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Background: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system. Results: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes. Conclusions: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. A1iT8gFKWRifc6GWDf3ih6 Video Abstract [ABSTRACT FROM AUTHOR]

Division of labor can evolve when social groups benefit from the functional specialization of its members. Recently, a novel means of coordinating the division of labor was found in the antibiotic‐producing bacterium Streptomyces coelicolor, where specialized cells are generated through large‐scale genomic re‐organization. We investigate how the evolution of a genome architecture enables such mutation‐driven division of labor, using a multiscale computational model of bacterial evolution. In this model, bacterial behavior—antibiotic production or replication—is determined by the structure and composition of their genome, which encodes antibiotics, growth‐promoting genes, and fragile genomic loci that can induce chromosomal deletions. We find that a genomic organization evolves, which partitions growth‐promoting genes and antibiotic‐coding genes into distinct parts of the genome, separated by fragile genomic loci. Mutations caused by these fragile sites mostly delete growth‐promoting genes, generating sterile, and antibiotic‐producing mutants from weakly‐producing progenitors, in agreement with experimental observations. This division of labor enhances the competition between colonies by promoting antibiotic diversity. These results show that genomic organization can co‐evolve with genomic instabilities to enable reproductive division of labor. Synopsis: A computational model of the multicellular bacteria Streptomyces reveals that if antibiotic production trades off with replication, genome architecture can evolve to support a mutation‐driven division of labor.In silico bacterial colonies divide labor between replication and antibiotic production by evolving a genome architecture that physically segregates genes for these different functions and allows them to be dissociated due to mutations at fragile sites.Division of labor is driven by mutations and is reminiscent of the division between germ and soma in multicellular eukaryotes: One class of cells specializes in reproduction, while the other class, comprising the mutants, focuses on costly antibiotic production.In this system, which replicates dynamics observed in S. coelicolor, mutant cells effectively function as soma by enhancing colony fitness, despite being sterile. [ABSTRACT FROM AUTHOR]

The genetic basis underlying loss‐of‐virulence mutations that arise among natural phytopathogen populations is not well documented. In this study, we examined the virulence of 377 isolates of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) that were isolated from 76 kiwifruit orchards suffering from bacterial canker disease. Eighty‐four nonpathogenic isolates were identified in 40 orchards. A nonpathogenic isolate G166 was found to be defective in hrpL transcription and the downstream type III secretion system (T3SS)‐dependent phenotypes. Comparative genomics and complementary expression assay revealed that a single‐base "G" insertion in the hrpL promoter blocks gene transcription by reducing promoter activity. The electrophoretic mobility shift assay showed that the genetic variation impairs σ54/promoter binding during gene transcription under hrp‐inducing conditions, resulting in lower expression of hrpL. A PCR‐restriction fragment length polymorphism assay was performed to trace the evolutionary history of this mutation, which revealed the independent onset of genetic variations in natural Psa3 populations. We also found that nonpathogenic variants outperformed virulent Psa3 bacteria for both epiphytic and apoplast colonization of kiwifruit leaves in mixed inoculations. Our study highlights a novel mechanism for loss of virulence in Psa3 and provides insight into bacterial adaptive evolution under natural settings. [ABSTRACT FROM AUTHOR]

The use of antibacterial and antifouling materials is widely being investigated to combat the increasing risk associated with bacterial infections and the evolution of drug‐resistant bacteria. Efficient antibacterial materials can be fabricated by mimicking the topography found on the surface of natural antibacterial materials. Natural materials such as the wings of cicadas and dragonflies have evolved to use the structural features on their surface to attain bactericidal properties. The nanopillars/nanospikes present on these natural materials physically damage the bacterial cells that settle on the nanostructures resulting in cell lysis and death. This article reviews the role of nanostructures found on the surface of some of these natural antibacterial and antifouling materials such as lotus leaf, cicadas and dragonflies wings, shark skin, and rose petals. These natural structures provide guidelines for the design of synthetic bio‐inspired materials. This review article also presents some novel fabrication techniques used to produce biomimetic micro‐ and nano‐structures on synthetic material surfaces. The role of size, shape, aspect ratio, and spacing between the micro/nano‐structures on the bactericidal properties is also discussed. Finally, the review is finished with the author's view on the future of the field. [ABSTRACT FROM AUTHOR]

Summary: Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence.Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus.Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface.The phyllosphere provides a dynamic environment for prophage‐mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome‐based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases. [ABSTRACT FROM AUTHOR]

During the initiation step of bacterial genome replication, replicative helicases depend on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, most bacteria do not contain any of these genes, which are domesticated phage elements that have replaced the ancestral and unrelated loader gene dciA several times during evolution. To understand how DciA assists the loading of DnaB, the crystal structure of the complex from Vibrio cholerae was determined, in which two VcDciA molecules interact with a dimer of VcDnaB without changing its canonical structure. The data showed that the VcDciA binding site on VcDnaB is the conserved module formed by the linker helix LH of one monomer and the determinant helix DH of the second monomer. Interestingly, DnaC from Escherichia coli also targets this module onto EcDnaB. Thanks to their common target site, it was shown that VcDciA and EcDnaC could be functionally interchanged in vitro despite sharing no structural similarity. This represents a milestone in understanding the mechanism employed by phage helicase loaders to hijack bacterial replicative helicases during evolution. [ABSTRACT FROM AUTHOR]

