The release of anthropogenic chemicals into the environment is vast and frequently hazardous. For instance, millions of kg of antibiotics are used each year in agriculture in the US and are released into the environment, and correlates with and likely contributes to antibiotic resistance in human pathogens, rendering some infections as untreatable. A second class of chemicals is persistent organic pollutants, such as dioxins, which are immune disruptors and are priority pollutants requiring remediation from the environment. Bacteria respond to chemical perturbation, in order to survive, in many ways: activation of antibiotic resistance genes (ARGs), horizontal gene transfer, transcription of degradative pathway genes, and other related systems such as toxic shock response. Often we use molecular methods to monitor the bacterial community responses and we have reviewed, analyzed, developed and validated hundreds of PCR primer sets specific to ARGs and aromatic carbon metabolism. We have found that in-feed antibiotics increase the abundance and diversity of ARGs both in individual swine, as well as farm-wide in manure, compost and soil amended with compost. Resistance gene abundance correlates with transposase abundance, indicating that the resistance genes may be genetically mobile and represents a potential risk to medical antibiotic treatment in humans. Using gene-targeted metagenomics we see that the diversity of dioxygenases which degrade dioxins exist in a greater extent than we currently have characterized. We went on to isolate a novel dibenzofuran-degrading consortium consisting of Agromyces sp., Bacillales sp. and Comamonadaceae sp, which completely degrade dibenzofuran. This consortium can also cometabolize chlorinated dioxins including 2,3- dichlorodibenzo-p-dioxin. Microorganisms respond to anthropogenic pollution in order to survive; however, the response may have positive or negative human implications, both threatening human health (in the case of antibiotic resistance genes) or aid in the removal of toxic chemicals (in the case of dioxins).
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