Abstract
The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e., the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which—despite their frequent occurrence in a large number of bacteria—are largely neglected in prevalent plasmidome conceptions.
Highlights
Ecological impacts of plasmids are beyond doubt
Recording of extra-chromosomal genetic elements of bacterial populations from diverse environments includes culture-dependent or -independent approaches. While the former is self-explanatory, for the latter several methods have proven to facilitate detection and subsequent characterization of novel accessory genetic elements; such as the exogenous plasmid isolation by biparental matings (Bale et al, 1988). It relies on the transfer, replication as well as the expression of selectable markers, or triparental matings (Hill et al, 1992; Smalla et al, 2006) which is based on the ability of Linear plasmids and plasmidome genetic elements to transfer small mobilisable plasmids carrying selectable markers into a new recipient
The plasmidome refers to the entire plasmid DNA of an environmental sample independent of cultivation but should—as a matter —include the elements isolated from bacteria that have been isolated and cultured
Summary
Ecological impacts of plasmids are beyond doubt. In a given environment such accessory genetic elements (when they have the capacity to integrate into the genome occasionally termed episomes) commonly carry information that is—under given circumstances—beneficial for their prokaryotic host cells. Plasmid-encoded qualities include virulence factors, resistance to antibiotics, production of antimicrobials, degradation of xenobiotics, and functions involved in bacteria–host interactions (Smalla et al, 2000c). Those conferring conjugative capabilities facilitate horizontal gene transfer. Recording of extra-chromosomal genetic elements of bacterial populations from diverse environments includes culture-dependent or -independent approaches While the former is self-explanatory, for the latter several methods have proven to facilitate detection and subsequent characterization of novel accessory genetic elements; such as the exogenous plasmid isolation by biparental matings (Bale et al, 1988). It relies on the transfer, replication as well as the expression of selectable markers, or triparental matings (Hill et al, 1992; Smalla et al, 2006) which is based on the ability of
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