A variety of secondary metabolites contributing to plant growth are synthesized by bacterial nonribosomal peptide synthases (NRPSs). Among them, the NRPS biosynthesis of surfactin is regulated by the SrfA operon. To explore the molecular mechanism for the diversity of surfactins produced by bacteria within the genus Bacillus, we performed a genome-wide identification study focused on three critical genes of the SrfA operon—SrfAA, SrfAB and SrfAC—from 999 Bacillus genomes (belonging to 47 species). Gene family clustering indicated the three genes can be divided into 66 orthologous groups (gene families), of which a majority comprised members of multiple genes (e.g., OG0000009 had members of all three SrfAA, SrfAB and SrfAC genes), indicating high sequence similarity among the three genes. Phylogenetic analyses also found that none of the three genes formed monophyletic groups, but were usually arranged in a mixed manner, suggesting the close evolutionary relationship among the three genes. Considering the module structure of the three genes, we propose that self-duplication, especially tandem duplications, might have contributed to the initial establishment of the entire SrfA operon, and further gene fusion and recombination as well as accumulated mutations might have continuously shaped the different functional roles of SrfAA, SrfAB and SrfAC. Overall, this study provides novel insight into metabolic gene clusters and operon evolution in bacteria. [ABSTRACT FROM AUTHOR]

The nonstandard use of disinfectants can lead to the disinfectant resistance of bacteria and even increase antibiotic resistance. However, compared with the study of antibiotic resistance, studies of bacterial resistance to disinfectants are relatively few in number. In this study, we explored the standard strain screening procedure for the evaluation of disinfection efficacy. Staphylococcus aureus strains with different sources and substrates were selected from the National Pathogen Resource Center of China and screened the standard strains that could evaluate the long-term bacteriostatic effect of the chlorine-containing disinfectants through the determination of the physical properties, genome-based safety evaluation, and disinfection test evaluation. In this process, one S. aureus strain was more resistant to the long-term bacteriostasis of chlorine-containing disinfectants than the other strains. This strain and the standard strain ATCC 6538 were cultured in the medium containing a low concentration of chlorine-containing disinfectant synchronously. Then, comparative transcriptome analysis was carried out to investigate the potential mechanism of a high tolerance to chlorine-containing disinfectants. The pathway of significant differential expression is related to the oxocarboxylic acid metabolic mechanism, amino acid metabolic mechanism, and pyrimidine mechanism, which may be the molecular mechanism of S. aureus evolution to adapt to chlorine-containing disinfectants. Our study established a technical process for screening and evaluating standard strains for disinfection, which also provided a reference for studying the bacterial evolution mechanism toward chlorine tolerance. [ABSTRACT FROM AUTHOR]

Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.

Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integronintegrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells. [ABSTRACT FROM AUTHOR]

Bacterial cell filamentation is a morphological change wherein cell division is blocked, which can improve bacterial survival under unfavorable conditions (e.g., antibiotic stress that causes DNA damage). As an extrachromosomal DNA molecule, plasmids can confer additionally advantageous traits including antibiotic resistance on the host. However, little is known about whether plasmids could shift bacterial morphological responses to antibiotic stress. Here, it is reported that plasmid‐free cells, rather than plasmid‐bearing cells, exhibit filamentation and asymmetrical cell division under exposure to sub‐inhibitory concentrations of antibiotics (ciprofloxacin and cephalexin). The underlying mechanism is revealed by investigating DNA damage, cell division inhibitor sulA, the SOS response, toxin‐antitoxin module (parDE) located on plasmids, and efflux pumps. Significantly higher expression of sulA is observed in plasmid‐free cells, compared to plasmid‐bearing cells. Plasmid carriage enables the hosts to suffer less DNA damage, exhibit stronger efflux pump activities, and thus have a higher antibiotic tolerance. These benefits are attributed to the parDE module that mediates stress responses from plasmid‐bearing cells and mainly contributes to cell morphological changes. Collectively, the findings demonstrate that plasmids can confer additional innate defenses on the host to antibiotics, thus advancing the understanding of how plasmids affect bacterial evolution in hostile environments. [ABSTRACT FROM AUTHOR]

The article presents a study which explores how machine learning enables prediction of metabolic system evolution in bacteria. It mentions that evolution prediction as a long-standing goal in evolutionary biology, with potential impacts on strategic pathogen control, genome engineering, and synthetic biology.

Myriad ecological and evolutionary factors can influence whether a particular parasite successfully transmits to a new host during a disease outbreak, with consequences for the structure and diversity of parasite populations. However, even though the diversity and evolution of parasite populations are of clear fundamental and applied importance, we have surprisingly few studies that track how genetic structure of parasites changes during naturally occurring outbreaks in non‐human populations. Here, we used population genetic approaches to reveal how genotypes of a bacterial parasite, Pasteuria ramosa, change over time, focusing on how infecting P. ramosa genotypes change during the course of epidemics in Daphnia populations in two lakes. We found evidence for genetic change – and, therefore, evolution – of the parasite during outbreaks. In one lake, P. ramosa genotypes were structured by sampling date; in both lakes, genetic distance between groups of P. ramosa isolates increased with time between sampling. Diversity in parasite populations remained constant over epidemics, although one epidemic (which was large) had low genetic diversity while the other epidemic (which was small) had high genetic diversity. Our findings demonstrate that patterns of parasite evolution differ between outbreaks; future studies exploring the feedbacks among epidemic size, host diversity, and parasite genetic diversity would improve our understanding of parasite dynamics and evolution. [ABSTRACT FROM AUTHOR]

