Antibiotics are used in animal livestock production for therapeutic treatment of disease and at subtherapeutic levels for growth promotion and improvement of feed efficiency. It is estimated that approximately 75% of antibiotics are not absorbed by animals and are excreted in waste. Antibiotic resistance selection occurs among gastrointestinal bacteria, which are also excreted in manure and stored in waste holding systems. Land application of animal waste is a common disposal method used in the United States and is a means for environmental entry of both antibiotics and genetic resistance determinants. Concerns for bacterial resistance gene selection and dissemination of resistance genes have prompted interest about the concentrations and biological activity of drug residues and break-down metabolites, and their fate and transport. Fecal bacteria can survive for weeks to months in the environment, depending on species and temperature, however, genetic elements can persist regardless of cell viability. Phylogenetic analyses indicate antibiotic resistance genes have evolved, although some genes have been maintained in bacteria before the modern antibiotic era. Quantitative measurements of drug residues and levels of resistance genes are needed, in addition to understanding the environmental mechanisms of genetic selection, gene acquisition, and the spatiotemporal dynamics of these resistance genes and their bacterial hosts. This review article discusses an accumulation of findings that address aspects of the fate, transport, and persistence of antibiotics and antibiotic resistance genes in natural environments, with emphasis on mechanisms pertaining to soil environments following land application of animal waste effluent.

To monitor the dissemination of resistance genes into the environment, we determined the occurrence of tetracycline resistance (Tc r ) genes in groundwater underlying two swine confinement operations. Monitoring well networks (16 wells at site A and 6 wells at site C) were established around the lagoons at each facility.

Elevated concentrations of sodium (Na+) and chloride (Cl-) in surface and ground water are common in the United States and other countries, and can serve as indicators of, or may constitute, a water quality problem. We have characterized the most prevalent natural and anthropogenic sources of Na+ and Cl- in ground water, primarily in Illinois, and explored techniques that could be used to identify their source. We considered seven potential sources that included agricultural chemicals, septic effluent, animal waste, municipal landfill leachate, sea water, basin brines, and road deicers. The halides Cl-, bromide (Br), and iodide (I) were useful indicators of the sources of Na+-Cl- contamination. Iodide enrichment (relative to Cl-) was greatest in precipitation, followed by uncontaminated soil water and ground water, and landfill leachate. The mass ratios of the halides among themselves, with total nitrogen (N), and with Na+ provided diagnostic methods for graphically distinguishing among sources of Na+ and Cl- in contaminated water. Cl/Br ratios relative to Cl- revealed a clear, although overlapping, separation of sample groups. Samples of landfill leachate and ground water known to be contaminated by leachate were enriched in I and Br; this provided an excellent fingerprint for identifying leachate contamination. In addition, total N, when plotted against Cl/Br ratios, successfully separated water contaminated by road salt from water contaminated by other sources.

Antibiotics are used at therapeutic levels to treat disease; at slightly lower levels as prophylactics; and at low, subtherapeutic levels for growth promotion and improvement of feed efficiency. Over 88% of swine producers in the United States gave antimicrobials to grower/finisher pigs in feed as a growth promoter in 2000. It is estimated that ca. 75% of antibiotics are not absorbed by animals and are excreted in urine and feces. The extensive use of antibiotics in swine production has resulted in antibiotic resistance in many intestinal bacteria, which are also excreted in swine feces, resulting in dissemination of resistance genes into the environment. To assess the impact of manure management on groundwater quality, groundwater samples have been collected near two swine confinement facilities that use lagoons for manure storage and treatment. Several key contaminant indicators - including inorganic ions, antibiotics, and antibiotic resistance genes - were analyzed in groundwater collected from the monitoring wells. Chloride, ammonium, potassium, and sodium were predominant inorganic constituents in the manure samples and served as indicators of groundwater contamination. Based on these analyses, shallow groundwater has been impacted by lagoon seepage at both sites. Liquid chromatography-mass spectroscopy (LC-MS) was used to measure the dissolved concentrations of tetracycline, chlortetracycline, and oxytetracycline in groundwater and manure. Although tetracyclines were regularly used at both facilities, they were infrequently detected in manure samples and then at relatively trace concentrations. Concentrations of all tetracyclines and their breakdown products in the groundwater sampled were generally less than 0.5 microg/L. Bacterial tetracycline resistance genes served as distinct genotypic markers to indicate the dissemination and mobility of antibiotic resistance genes that originated from the lagoons. Applying PCR to genomic DNA extracted from the lagoon and groundwater samples, four commonly occurring tetracycline (tet) resistance genes - tet(M), tet(O), tet(Q), and tet(W) - were detected. The detection frequency of tet genes was much higher in wells located closer to and down-gradient from the lagoons than in wells more distant from the lagoons. These results suggested that in the groundwater underlying both facilities tetracycline resistance genes exist and are somewhat persistent, but that the distribution and potentially the flux for each tet gene varied throughout the study period.

