Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

A cryptic plasmid is among the most numerous genetic elements in the human gut

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.

Fresh produce as a reservoir of antimicrobial resistance genes: A case study of Switzerland

Antimicrobial resistance (AMR) can be transferred to humans through food and fresh produce can be an ideal vector as it is often consumed raw or minimally processed. The production environment of fresh produce and the agricultural practices and regulations can vary substantially worldwide, and consequently, the contamination sources of AMR. In this study, 75 imported and 75 non-imported fresh produce samples purchased from Swiss retailers were tested for the presence of antimicrobial resistant bacteria (ARB) and antimicrobial resistance genes (ARGs). Moreover, the plasmidome of 4 selected samples was sequenced to have an insight on the diversity of mobile resistome. In total, 91 ARB were isolated from fresh produce, mainly cephalosporin-resistant Enterobacterales (n = 64) and carbapenem-resistant P. aeruginosa (n = 13). All P. aeruginosa, as well as 16 Enterobacterales' isolates were multidrug-resistant. No differences between imported and Swiss fresh produce were found regarding the number of ARB. In 95 % of samples at least one ARG was detected, being the most frequent sul1, blaTEM, and ermB. Abundance of sul1 and intI1 correlated strongly with the total amount of ARGs, suggesting they could be good indicators for AMR in fresh produce. Furthermore, sul1 correlated with the fecal marker yccT, indicating that fecal contamination could be one of the sources of AMR. The gene sulI was significantly higher in most imported samples, suggesting higher anthropogenic contamination in the food production chain of imported produce. The analyses of the plasmidome of coriander and carrot samples revealed the presence of several ARGs as well as genes conferring resistance to antiseptics and disinfectants in mobile genetic elements. Overall, this study demonstrated that fresh produce contributes to the dissemination of ARGs and ARB.

Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1896 mobilisable and 8970 non-mobilisable plasmids. The UWSs' plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

Characterization of the Environmental Plasmidome of the Red Sea

Plasmids contribute to microbial diversity and adaptation, providing microorganisms with the ability to thrive in a wide range of conditions in extreme environments. However, while the number of marine microbiome studies is constantly increasing, very little is known about marine plasmids, and they are very poorly represented in public databases. To extend the repertoire of environmental marine plasmids, we established a pipeline for the de novo assembly of plasmids in the marine environment by analyzing available microbiome metagenomic sequencing data. By applying the pipeline to data from the Red Sea, we identified 362 plasmid candidates. We showed that the distribution of plasmids corresponds to environmental conditions, particularly, depth, temperature, and physical location. At least 7 of the 362 candidates are most probably real plasmids, based on a functional analysis of their open reading frames (ORFs). Only one of the seven has been described previously. Three plasmids were identified in other public marine metagenomic data from different locations all over the world; these plasmids contained different cassettes of functional genes at each location. Analysis of antibiotic and metal resistance genes revealed that the same positions that were enriched with genes encoding resistance to antibiotics were also enriched with resistance to metals, suggesting that plasmids contribute site-dependent phenotypic modules to their ecological niches. Finally, half of the ORFs (50.8%) could not be assigned to a function, emphasizing the untapped potential of the unique marine plasmids to provide proteins with multiple novel functions. IMPORTANCE Marine plasmids are understudied and hence underrepresented in databases. Plasmid functional annotation and characterization is complicated but, if successful, may provide a pool of novel genes and unknown functions. Newly discovered plasmids and their functional repertoire are potentially valuable tools for predicting the dissemination of antimicrobial resistance, providing vectors for molecular cloning and an understanding of plasmid-bacterial interactions in various environments.

A mathematician's guide to plasmids: an introduction to plasmid biology for modellers

Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.

Microbial diversity and geochemistry of groundwater impacted by steel slag leachates

To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m³ steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.

