Title: “Identifying mobile plasmids in-situ in various ecosystems”
Authors: Alvah Zorea, Sarah Morais, Orly Gershoni-Yahalom, David Pellow, Maraike Probst, Ron Shamir, Benyamin Rosental, Natalie Elia, Itzik Mizrahi
Abstract: Microbes have various ways of communication, one of which involves transferring plasmids between and among bacterial species- a process termed horizontal gene transfer. This extraordinary phenomenon enables rapid bacterial evolution and gain of function, such as antibiotic resistance. Thus, an increase in horizontal gene transfer rates can be critical in determining the functionality of a given bacterial population. To investigate the influence of plasmid mobility in various environments, it is essential to identify these plasmids within their host cells (in-situ). To this end, we developed a novel method that employs computational tools together with a molecular procedure based on a modification of the Fluorescent in-situ Hybridization protocol to target plasmids in their microbial hosts in natural environments. This novel method increases sensitivity and enables the detection of low-copy number plasmids as well as the identification of several plasmid types within the same microbial cell.
Title: “Characterization of the Environmental Plasmidome of the Red Sea”
Authors: Lucy Androsiuk, Tal Shay, Shay Tal
Abstract: Plasmids contribute to microbial diversity and adaptation, providing microorganisms with the ability to thrive in a wide range of conditions in extreme environments. In my study, we focus on environmental marine plasmids, which are poorly represented in public databases. However, there is an increasing number of marine microbiome studies, enriching the knowledge about microbial communities in various marine environments. Therefore, we established a pipeline for de novo assembly of plasmids in marine environment analyzing available microbiome metagenomic sequencing data. We identified 362 plasmid candidates in the Red Sea and show that plasmids distribution corresponds to physical environmental conditions, particularly, depth, temperature and physical location. At least 7 of the 362 candidates are most probably real plasmids, based on functional analysis of their open reading frames (ORFs). Only one of them was previously described. Three plasmids were identified in other available metagenomic data from locations all over the world, containing different cassettes of functional genes. We observed that most of the ORFs (83%) cannot be assigned to function, emphasizing the uniqueness of marine plasmids and the lack of knowledge. We believe that plasmid dynamics can be studied in mariculture system as model for environmental niche. To analyze, whether fish serve as plasmids disseminators in the sea, we grew seabream in regular conditions and sampled their scales and intestines after acclimatization period. We sampled incoming, tank and outcoming water to detect whether the plasmids are not introduced into the tank within the filtered UV-treated water, whether the plasmids are secreted by fish into water, and whether the plasmids are contaminating the wastewater after wastewater treatment. The analysis on this data is yet to be performed.
Title: “Horizontal plasmid transfer shapes the resistome in intensive frog farms”
Authors: Mei Zhuang, Waner Yan, Yifei Xiong, Zhilin Wu, Yuping Cao, Liang Chen, Edmond Sanganyado, Bupe A. Siame, Kashi Yechezkel, Ka Yin Leung2
Abstract: Background: The accumulation of antibiotic resistance (AR) through horizontal plasmid transfer (HPT) is not only a public health issue but can also threaten food security as well as environmental health. However, the evidence in the literature to implicate HPT as a major driving force shaping resistome in unique environmental niches, promoting bacterial evolution and environmental adaptation is scarce. Results: Combining with antibiotic susceptibility testing, metagenomic analysis of sediments from five intensive frog farms revealed Escherichia coli and Edwardsiella tarda as core multidrug resistant (MDR) bacteria. Totally 250 plasmids carrying diverse ARGs were identified by ninety-five genomes analysis of E. coli, E. tarda, and other species (mainly Citrobacter and Klebsiella). Large plasmids harbored by MDR bacteria were majorly conjugative (57%) and had multi-replicons. We present strong evidence that ARGs on plasmids conferred the multi-antibiotic resistance phenotype. The majority of the 250 detected plasmids fell into 32 distinct groups that tracked the spread of ARGs via horizontal plasmid transfer (HPT). These plasmids were co-habit and transferable inter/intra-species. Public datasets BLAST searched results revealed similar plasmids in various environment niches globally. Conclusion: Our findings support the hypothesis that horizontal plasmid transfer (HPT) is a key mechanism shaping the resistome in frog farms and that plasmidome studies can reveal HPT mechanisms involved in spreading ARB, ARGs, and other virulence genes in the agriculture microbiome.