Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes

Abstract

Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-hostrange plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (␤ and ) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1␤ plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1␤ plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1␤ plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.

A Novel Mercuric Reductase from the Unique Deep Brine Environment of Atlantis II in the Red Sea

“…We then compared the catalytic properties of the enzymes, and we performed comprehensive site-directed mutagenesis to dissect and understand the structural features that contribute to the enzyme's halophilicity, thermostability, and high resistance to Hg 2ϩ . The results show that the amino acid sequence of MerA ATII-LCL differs from that of its mesophilic ortholog from an uncultured soil microorganism (35) by just 9%. Yet, the two enzymes differ strikingly in their properties and responses to three abiotic factors.…”

“…An ORF that showed Ͼ90% homology to a mercuric reductase from a soil bacterium (35) was identified in the assembled reads. To rule out the possibility that the ATII-LCL MerA ORF sequence obtained from assembled metagenomic reads might be the product of chimeric sequences, we decided to amplify the sequence of the identified ORF using ATII-LCL environmental DNA and two perfectly matched oligonucleotides deduced from the sequence of the soil and ATII-LCL orthologs.…”

“…The metagenome-derived MerA enzyme from the ATII-LCL described here reveals simple and limited alterations in the primary structure of the protein relative to that of an ortholog from a terrestrial environment (35). These are reflected in critical shifts in the catalytic properties of the enzyme that allow for efficient function under the extreme conditions of its marine habitat.…”

Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

“…Studies that selected for plasmids carrying specific traits appear to show noticeably lower plasmid diversity. For example, at least 14 of the 19 BHR plasmids captured from agricultural soils belonged to the IncP-1 group (76,77). Of the 12 plasmids captured from activated sludge, 10 were members of the IncP-1 group (66).…”

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

“…Plasmid survival under positive selection has important consequences because plasmids can carry many accessory genes (e.g., ref. 29), not all of which are selected at any given time. Interspecific conjugation also provides opportunity for plasmid recombination with resident genetic elements, enhancing genomic diversification (2).…”