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.

Lineage‐specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group

“…This can be explained by multiple factors, including plasmid chromosomal integration or technical difficulties when isolating very large plasmids from bacteria using methods designed principally for high‐copy small plasmids. Indeed, despite methods available (Kado & Liu, ), obtaining correctly closed genomes of large plasmids remains a methodological challenge (Smalla, Jechalke, & Top, ). Nevertheless, our approach allowed plasmid and chromosomal sequence to be discriminated.…”

Fitness Costs of Plasmids: a Limit to Plasmid Transmission

“…Plasmids are widely distributed across prokaryotes, and help bacteria adapt to a myriad of different environments, conditions, and stresses (3,4), playing a key role in bacterial ecology and evolution (5)(6)(7). The most vivid testimony to the power of plasmids as catalysts for bacterial adaptation is their role in the spread of antibiotic resistance among clinical pathogens (8), which has emerged as a major health problem over the past decades (9).…”

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome

“…Besides, specific methods for genetic labeling allow capturing plasmid sequences in recipient cells for subsequent analysis (reviewed in Ref. ). Classical techniques also use experimentally introduced recipient cells, which receive plasmids from the donor community.…”