Simple Summary: Antibiotic resistance has become one of the biggest threats to global health. The occurrence of resistance is a natural phenomenon of bacterial evolution, but their inappropriate use in humans and the environment is hastening the process at a reckless speed. The speed of developing resistance is at par or, in fact, more than the speed of novel antibiotic development. Most of the big pharmaceutical companies have left antibiotic research due to the high risk of failure and poor return on investment. Antibiotic research is mostly carried out by academic institutes and small- and medium-sized enterprises. However, they lack sufficient funds to take the compounds from early-and-mid-stage to clinical trials and market. To make this possible, several government and non-government organizations worldwide have come forward to incentivize research through push funding mechanisms. The positive impact of these mechanisms, which started around a decade ago, is now visible, with fair improvements in research pipelines in the last five years. However, a large landscape of push incentives across the globe and staggered funding across different stages of development make the process complex. Efforts in various forms are now being implemented and proposed to streamline and smoothen push funding mechanisms for reinvigorating antibiotic research. The growing need for effective antibiotics is attributed to the intrinsic ability of bacteria to develop survival mechanisms. The speed at which pathogens develop resistance is at par or even faster than the discovery of newer agents. Due to the enormous cost of developing an antibiotic and poor return on investment, big pharmaceutical companies are stepping out of the antibiotic research field, and the world is now heading towards the silent pandemic of antibiotic resistance. Lack of investment in research has further led to the anemic antibiotic pipeline. To overcome these challenges, various organizations have come forward with push funding to financially assist antibiotic developers. Although push funding has somewhat reinvigorated the dwindled field of antibiotic development by bearing the financial risks of failure, the landscape is still large and staggered. Most of the funding is funneled towards the early stages; however, to carry the promising compounds forward, equal or more funding is required formid- and late-stage research. To some extent, the complexity associated with accessing the funding mechanisms has led to their underutilization. In the present review, we discuss several major push funding mechanisms, issues in their effective utilization, recent strategies adopted, and a way forward to streamline funding in antibiotic research. [ABSTRACT FROM AUTHOR]

The use of biostimulants in the bioremediation of polluted soils in order to eliminate/reduce the toxic effects of pesticides on the soil is currently a very common environmental practice. In this study, we studied the bioremediation effect of three biostimulants obtained from sewage sludge by way of an enzymatic hydrolysis and fermentation process in a diuron-contaminated soil for 55 days under laboratory conditions. During this period of time, the enzymatic activities, bacterial community and the evolution of diuron in the soil were analyzed. Compared with the unpolluted soil, the application of diuron decreased the dehydrogenase, β-glucosidase and phosphatase activities by 60%, 40.7%, and 60.6%, respectively. The Gram-positive bacterial population was decreased by 48.5%, while the Gram-negative population was decreased by 57.7% and the fungal population was decreased by 54.3%. The application of the three biostimulants to the soil decreased the diuron concentration. However, this decrease was higher when the biostimulant obtained by enzymatic hydrolysis was applied. This may be due to the fact that this biostimulant contains a higher quality of low molecular weight proteins than the other two biostimulants obtained by fermentation processes. [ABSTRACT FROM AUTHOR]

Bacterial keratitis can lead to intraocular infection and even blindness without prompt and potent treatments. Currently, clinical abuse of antibiotics encouraged the evolution of resistant bacteria. Conventional antibiotic eye drops based keratitis treatment has been heavily restricted due to the lack of bactericidal efficiency and easy induction of bacterial resistance. Hence, developing an effective treatment strategy for bacterial keratitis is of great significance. In this work, we investigated ε-poly-L-lysine (EPL)-modified polydopamine (PDA) nanoparticles (EPL@PDA NPs)-mediated antibacterial photothermal therapy (aPTT), to cope with methicillin-resistant Staphylococcus aureus (MRSA)-induced keratitis. The surface modification of cationic peptide EPL enables EPL@PDA NPs to specifically target negatively charged MRSA and induces local hyperthermia to kill the bacteria under low ambient temperature. Under nearinfrared (NIR) irradiation, the sterilization efficiency of EPL@PDA NPs suspension for MRSA in vitro was up to 99.96%. The EPL@PDA-mediated aPTT presented potent antibacterial efficacy in treating MRSA-induced keratitis with little corneal epithelial cytotoxicity and good biocompatibility. In conclusion, the bacterial-targeting aPTT platform in this work provides a prospective method for the management of MRSAinduced refractory bacterial keratitis. [ABSTRACT FROM AUTHOR]

Composting is an excellent way to recycle biogas residues into a stable, non-toxic agricultural end product. In this study, the dynamic changes of physical–chemical parameters and bacterial community in three groups of bioaugmentation composting systems at different moisture contents (MC) of 50% (MC50), 60% (MC60) and 70% (MC70) were monitored. The differences of bacterial communities in composts with different initial MC were compared, and the interaction between biological and non-biological parameters was also explored. The results revealed that after 30 days of composting, the biogas residues compost in MC60 reached highest temperature of 64 °C, total Kjeldahl nitrogen (TKN) of 2%, seed germination index (GI) of 110%, and the longest thermophilic period duration of 5 days (55 °C). Additionally, the result of high-throughput sequencing showed that the diversity of bacterial communities in MC60 was the highest, and the abundance of Actinobacteria (16.93–52.63%), Firmicutes (8.71–56.75%), and Proteobacteria (16.88–46.95%) in all groups were the highest at phylum level. The LEfSe analysis indicated that the abundance of Ochrobactrum and Cellulomonadaceae in MC60 was significantly (p < 0.05) higher than with other treatments. Moreover, canonical correspondence analysis (CCA) indicated thermophilic period duration is significantly (p < 0.05) positively correlated with Paenibacillus. Besides, it was found the relative abundance of Nocardiopsis and Georgenia has a significant (p < 0.01) correlation with the fertilizer efficiency of compost. These results showed that controlling the initial moisture content at 60% can improve the maturity and fertilizer efficiency of compost, and enable the bacteria beneficial to composting to gain the advantage of proliferation. [ABSTRACT FROM AUTHOR]

Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991–3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses—amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution. [ABSTRACT FROM AUTHOR]

Madagascar's flora and fauna have evolved in relative isolation since the island split from the African and Indian continents. When the last common ancestors of lemurs left Africa between 40 and 70 million years ago, they carried a subset of the viral diversity of the mainland population within them, which continued to evolve throughout the lemur radiation. Relative to other primate radiations, we know very little about the past or present viral diversity of lemurs, particularly mouse lemurs. Using high-throughput sequencing, we identified two gammaretroviruses and three betaretroviruses in the genomes of four species of wild mouse lemurs. The two gammaretroviruses and two betaretroviruses have not previously been described. One betaretrovirus was previously identified. All identified viruses are present in both Lorisiformes and Lemuriformes but absent from haplorrhine primates. The estimated ages of these viruses are consistent with the estimated divergence dates of the host lineages, suggesting they colonized the lemur genome after the Haplorrhine–Strepsirrhine split, but before the Lorisiformes–Lemuriformes split and before the colonization of Madagascar. The viral phylogenies connect multiple lineages of retroviruses from non-lemur and non-Madagascar-native species, suggesting substantial cross-species transmission occurred deep in the primate clade prior to its geographic dispersal. These phylogenies provide novel insights into known retroviral clades. They suggest that the origin of gammaretroviruses in rodents or bats may be premature and that the Jaagsiekte sheep virus clade may be older and more broadly distributed among mammals than previously thought. [ABSTRACT FROM AUTHOR]

Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR. [ABSTRACT FROM AUTHOR]

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Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non- conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ ggMOB/ [ABSTRACT FROM AUTHOR]

Viruses that infect bacteria, called phages, shape the composition of bacterial communities and are important drivers of bacterial evolution. We recently showed that temperate phages, when residing in bacteria (i.e., prophages), are capable of manipulating the bacterial cell-to-cell communication process called quorum sensing (QS). QS relies on the production, release, and population-wide detection of signaling molecules called autoinducers (AI). Gram-negative bacteria commonly employ N-acyl homoserine lactones (HSL) as AIs that are detected by LuxR-type QS receptors. Phage ARM81ld is a prophage of the aquatic bacterium Aeromonas sp. ARM81, and it encodes a homolog of a bacterial LuxR, called LuxRARM81ld. LuxRARM81ld detects host Aeromonas-produced C4-HSL, and in response, activates the phage lytic program, triggering death of its host and release of viral particles. Here, we show that phage LuxRARM81ld activity is modulated by noncognate HSL ligands and by a synthetic small molecule inhibitor. We determine that HSLs with acyl chain lengths equal to or longer than C8 antagonize LuxRARM81ld. For example, the C8-HSL AI produced by Vibrio fischeri that coexists with Aeromonads in aquatic environments, binds to and inhibits LuxRARM81ld, and consequently, protects the host from lysis. Coculture of V. fischeri with the Aeromonas sp. ARM81 lysogen suppresses phage ARM81ld virion production. We propose that the cell density and species composition of the bacterial community could determine outcomes in bacterial-phage partnerships. [ABSTRACT FROM AUTHOR]

Cyanobacteria rely on CO2-concentrating mechanisms (CCMs) to grow in today's atmosphere (0.04% CO2). These complex physiological adaptations require ≈15 genes to produce two types of protein complexes: inorganic carbon (Ci) transporters and 100+ nm carboxysome compartments that encapsulate rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting any of these genes prohibit growth in ambient air. If any plausible ancestral form--i.e., lacking a single gene--cannot grow, how did the CCM evolve? Here, we test the hypothesis that evolution of the bacterial CCM was "catalyzed" by historically high CO2 levels that decreased over geologic time. Using an E. coli reconstitution of a bacterial CCM, we constructed strains lacking one or more CCM components and evaluated their growth across CO2 concentrations. We expected these experiments to demonstrate the importance of the carboxysome. Instead, we found that partial CCMs expressing CA or Ci uptake genes grew better than controls in intermediate CO2 levels (≈1%) and observed similar phenotypes in two autotrophic bacteria, Halothiobacillus neapolitanus and Cupriavidus necator. To understand how CA and Ci uptake improve growth, we model autotrophy as colimited by CO2 and HCO3 -, as both are required to produce biomass. Our experiments and model delineated a viable trajectory for CCM evolution where decreasing atmospheric CO2 induces an HCO3 - deficiency that is alleviated by acquisition of CA or Ci uptake, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity. [ABSTRACT FROM AUTHOR]