Efficient Suppression of Natural Plasmid-Borne Gene Expression in Carbapenem-Resistant Klebsiella pneumoniae Using a Compact CRISPR Interference System

There is an urgent need for efficient tools for genetic manipulation to assess plasmid function in clinical drug-resistant bacterial strains. To address this need, we developed an all-in-one CRISPR interference (CRISPRi) system that easily inhibited the gene expression of a natural multidrug-resistant plasmid in an sequence type 23 (ST23) Klebsiella pneumoniae isolate. We established an integrative CRISPRi system plasmid, pdCas9gRNA, harboring a dcas9 gene and a single guide RNA (sgRNA) unit under the control of anhydrotetracycline-induced and J23119 promoters, respectively, using a one-step cloning method. This system can repress the single resistance gene bla_NDM-1, with a >1,000-fold reduction in the meropenem MIC, or simultaneously silence the resistance genes bla_NDM-1 and bla_SHV-12, with a 16-fold and 8-fold respective reduction in the meropenem and aztreonam MIC on a large natural multidrug-resistant pNK01067-NDM-1 plasmid in an ST23 K. pneumoniae isolate. Furthermore, an sgRNA targeting the bla_NDM-1 promoter region can silence the entire bla_NDM-1-ble_MBL-trpF operon, confirming the existence of the operon. We also used this tool to knock down the multicopy resistance gene bla_KPC-2 in pathogenic Escherichia coli, increasing the susceptibility to meropenem. In a word, the all-in-one CRISPRi system can be used for efficient interrogation of indigenous plasmid-borne gene functions, providing a rapid, easy genetic manipulation tool for clinical K. pneumoniae isolates.

Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts

Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.

Delivering the Promise of Gene Therapy with Nanomedicines in Treating Central Nervous System Diseases

Central Nervous System (CNS) diseases, such as Alzheimer's diseases (AD), Parkinson's Diseases (PD), brain tumors, Huntington's disease (HD), and stroke, still remain difficult to treat by the conventional molecular drugs. In recent years, various gene therapies have come into the spotlight as versatile therapeutics providing the potential to prevent and treat these diseases. Despite the significant progress that has undoubtedly been achieved in terms of the design and modification of genetic modulators with desired potency and minimized unwanted immune responses, the efficient and safe in vivo delivery of gene therapies still poses major translational challenges. Various non-viral nanomedicines have been recently explored to circumvent this limitation. In this review, an overview of gene therapies for CNS diseases is provided and describes recent advances in the development of nanomedicines, including their unique characteristics, chemical modifications, bioconjugations, and the specific applications that those nanomedicines are harnessed to deliver gene therapies.

Plasmidome analysis of a hospital effluent biofilm: Status of antibiotic resistance

Plasmids are widely involved in the dissemination of characteristics within bacterial communities. Their genomic content can be assessed by high-throughput sequencing of the whole plasmid fraction of an environment, the plasmidome. In this study, we analyzed the plasmidome of a biofilm formed in the effluents of the teaching hospital of Clermont-Ferrand (France). Our analysis discovered >350 new complete plasmids, with a length ranging from 1219 to 40,193 bp. Forty-two plasmid incompatibility (Inc) groups were found among all the plasmid contigs. Ten large plasmids, described here in detail, were reconstructed from plasmid contigs, seven of which carried antibiotic resistance genes. Four plasmids potentially confer resistance to numerous families of antibiotics, including carbapenems, aminoglycosides, colistin, and chloramphenicol. Most of these plasmids were affiliated to Proteobacteria, a phylum of Gram-negative bacteria. This study therefore illustrates the composition of an environmental mixed biofilm in terms of plasmids and antibiotic resistance genes.

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

BACKGROUND

Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms.

METHODS

To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years.

RESULTS

Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment.

CONCLUSIONS

Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.

Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions

Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.