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The adsorption and desorption of atrazine (2‐chloro‐4‐ethylamino‐6‐isopropylamino‐s‐triazine) and a primary metabolite, deethylatrazine (2‐amino‐4‐chloro‐6‐isopropylamino‐s‐triazine; DEA), by low organic C (≤ 3.3 g kg−1) materials were measured by batch‐equilibrium techniques. The adsorbents were samples of glacial outwash sand, till, and stream sediments. The adsorption of both atrazine and DEA conformed to linear isotherms. The adsorption of atrazine by most of the adsorbents yielded apparent Koc values that were in excess of those based on surface agricultural soils. Adsorption correlated with only the pH of the sand‐water suspensions. The desorption of atrazine was hysteretic under the conditions of the measurement. DEA had a lower affinity for the same adsorbents; the mean ratio of Kd values of DEA to those of atrazine was 0.37 ± 0.20. DEA adsorption did not correlate with organic C, surface area, clay content of the adsorbents, or with the pH of the suspensions. DEA adsorption, unlike atrazine, tended to be reversible. There was a linear relationship between the adsorption constants of atrazine and those of DEA.

RNA methylase genes are common antibiotic resistance determinants for multiple drugs of the macrolide, lincosamide, and streptogramin B (MLS(B)) families. We used molecular methods to investigate the diversity, distribution, and abundance of MLS(B) methylases in waste lagoons and groundwater wells at two swine farms with a history of tylosin (a macrolide antibiotic structurally related to erythromycin) and tetracycline usage. Phylogenetic analysis guided primer design for quantification of MLS(B) resistance genes found in tylosin-producing Streptomyces (tlr(B), tlr(D)) and commensal/pathogenic bacteria (erm(A), erm(B), erm(C), erm(F), erm(G), erm(Q)). The near absence of tlr genes at these sites suggested a lack of native antibiotic-producing organisms. The gene combination erm(ABCF) was found in all lagoon samples analyzed. These four genes were also detected with high frequency in wells previously found to be contaminated by lagoon leakage. A weak correlation was found between the distribution of erm genes and previously reported patterns of tetracycline resistance determinants, suggesting that dissemination of these genes into the environment is not necessarily linked. Considerations of gene origins in history (i.e., phylogeny) and gene distributions in the landscape provide a useful "molecular ecology" framework for studying environmental spread of antibiotic resistance.

SummaryA low-diversity microbial community, dominated by the γ-proteobacterium Halomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50°C, pH 8, 181 bars pressure). These highly porous and permeable quartz arenite sandstones are directly analogous to reservoirs around the world targeted for largescale hydrocarbon extraction, as well as subsurface gas and carbon storage. A new downhole lowcontamination subsurface sampling probe was used to collect in situ formation water samples for microbial environmental metagenomic analyses. Multiple lines of evidence suggest that this H. sulfidaerisdominated subsurface microbial community is indigenous and not derived from drilling mud microbial contamination. Data to support this includes V1-V3 pyrosequencing of formation water and drilling mud, as well as comparison with previously published microbial analyses of drilling muds in other sites. Metabolic pathway reconstruction, constrained by the