title: Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization.
abstract: 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.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511; Division for Marine and Environmental Research, Rudjer Boskovic Institute, Zagreb 10000, Croatia; and.
authors.forename: Nikolina
authors.initials: N
authors.lastname: Udikovic-Kolic
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511; Biosafety Research, State Laboratory Basel, 4012 Basel, Switzerland.
authors.forename: Fabienne
authors.initials: F
authors.lastname: Wichmann
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511;
authors.forename: Nichole A
authors.initials: NA
authors.lastname: Broderick
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511; jo.handelsman@yale.edu.
authors.forename: Jo
authors.initials: J
authors.lastname: Handelsman
mesh_terms: D000383:Agriculture; D000818:Animals; D000900:Anti-Bacterial Agents / Q000737:chemistry; D001419:Bacteria / Q000235:genetics*; D002417:Cattle; D024881:Drug Resistance, Bacterial; D017753:Ecosystem; D005798:Genes, Bacterial; D023281:Genomics; D008372:Manure; D056186:Metagenomics; D008969:Molecular Sequence Data; D011549:Pseudomonas / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000737:chemistry; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D013449:Sulfonamides / Q000737:chemistry; D013552:Swine; D001618:beta-Lactamases / Q000737:chemistry
chemical_list: D000900:Anti-Bacterial Agents; D008372:Manure; D012336:RNA, Ribosomal, 16S; D012987:Soil; D013449:Sulfonamides; D001618:beta-Lactamases
keywords: dairy cow manure; β-lactam antibiotics