title: Plasmid Detection, Characterization, and Ecology.
abstract: Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Jechalke
authors.affiliation: University of Idaho, Department of Biological Sciences, 875 Perimeter MS 3051, Moscow, Idaho 83844-3051.
authors.forename: Eva M
authors.initials: EM
authors.lastname: Top
mesh_terms: D000220:Adaptation, Biological; D001419:Bacteria / Q000235:genetics*; D004463:Ecology; D004783:Environmental Microbiology; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D058507:Host Specificity; D010957:Plasmids / Q000032:analysis* / Q000096:biosynthesis* / Q000145:classification