In recent decades, there has been an increase in environmental problems caused by cosmetic products derived from toxic substances. Based on this issue, researchers and developers of new beauty cosmetics are looking for new natural alternatives that work well for the consumer and have biodegradable characteristics. This systematic review highlights the major publications of bacterial cellulose used strictly for cosmetics in the last 10 years. Bacterial cellulose is a natural product with great cosmetic properties and low cost that has shown excellent results. This study aimed at collecting rigorous information on bacterial cellulose in the cosmetic field in the last decade to produce a systematized review. A comprehensive search was conducted with selected descriptors involving the topic of "bacterial cellulose", "cosmetics", "clean beauty", and "skin mask". Seventy studies were found, which went through exclusion criteria that selected only those related to the topic that was searched. In the 12 remaining studies that met the criteria, bacterial cellulose showed conditions for use as a mask-forming product for facial care. The increase in the number of publications concerning bacterial cellulose in cosmetics in the last ten years is a strong indicator that this is a growing area for both research and the industry. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs) are critical elements of cell–cell communication. Here, we characterized the outer membrane vesicles (OMVs) released by specific clones of Escherichia coli isolated from the Long-Term Evolution Experiment after 50,000 generations (50K) of adaptation to glucose minimal medium. Compared with their ancestor, the evolved clones produce small OMVs but also larger ones which display variable amounts of both OmpA and LPS. Tracking ancestral, fluorescently labelled OMVs revealed that they fuse with both ancestral- and 50K-evolved cells, albeit in different proportions. We quantified that less than 2% of the cells from one 50K-evolved clone acquired the fluorescence delivered by OMVs from the ancestral strain but that one cell concomitantly fuses with several OMVs. Globally, our results showed that OMV production in E. coli is a phenotype that varies along bacterial evolution and question the contribution of OMVs-mediated interactions in bacterial adaptation. [ABSTRACT FROM AUTHOR]

Biofilm structures are the main mode of evolutionary reproductive adaptation of bacteria, and even these features alone, are sufficient to make them the focus of genetic and physiological studies. As this life form is a multicellular-like life form coordinated by genetic and physiological programming, it is quite different from the planktonic form. In bacterial biofilms, which are often composed of more than one species in nature, there is a clear division of labor, nutrient channels, and a language (signaling) established between the cells forming the biofilm. On the other hand, biofilms, especially formed by pathogens, cause important industrial and clinical problems due to their high resistance to environmental stress conditions. Obtaining new data on the molecular basis of bacterial evolution and understanding the intra- and inter-species ecosystem relations in this context, as well as finding permanent solutions to the serious problems they create, are directly related to a detailed understanding of the genetic regulation of bacterial biofilm structures. Today, it is becoming increasingly certain that environmental signals effective in the transition from planktonic form to biofilm form and their receptor/response molecules are generally managed by similar systems and global regulator molecules in bacteria. In this sense; Besides the quorum sensing (QS) systems, cyclic adenosine monophosphate-catabolite suppressor protein (cAMP-CRP) and bis-(3′–5′) cyclic dimeric guanosine monophosphate (c-di-GMP) signaling molecules are of critical importance. In this review article, current information on bacterial biofilms is summarized and interpreted based on this framework. [ABSTRACT FROM AUTHOR]

Copyright of Journal of China University of Petroleum is the property of China University of Petroleum and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Journal of Univesity of Thi-Qar is the property of Republic of Iraq Ministry of Higher Education & Scientific Research (MOHESR) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Accumulation of toxic organic has posed a substantial pressure on the proliferation of bacterial resistance. While aromatic organics have been demonstrated to enhance the antibiotic resistance in bacteria, no information is yet available on the effects of non-aromatic organics on the variations of bacterial resistance. Here, we investigated the effects of a typical ketone (i.e., methylisobutanone (MIBK)) on the variations of antibiotic resistance in Escherichia coli (E. coli). The results showed that the growth of resistant E. coli under environmental concentration of 50 μg/L MIBK was firstly inhibited as explained by the transient disruption in the cell membrane and then recovered possibly due to the reactive oxygen species. Exposure to 50 μg/L MIBK gradually raised the abundance of representative resistance gene (ampR) in E. coli. In contrast, the high concentration of 50 mg/L MIBK continuously inhibited the growth of resistant E. coli by disrupting cell membrane and notably promoted the proliferation of ampR through enhancing the horizontal transformation and up-regulating the expression of efflux pump gene. These findings provided the first evidence for the evolution of bacterial resistance in response to ketone organics. [ABSTRACT FROM AUTHOR]

Bacteria of the order Corynebacteriales including pathogens such as Mycobacterium tuberculosis and Corynebacterium diphtheriae are characterized by their complex, multi-layered envelope. In addition to a peptidoglycan layer, these organisms possess an additional polysaccharide layer made of arabinogalactan and an outer membrane layer composed predominantly of long-chain fatty acids called mycolic acids. This so-called mycolata envelope structure is both a potent barrier against antibiotic entry into cells and a target of several antibacterial therapeutics. A better understanding of the mechanisms underlying mycolata envelope assembly therefore promises to reveal new ways of disrupting this unique structure for the development of antibiotics and antibiotic potentiators. Because they engage with receptors on the cell surface during infection, bacteriophages have long been used as tools to uncover important aspects of host envelope assembly. However, surprisingly little is known about the interactions between Corynebacteriales phages and their hosts. We therefore made use of the phages Cog and CL31 that infect Corynebacterium glutamicum (Cglu), a model member of the Corynebacteriales, to discover host factors important for phage infection. A high-density transposon library of Cglu was challenged with these phages followed by transposon sequencing to identify resistance loci. The analysis identified an important role for mycomembrane proteins in phage infection as well as components of the arabinogalactan and mycolic acid synthesis pathways. Importantly, the approach also implicated a new gene (cgp_0396) in the process of arabinogalactan modification and identified a conserved new factor (AhfA, Cpg_0475) required for mycolic acid synthesis in Cglu. [ABSTRACT FROM AUTHOR]

