Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology

Abstract

IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.

Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

“…Identity cutoff for visual representation was 80%. The plasmids pMLUA1 and pMOL98 are shown as close relatives of pALTS27/pALTS32 and pALTS28, respectively, while R751 and pTL50 ( Shintani et al, 2020 ) are shown as the respective plasmid archetypes of the IncP-1β and IncP-1ɛ groups. Replication, Mating Pair Formation, DNA Transfer, Maintenance and Control, Accessory, and Unknown.…”

Importance of N-Acyl-Homoserine Lactone-Based Quorum Sensing and Quorum Quenching in Pathogen Control and Plant Growth Promotion

“…Horizontal gene transfer (HGT) in the phytosphere is known to occur frequently due to high metabolic activity, microbial density, and positive selection in the rhizosphere/phytosphere [22]. In addition, mobile genetic elements (MGE) such as plasmids of the Inc-P1-group can mediate the exchange between bacterial cells in the rhizosphere, and can thus contribute to the plasticity and dynamic of the genetic content of bacteria [23]. In addition, phenotypic switching (PS) is an ongoing process with much higher probability than HGT, plasmid transfer through MGE, or spontaneous mutations [24].…”

Rhizospheric Communication through Mobile Genetic Element Transfers for the Regulation of Microbe–Plant Interactions

“…Horizontal gene transfer (HGT) among bacteria is a widely known mechanism of MGE transfer in the rhizosphere [27,28]. Among soil bacteria, HGT is a common strategy to spread adaptation-related genes such as those related to antibiotic resistance and heavy metal resistance [29][30][31]. Soil contamination by antibiotics and heavy metals is becoming more widespread as a result of increased anthropogenic activities [32].…”

“…MGE transfers among bacteria for spreading antibiotic and heavy metal resistance are typical examples of MGE-transfer-mediated adaptation to the environment [27,[29][30][31]80]. Cross-kingdom MGE transfers also promote adaptation to the environment.…”