S., Heuer H., Siemens J., Amelung W., Smalla K.
  
• 2014. Structural and functional response of the soil bacterial community to application of manure from difloxacin-treated pigs. FEMS Microbiology Letters, Vol. 348. 2014, Issue 2, Pp. 127 - 132.
  Jechalke S., Focks A., Rosendahl I., Groeneweg J., Siemens J., Heuer H., Smalla K.
  
• 2014. Widespread dissemination of class 1 integron components in soils and related ecosystems as revealed by cultivation-independent analysis. Frontiers Microbiology, Vol. 4. 2014: 420.
  Jechalke S., Schreiter S., Wolters B., Dealtry S., Heuer H., Smalla K.