With the continuous evolution of bacteria and the constant use of traditional antibiotics, the emergence of drug-resistant bacteria and super viruses has attracted worldwide attention. Antimicrobial therapy has become the most popular and important research field at present. Coordination Polymer (CP) and/or metal-organic framework (MOF) platforms have the advantages of a high biocompatibility, biodegradability, and non-toxicity, have a great antibacterial potential and have been widely used in antibacterial treatment. This paper reviewed the mechanism and antibacterial effect of three typical MOFs (pure Ag-MOFs, hybrid Ag-MOFs, and Ag-containing-polymer @MOFs) in silver-based coordination polymers. At the same time, the existing shortcomings and future views are briefly discussed. The study on the antibacterial efficacy and mechanism of Ag-MOFs can provide a better basis for its clinical application and, meanwhile, open up a novel strategy for the preparation of more advanced Ag-contained materials with antibacterial characteristics. [ABSTRACT FROM AUTHOR]

The synthesis of magnetosomes in magnetotactic bacteria (MTB) represents probably one of Earth's most ancient forms of biomineralization. The evolution of magnetosomes and the origin of magnetotaxis date back to the Archean Eon, 4.4–2.5 Ga ago. Magnetosomes consist of fine magnetite nanocrystals coated with a lipidic envelope. Their findings in eukaryotic cells and animals support the evolutionary success of otherwise energetically very demanding biocrystallization. Moreover, the conservation of magnetite biomineralization genes in all domains of life has been proposed very recently. Therefore, it is not surprising that magnetosomes have attracted attention from various scientific fields, including mineralogy, microbiology, biochemistry, biophysics, and bioengineering. Here, we review the most recent iron flow findings that lead to magnetite nanocrystals' biomineralization in MTB. We emphasize the historical milestones that formed the evolution of magnetosomes and magnetotaxis functionality. Finally, we discuss the usability of these unique structures in biomedical, biotechnological, environmental, and nutritional applications. [ABSTRACT FROM AUTHOR]

Microplastics (MPs) contaminate the global marine and terrestrial ecosystems. This environmental contamination can enter the food chain, with MPs found in drinking water, fishery products and other food categories. Consequently, ingestion is considered the main route of human exposure to MPs. Concerns exist on the potential of MPs to act as vectors for pathogenic bacteria, possibly threatening microbial food safety. Starting from the current evidence on foodborne pathogens associated with MPs, we review the state of knowledge on the putative role of MPs in enhancing harmful bacterial traits and transporting them to humans. Finally, we focus on the simultaneous uptake of MPs and pathogens in the human gut. Overall, we identify major knowledge gaps, both on the mechanisms and the possible health outcomes. The scarce and inconclusive results regarding the effect of MPs on microbial virulence and evolution, together with the insufficient knowledge about the attachment of microbial toxins to MPs, highlight the need for further studies. We conclude that biofilm-coated MPs in foodstuffs may pose several risks to food safety, but further research will be essential to determine the extent of their effect on human health. [Display omitted] • Micro- and nanoplastics are present as contaminants in the food chain. • Foodborne pathogens and biotoxins have been identified on (micro)plastics biofilms. • Micro- and nanoplastics can affect bacterial virulence and other harmful traits. • The uptake of microplastics carrying pathogens may impact on human health. [ABSTRACT FROM AUTHOR]

Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions. [Display omitted] • Apo DdmD assembles as an autoinhibited dimer for plasmid nicking • DdmE is a DNA-guided, DNA-targeting Argonaute-like protein and prefers short guides • DdmE recruits DdmD dimer to target plasmids by DNA-guided DNA targeting • DdmD transitions from dimer to monomer upon DNA binding for translocation and cleavage As a component of a bacterial anti-plasmid defense system, DdmE is an Argonaute-like protein that functions as a DNA-guided DNA-targeting module. It recruits DdmD, an autoinhibited dimer with helicase and nuclease domains, to target DNA. Upon targeting, DdmD transitions from dimer to monomer for translocation and cleavage. [ABSTRACT FROM AUTHOR]

IncQ-type plasmids have become important vectors in the dissemination of bla GES among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different bla GES variants from human and environmental sources. The bla GES variants were identified using polymerase chain reaction (PCR) in Aeromonas veronii isolated from hospital effluent and Klebsiella variicola isolated from a rectal swab of a patient admitted to the cardiovascular intensive care unit in a different hospital. Antimicrobial-susceptibility testing and transformation experiments were performed for phenotypic analysis. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms. The comparative analysis of plasmids was performed using BLASTn, and the IncQ1 plasmids showed a high identity and similar size. A. veronii harbored bla GES-7 in a class 1 integron (In2061), recently described by our group, and K. variicola carried bla GES-5 in the known class 1 integron. Both integrons showed a fused gene cassette that encodes resistance to aminoglycosides and fluoroquinolones, with an IS 6100 truncating the 3′-conserved segment. The fused genes are transcribed together, although the attC site is disrupted. These gene cassettes can no longer be mobilized. This study revealed a mobilome that may contribute to the dissemination of GES-type β-lactamases in Brazil. Class 1 integrons are hot spots for bacterial evolution, and their insertion into small IncQ-like plasmids displayed successful recombination, allowing the spread of bla GES variants in various environments. Therefore, they can become prevalent across clinically relevant pathogens. • High-identity IncQ1 plasmids noted in isolates from human and environmental sources. • Overall, two plasmids identified harboring different GES-types. • Klebsiella variicola carrying GES-carbapenemase in class 1 integron (In2005). • Underestimation of the true prevalence of GES-producing isolates. [ABSTRACT FROM AUTHOR]

