Plasmids foster diversification and adaptation of bacterial populations in soil

Abstract

It is increasingly being recognized that the transfer of conjugative plasmids across species boundaries plays a vital role in the adaptability of bacterial populations in soil. There are specific driving forces and constraints of plasmid transfer within bacterial communities in soils. Plasmid-mediated genetic variation allows bacteria to respond rapidly with adaptive responses to challenges such as irregular antibiotic or metal concentrations, or opportunities such as the utilization of xenobiotic compounds. Cultivation-independent detection and capture of plasmids from soil bacteria, and complete sequencing have provided new insights into the role and ecology of plasmids. Broad host range plasmids such as those belonging to IncP-1 transfer a wealth of accessory functions which are carried by similar plasmid backbones. Plasmids with a narrower host range can be more specifically adapted to particular species and often transfer genes which complement chromosomally encoded functions. Plasmids seem to be an ancient and successful strategy to ensure survival of a soil population in spatial and temporal heterogeneous conditions with various environmental stresses or opportunities that occur irregularly or as a novel challenge in soil.

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

“…It is tempting to explain the persistence of plasmids and other mobile genetic elements by the benefits they bring to a bacterial community, for example as a communal gene pool (3) or by increasing robustness to environmental uncertainty (14). However, it is hard to envisage how selection might maintain mobile elements for the benefit of the community in the long term if they are costly for the individual cell in the short term (5).…”

“…Plasmids can be shared by a considerable fraction of the microbial community (13), but surprisingly there have been few experimental tests of how the presence of alternative hosts affects plasmid population dynamics, particularly over periods longer than a few days. Moreover, most studies of plasmid dynamics have been performed in well-mixed rich laboratory media, which do not adequately represent the physical structure or nutrient availability in most natural microbial communities (14,15). Structured communities may present fewer opportunities for plasmid donors to encounter recipients, but clustering of genotypes in space may promote species coexistence (16) and also allow plasmids to rapidly sweep through naïve recipient populations once encountered (17,18).…”

Antibiotic resistance genes in manure-amended soil and vegetables at harvest

“…Manure has been shown to promote the horizontal transfer of ARGs in soils [12]. Furthermore, the rhizosphere of plant is also known as a hot spot of gene transfer [13,14]. The rhizosphere soil is quite different from the bulk soil in their properties, microbial composition, and activity.…”

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

“…For example, extensive gene sharing has been observed throughout the commensal human microbiome, including sharing of genes that enable nutrient acquisition from novel food sources (Hehemann et al, 2010;Smillie et al, 2011), and pathogenicity islands and antibiotic resistance genes in pathogenic microbes Hiramatsu et al, 2001;Forsberg et al, 2012). There is evidence of extensive HGT in other natural habitats, such as soil (Coombs and Barkay, 2004;Heuer and Smalla, 2012) and aquatic environments (McDaniel et al, 2010;Frischer et al, 1994). Although these studies offer valuable insights into the frequency and potential impact of genes that can be transferred in microbial communities, the complexity of these systems makes difficult any further examination of the effects of these HGT events on their evolution and ecology.…”