Plasmid Detection, Characterization, and Ecology

Abstract

Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. To reduce the cost of plasmid carriage, it is thought that 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 towards environmental change. 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 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.

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera

“…A recently discovered group of BHR plasmids are the PromA plasmids, most of which were isolated by exogenous plasmid capture (Schneiker et al, 2001;Tauch et al, 2002;Van der Auwera et al, 2009;Li et al, 2014;Thomas et al, 2017;Yanagiya et al, 2018), hence originated from unknown hosts. Exogenous plasmid isolation allows capturing conjugative as well as mobilizable plasmids from environmental microorganisms by means of biparental and triparental matings without the need to cultivate the host (Smalla et al, 2015). A few PromA plasmids also originated from proteobacterial isolates (Ito and Iizuka, 1971;Mela et al, 2008;Van der Auwera et al, 2009).…”

Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches

“…Whereas our primers designed to amplify the specific DNA parts, the virtual sequencing allows targeting the random areas, which enables it to be used for de novo sequencing of random DNA fragments. For the experimental generation of truly novel plasmids in their native host, where the genetic material requires a correct assembly, it might be necessary to enrich and purify the plasmid DNA [37]. This can be achieved by closing the sequence gaps between contigs by PCR-amplification and subsequent Sanger sequencing of the PCR-product [37].…”

“…For the experimental generation of truly novel plasmids in their native host, where the genetic material requires a correct assembly, it might be necessary to enrich and purify the plasmid DNA [37]. This can be achieved by closing the sequence gaps between contigs by PCR-amplification and subsequent Sanger sequencing of the PCR-product [37]. In our case, to provide consistent results, we used the same conditions for each experiment, including the design of primers with the same melting temperature, reaction time, and amount of reaction mixture.…”

The plasmid diversity ofAcinetobacter bereziniaeHPC229 provides clues on the ability of the species to thrive on both clinical and environmental habitats

“…Still, a caveat of these schemes is that plasmids lacking Rep or MOB genes escape classification schemes [6]. In this context, the rapid advance of whole genome sequence methodologies (WGS), by providing complete (or near-complete) plasmid sequences, has helped to overcome in part these limitations by providing valuable insights into the evolution of the accesory regions of the plasmids present in particular bacterial groups [7]. Thus, the characterization not only of the plasmid backbone but also of accesory genes including the complete repertoire of mobile genetic elements, and the identification of potential recombinatorial hot spots in the plasmid sequence, may provide many clues on the evolutionary processes that shaped their structures and drove their persistence in a given bacterial group, as well as their potentiality of dissemination to novel hosts [8-12].…”