Water disinfection practices have long been established as a critical engineering intervention for controlling pathogen transmission and safeguarding individual and public health. However, recent discoveries have unveiled the significant role disinfection and post-disinfection play in accelerating the development of resistance to disinfectants and antimicrobial drugs within bacterial and viral communities in the environment. This phenomenon, in turn, may facilitate the emergence of persistent microbes and those with new genetic characteristics. These microbes may thrive in host environments with increased infectivity and resistance, posing challenges to current medical treatments and jeopardizing human health. In this perspective, we illuminate the intricate interplay between aquatic environments, microbes, and hosts and how microbial virulence evolves across the environment and host under the pressure of disinfection and post-disinfection conditions. We aim to draw attention to the previously overlooked potential risks associated with disinfection in driving the virulence evolution of bacteria and viruses, establish connections between pathogens in diverse environments and hosts within the overarching framework of the One Health concept, and ultimately provide guidelines for advancing future water disinfection technologies to effectively curb the spread of infectious diseases. [Display omitted] • Microbes can evolve under disinfection and post-disinfection conditions. • Evolved microbes may pose health risks upon entry into human hosts. • Tracing the trajectory of microbial evolution helps assess disinfection risks. [ABSTRACT FROM AUTHOR]

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4 %) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture. [Display omitted] • Organic fertilizers increased the soil ARGs abundance but suppressed their migration into crops. • The evolution of indigenous bacteria in soil was more inclined to the K strategy. • The pH, EC, and nutrients as key drivers influenced the ARGs abundance. • Composition of conjugators showed differential selection of resistant plasmids by endophytes. [ABSTRACT FROM AUTHOR]

The rapid development of economy and technology caused numerous irreversible effects on the environment, and the rational use and storage of existing resources have became an indispensable process in modern development. Energy storage through supercapacitors can effectively alleviate part of the energy crisis. Here, the effects of heating rates on the morphology of carbonized bacterial cellulose (CBC) carbon and its electrochemical properties were studied and CBC-5 (heating rate of 5 ℃/min) with porous structure was confirmed to be supporting material for loading MnO 2. The specific capacitance of CBC-5@MnO 2 composites was high up to 190 F g−1 at 1 A g−1, and its capacitance retention rate was up to 96.6% after 8000 cycles. The superior electrochemical performance cannot be achieved without the cooperative effect among the metal oxides and carbon materials, which also benefits from the fast transport of ions and electrons in solution. The assembled CBC-5//CBC-5@MnO 2 -6 h hybrid supercapacitors exhibited largest energy density and power density values of 44.5 Wh kg−1 (at 0.2 A g−1) and 11111.1 W kg−1 (at 10 A g−1), respectively. The assembled button cells can light up small LED bulbs for at least 10 min. The porous bacterial cellulose carbon can provided possibilities for high electrode design. [Display omitted] • Morphology change of carbonized bacterial cellulose (CBC) affected by heating rate was clarified. • CBC-5 exhibited a three-dimensional channel structure and large specific surface area. • Homogeneous MnO 2 nanospheres were loaded onto CBC by adjusting hydrothermal time. • The device shows energy density of 44.5 Wh kg−1and power density of 11,111.1 W kg−1. • A button cell was assembled to light an LED lamp for nearly 20 min [ABSTRACT FROM AUTHOR]

• Primary vectors of HGT differed between surface-water and groundwater biofilters. • Functional redundancy trends differed in surface-water and groundwater biofilters. • Virulent phages drove bacterial evolution through synergistic interactions. • Genes related to water purification and microbial/chemical risks were enriched. Biofiltration in drinking water treatment (BDWT) are popular as it holds promise as an alternative to chemical treatments, yet our understanding of the key drivers and trends underlying bacterial evolution within this process remains limited. While plasmids and phages are recognized as the main vectors of horizontal gene transfer (HGT), their roles in shaping bacterial evolution in BDWT remain largely unknown. Here we leverage global metagenomic data to unravel the primary forces driving bacterial evolution in BDWT. Our results revealed that the primary vector of HGT varies depending on the type of source water (groundwater and surface water). Both plasmids and phages accelerated bacterial evolution in BDWT by enhancing genetic diversity within species, but they drove contrasting evolutionary trends in functional redundancy in different source water types. Specifically, trends towards and away from functional redundancy (indicated as gene-protein ratio) were observed in surface-water and groundwater biofilters, respectively. Virulent phages drove bacterial evolution through synergistic interactions with bacterial species capable of natural transformation and with certain natural compounds that disrupt bacterial cytoplasmic membranes. Genes relating to water purification (such as Mn(II)-oxidizing genes), microbial risks (antibiotic resistance genes), and chemical risk (polycyclic aromatic hydrocarbons) were enriched via HGT in BDWT, highlighting the necessity for heighted focus on these useful and risky objects. Overall, these discoveries enhance our understanding of bacterial evolution in BDWT and have implications for the optimization of water treatment strategies. [Display omitted] [ABSTRACT FROM AUTHOR]