Initial behaviors and removal of extracellular plasmid gene in membrane bioreactor

Extracellular antibiotic resistance genes (eARG) are considered to play an important role in spread of antimicrobial resistance (AMR) in wastewater treatment and water environment. Membrane bioreactor (MBR) reportedly has better removal of ARGs in wastewater than conventional activated sludge process. However, removal of eARG is possibly limited because eARG is small to pass through microfiltration (MF) membranes. To evaluate potential removal of eARG in MBR, this study aimed to understand the initial behaviors of eARG received in MBR. The recombinant plasmid with artificial marker gene was spiked in lab-scale MBR to trace fate of eARG in MBR. Among 10 ¹⁰ copies/L of the spiked gene, 2.6 × 10⁹ copies/L was adsorbed on sludge particles at 6 h after spiking, while only 2.2 × 10⁸-3.6 × 10⁸ copies/L of the spiked gene was remained but constant in sludge liquid phase from 6 until 48 h. This result suggests that adsorption on sludge particles served as the main mechanism to govern the initial fate of eARG in MBR. Meanwhile, the spiked gene concentrations in membrane permeate was lower than sludge liquid phase and decreased overtime, suggesting retention of eARG in membrane filtration. Total LRV of the spiked extracellular gene were 3.4 ± 0.8 log at 48 h after spiking. LRV by adsorption corresponded to 1.7 ± 0.7 log constantly since 3 h after spiking, while LRV by membrane filtration increased from 0 to 1.7 ± 0.6 log. Linear correlation of LRV by membrane filtration with transmembrane pressure (TMP) suggested that foulant deposition on membrane governs removal of eARG by membrane filtration in MBR.

Assessment of the plasmidome of an extremophilic microbial community from the Diamante Lake, Argentina

Diamante Lake located at 4589 m.a.s.l. in the Andean Puna constitutes an extreme environment. It is exposed to multiple extreme conditions such as an unusually high concentration of arsenic (over 300 mg L^-1) and low oxygen pressure. Microorganisms thriving in the lake display specific genotypes that facilitate survival, which include at least a multitude of plasmid-encoded resistance traits. Hence, the genetic information provided by the plasmids essentially contributes to understand adaptation to different stressors. Though plasmids from cultivable organisms have already been analyzed to the sequence level, the impact of the entire plasmid-borne genetic information on such microbial ecosystem is not known. This study aims at assessing the plasmidome from Diamante Lake, which facilitates the identification of potential hosts and prediction of gene functions as well as the ecological impact of mobile genetic elements. The deep-sequencing analysis revealed a large fraction of previously unknown DNA sequences of which the majority encoded putative proteins of unknown function. Remarkably, functions related to the oxidative stress response, DNA repair, as well as arsenic- and antibiotic resistances were annotated. Additionally, all necessary capacities related to plasmid replication, mobilization and maintenance were detected. Sequences characteristic for megaplasmids and other already known plasmid-associated genes were identified as well. The study highlights the potential of the deep-sequencing approach specifically targeting plasmid populations as it allows to evaluate the ecological impact of plasmids from (cultivable and non-cultivable) microorganisms, thereby contributing to the understanding of the distribution of resistance factors within an extremophilic microbial community.

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria. The publicly available WGS enabled mapping bacterial hosts to several viral sequences. The WGS of groundwater isolates increased the depth of host prediction by allowing host identification at the strain level. The latter included 4 viruses that were almost entirely (>99% query coverage, >99% identity) identified as integrated in the genomes of Pseudomonas, Acidovorax, and Castellaniella strains, resulting in high-confidence host assignments. Lastly, 21 of these viruses carried putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they are key players in microbial adaption to environmental stress. IMPORTANCE To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.

