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United States Department of Agriculture

Agricultural Research Service

Title: Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a three-year period

item Koike, S
item Krapac, I
item Oliver, H
item Yannarell, A
item Chee Sanford, Joanne
item Aminov, R
item Mackie, R

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/7/2007
Publication Date: 8/1/2007
Citation: Koike, S., Krapac, I.G., Oliver, H.D., Yannarell, A.C., Chee Sanford, J.C., Aminov, R.I., Mackie, R.I. 2007. Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a three-year period. Applied and Environmental Microbiology. 73(15):4813-4823.

Interpretive Summary: Agricultural soils routinely receive chemical and microbiological inputs through the practice of manure recycling. Microbial processes such as nutrient cycling, herbicide degradation, microbe-microbe interactions, plant-microbe interactions, and cell survival may be directly impacted from the dynamic changes occurring in these soil environments due to external inputs. In this study, we investigated the molecular ecology of tetracycline resistance genes in groundwater underlying two large farms, which routinely apply manure to crop fields at the sites. Antibiotic resistance genes are part of mobile elements that can be transferred between bacteria, frquently along with other important genes such as herbicide degradation genes or metal resistances. Antibiotic resistance genes are also thought to confer a higher competive advantage of bacteria, which may affect the composition of the native soil microbial population. In addition, antibiotic resistances may be important mechanisms in plant root and seed zones, which may in turn affect plant development and microbial growth. The results showed elevated presence and persistence of tetracycline resistance genes following external inputs, however, natural microbial populations also maintained a background level of genes. The impact of this study revealed new knowledge about how genetic elements are maintained in natural environments, and how native populations can adapt to the ecological conditions that surround them. This study was the first long term study to examine the dynamics of genes that may be associated with other important agricultural processes mediated by microbes, and in a broader sense, suggests a mechnism of how native soil microorganisms might acquire and maintain new traits that allow a competitive advantage for their survival and growth.

Technical Abstract: To monitor the dissemination of resistance genes into the environment we determined the occurrence of tetracycline resistance genes (Tcr) in groundwater underlying two swine confinement operations. Monitoring well networks (sixteen wells at Sites A and six wells at Site C) were established around the lagoons at each facility. Groundwater (n = 124) and lagoon (n = 12) samples were collected from the two sites at six sampling times from 2000 through 2003. Total DNA was extracted and PCR was used to detect seven Tcr [tet(M), tet(O), tet(Q), tet(W), tet(C), tet(H) and tet(Z)]. The concentration of Tcr was quantified by real-time qPCR. To confirm the Tcr source in groundwater, comparative analysis of tet(W) gene sequences was performed on groundwater and lagoon samples. All seven Tcr were continually detected in groundwater during the three-year monitoring period at both sites. At Site A, elevated detection frequency and concentration for Tcr were observed in the wells located down-gradient of the lagoon. Comparative analysis of tet(W) sequences revealed that the impacted groundwater contained gene sequences almost identical (99.8% identity) to those found in the lagoon, but these genes were not found in background libraries. Novel sequence clusters and unique indigenous resistance gene pools were also found in the groundwater. Thus, antibiotic resistance genes in groundwater are affected by swine manure, but they are also part of the indigenous gene pool.

Last Modified: 06/26/2017
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