Once used synonymously with the term apoptosis, PCD processes in animals are now divided into separate pathways of apoptosis, necroptosis, pyroptosis, and others [[3]]. A defining feature of multicellular life is the utilization of programmed cell death (PCD) [[1]]. Such systems may be analogous to phage holin-endolysin systems, but these effectors also bear some similarities to type VI secretions systems involved in bacteria-bacteria conflict [[39]]. Utilization of membrane pores in bacteria-phage conflict may have provided a template for the evolution of multiple cell death processes in eukaryotes. [Extracted from the article]

Methicillin-resistant Staphylococcus aureus (MRSA), a major human pathogen, uses the prophage-encoded tarP gene as an important immune evasion factor. TarP glycosylates wall teichoic acid (WTA) polymers, major S. aureus surface antigens, to impair WTA immunogenicity and impede host defence. However, tarP phages appear to be restricted to only a few MRSA clonal lineages, including clonal complexes (CC) 5 and 398, for unknown reasons. We demonstrate here that tarP-encoding prophages can be mobilized to lysogenize other S. aureus strains. However, transfer is largely restricted to closely related clones. Most of the non-transducible clones encode tarM, which generates a WTA glycosylation pattern distinct from that mediated by TarP. However, tarM does not interfere with infection by tarP phages. Clonal complex-specific Type I restriction-modification systems were the major reasons for resistance to tarP phage infection. Nevertheless, tarP phages were found also in unrelated S. aureus clones indicating that tarP has the potential to spread to distant clonal lineages and contribute to the evolution of new MRSA clones. [ABSTRACT FROM AUTHOR]

Integrative and conjugative elements (ICEs) serve as major drivers of bacterial evolution. These elements often confer some benefit to host cells, including antibiotic resistance, metabolic capabilities, or pathogenic determinants. ICEs can also have negative effects on host cells. Here, we investigated the effects of the ICE (conjugative transposon) Tn916 on host cells. Because Tn916 is active in a relatively small subpopulation of host cells, we developed a fluorescent reporter system for monitoring activation of Tn916 in single cells. Using this reporter, we found that cell division was arrested in cells of Bacillus subtilis and Enterococcus faecalis (a natural host for Tn916) that contained an activated (excised) Tn916. Furthermore, most of the cells with the activated Tn916 subsequently died. We also observed these phenotypes on the population level in B. subtilis utilizing a modified version of Tn916 that can be activated in the majority of cells. We identified two genes (orf17 and orf16) in Tn916 that were sufficient to cause growth defects in B. subtilis and identified a single gene, yqaR, that is in a defective phage (skin) in the B. subtilis chromosome that was required for this phenotype. These three genes were only partially responsible for the growth defect caused by Tn916, indicating that Tn916 possesses multiple mechanisms to affect growth and viability of host cells. These results highlight the complex relationships that conjugative elements have with their host cells and the interplay between mobile genetic elements. Author summary: Horizontal gene transfer, often mediated by mobile genetic elements, facilitates bacterial evolution. Integrative and conjugative elements (ICEs) are mobile genetic elements that encode machinery to transfer the element from a donor bacterium to a neighboring cell, thereby generating a new bacterial host. ICEs are the most prevalent type of conjugative element and confer novel traits, including antibiotic resistances and symbiotic, pathogenic, or metabolic capabilities. Early-discovered ICEs were identified by the benefits they provide to their host cells. Tn916, the first-described ICE, was identified due to its ability to spread tetracycline resistance in clinical isolates of Enterococcus. However, conjugative elements can also incur a cost to their hosts. Here, we report that the activated form of Tn916 causes growth arrest and cell death in two bacterial hosts: Bacillus subtilis, which has been used for many studies of the element; and Enterococcus faecalis, a natural host of the element. We demonstrate that these deleterious effects in B. subtilis are due, at least in part, to interactions between components of the Tn916 conjugation machinery and a co-resident prophage-like element. Our findings highlight the complex nature of interactions that can occur between an integrative and conjugative element, its host, and other horizontally acquired elements. [ABSTRACT FROM AUTHOR]

Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage satellites that were packaged as concatemeric repeats within naturally occurring bacteriophage particles in seawater. These same phage-parasitizing mobile elements were found integrated in the genomes of dominant co-occurring bacterioplankton species. Like known phage satellites, many marine phage satellites encoded genes for integration, DNA replication, phage interference, and capsid assembly. Many also contained distinctive gene suites indicative of unique virus hijacking, phage immunity, and mobilization mechanisms. Marine phage satellite sequences were widespread in local and global oceanic virioplankton populations, reflecting their ubiquity, abundance, and temporal persistence in marine planktonic communities worldwide. Their gene content and putative life cycles suggest they may impact host-cell phage immunity and defense, lateral gene transfer, bacteriophage-induced cell mortality and cellular host and virus productivity. Given that marine phage satellites cannot be distinguished from bona fide viral particles via commonly used microscopic techniques, their predicted numbers (~3.2 × 1026 in the ocean) may influence current estimates of virus densities, production, and virusinduced mortality. In total, the data suggest that marine phage satellites have potential to significantly impact the ecology and evolution of bacteria and their viruses throughout the oceans. We predict that any habitat that harbors bacteriophage will also harbor similar phage satellites, making them a ubiquitous feature of most microbiomes on Earth. [ABSTRACT FROM AUTHOR]