A Peek into the Plasmidome of Global Sewage

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impact the ecology and evolution of bacteria and can significantly influence the burden of infectious diseases. Insight about the identity and functions encoded on plasmids on the global scale are largely lacking. Here, we investigate the plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project. We obtained 105-Gbp Oxford Nanopore and 167-Gbp Illumina NextSeq DNA sequences from plasmid DNA preparations and assembled 165,302 contigs (159,322 circular). Of these, 58,429 carried genes encoding for plasmid-related and 11,222 for virus/phage-related proteins. About 90% of the circular DNA elements did not have any similarity to known plasmids. Those that exhibited similarity had similarity to plasmids whose hosts were previously detected in these sewage samples (e.g., Acinetobacter, Escherichia, Moraxella, Enterobacter, Bacteroides, and Klebsiella). Some AMR classes were detected at a higher abundance in plasmidomes (e.g., macrolide-lincosamide-streptogramin B, macrolide, and quinolone) compared to the respective complex sewage samples. In addition to AMR genes, a range of functions were encoded on the candidate plasmids, including plasmid replication and maintenance, mobilization, and conjugation. In summary, we describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes. Moreover, the obtained data could provide further valuable insight into the ecology and evolution of microbiomes, knowledge about AMR transmission, and the discovery of novel functions.

IMPORTANCE This is, to the best of our knowledge, the first study to investigate plasmidomes at a global scale using long read sequencing from complex untreated domestic sewage. Previous metagenomic surveys have detected AMR genes in a variety of environments, including sewage. However, it is unknown whether the AMR genes were present on the microbial chromosome or located on extrachromosomal elements, such as plasmids. Using our approach, we recovered a large number of plasmids, of which most appear novel. We identified distinct AMR genes that were preferentially located on plasmids, potentially contributing to their transmissibility. Overall, plasmids are of great importance for the biology of microorganisms in their natural environments (free-living and host-associated), as well as for molecular biology and biotechnology. Plasmidome collections may therefore be valuable resources for the discovery of fundamental biological mechanisms and novel functions useful in a variety of contexts.

Plasmidome AMR screening (PAMRS) workflow: a rapid screening workflow for phenotypic characterization of antibiotic resistance in plasmidomes

Background: Phenotypic characterization of antimicrobial resistance (AMR) in bacteria has remained the gold standard for investigation and monitoring of what resistance is present in an organism. However, the process is laborious and not attractive for screening multiple plasmids from a microbial community (plasmidomes). Instead, genomic tools are used, but a major bottle neck that presence of genes does not always translate into phenotypes. Methods: We designed the plasmidome AMR screening (PAMRS) workflow to investigate the presence of antibiotic resistant phenotypes in a plasmidome using Escherichia coli as a host organism. Plasmidomes were extracted from the faecal matter of chicken, cattle and humans using commercial plasmid extraction kits. Competent E. coli cells were transformed and evaluated using disk diffusion. Thirteen antibiotic resistant phenotypes were screened. Results: Here, we show that multiple antibiotic resistant phenotypes encoded by plasmids can be rapidly screened simultaneously using the PAMRS workflow. E. coli was able to pick up to 7, 5 or 8 resistant phenotypes from a single plasmidome from chicken, cattle or humans, respectively. Resistance to ceftazidime was the most frequently picked up phenotype in humans (52.6%) and cattle (90.5%), whereas in chickens, the most picked up resistant phenotype was resistance to co-trimoxazole, ceftriaxone and ampicillin (18.4% each). Conclusions: This workflow is a novel tool that could facilitate studies to evaluate the occurrence and expression of plasmid-encoded antibiotic resistance in microbial communities and their associated plasmid-host ranges. It could find application in the screening of plasmid-encoded virulence genes.

An improved direct metamobilome approach increases the detection of larger-sized circular elements across kingdoms

Mobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate genetic diversity. MGEs serve as a vast communal gene pool and include DNA elements such as plasmids and bacteriophages (phages) among others. These mobile DNA elements represent a human health risk as they can introduce new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting environmental circular MGEs, referred to as metamobilomes, may broaden our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomics is affected by a severe bias towards small circular elements, introduced by multiple displacement amplification (MDA). MDA is typically used to overcome limiting DNA quantities after the removal of non-circular DNA during library preparations. By examining the relationship between sequencing coverage and the size of circular MGEs in paired metamobilome datasets with and without MDA, we show that larger circular elements are lost when using MDA. This study is the first to systematically demonstrate that MDA is detrimental to detecting larger-sized plasmids if small plasmids are present. It is also the first to show that MDA can be omitted when using enzyme-based DNA fragmentation and PCR in library preparation kits such as Nextera XT® from Illumina.

Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data

Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.

Characterization of putative circular plasmids in sponge-associated bacterial communities using a selective multiply-primed rolling circle amplification

Plasmid transfers among bacterial populations can directly influence the ecological adaptation of these populations and their interactions with host species and environment. In this study, we developed a selective multiply-primed rolling circle amplification (smRCA) approach to enrich and characterize circular plasmid DNA from sponge microbial symbionts via high-throughput sequencing (HTS). DNA (plasmid and total community DNA) obtained from sponge (Cinachyrella sp.) samples and a bacterial symbiont (Vibrio sp. CyArs1) isolated from the same sponge species (carrying unknown plasmids) were used to develop and validate our methodology. The smRCA was performed during 16 hr with 141 plasmid-specific primers covering all known circular plasmid groups. The amplified products were purified and subjected to a reamplification with random hexamer primers (2 hr) and then sequenced using Illumina MiSeq. The developed method resulted in the successful amplification and characterization of the sponge plasmidome and allowed us to detect plasmids associated with the bacterial symbiont Vibrio sp. CyArs1 in the sponge host. In addition to this, a large number of small (<2 kbp) and cryptic plasmids were also amplified in sponge samples. Functional analysis identified proteins involved in the control of plasmid partitioning, maintenance and replication. However, most plasmids contained unknown genes, which could potentially serve as a resource of unknown genetic information and novel replication systems. Overall, our results indicate that the smRCA-HTS approach developed here was able to selectively enrich and characterize plasmids from bacterial isolates and sponge host microbial communities, including plasmids larger than 20 kbp.

First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna

Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O₂ pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.

Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater

The goal of the present work was to investigate the physicochemical and radiochemical conditions and the microbial diversity in groundwater collected near the Lake Karachai (Russia), which was formerly used for the disposal of liquid radioactive waste, to isolate the dominant bacteria, and to determine their taxonomy and the physiological characteristics responsible for their adaptation to this environment. Groundwater samples contained high concentrations of acetate, oxalate, nitrate, and sulfate, as well as radionuclides. High-throughput sequencing and analysis of the clone libraries revealed lower microbial diversity in the most strongly contaminated groundwater and a predominance of bacteria of the genera Polynucleobacter, Pusillimonas, Candidatus Pelagibacter, and of the candidate phylum Parcubacteria; these groups include species with an ultra small cell size. Archaeal sequences in the libraries belonged to ammonium oxidizers of the phylum Thaumarchaeota and methanogens of the phylum Euryarchaeota. Pure cultures of obligate and facultative ultramicrobacteria belonging to the genera Chryseobacterium, Microbacterium, Salinibacterium, Pusillimonas, Roseomonas, and Janibacter were isolated from water samples. In genomes of Pusillimonas and Roseomonas strains the genes associated with nitrate reduction, resistance to heavy metals and metalloids were revealed. Several isolates are able to participate in the geochemical process of nitrate conversion to N2 using acetate; this results in decreasing redox potential, which in turn may stimulate radionuclide reduction and decrease radionuclide migration in groundwater.

Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome's capacity to take up environmental DNA enables rapid adaptation to environmental stresses.IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.

Efficient reduction of antibiotic residues and associated resistance genes in tylosin antibiotic fermentation waste using hyperthermophilic composting

Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria.

A marine plasmid hitchhiking vast phylogenetic and geographic distances

Horizontal gene transfer (HGT) is the movement of genetic material between organisms other than by reproduction, which plays an important role in bacterial evolution. Often, mobile genetic elements such as plasmids are involved in HGT. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized plasmid that is found with 100% sequence identity in multiple distinct bacterial genera obtained from geographically separated locations. This is the only known instance where actual nucleotide identity and not only high synteny has been described for plasmids in environmental organisms. Furthermore, we provide experimental evidence for the potential of this plasmid to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.

Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.