An Environmental Escherichia coli Strain Is Naturally Competent to Acquire Exogenous DNA

Abstract

The diffusion of antibiotic resistance determinants in different environments, e.g., soil and water, has become a public concern for global health and food safety and many efforts are currently devoted to clarify this complex ecological and evolutionary issue. Horizontal gene transfer (HGT) has an important role in the spread of antibiotic resistance genes (ARGs). However, among the different HGT mechanisms, the capacity of environmental bacteria to acquire naked exogenous DNA by natural competence is still poorly investigated. This study aimed to characterize the ability of the environmental Escherichia coli strain ED1, isolated from the crustacean Daphnia sp., to acquire exogenous DNA by natural competence. Transformation experiments were carried out varying different parameters, i.e., cell growth phase, amount of exogenous DNA and exposition to artificial lake water (ALW) and treated wastewater to mimic environmentallike conditions that may be encountered in the agri-food system. Results were compared with those showed by the laboratory E. coli strain DH5α. Our experimental data, supported by genomic sequencing, showed that, when exposed to pure water, ED1 strain was able to acquire exogenous DNA with frequencies (10 −8-10 −9) statistically higher than the ones observed for DH5α strain (10 −10). Interestingly, higher values were retrieved for ED1 than DH5α strains exposed to ALW (10 −7 vs. 10 −9 , respectively) or treated wastewater (10 −8 vs. 10 −10 , respectively). We tested, therefore, ED1 strain ability to colonize the rhizosphere of lettuce, a model plant representative of rawconsumed vegetables of high economic importance in the ready-to-eat food industry. Results showed that ED1 strain was able to efficiently colonize lettuce rhizosphere, revealing a stable colonization for 14 days-long period. In conclusion, ED1 strain ability to acquire exogenous DNA in environmental-like conditions by natural competence, combined with its ability to efficiently and stably colonize plant rhizosphere, poses the attention to food and human safety showing a possible route of diffusion of antibiotic resistance in the agri-food system, sustaining the "One Health" warnings related to the antibiotic spread.

Outer Membrane Vesicles Derived from Klebsiella pneumoniae Are a Driving Force for Horizontal Gene Transfer

“…Current knowledge of HGT is based on three widely described mechanisms for the exchange of genetic material between bacteria: transformation, conjugation and transduction [5][6][7]. Transformation involves the natural uptake of naked DNA from an extracellular environment; this phenomenon occurs when cells are in a physiological state of competence, regulated by 20-50 proteins [8,9]. Conjugation is a DNA transfer mechanism through the sexual pilus and requires cell-to-cell contact [10].…”

Zooplankton as a Transitional Host for Escherichia coli in Freshwater

“…Purified DNA was sequenced on a NovaSeq Illumina Platform (IGA Technologies, Padova, Italy), providing a total of 10 and 15 million output reads for ED1 and ED157, respectively. One of these two genomes was already mentioned in a previous article ( 66 ). Briefly, reads were first trimmed using Trimmomatic ( 67 ) and the genomes were assembled using SPAdes default parameters ( 68 ), obtaining totals of 54 and 59 assembled contigs of >1 Kb, respectively.…”

“…The ED1 genome was deposited into the NCBI GenBank database under the accession no. JAAWVB00000000 ( 66 ). The ED157 Genome Shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no.…”

ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review

“…The use of different growth media does not allow the sizing of the amount of protein available nor the visualization of the form of expression or distribution in the plant material (Banchi et al, 2019;Porto et al, 2014). The uidA gene with its associated protein is found in a wide variety of organisms, including E. coli and several other microbes, including other microorganisms of the digestive tract and soil bacteria (Porto et al, 2014;Riva et al, 2020). The work of GUS is common in all vertebrate tissues, with high activity in the kidney, liver and spleen (Xu et al, 2020).…”